title: LG15_input

data_processing:
none provided by the submitter
Assembly: hg38
Supplementary files format and content: UCSC bigwig

source_name: Microglia

extract_protocol:
PU.1+ nuclei were isolated according Nott et al., Nature Protocols 2021.
Chromatin immunoprecipitation (ChIP) for H3K27ac was performed as previously described 48. Fixed, sorted nuclei (~200,000 nuclei per sample) were resuspended in 130 μl ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail). Chromatin was sheared by sonication using a Covaris E220 focused-ultrasonicator (Covaris, MA) with the following setting: time, 240 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0). The lysates were adjusted to 250 μl with LB3 and further diluted with 25 μl 10% Triton X-100 (final concentration 1%). Samples were spun down at maximum speed at 4℃ for 10 minutes. For DNA input control, 3 μl of the lysate were taken and volume adjusted to 25 μl with TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) and stored at 4℃ until library preparation. For immunoprecipitation, 20 μl of Dynabeads Protein A (ThermoFisher Scientific, 10001D) and H3K27ac antibody (2 μl serum; ActiveMotif, 39135) was added to the diluted lysates and rotated overnight at 4°C. Beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA), twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), once with TE-NaCl (10 mM Tris-HCl pH8, 1 mM EDTA, 50 mM NaCl) and finally resuspended in 25 μl TT. Libraries from ChIP and DNA input samples were prepared with the NEBNext Ultra II DNA library prep kit (NEB) reagents according to the manufacturer’s protocol on the beads suspended in 25 µL TT (10 mM Tris/HCl pH7.5, 0.05% Tween-20), with reagent volumes reduced by half. Next, DNA was eluted and crosslinks reversed by adding 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl EDTA, 1 µl proteinase K (20 mg/ml), 20 µl water, incubating for 1 hour at 55°C , then 30 minutes to overnight at 65°C. DNA was purified using 2 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 1.5 M NaCl to a final of 12% PEG, eluted with 12.5 µl TT. DNA contained in the eluate was then amplified for 14 cycles in 25 µl PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 225-350 bp, purified, and single-end sequenced using an Illumina NovaSeq 6000.

value: Microglia

value: input


title: LG14_input

status: Public on Feb 01 2024

type: SRA

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

country: USA

institute: UCSD

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: chip antibody


title: RRP40_2

city: Atlanta

first: Anita

middle: H.

last: Corbett

state: Georgia

address: 1510 Clifton Road

department: Biology

institute: Emory University

library_source: transcriptomic

data_processing:
Trimming: NovaSeq paired-end 150-bp reads were adaptor trimmed.
Alignment: Reads were mapped to the S. cerevisiae S288C genome assembly R64-1-1, annotated with CUTs and SUTs (Xu et al. Nature. 2009) using the STAR RNA-seq aligner [v2.6.1d]
Counting: Reads were assigned to gene features (Gene_ID) and counted using featureCounts [v1.22.2; Liao et al. Bioinformatics. 2014)].
Expression estimates: Transcript and gene expression estimates were measured using StringTie [v2.1.7; Pertea et al. Nature Biotechnol.]
Differential gene expression analysis: DE analysis on raw read counts was performed using DESeq2 R package [v1.38.1; (Love et al. Genome Biology. 2014)]
Assembly: S. cerevisiae S288C R64-1-1
Supplementary files format and content: Gene Counts_Comma-separated values (CSV) files contain raw gene counts for each sample produced using featureCounts
Supplementary files format and content: DESeq2_Comma-separated values (CSV) files contain normalized abundance measurements generated using DESeq2

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: MATa ura3Δ0 leu2Δ0 his3Δ1 rrp40Δ::NEO [RRP40, LEU2, CEN6, pRS315]

growth_protocol: S. cerevisiae rrp∆ cells containing wildtype RRP or mutant rrp plasmid (pRS315, LEU2, CEN6) were grown in 10 mL Leu- minimal media in triplicate at 37°C for 5hr.

extract_protocol:
Total RNA extracted from S. cerevisiae cells using Zymo kit (Zymo Research) and rRNA was removed according to method described in Bogdanova et al. Normalization of Full-Length-Enriched cDNA, in cDNA Libraries: Methods and Applications (2011) with some modifications.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat# R3000; Zymo Research)

treatment_protocol: Growth in Leu- Glu media at 37°C for 5hr

value: BY4741 haploid

tag: genotype

value: MATa ura3delta0 leu2delta0 his3delta1 rrp40delta::NEO [RRP40, LEU2, CEN6, pRS315]


title: Growth_dkhpB_M_3

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description: single-end

data_processing:
Reads from the RNA-seq experiments were trimmed and filtered using the FASTX toolkit (v.0.10.1; http://hannonlab.cshl.edu/fastx_toolkit). Mapping was performed using READemption (v.1.01)(Förstner et al., 2014) against the genome sequence for F. nucleatum subsp. nucleatum ATCC 23726 (NZ_CP028109.1) downloaded from the National Center for Biotechnology Information (NCBI). Differential gene expression analysis was carried using DEseq2 (v.1.18.01) (Love et al., 2014). All analysis for each was carried for biological triplicates and considered significant with a false-discovery rate ≤ 0.05.
Assembly: NZ_CP028109.1
Supplementary files format and content: wiggle

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

source_name: cells were grown to mid-exponential phase prior to harvest

growth_protocol: All bacteria were grown in Columbia broth.

extract_protocol:
Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and snap-frozen at –80°C if not directly processed. The bacterial solution was centrifuged for 20min, 4500rpm at 4°C and the supernatant was completely discarded. Cells were suspended in 600μl of 10mg/ml lysozyme in TE buffer (pH8.0) and incubated at 37°C for 10min. Next, 60μl of 10% w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64°C, 1-2min before adding 66μl 3MNaOAc, pH5.2. Next, 750μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5min. at 64°C. Samples were briefly placed on ice to cool before centrifugation for 15min, 13,000rpm at 4°C. The aqueous layer was transferred into a 2ml phase lock gel tube (Eppendorf), 750μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12min, 13,000rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3MNaOAc, pH6.5) was added and incubated overnight at -20°C. Precipitated RNA was harvested by centrifugation, washed with cold 75% v/v ethanol and air-dried. Purified RNA was resuspended in 50µl RNase-free water and stored at -80°C.
For preparation cDNA library of the immunoprecipitated RNA samples, NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) was used. Briefly, 3.5 μl of RNA was mixed with 1 μl of 3’ SR Adaptor (diluted 1:10 in nuclease-free water) and incubated in a preheated thermal cycler for 2 min at 70 °C.  The samples were transferred to ice and added with the premixed 3’ ligation mix (5 μl 3’ Ligation Reaction Buffer, 1.5 μl 3’ Ligation Enzyme Mix). The ligation mixture was then incubated for 1 h at 25 °C. 0.25 μl of SR RT Primer and 2.5 μl nuclease-free water were added to the mixture and incubated at 75 °C for 5 min, 37 °C for 15 min and followed by 25 °C for 15 min. To ligate the 5’ SR adaptor, the 5’ ligation mixture (0.5 μl 1:10 diluted 5’ SR Adaptor, 0.5 μl 10x 5’ ligation reaction buffer, 1.25 μl 5’ ligation enzyme mix) was added to each sample and incubated for 1 h at 25 °C. For synthesis first strand of cDNA, reverse transcription mix (4 μl first strand synthesis reaction buffer, 0.5 μl murine RNase inhibitor, 0.5 μl M-MLV reverse transcriptase) was added to each reaction and incubated for 1 h at 50 °C followed by 15 min at 70 °C to inactivate the reverse transcription reaction. 5 μl of cDNA was then proceeded to PCR amplification with the PCR mix (12.5 μl LongAmp Taq 2x master mix, 0.625 μl SR primer, 6.25 μl nuclease-free water) and 0.625 μl index (X) primer. PCR program (30s at 94°C, 15 s at 94 °C, 30 s at 62 °C and 15 s at 70 °C for 19 cycles, 5 s at 70 °C) was carried out. PCR products were mixed with 25 μl of GLII buffer and loaded on 6 % polyAcrylamide gel containing 8 M urea. After staining the gel for 10 min in 1x TBE buffer with a 1:10,000 dilution of SYBR Gold Nucleic Acid Gel Stain (Invitrogen), the bands in the range of 130- 1000 bp were cut into small pieces and transfer to a 2 ml LoBind tube. 500 μl of DNA elution buffer was added and incubated at the room temperature for 2 h. After transferring the elute and the gel debris to centrifuge tube filters (Sigma) and centrifugation (5000 rpm, 1 min), the elute was recovered by adding 1 μl liner acrylamide (NEB) and precipitating in ethanol at -80°C for 1 h. After precipitation, the pellet was washed with 80% ethanol and resuspended in 12 μl nuclease free water (NEB). 1 μl of the prepared cDNA library was subjected to Bioanalyzer analysis.   Amplified cDNAs were pooled and sequenced on an illumine NextSeq 2000 platform by the CoreUnit Sysmed from the University of Wuerzburg.

tag: strain

value: deletion of KhpB

tag: tissue


title: rrp40_S87A_1

source_name: MATa ura3Δ0 leu2Δ0 his3Δ1 rrp40Δ::NEO [rrp40-S87A, LEU2, CEN6, pRS315]

value: MATa ura3delta0 leu2delta0 his3delta1 rrp40delta::NEO [rrp40-S87A, LEU2, CEN6, pRS315]


title: RRP40_1


title: rrp40_W195R_3

source_name: MATa ura3Δ0 leu2Δ0 his3Δ1 rrp40Δ::NEO [rrp40-W195R, LEU2, CEN6, pRS315]

value: MATa ura3delta0 leu2delta0 his3delta1 rrp40delta::NEO [rrp40-W195R, LEU2, CEN6, pRS315]


title: RRP40_3


title: Germinating seed, 6h light, rep2, RNA-seq

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

description:
L6_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L6.RNAseq.plus.bw
L6.RNAseq.minus.bw

data_processing:
Reads were trimmed using HOMER v4.11.1 with the following command: homerTools trim -pe -3 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -mis 2 -minMatchLength 4 -min 20. Trimmed reads were mapped to the TAIR10 genome sequence using STAR v2.7.9a with the following options: –outSAMstrandField intronMotif –outMultimapperOrder Random –outSAMmultNmax 1 –outFilterMultimapNmax 10000 –limitOutSAMoneReadBytes 10000000.
De novo transcript reconstruction was performed using a combination of two approaches. First, stringtie v2.1.4 was used with the total RNA-seq BAM files with the following options to generate de novo transcripts: -m 150 -s 1 -f 0.01. Additionally, the TSS peak summits were used to guide the creation of putative transcripts via the –ptf option. The resulting GTF files were merged from all samples and transcripts overlapping existing Araport11 transcripts filtered out using gffcompare v0.12.6. In a second approach, all total RNA-seq BAM files were filtered to remove reads with a MAPQ of less than 10, soft-clipping, or gaps, and then merged into a single file using samtools v1.14 and custom AWK scripts. A HOMER format tag directory was created using makeTagDirectory from HOMER v4.11.1, and de novo transcript reconstruction performed using findPeaks with the options -style groseq -tssSize 100 -minBodySize 100 -endFold 2078. Transcripts overlapping existing Araport11 transcripts were filtered out using gffcompare. The final HOMER and stringtie transcripts were imported into R v4.3.1 to generate a unified non-overlapping set of putative transcripts of lengths greater or equal to 200 bp, as well filtering those out whose TSS was not within 50 bp of a TSS peak discovered from the csRNA-seq, using base Bioconductor packages. The final transcript set was obtained by first converting the putative transcript set from GTF to GFF3 format using gffread v0.12.7, concatenating with the Araport11 annotations in GFF3 format, and finally sorted using GFF3sort v1.0.0.
TMM-normalized counts per million (CPM) from all samples were obtained by first reading the counts into R v4.3.1, then normalizing them using the calcNormFactors and cpm functions from the edgeR package.
Coverage tracks in bedGraph format were generated from the tag directories using the makeUCSCfile program from HOMER v4.11.1. The csRNA-seq files were further converted to bigWig using R v4.3.1 with the edgeR package to TMM-normalize the signal density.
Assembly: TAIR10
Supplementary files format and content: De novo transcripts are stored using the GFF3 format.
Supplementary files format and content: Transcript tab-separated quantification tables contain a column of transcript names and columns of counts for each RNA-seq sample.
Supplementary files format and content: RNA-seq read pileups per strand are provided in bigWig format.

organism: Arabidopsis thaliana

source_name: Seeds

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized using the gas product of 100 mL of bleach mixed with 3 mL hydrochloric acid for 1 h, followed by stratification in water in the dark at 4 ˚C. Seeds were grown in 50 mL liquid ½ MS in 125 mL Erlenmeyer flasks, shaking at 180 RPM, in continuous light at 22 ˚C.

extract_protocol:
50 mg of sample (or 25 mg for dry seeds) was flash-frozen in liquid nitrogen and ground to a powder with a mortar and pestle. 1.5 mL of extraction buffer (EB; 100 mM Tris-HCl pH 9.5, 150 mM NaCl, 5 mM EDTA pH 8, 1% sarkosyl) was prepared per sample, and 7.5 µL beta-mercaptoethanol was added to each EB aliquot and briefly vortexed. After addition of the EB to the frozen ground tissue powder, the homogenate was mixed vigorously and left on ice for 10 min, with intermittent vortexing. This was followed by a 10 min max-speed centrifugation at 4 ˚C in a benchtop centrifuge. 1 mL of supernatant (avoiding the starchy upper-most layer) was transferred to a new tube and mixed with 1 mL chloroform. Following a 15 s vortexing step, the mixture was centrifuged as before and 900 µL of the upper phase transferred to a new tube. To this was added 90 µL 3 M NaOAc and 1 mL Tris-buffered phenol-chloroform, followed by vortexing for 15 s and another centrifugation as before. As much clear supernatant as possible was moved to a new tube and gently mixed by inversion with an equal volume isopropanol and incubated at 4 ˚C for 1 h. The precipitated RNA was pelleted by a 20 min max-speed centrifugation at 4 ˚C. The supernatant was discarded and the pellet washed with 800 µL ice-cold 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was discarded, further removed with a pipette after pulse-spinning, and left inverted to dry for 2 min. The pellet was dissolved in 100 µL nuclease-free water, to which 10 µL DNaseI buffer (ThermoFisher Scientific), 5 µL DNaseI (ThermoFisher Scientific), and 1 µL RiboLock (ThermoFisher Scientific) was added and left to incubate at 37 ˚C for 30 min. The resulting DNA-free RNA was isolated using a modified RNA purification protocol. Briefly, 240 µL nuclease-free water was added to the DNaseI reaction alongside 40 µL solubilization buffer (200 mM Tris-HCl pH 7.5, 10 mM EDTA pH 8, 5% SDS) and vortexed. Afterwards 40 µL 3 M NaOAc and 800 µL Tris-buffered phenol-chloroform was added and again vortexed for 15 s, followed by a max-speed centrifugation for 5 min at 4 ˚C. The supernatant was transferred to a new tube containing 800 µL chloroform and vortexed for 15 s, followed by another centrifugation as before. The supernatant was again transferred to a new tube, this time to one containing 1 mL ice-cold ethanol, gently mixed by inversion, and left at -80 ˚C overnight. The following day the tube was centrifuged as before for 20 min. The supernatant was discarded and the pellet was washed with 800 µL 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was removed, and again removed using a pipette after pulse spinning. After leaving the tubes to dry inverted for 2 min, the pellet was dissolved in 27 µL nuclease-free water (of which 1.5 µL was used for quantification with a NanoDrop (ThermoFisher Scientific)) and stored at -80 ˚C. RNA integrity was assessed by running 1 µg RNA in a denaturing RNA gel and 100 ng RNA with a Bioanalyzer RNA analysis chip (Agilent).
Total RNA was rRNA-depleted and library preparation was performed using the TruSeq Stranded Total RNA library preparation kit with Ribo-Zero (Illumina) following the manufacturer's protocol.

value: Seeds


title: Germinating seed, 72h stratification, rep2, RNA-seq

description:
S72_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
S72.RNAseq.plus.bw
S72.RNAseq.minus.bw


title: LG15

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger atac v1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: fragment tsv from cell ranger atac of 10X

source_name: Frontal cortex (BA9)

extract_protocol:
Human frontal cortex was homogenized by gentle manual dissociation on ice as described previously (Gosselin et al., 2017). Briefly, samples were dissociated in isolation buffer consisting of HBSS without magnesium and calcium (Life Technologies, 14175-095), 1% bovine serum albumin, and 1mM EDTA using a 2 ml polytetrafluoroethylene douncer and pestle (Wheaton, 358026). Myelin and debris was …by resuspension of the pellet in 37% isotonic Percoll (Sigma, P4937), and centrifuged at 600 x g for 30 min at 14°C with no acceleration and deceleration. Pelleted cells were washed twice with isolation buffer, filtered through a 70 µm strainer. Cells were then incubated in 1:100 with a Fc receptor blocking antibody (Human TruStain FcX) for 30 min at 4°C, and then with CD11b-PE (Biolegend), and CD45-APC (Biolegend). DAPI was used as live/dead staining. After staining, cells were centrifuged and resuspended in isolation buffer and kept on ice until FACS. CD45+ cells were sorted using Sony SA900 (100- µm nozzle, purity mode, sample chilling).
Library was performed according to the manufacter’s instructions (single cell ATAC-seq v1 protocol, 10x Genomics). Cells were permeabilized using lysis buffer (10 mM Tris-HCl pH 7.4 (15567027, Thermo Fischer Scientific), 10 mM NaCl (ICN15194401, Fischer Scientific), 3 mM MgCl2 (194698, Mp Biomedicals Inc.), 0.1% Tween 20 (P7949, Sigma), 0.1% IGEPAL-CA630 (I8896, Sigma), 0.01% Digitonin (G9441, Promega), and 1% BSA in nuclease free water) and incubated for 5 minutes on ice. Permeabilized nuclei were washed using washing buffer (lysis buffer without IGEPAL-CA630 and Digitonin), centrifuged for 5 minutes at 500 rcf and resuspended in Nuclei buffer (10x Genomics). An aliquot was mixed with Trypan Blue and counted using a hemocytometer. Up to 10,000 nuclei were tagmented before loading onto a Chromium Controller; libraries were generated according to manufacturer specifications ((Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1, 1000175; Chromium Next GEM Chip H Single Cell Kit, 1000162; Single Index Kit N Set A, 1000212, 10x Genomics)). Libraries were amplified for 10 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was inspected using the High Sensitivity D1000 ScreenTape assay on a Tapestation 4200 (Agilent). Libraries were sequenced using an Illumina NovaSeq 6000 using the following read lengths: Read 1: 50 cycles, Read 2: 50 cycles, Index 1: 8 cycles, Index 2: 16 cycles.

value: CD45+ cells

value: Frontal cortex (BA9)

value: Male

tag: age

value: 88 years


title: Growth_dkhpB_M_2

description: single-end

value: cells were grown to mid-exponential phase prior to harvest


title: Growth_dkhpB_M_1

description: single-end


title: LG15_H3K27ac

value: H3K27ac polyclonal (Active Motif, Catalog No:39135)


title: Germinating seed, 6h light, rep1, RNA-seq

description:
L6_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L6.RNAseq.plus.bw
L6.RNAseq.minus.bw


title: rrp4_G226D_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp4Δ::NEO [rrp4-G226D, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp4delta::NEO [rrp4-G226D, LEU2, CEN6, pRS315]


title: Germinating seed, 72h stratification, rep1, RNA-seq

description:
S72_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
S72.RNAseq.plus.bw
S72.RNAseq.minus.bw


title: Growth_dkhpA_S_3

description: single-end

source_name: cells were grown to stationary phase prior to harvest

value: deletion of KhpA


title: Growth_dkhpA_S_2

description: single-end

value: cells were grown to stationary phase prior to harvest


title: Germinating seed, 24h stratification, rep2, RNA-seq

description:
S24_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
S24.RNAseq.plus.bw
S24.RNAseq.minus.bw


title: LG05_input

value: Microglia


title: LG14_H3K27ac


title: LG05_H3K27ac


title: Germinating seed, 24h stratification, rep1, RNA-seq

description:
S24_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
S24.RNAseq.plus.bw
S24.RNAseq.minus.bw


title: HeLa cells_clone 41

city: Seoul

first: HyunHo

last: cha

address: 222, Wangsimni-ro, Seongdong-gu

department: Biomedical Science

country: South Korea

institute: hanyang university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC v0.11.7 and Trimmomatic v0.38, then mapped to hg19 whole genome using HISAT2 v2.1.0
And then, transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016)
Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes)
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa

extract_protocol:
RNA was isolated using Trizol® reagent (Thermo Fisher Scientific, Waltham, MA, USA)
Library construction was performed by Macrogen Inc. (Macrogen, Seoul, Korea). 1 µg of total RNA was used to construct cDNA libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA).

tag: cell line

value: HeLa

value: Human cervix epitheloid carcinoma

value: UPF1 knock out


title: Growth_dkhpA_S_1

description: single-end


title: Growth_dkhpA_M_3

description: single-end


title: Dry seed, rep2, RNA-seq

description:
DS_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
DS.RNAseq.plus.bw
DS.RNAseq.minus.bw


title: RRP4_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp4Δ::NEO [RRP4, LEU2, CEN6, pRS315]

value: BY4741 haploid

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp4delta::NEO [RRP4, LEU2, CEN6, pRS315]


title: rrp4_G226D_1


title: rrp4_G226D_2


title: RRP4_2


title: HeLa cells_clone 9


title: Growth_dkhpA_M_2

description: single-end


title: Seedling, 57h light, rep2, ATAC-seq

description:
L57_2_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L57.ATACseq.bw

data_processing:
Reads were trimmed using fastp v0.23.4 for the adapter sequence CTGTCTCTTATACACATCT. Trimmed reads were mapped to the TAIR10 genome sequence using bowtie2 v2.4.4 with the following options: –very-sensitive -X 2000 –dovetail. Non-nuclear reads, reads overlapping with a manually curated blacklist, and reads with a MAPQ score of less than 10 were discarded using samtools v1.14. The remaining reads were deduplicated using Genrich v0.6.1 and the accompanying getReads.py script. The filtered BAM was converted into BED format using bedtools v2.30.0.
ACR peaks were called using MACS3 v3.0.0b3 with the following command: macs3 callpeak –nomodel –shift -100 –extsize 200 -g 1.191e8 –keep-dup all -p 0.05 -f BED. To create a final set of peaks from all samples, peaks were first filtered to only keep those with a q value of less than 0.05 and those which were present in both replicates, and finally merged using bedtools v2.30.0. To identify peak summits, reads were resized to 200 bp centered from the start position, merged from all samples, and converted into bedGraph format using bedtools. This was then read into R v4.3.1 and the single nucleotide coordinate containing the maximum pileup value identified within each peak using base Bioconductor packages.
To create normalized bigWig tracks for each time-point reads from both replicates were first merged and resized to 50 bp centered from the start position, then reads counted in 10 bp bins along the genome before being converted into bedGraph format with bedtools v2.30.0. This was read into R v4.3.1 and the read counts per bin normalized using the normOffsets function (with weights for bins outside of peak regions set to 0) and calculateCPM function from the csaw package before being exported in bigWig format.
To obtain a normalized reads per million (RPM) table of all individual peaks, raw read counts were first obtained using bedtools, read into R v4.3.1, and normalized using the normOffsets and calculateCPM functions from the csaw package.
Assembly: TAIR10
Supplementary files format and content: Accessible chromatin region (ACR) tab-separated quantification tables contain a column of peak names and columns of counts for each sample.
Supplementary files format and content: Read pileups are provided in bigWig format.

source_name: Seedlings

extract_protocol:
Germinating seeds were placed between two microscope slides with a small drop of water which were rotated and squeezed together with gentle force until the embryos were released from within the seed. The mixture of embryos and seed coats were then kept in a small beaker containing 4 mL ice-cold water until all of the sample had been processed (1-2 g starting material). Following this, 4 mL 80% sucrose was added and mixed gently by inversion. The solution was split into two 5 mL microcentrifuge tubes and centrifuged at 3,000 x g for 10 min in a cooled benchtop centrifuge (4 ˚C). The embryo-containing supernatant was filtered through a piece of miracloth (EMD Millipore), washed with ice-cold water, and briefly dried from below using a piece of paper towel to absorb excess water. The embryos were flash frozen in a mortar and ground to a fine powder with a pestle. Approximately 500 mg of frozen ground tissue powder was added to 10.5 mL ice-cold nuclear purification buffer (NPB; 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine) with added cOmplete Mini EDTA-free protease inhibitor cocktail (Merck) in a chilled mortar and ground with a chilled pestle. The homogenate was collected with a 10 mL serological pipette and passed through a 100 µm cell strainer, as well as a 40 µm cell strainer, into a 15 mL Falcon tube (Corning) kept on ice. The tube was centrifuged at 1,200 x g for 10 min in a cooled benchtop centrifuge (4 ˚C). The supernatant was discarded and the pellet gently resuspended in 1 mL ice-cold nuclear extraction buffer 2 (NEB2; 0.25 M sucrose, 10 mM Tris-HCl pH 8, 10 mM MgCl2, 1% Triton X-100) with added cOmplete Mini EDTA-free protease inhibitor cocktail (Merck) and transferred to a cooled 1.5 mL microcentrifuge tube. The tube was centrifuged at 12,000 x g for 10 min in a cooled benchtop centrifuge (4 ˚C). The supernatant was removed and the pellet resuspended in 300 µL ice-cold NEB2. This was then pipetted as a layer above 300 µL of nuclear extraction buffer 3 (NEB3; 1.7 M sucrose, 10 mM Tris-HCl pH 8, 2 mM MgCl2, 0.15% Triton X-100) with added cOmplete Mini EDTA-free protease inhibitor cocktail (Merck) in a new 1.5 mL microcentrifuge tube. The tube was centrifuged at 16,000 x g for 10 min in a cooled benchtop centrifuge (4 ˚C). The supernatant was removed, the pellet resuspended in 500 µL ice-cold NPB and transferred to a new 1.5 mL microcentrifuge tube. Nuclei concentration and quality was determined using fluorescence microscopy. Briefly, 1 µL DAPI (0.2 µg/µL) was added to 25 µL nuclei in a 0.5 mL microcentrifuge tube and kept in the dark on ice. A fluorescence microscope was used to count nuclei from 10 µL of the DAPI-stained nuclei inside a Neubauer Improved chamber (Merck).
Tagmentation and library preparation was performed following the manufacturers instructions in the Diagenode Tagmentation kit (Diagenode). Approximately 50,000 nuclei were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 1,000 x g for 10 min in a cooled benchtop centrifuge (4 ˚C). The nuclei pellet was gently resuspended in 50 µL tagmentation mastermix (25 µL 2X Tagmentation buffer (Diagenode), 16.5 µL PBS pH 7.4, 5 µL nuclease-free water, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, 2.5 µL loaded Tagmentase (Diagenode)) and incubated at 37 ˚C for 30 min, mixing gently every 5 min. The reaction was terminated by the addition of 250 µL Binding Buffer (Diagenode), mixing by pipetting up and down. The mixture was transferred to a Diagenode MicroCHIP Diapure spin column placed in a collection tube (Diagenode) and centrifuged at 10,000 x g for 30 s in a benchtop centrifuge. The flow-through was discarded and 200 µL Wash Buffer (Diagenode) added to the column. The tube was centrifuged as before, flow-through discarded, and the wash step repeated once more. The column was transferred to a 1.5 mL LoBind tube (Eppendorf) and 12 µL DNA Elution Buffer (Diagenode) added directly to the column matrix. The tube was centrifuged once more as before and the final DNA elution stored at -20 ˚C. For library preparation, 10 µL of sample DNA was mixed with 14 µL of nuclease-free water, 25 µL 2X NEBNext PCR mix (New England Biolabs), and 1 µL of a primer index pair from the 24 UDI For Tagmented Libraries - Set I (Diagenode). A first PCR was performed in a thermocycler using the following conditions: 5 min at 72 ˚C, 30 s at 98 ˚C, 5 cycles of 10 s at 98 ˚C, 30 s at 63 ˚C, and 1 min at 72 ˚C. The number of additional required amplification cycles for each sample was determined before continuing. 5 µL of the PCR reaction mix was combined with 5 µL NEBNext PCR mix (New England Biolabs), 3.75 µL nuclease-free water, 1 µL Evagreen dye (Biotium), and 0.25 µL of the previous primer index pair (Diagenode). A qPCR was performed using the following conditions: 30 s at 98 ˚C, and 20 cycles of 10 s at 98 ˚C, 30 s at 63 ˚C, and 1 min at 72 ˚C. The number of cycles was plotted on the x-axis against the fluorescence readout on the y-axis. The point in the curve at which the reaction reached one-third its maximum fluorescence was found, with the matching cycle number (rounded down to the nearest integer value) used as the final number of additional amplification cycles. This was done by placing the PCR reaction back into the thermocycler, heating to 98 ˚C for 30 s, followed by the same cycling conditions as before for the determined number of additional cycles. DNA purification was performed by the addition of 67.5 µL AMPure XP beads (Beckman Coulter) to the PCR reaction in a 1.5 mL LoBind tube (Eppendorf) and vortexed for 1 s. After incubating at RT for 5 min, the tube was placed in a magnetic rack for another 5 min. The supernatant was removed and replaced with 200 µL 80% ethanol, incubating for 30 s. The ethanol wash step was repeated once. The beads were then air-dried for up to 5 min, after which the tube was removed from the magnetic rack and the beads resuspended in 30 µL DNA Elution Buffer (Diagenode) by tapping. This was incubated at RT for 5 min before being placed in the magnetic rack for another 5 min. 28 µL of the elute was transferred to a new 1.5 mL LoBind tube (Eppendorf) and stored at -20 ˚C. 1 µL was used for quantification and quality control using a Bioanalyzer High Sensitivity DNA chip (Agilent).

value: Seedlings

tag: treatment

value: Seedling, 57h light


title: Growth_dkhpA_M_1

description: single-end


title: Dry seed, rep1, RNA-seq

description:
DS_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
DS.RNAseq.plus.bw
DS.RNAseq.minus.bw

value: Seeds


title: RRP4_1


title: Huh7 cells_control_replicate 2

value: Human hepatocellular carcinoma

value: control


title: rra1∆_pH7_5_biological_replicate_2

city: Durham

first: J Andrew

last: Alspaugh

state: NC

address: 337 Sands Research Building, 303 Research Drive, DUMC 102359

institute: Duke University

data_processing:
Quality control was assessed by FastQC.
Reads were trimmed for adaptor sequences and filtered using "fastq-mcf" with the following parameters: -q 20 , -x 0.5.  Trimmed and filtered reads were aligned to the Malassezia sympodialis ATCC 42132 genome using "STAR" with the following parameters: --quantMode GeneCounts, --alignIntronMax 5000, --outSJfilterIntronMaxVsReadN 500 1000 2000.
Bam files were sorted, indexed, and merged using "Samtools". Duplicate reads were removed from bam files using "picard".
Differential expression analyses were performed in R using an RNA‐Seq Bioconductor (Love 2015, F1000Res) workflow followed by the DESeq2 package with a false discovery rate (FDR) of 5% (Love 2014, Genome Biol).
Assembly: GCA_900149145.1
Supplementary files format and content: Comma-delimited text file including raw counts for each sample.

molecule: polyA RNA

organism: Malassezia sympodialis

growth_protocol: WT, rim101∆, and rra1∆ cells were incubated at 30°C with shaking in mDixon media to mid-logarithmic growth phase.

extract_protocol:
Cultures were harvested by centrifugation at 4000 rpm for 10 min at 4˚C, then washed once with cold sterile H2O. Cell pellets were flash frozen in a dry ice-ethanol bath and lyophilized overnight. RNA was extracted from the lyophilized pellets via a Trizol-chloroform extraction (Invitrogen). The resulting RNA was treated with DNase I (New England Biolabs) for 30 min at 37˚C as described, then re-purified using Trizol and chloroform.
An mRNA library was prepared using a Kapa Stranded mRNA-Seq library prep kit. Stranded mRNA-Seq was performed on an Illumina HiSeq 4000 with 50-bp single-end reads.

treatment_protocol: Cultures were pelleted and resuspended at an OD600 of 2.5 in 20 mL of media: either DMEM supplemented with 10% FBS, mDixon media buffered to pH 4, or mDixon media buffered to pH 7.5. Cells were incubated at 30°C for 90 minutes with shaking.

tag: condition


title: liver,CW2

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

country: China

institute: Northeast Normal University

data_processing:
Raw sequencing data format was shown as “.fastq” and the joint sequence (adapter) was removed from the original tags using CUTADAPT 1.9. Low quality and repetitive sequences were filtered to obtain clean data. De novo splicing in TRINITY tool (Version 2.4.0) was selected to assemble the clean reads and then the software was used to perform the transcript clustering based on shared sequences contents. The longest transcript in each cluster was regarded as one Unigene. All obtained Unigenes were annotated based on known databases. Quantitative assessment for transcripts per million (TPM) of each Unigene was executed with the SALMON package.
Assembly: Trinity.gene.fasta
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Hipposideros armiger

source_name: liver

extract_protocol:
Commercial RNA simple extraction kit (DP419, TIANGEN, China) was selected to extract the total RNA in liver tissues. 60 mg fresh tissue was ground by high-speed homogenizer (DHFSTPRP-32D, LAWSON, China) with 1 mL lysis buffer RZ to obtain homogenate and then trichloromethane was added. After staying at room temperature for 4 min, the mixture was centrifuged at 12000 rpm to obtain the aqueous phase that was mixed with absolute ethyl alcohol. RD solution was used to remove residual protein impurity in RNA samples and the purified total RNA was stored at RNase-free tubes after repeated centrifugation.
When RNA integrity number > 7.0 and A260/280 > 1.8, messenger RNA (mRNA) with poly A was caught using oligo(dT) dynabeads (25-61005, THERMO FISHER, USA) and then broken into fragmentation with the specific kit (E6150S, NEBNEST, USA). Double-strands complementary DNA was synthesized based on the reverse transcriptase and E. coli DNA polymerase I that were provided by LIANCHUAN BIO TECHNOLOGIES Co., LTD (Hangzhou, China). Paired-ends of the complementary DNA were added with a “A” base, which could combine with the adapter sequence. After the second strand was digested, the sequencing library (300±50 bp) was established by amplifying the target sequences.

value: liver

tag: Sex

value: male

value: adult

value: WT

value: heavy metals exposure


title: Seedling, 57h light, rep1, ATAC-seq

description:
L57_1_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L57.ATACseq.bw


title: rra1∆_pH7_5_biological_replicate_3


title: Germinating seed, 26h light, rep2, ATAC-seq

description:
L26_2_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L26.ATACseq.bw

value: Germinating seed, 26h light


title: skin derived strain s27777 in 2% oxygen, biological replicate 2

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, normalization of retrieved counts and fold change calculation between groups were performed by DESeq2 package.
Assembly: Malassezia globosa CBS 7966 (GCF_000181695.2)
Supplementary files format and content: Normalized counts, fold change values and related p-values were listed as a tsv format for each comparison.
Supplementary files format and content: Counts, RPKM and TPM values are represented as a tsv format for each sample.

organism: Malassezia globosa

extract_protocol:
Total RNA was extracted using RiboPure-Yeast Kit (Ambion, #AM1926) following manufacturer's instructions.
Library was constructed using Illumina TruSeq RNA Library Prep Kit V2 following manufacturer's instructions.

value: 2percent oxygen


title: Huh7 cells_lncRNA-HEIH_replicate 1

value: lncRNA-HEIH overexpression


title: HeLa cells_WT

value: HeLa

value: Human cervix epitheloid carcinoma


title: rra1∆_pH7_5_biological_replicate_1


title: skin derived strain s27777 in 2% oxygen, biological replicate 1


title: Huh7 cells_control_replicate 1


title: rra1∆_pH4_biological_replicate_3

value: pH 4


title: Germinating seed, 26h light, rep1, ATAC-seq

description:
L26_1_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L26.ATACseq.bw


title: Huh7 cells_lncRNA-HEIH_replicate 2


title: skin derived strain s27777 in 20% oxygen, biological replicate 2

value: 20percent oxygen


title: WN cells, DMSO, rep3

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

data_processing:
Trimmomatic (version 0.36) was used to process raw reads
reads were aligned to GRCh38 using STAR-aligner (version 2.6.1d)
Aligned reads were counted using featureCounts of subread (version 1.5.3), with the -exon flag
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: NBL-W-N

growth_protocol: Cells were grown at 5% CO2 in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using TRIzol® reagent (Life Technologies) according to the manufacture’s protocol
Strand-specific RNA-SEQ libraries were prepared using an oligo-dT based RNA-SEQ library protocol (Illumina/NEB/Kapa provided).

treatment_protocol: Cells were treated with tazemetostat 600nM or DMSO for 72 hours.

value: NBL-W-N

value: neuroblastoma cell line, MYCN-amplified

value: DMSO

tag: time

value: Day 3


title: WN cells, DMSO, rep2


title: rra1∆_pH4_biological_replicate_1


title: skin derived strain s27541 in 2% oxygen, biological replicate 2


title: skin derived strain s27777 in 20% oxygen, biological replicate 1


title: Germinating seed, 6h light, rep1, ATAC-seq

description:
L6_1_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L6.ATACseq.bw

value: Seeds

value: Germinating seed, 6h light


title: WN cells, DMSO, rep1


title: Dry seed, rep2, ATAC-seq

description:
DS_2_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
DS.ATACseq.bw

value: Dry seed


title: WN cells, taz, rep3

value: tazemetostat 600nm


title: rra1∆_DMEM_biological_replicate_3

value: DMEM


title: skin derived strain s27541 in 20% oxygen, biological replicate 2


title: WN cells, taz, rep2

value: WT


title: Dry seed, rep1, ATAC-seq

description:
DS_1_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
DS.ATACseq.bw


title: ABLab_RNA_seq_NABC708_MMS_40min_replicate2

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

data_processing:
Raw reads for the ChIP-seq results were obtained as fastq files. BWA was used in order to align the reads to the Caulobacter genome (accession number: NC_011916.1).
The aligned reads in  .bam format were converted into a .bed file format using the bamtobed option of Bedtools. Coverage was further calculated using BEDTools.
RPKM was further calculated for the samples using a custom python script.
Assembly: NC_011916.1
Supplementary files format and content: Files ending with .csv:  RPKM from RNA-seq data (column 1: gene name, column 2: RPKM)

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Overnight cultures ofCaulobactercells were back-diluted to 0.025 OD600in PYE media and grown at 30°C for 3 hours.

extract_protocol:
For RNA extraction, harvested  cells were spun down, the cell pellets were snap frozen and stored at -80°C. RNA was then extracted from these cell pellets according to a previous study (Badrinarayanan et al, 2017). RNA was isolated using Trizol extraction and purified via the Direct-zol RNA MiniPrep (Zymo, Cat. no. R2052) kit. The extracted RNA was treated with DNAse in order to remove the presence of genomic DNA from the sample. Total RNA was then purified using the RNA Clean & Concentrator-25 (Zymo, Cat. no. R1018) kit. Integrity of the RNA was assessed using Bioanalyzer instrument. mRNA was isolated from the total sample using the RiboMinus kit (Thermo, Cat. no. K155004) and submitted for sequencing.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® with sample prep beads (Cat no: E7765L)

treatment_protocol: 3 hours post back-dilution, when OD600of culture was ∼0.1, DNA damage (MMS (1.5mM) / MMC (0.25 μg/ml) / norfloxacin (8 μg/ml)) was introduced. Samples were collected at 0, 20 and 40 minutes post damage introduction.

value: Caulobacter crecentus CB15N

value: mixed population, exponential phase

value: CB15N; delta-cada2


title: skin derived strain s27541 in 2% oxygen, biological replicate 1

value: 2percent oxygen


title: rra1∆_DMEM_biological_replicate_2


title: ABLab_RNA_seq_NABC708_MMS_40min_replicate1


title: rra1∆_DMEM_biological_replicate_1


title: WN cells, taz, rep1


title: Germinating seed, 6h light, rep2, ATAC-seq

description:
L6_2_ATAC
Accessible DNA
peaks.ATACseq.bed
counts.raw.ATACseq.tsv
counts.cpm.ATACseq.tsv
L6.ATACseq.bw


title: ABLab_RNA_seq_NABC708_MMS_20min_replicate2


title: rra1∆_pH4_biological_replicate_2


title: gut derived strain g37189 in 2% oxygen, biological replicate 1


title: ABLab_RNA_seq_NABC708_MMS_20min_replicate1


title: BE2 cells, DMSO, rep3


title: rim101∆_pH7_5_biological_replicate_3


title: gut derived strain g37189 in 2% oxygen, biological replicate 2


title: rim101∆_pH7_5_biological_replicate_1


title: gut derived strain g37189 in 20% oxygen, biological replicate 2


title: ABLab_RNA_seq_NABC708_MMS_0min_replicate2


title: rim101∆_pH4_biological_replicate_3


title: BE2 cells, DMSO, rep1


title: skin derived strain s27541 in 20% oxygen, biological replicate 1


title: BE2 cells, taz, rep3


title: rim101∆_pH4_biological_replicate_2


title: rim101∆_pH4_biological_replicate_1


title: ABLab_RNA_seq_NABC707_MMS_40min_replicate2

value: CB15N; delta-cada1


title: ABLab_RNA_seq_NABC708_MMS_0min_replicate1


title: gut derived strain g37188 in 2% oxygen, biological replicate 2


title: rim101∆_pH7_5_biological_replicate_2


title: gut derived strain g37188 in 2% oxygen, biological replicate 1


title: BE2 cells, taz, rep2


title: ABLab_RNA_seq_NABC707_MMS_20min_replicate2


title: gut derived strain g37188 in 20% oxygen, biological replicate 2


title: ABLab_RNA_seq_NABC707_MMS_40min_replicate1


title: BE2 cells, taz, rep1


title: WS cells, control, rep3

source_name: NBL-W-S

value: NBL-W-S

value: Day 0


title: rim101∆_DMEM_biological_replicate_2


title: WS cells, control, rep2


title: gut derived strain g37188 in 20% oxygen, biological replicate 1

value: 20percent oxygen


title: ABLab_RNA_seq_NABC707_MMS_20min_replicate1


title: BE2 cells, DMSO, rep2

value: neuroblastoma cell line, MYCN-amplified


title: ABLab_RNA_seq_NABC707_MMS_0min_replicate2


title: gut derived strain g37189 in 20% oxygen, biological replicate 1


title: rim101∆_DMEM_biological_replicate_1


title: rim101∆_DMEM_biological_replicate_3


title: WN cells, control, rep3

value: NBL-W-N


title: ABLab_RNA_seq_NABC707_MMS_0min_replicate1


title: WT_pH7_5_biological_replicate_2


title: WT_pH7_5_biological_replicate_1


title: WN cells, control, rep2


title: WN cells, control, rep1


title: ABLab_RNA_seq_NABC2_MMS_40min_replicate2

value: CB15N; delta-recA


title: SY5Y cells, control, rep3

value: neuroblastoma cell line, MYCN-non-amplified


title: ABLab_RNA_seq_NABC2_MMS_20min_replicate1


title: WT_pH4_biological_replicate_2

value: pH 4


title: WT_pH4_biological_replicate_3


title: WT_pH7_5_biological_replicate_3


title: ABLab_RNA_seq_NABC2_MMS_20min_replicate2


title: WS cells, control, rep1


title: WT_pH4_biological_replicate_1


title: SY5Y cells, control, rep1


title: SY5Y cells, control, rep2


title: WT_DMEM_biological_replicate_3


title: ABLab_RNA_seq_NABC2_MMS_40min_replicate1


title: SHEP cells, control, rep2

source_name: SHEP

value: SHEP


title: ABLab_RNA_seq_NABC2_MMS_0min_replicate2


title: WT_DMEM_biological_replicate_1


title: ABLab_RNA_seq_CB15N_MMS_40min_replicate1


title: SHEP cells, control, rep3


title: AP64, 8 hours after the shift to light, dark control rep2

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.

data_processing:
Raw reads were processed, and differential gene expression was assessed as described before (Kopejtka et al., 2020).
Quality filtered reads were mapped to the G. phototrophica AP64T genome (GenBank accession number GCF_000695095.2) using bowtie2.
Normalization and identification of significantly differentially regulated genes (FDR < 0.01) was performed with edgeR.
Assembly: GCF_000695095.2
Supplementary files format and content: text file includes counts for each sample

organism: Gemmatimonas phototrophica

growth_protocol: G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of the experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown aerobically at dark.

extract_protocol:
Cells from triplicate cultures were harvested by centrifugation, resuspended in 1 mL PGTX extraction solution (Pinto et al., 2009) and immediately frozen in liquid nitrogen. RNA was extracted as described earlier (Kopejtka et al., 2020).
Libraries were generated according to the protocol of Shishkin et al. (2015) including rRNA removal with the RiboZero Kit (Illumina, USA) and sequenced on a NovaSeq 6000 (Illumina, USA) in paired-end mode with 100 cycles in total.

treatment_protocol: After reaching approx. OD600 = 0.2 cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1 for 2, 4, and 8 hours


title: WT_DMEM_biological_replicate_2


title: ABLab_RNA_seq_CB15N_MMS_20min_replicate1


title: ABLab_RNA_seq_CB15N_MMS_40min_replicate2


title: NBLS cells, control, rep2

source_name: NBL-S

value: NBL-S

value: neuroblastoma celll line, MYCN-overexpressing


title: ABLab_RNA_seq_NABC2_MMS_0min_replicate1


title: SHEP cells, control, rep1

value: WT


title: AP64, 8 hours after the shift to light, dark control rep3


title: AP64, 8 hours after the shift to light, rep3

value: 8 hours after the shift to light


title: NBLS cells, control, rep3


title: ABLab_RNA_seq_CB15N_MMS_20min_replicate2

value: Caulobacter crecentus CB15N

value: mixed population, exponential phase


title: SGBS_day11_rep10_oxBS (450k)

type: genomic

city: Heidelberg

first: Clarissa

last: Feuerstein-Akgoz

address: Im Neuenheimer Feld 280

institute: DKFZ

hyb_protocol: DNA samples (0.7-1.5 ng) were bisulfite (BS)- and oxidative bisulfite (oxBS)-treated using the TrueMethyl Array Kit (CEGX) according to the manufacturer’s instructions in the User Guide Version 2 (Feb 2015) as described by Gross et al. (2017) and hybridized to  Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Quality control, data preprocessing and data normalization were done using the RnBeads R package. Briefly, raw IDAT files were used as input and preprocessed separately for BS and oxBS data. Probes were filtered for a detection p-value threshold of 0.01, cross-reactive probes were removed (Chen et al., 2013) and remaining data was normalized using the beta-mixture quantile normalization (BMIQ) method.
Data represent BS and oxBS beta values after filtering for low quality and cross-reactive probes and performing beta-mixture quantile normalization (BMIQ).

label: Cy5 and Cy3

source_name: SGBS cells at day 11 of adipocyte differentiation

label_protocol: Standard Illumina Protocol

growth_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) pre-adipocytes were grown to confluency in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12Nutrient Mixture (Ham) supplemented with 10 % fetal bovine serum  (FBS), 33 µM biotin, 17 µM pantothenate, 100 U/ml penicillin, 100 µg/ml streptomycin, 1ng/µl fibroblast growth factor (FGF) 1, and 90 µg/ml heparin. Three days post-confluency (day 0), SGBS cells were washed three times with PBS and stimulated to differentiate with serum-free growth medium, supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM rosiglitazone/BRL49653, 500 µM 1-methyl-3-isobuthylxanthine (IBMX), 250 nM dexamethasone (Dex), and 0.01 mg/ml human transferrin. After 6 days, FGF-1, Heparin, IBMX, Dex, rosiglitazone were removed from the medium. Cells were harvested at day 0, 1, 7 and 11.

extract_protocol: DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an RNase A digest (RNase A solution, Qiagen) and Proteinase K digest  (Puregene Proteinase K, Qiagen). DNA  quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).

value: SGBS preadipocyte cell line

value: day 11

tag: experiment

tag: replicate

tag: conversion

value: oxBS


title: AP64, 8 hours after the shift to light, dark control rep1


title: SGBS_day11_rep11_oxBS (450k)


title: ABLab_ChIP_seq_CB15N_2h_anti_FLAG_replicate2

data_processing:
Raw reads for the ChIP-seq results were obtained as fastq files. BWA was used in order to align the reads to the Caulobacter genome.
The aligned reads in  .bam format were converted into a .bed file format using the bamtobed option of Bedtools.
Normalised coverage at each nucleotide position was calculated using the Bedtools genomecov command with -scale option.
ChIP-seq profiles from these coverage files were plotted using a custom python script.
Peakzilla was used in order to identify bona fide enrichment peaks. bed files from cada2 3xflag or rpoC 3xflag ChIP-seq under MMS exposure were compared to untagged wild type (CB15N) cells treated under identical conditions for peak-calling.
Assembly: NC_011916.1
Supplementary files format and content: Files ending with _coverage.csv:  nucleotide-resolution coverage (in rpm) from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

source_name: mixed population, exponential phase

growth_protocol: Overnight Caulobacter crescentus cultures were sub-inoculated to OD600 of  0.025, cultures were grown at 30°C for  3 hrs with shaking at 250rpm.

extract_protocol:
Cells were fixed with formaldehyde (final concentration of 1%) at room temperature for 30 min, then quenched with 0.125 M glycine for another 15 min at room temperature for ChIP-seq.
NEB NEXT UltraII library preparation kit

treatment_protocol: Upon reaching  ~OD600 of 0.1, MMS (final concentration of 1.5 mM) was added, and the cultures were outgrowth for another 2 hours before fixation with formaldehyde. Controls of no MMS treatment were also included.

tag: synonym

value: Caulobacter crescentus


title: ABLab_RNA_seq_CB15N_0min_replicate2


title: BE2 cells, control, rep2

value: Day 0


title: ABLab_RNA_seq_CB15N_0min_replicate1


title: SGBS_day07_rep10_oxBS (450k)

source_name: SGBS cells at day 7 of adipocyte differentiation

value: day 7


title: BE2 cells, control, rep3

value: neuroblastoma cell line, MYCN-amplified


title: AP64, 8 hours after the shift to light, rep1


title: NBLS cells, control, rep1


title: ABLab_ChIP_seq_CB15N_2h_anti_FLAG_replicate1


title: ABLab_ChIP_seq_CB15N_0h_anti_FLAG_replicate2


title: SGBS_day07_rep09_oxBS (450k)


title: AP64, 4 hours after the shift to light, dark control rep3


title: BE2 cells, control, rep1


title: AP64, 4 hours after the shift to light, dark control rep2


title: 5S cells, control, rep3


title: ABLab_ChIP_seq_CB15N_0h_anti_FLAG_replicate1


title: AP64, 8 hours after the shift to light, rep2


title: SGBS_day01_rep11_oxBS (450k)

source_name: SGBS cells at day 1 of adipocyte differentiation

value: day 1


title: AP64, 4 hours after the shift to light, dark control rep1


title: 5S cells, control, rep2


title: SGBS_day07_rep11_oxBS (450k)


title: SGBS_day11_rep09_oxBS (450k)


title: 5S cells, control, rep1


title: 55N cells, control, rep3


title: ABLab_ChIP_seq_NABC741_2h_anti_FLAG_replicate2


title: AP64, 4 hours after the shift to light, rep3

value: 4 hours after the shift to light


title: SGBS_day11_rep11_BS (450k)

value: BS


title: ABLab_ChIP_seq_NABC741_0h_anti_FLAG_replicate2


title: ABLab_ChIP_seq_NABC741_2h_anti_FLAG_replicate1


title: AP64, 4 hours after the shift to light, rep2


title: SGBS_day11_rep09_BS (450k)


title: AP64, 4 hours after the shift to light, rep1


title: 55N cells, control, rep2


title: SGBS_day01_rep10_oxBS (450k)


title: ABLab_ChIP_seq_NABC741_0h_anti_FLAG_replicate1


title: AP64, 2 hours after the shift to light, dark control rep3


title: SGBS_day00_rep11_oxBS (450k)

source_name: SGBS cells at day 0 of adipocyte differentiation

value: day 0


title: SGBS_day00_rep10_oxBS (450k)


title: 09-02_sRNA-seq_ubp3-OE

city: Cold Spring Harbor

first: Hyun Soo

last: Kim

state: New York

address: 1 Bungtown Rd

department: Plant

institute: Cold Spring Harbor Laboratory

data_processing:
ChIP-seq reads were trimmed using Trimmomatic, mapped to S. pombe genome using Bowtie2. Bigwig files were generated using bamCoverage and visualized in IGV genome browser. Total ChIP-seq read counts for defined region were analyzed using MultiBigwigSummary or MultiBamSummary.
sRNA-seq reads were adapter-trimmed using FASTX-Toolkit, keeping a minimum read size of 15 nt, and mapped to the S. pombe genome using Bowtie  allowing up to 1 mismatch. The strand-specific genomic coverage was calculated using Bedtools41 and represented in 20 nt windows.
Assembly: ASM294v2
Supplementary files format and content: Bigwig
Supplementary files format and content: Bedgraph

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: All yeast cells were grown in rich medium (YES)

extract_protocol:
Chromatin Immunoprecipitation (ChIP) experiments were performed as previously described29. Briefly, freshly grown 40 ml cells in YES were fixed with 1% formaldehyde from 37% stock (Sigma F8775) for 20 min at room temperature for H3K9me2, H3K9me3, RNA Pol II, Ago1 and Chp1 ChIP. For Swi6 and 3xFlag-Clr4 ChIP, 40 ml cells were pre-incubated at 18 °C for 2 h and fixed with 1.45% Formaldehyde from 16% stock (ThermoFisher 28908) for 30 min at 18 °C. Cells were quenched with 360 mM glycine and 2.4 mM Tris for 5 min. Whole-cell extracts (WCE) were prepared using FastPrep-24 and sonicated using Covaris. 1~2 μg of antibodies like anti-H3K9me2 (Abcam ab1220), anti-H3K9me3 (Absolute Antibody Ab00700-1.26), anti-RNA polymerase II (BioLegend 904001), Swi6 (Abcam ab188276), Ago1 (Abcam Ab18190), Chp1 (Abcam ab18191) and anti-Flag (Sigma F1804) were pre-incubated with 50 μl Protein A and Protein G sepharose (GE 17513801 and 17061801) mix for 3~4 h and then incubated with sheared chromatin overnight at 4 °C. After washing, bead-antibody-chromatin mixture were treated with Proteinase K (ThermoFisher 100005393) for 1 h ant 42 °C and incubated 5~6 h at 65 °C to reverse cross-links. DNA was cleaned up using ChIP DNA Clean & Concentrator (Zymo Research D5205) and subsequently used for qPCR or ChIP-Seq. For sRNA-seq, Total RNAs were purified from freshly grown yeast cells using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymoresearch R2014) and sRNA were enriched using RNA Clean & Concentrator (Zymoresearch R1013).
ChIP-Seq libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) and barcoded multiplex libraries were sequenced using Illumina MiSeq platform, which generates paired-end 101 bp reads. sRNA libraries were constructed using NEBNext Small RNA Library Prep Set for Illumina (NEB E7330) and barcoded multiplex libraries were sequenced using Illumina MiSeq platform, which generates single-end 36 nt reads.

value: yeast cells

tag: description


title: SGBS_day01_rep09_oxBS (450k)


title: 55N cells, control, rep1


title: 09-01_sRNA-seq_WT


title: ABLab_ChIP_seq_NABC718_2h_anti_FLAG_replicate1

value: CB15N; cada2-flag::specR


title: SGBS_day07_rep11_BS (450k)


title: ABLab_ChIP_seq_NABC718_2h_anti_FLAG_replicate2


title: Group3_3

city: Hefei

first: Rongrong

last: Qin

address: Jinzhai Street

institute: University of Science and Technology of China

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: tab-delimited text files include readcount values for each Sample …

source_name: Primary NK cells

growth_protocol: The enriched NK cells from PBMC of healthy volunteers were cultured in the presence of rhIL-2 (100 U/mL) in culture medium (RPMI 1640 medium supplemented with penicillin -streptomycin (100 µL/mL) and 10% human fetal bovine serum (FBS)), in a 37◦C, 95% humidity, 5%CO2 incubator.

extract_protocol:
Retinas 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

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: Primary NK cells

value: lymphocytes

value: WT

value: exposed to tacrolimus + sirolimus + corticosteroid

value: Day 3


title: AP64, 2 hours after the shift to light, dark control rep2


title: SGBS_day11_rep10_BS (450k)

value: SGBS preadipocyte cell line

value: day 11


title: Group3_2


title: SGBS_day07_rep10_BS (450k)


title: AP64, 2 hours after the shift to light, dark control rep1


title: ABLab_ChIP_seq_NABC718_0h_anti_FLAG_replicate2

value: Caulobacter crescentus

value: mixed population, exponential phase


title: Group3_1


title: 08-05_sRNA-seq_clr4-2-4KtoR


title: 08-06_sRNA-seq_clr4-W31G


title: SIR2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

value: exposed to sirolimus

value: Day 9


title: ABLab_ChIP_seq_NABC718_0h_anti_FLAG_replicate1


title: AP64, 2 hours after the shift to light, rep3

value: 2 hours after the shift to light


title: SIR1

value: Day 8


title: 08-04_sRNA-seq_clr4-2-8KtoR


title: AP64, 2 hours after the shift to light, rep1


title: SGBS_day01_rep11_BS (450k)

value: day 1

value: BS


title: EVE2

value: exposed to everolimus

value: Day 7


title: EVE1

value: Primary NK cells

value: Day 6


title: SGBS_day01_rep09_BS (450k)


title: SGBS_day07_rep09_BS (450k)

value: day 7


title: SGBS_day01_rep10_BS (450k)


title: 08-02_sRNA-seq_ubc4-1

value: yeast cells


title: SGBS_day00_rep11_BS (450k)

value: day 0


title: WI38_RNA_PHARM_INHIB_RAS_DMOG_D07_REP2

type: RNA

city: CRETEIL

first: José Américo

middle: Nabuco Leva Ferreira

last: Freitas

address: 8 rue du Général Sarrail

country: France

institute: Institut Mondor de Recherche Biomedicale

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on the Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing: Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. Internal control probe sets were removed and average expression deciles over time-points were then defined independently for each treatment. Probes whose average expression was lower athan the 4th expression decile in both conditions were removed for subsequent analyses.

label: biotin

source_name: WI38, RASOIS_DMOG, D07

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: WI-38 fibroblasts (purchased from ATCC) were cultured in DMEM GLUTAMAX, high glucose (Gibco) medium containing 10% fetal bovine serum (FBS), and 1x PenStrep (Thermofischer) in a humidified incubator at 37 °C with a 5% atmospheric concentration of O2 and CO2. The medium was changed every 2 days. Cells were split as they reached a confluency of 70-80%.

treatment_protocol: DNA damage-induced senescence (DDIS) was triggered by etoposide treatment at a concentration of 20µM for two 2 days; cells were then washed and incubated with fresh medium without drug. For the matching samples, Rapamycin was added to fresh medium at a final concentration of 20 nM just before use. Cells were collected and processed at the indicated time points following the treatment.  RAS-OIS was induced by adding 400 nM 4-hydroxytamoxifen (4-OHT) to the culture medium, and  DMOG was added to fresh medium at a final concentration of 1 mM in the corresponding samples. As before, cells were collected and processed at the indicated time points following the treatment.

value: RAS-Oncogene Induced Senescence + Dimethyloxalylglycine

tag: timepoint


title: AP64, 2 hours after the shift to light, rep2

tag: cell type

value: WT


title: AP64, dark-adapted cells, rep2

value: dark-adapted cells


title: 08-01_sRNA-seq_WT


title: 08-03_sRNA-seq_cul4-1


title: WI38_RNA_PHARM_INHIB_RAS_DMOG_D07_REP1

extract_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on the Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)


title: SGBS_day00_rep10_BS (450k)

value: SGBS preadipocyte cell line


title: AP64, dark-adapted cells, rep1


title: WI38_RNA_PHARM_INHIB_RAS_DMOG_D04_REP1

source_name: WI38, RASOIS_DMOG, D04


title: WI38_RNA_PHARM_INHIB_RAS_DMOG_D04_REP2


title: AP64, dark-adapted cells, rep3


title: CRLT5

value: lymphocytes

value: CRLT group did not contain immunosuppressive drugs.

value: Day 5


title: 07-10_sRNA-seq_cul4-1 bdf2

value: cul4-1 bdf2delta


title: WI38_RNA_PHARM_INHIB_RAS_D07_REP2

source_name: WI38, RASOIS, D07

value: RAS-Oncogene Induced Senescence


title: TAC7_1

value: exposed to tacrolimus

value: Day 3


title: Ste8_2

value: exposed to corticosteroid


title: 07-11_sRNA-seq_epe1-OE


title: CRLT4

value: Primary NK cells

value: Day 4


title: 07-08_sRNA-seq_bdf2


title: 07-06_sRNA-seq_ubc4-1 epe1

value: ubc4-1 epe1delta


title: AP64, 8 hours after the shift to light, dark control rep3 [8D6]

treatment_protocol: After reaching approx. OD600 = 0.2 cultures were illuminated with photon flux density of 200 µmol photons m-2 s-1 for 2, 4, and 8 hours


title: AP64, 8 hours after the shift to light, rep2 [8L2]

value: 8 hours after the shift to light


title: AP64, 8 hours after the shift to light, dark control rep2 [8D5]


title: Ste8_1


title: 07-09_sRNA-seq_ubc4-1 bdf2

value: yeast cells

value: ubc4-1 bdf2delta


title: AP64, 8 hours after the shift to light, dark control rep1 [8D4]

value: WT


title: 07-05_sRNA-seq_epe1


title: TAC7_2


title: WI38_RNA_PHARM_INHIB_RAS_D04_REP2

source_name: WI38, RASOIS, D04


title: MMF5_1

value: exposed to mycophenolate mofetil


title: AP64, 8 hours after the shift to light, rep3 [8L3]


title: 07-07_sRNA-seq_cul4-1 epe1

value: cul4-1 epe1delta


title: WI38_RNA_PHARM_INHIB_RAS_D07_REP1


title: AP64, 4 hours after the shift to light, dark control rep3 [4D6]


title: MMF5_2

value: lymphocytes


title: WI38_RNA_PHARM_INHIB_RAS_D00_REP1

source_name: WI38, RASOIS, D00


title: Group4_3

value: exposed to tacrolimus + everolimus   +corticosteroid


title: AP64, 8 hours after the shift to light, rep1 [8L1]


title: WI38_RNA_PHARM_INHIB_RAS_D00_REP2


title: AP64, 4 hours after the shift to light, dark control rep2 [4D5]


title: WI38_RNA_PHARM_INHIB_RAS_D04_REP1


title: 07-03_sRNA-seq_ubc4-1


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_RAPAMYCIN_D14_REP2

source_name: WI38, DDIS_RAPA, D14

value: DNA Damage-Induced Senescence + Rapamycin


title: AP64, 4 hours after the shift to light, dark control rep1 [4D4]


title: 07-04_sRNA-seq_cul4-1


title: Group4_2


title: 06-08_Bdf2-Flag ChIP-seq_ubp3-OE

value: Bdf2-Flag ubp3-OE

value: chip_antibody:anti-Flag (Sigma F1804)


title: Group2_2

value: exposed to tacrolimus +mycophenolate mofetil  +corticosteroid


title: 07-02_sRNA-seq_dcr1


title: Group4_1

value: Day 3


title: AP64, 4 hours after the shift to light, rep3 [4L3]

value: 4 hours after the shift to light


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_RAPAMYCIN_D14_REP1


title: AP64, 4 hours after the shift to light, rep2 [4L2]


title: Group2_3

value: Primary NK cells


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_RAPAMYCIN_D07_REP1

source_name: WI38, DDIS_RAPA, D07


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_RAPAMYCIN_D07_REP2


title: Group2_1


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D14_REP2

source_name: WI38, DDIS, D14

value: DNA Damage-Induced Senescence


title: 06-07_Bdf2-Flag ChIP-seq_WT

value: Bdf2-Flag WT


title: AP64, 4 hours after the shift to light, rep1 [4L1]


title: AP64, 2 hours after the shift to light, dark control rep3 [2D6]


title: 06-06_Epe1-Flag ChIP-seq_ubp3-OE

value: Epe1-Flag ubp3-OE


title: AP64, 2 hours after the shift to light, dark control rep2 [2D5]


title: 06-05_Epe1-Flag ChIP-seq_WT

value: yeast cells

value: Epe1-Flag WT


title: CSA6_2

value: WT

value: exposed to cyclosporine A


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D14_REP1


title: CSA6_1


title: AP64, 2 hours after the shift to light, dark control rep1 [2D4]


title: CRLT1_3

value: CRLT group did not contain immunosuppressive drugs.


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D07_REP2

source_name: WI38, DDIS, D07


title: 07-01_sRNA-seq_WT


title: 06-04_H3K9me3 ChIP-seq_ubp3-OE

value: chip_antibody:anti-H3K9me3 (Absolute Antibody Ab00700-1.26)


title: CRLT1_2

value: lymphocytes


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D07_REP1


title: 06-03_H3K9me3 ChIP-seq_WT


title: AP64, 2 hours after the shift to light, rep2 [2L2]

value: 2 hours after the shift to light


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D00_REP1

source_name: WI38, DDIS, D00


title: AP64, 2 hours after the shift to light, rep1 [2L1]


title: CRLT1_1


title: AP64, dark-adapted cells, rep6 [P0D6]

value: dark-adapted cells


title: AP64, dark-adapted cells, rep5 [P0D5]


title: AP64, 2 hours after the shift to light, rep3 [2L3]


title: 06-01_H3K9me2 ChIP-seq_WT


title: P_00141 Remission cd19 enriched

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
Raw fastq files were processed by cellranger count https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count to generate single cell feature counts for each library.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature-barcode matrices in Hierarchical Data Format (HDF5) generated using cellranger.

source_name: Leukemia cells

extract_protocol:
Samples were subjected to scRNA seq library construction on the 10X Genomics platform using Chromium™ Single Cell 3' v3 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol.
scRNA seq library construction was performed according to the 10X Genomics's instructions.

tag: subject

value: leukemia


title: 05-07_Flag-Clr4 ChIP-seq_Clr4-AllKtoR

tag: genotype

value: chip_antibody:anti-Flag (Sigma F1804)


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T8_P18_REP2

growth_protocol: WI-38 fibroblasts (purchased from ATCC) were cultured in DMEM GLUTAMAX, high glucose (Gibco) medium containing 10% fetal bovine serum (FBS), and 1x PenStrep (Thermofischer) in a humidified incubator at 37 °C with a 5% atmospheric concentration of O2 and CO2. The medium was changed every 2 days. Cells were split as they reached a confluency of 70-80%.  Primary human myoblasts (SkMC) were isolated from a skeletal muscle biopsy of a healthy donor (PromoCell #C-12530, Lot 414Z025.11) and were purified with an immuno-magnetic sorting system using CD56/NCAM magnetic beads (Miltenyui Biotec #130-050-401) following the manufacturer’s specifications. The purified CD56-positive myoblasts were seeded in cell culture dishes coated with type I collagen (Sigma-Aldrich #C 8919) and cultured in the proliferation medium (DMEM-high glucose (Sigma # D6429), 20% FBS (Life Technologies #10270106), 50µg/ml gentamicin (Life technologies # 15750037), 0,5% Ultroser G (PALL # 15950-017) at 37°C with 5% CO2.

treatment_protocol: WI-38-ER:RASV12 fibroblasts were generated by retroviral transduction. RAS-OIS was induced by adding 400 nM 4-hydroxytamoxifen (4-OHT) to the culture medium. Cells were collected and processed at the indicated time points following the treatment. DNA damage-induced senescence (DDIS) was triggered by etoposide treatment at a concentration of 20µM for two 2 days. Cells were then washed and incubated with fresh medium without drug. Cells were collected and processed at the indicated time points following the treatment. Replicative senescence was obtained through proliferative exhaustion.

value: Replicative senescence


title: 05-06_Flag-Clr4 ChIP-seq_Clr4-W31G ubc4-1

value: Flag-Clr4-W31G ubc4-1

tag: strain


title: P_00150 Diagnosis


title: P_00141 Remission bulk


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T8_P18_REP2_BIS


title: AP64, dark-adapted cells, rep4 [P0D4]


title: WI38_RNA_PHARM_INHIB_ETOPOSIDE_D00_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T8_P18_REP1


title: 05-04_Flag-Clr4 ChIP-seq_cul4-1

tag: tissue

value: Flag-Clr4 cul4-1


title: 05-05_Flag-Clr4 ChIP-seq_Clr4-W31G


title: AP64, dark-adapted cells, rep3 [P0D3]


title: P_00141 Relapse


title: P_00141 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T7_P17_REP1


title: AP64, dark-adapted cells, rep2 [P0D2]


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T8_P18_REP1_BIS


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T7_P17_REP2


title: 05-02_Flag-Clr4 ChIP-seq_WT


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T6_P14_REP2


title: AP64, dark-adapted cells, rep1 [P0D1]


title: P_00091 Remission cd19 enriched


title: AP64, 10% O2, 8 hours after the shift to light, rep3

data_processing:
Raw reads were processed, and differential gene expression was assessed as described before (Kopejtka et al., 2020).
Quality filtered reads were mapped to the G. phototrophica AP64 genome (GenBank accession number GCF_000695095.2) using bowtie2.
Normalization and identification of significantly differentially regulated genes (FDR < 0.01) was performed with edgeR.
Assembly: GCF_000695095.2
Supplementary files format and content: text file includes counts for each sample

growth_protocol: G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of each experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown in triplicates at dark aerobically (20% O2) or semiaerobically (10% O2).

treatment_protocol: After reaching approx. OD600 = 0.2 cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1 for 2 and 8 hours

value: 8 hours after the shift to light, 10% O2


title: 05-01_Flag-Clr4 ChIP-seq_untag


title: AP64, 10% O2, 8 hours after the shift to light, rep2


title: P_00091 Relapse


title: 04-08_H3K9me3 ChIP-seq_clr4-AllKtoR


title: P_00091 Diagnosis


title: 04-07_H3K9me3 ChIP-seq_clr4-2-4KtoR


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T5_P12_REP2


title: AP64, 20% O2, 8 hours after the shift to light, rep3

value: 8 hours after the shift to light, 20% O2


title: AP64, 10% O2, 8 hours after the shift to light, rep1


title: 05-03_Flag-Clr4 ChIP-seq_ubc4-1

value: Flag-Clr4 ubc4-1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T5_P12_REP1


title: CU_L_78 Remission cd19 enriched


title: 04-06_H3K9me3 ChIP-seq_clr4-2-8KtoR

value: yeast cells


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T4_P8_REP2


title: 04-05_H3K9me3 ChIP-seq_WT


title: CU_L_78 Remission bulk


title: 04-04_H3K9me2 ChIP-seq_clr4-AllKtoR


title: P_00091 Remission bulk


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T6_P14_REP1


title: AP64, 10% O2, 2 hours after the shift to light, rep3

value: 2 hours after the shift to light, 10% O2


title: 06-02_H3K9me2 ChIP-seq_ubp3-OE


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T4_P8_REP1


title: P_00150 Relapse


title: 04-03_H3K9me2 ChIP-seq_clr4-2-4KtoR


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T3_P5_REP2


title: CU_L_78 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T3_P5_REP1


title: 04-02_H3K9me2 ChIP-seq_clr4-2-8KtoR


title: CU_L_349 Relapse


title: AP64, 10% O2, 2 hours after the shift to light, rep2

value: WT


title: AP64, 10% O2, 2 hours after the shift to light, rep1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T2_P3_REP2


title: AP64, 20% O2, 8 hours after the shift to light, rep2


title: CU_L_349 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T2_P3_REP1


title: CU_L_78 Relapse


title: 04-01_H3K9me2 ChIP-seq_WT


title: 03-06_H3K9me3 ChIP-seq_epe1-OE


title: AP64, 20% O2, 2 hours after the shift to light, rep3

value: 2 hours after the shift to light, 20% O2


title: AP64, 20% O2, 8 hours after the shift to light, rep1


title: CU_L_323 Relapse


title: AP64, 20% O2, 2 hours after the shift to light, rep2


title: 03-04_H3K9me3 ChIP-seq_WT


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T1_P1_REP2


title: CU_L_323 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T1_P1_REP1


title: CU_L_294 Remission cd19 enriched


title: AP64, 10% O2, dark-adapted cells, rep3

value: dark-adapted cells, 10% O2


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D21_REP2

source_name: WI38, RASOIS, D21

value: RAS-Oncogene Induced Senescence


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D21_REP1


title: 03-02_H3K9me2 ChIP-seq_cul4-1


title: CU_L_294 Remission bulk


title: 03-03_H3K9me2 ChIP-seq_epe1-OE


title: AP64, 10% O2, dark-adapted cells, rep2


title: CU_L_294 Relapse


title: AP64, 10% O2, dark-adapted cells, rep1


title: CU_L_277 Remission cd19 enriched


title: 03-01_H3K9me2 ChIP-seq_WT


title: AP64, 20% O2, dark-adapted cells, rep2

value: dark-adapted cells, 20% O2


title: 02-10_Bdf2-Flag_epe1-OE

value: Bdf2-Flag epe1-OE


title: CU_L_294 Diagnosis


title: AP64, 20% O2, 2 hours after the shift to light, rep1


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D14_REP1

source_name: WI38, RASOIS, D14


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D14_REP2


title: 02-09_Bdf2-Flag_cul4-1


title: 03-05_H3K9me3 ChIP-seq_cul4-1

value: chip_antibody:anti-H3K9me3 (Absolute Antibody Ab00700-1.26)


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D07_REP1


title: CU_L_277 Remission bulk

value: leukemia


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D07_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D04_REP2


title: 02-08_Bdf2-Flag_ubc4-1

value: chip_antibody:anti-Flag (Sigma F1804)


title: AP64, 20% O2, dark-adapted cells, rep1


title: CU_L_277 Relapse


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D04_REP1


title: CU_L_277 Diagnosis


title: 02-07_Bdf2-Flag_WT


title: CU_L_106 Remission cd19 enriched


title: AP64, 20% O2, dark-adapted cells, rep3


title: SAM_696_RNA-seq

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts

source_name: primary bladder tumor

extract_protocol:
Total RNA was isolated from tissue using TRI reagent based method.
Total RNA (500 ng) was processed for preparing whole transcriptome sequencing library. Enrichment of whole transcriptome RNA by depleting ribosomal RNA ( rRNA ) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

tag: age

tag: gender

value: female

tag: histologic type

value: Non-muscle invasive bladder cancer (NMIBC)

tag: progression

value: no


title: SAM_839_RNA-seq


title: CU_L_106 Remission bulk


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D02_REP2

source_name: WI38, RASOIS, D02

tag: cell line

tag: treatment


title: 02-05_Epe1-Flag_epe1-OE

source_name: yeast cells

value: Epe1-Flag epe1-OE


title: CU_L_106 Relapse


title: 02-04_Epe1-Flag_cul4-1

value: Epe1-Flag cul4-1


title: CU_L_106 Diagnosis


title: 02-03_Epe1-Flag_ubc4-1

value: Epe1-Flag ubc4-1


title: SAM_708_RNA-seq

value: male


title: SAM_660_RNA-seq


title: 02-01_Epe1-Flag_untag

value: yeast cells


title: SAM_689_RNA-seq


title: SAM_657_RNA-seq


title: 02-06_Bdf2-Flag_untag

value: WT


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D00_REP2


title: COG9 Remission cd19 enriched


title: SAM_653_RNA-seq


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D02_REP1


title: SAM_672_RNA-seq


title: COG9 Remission bulk


title: 01-18_Rpb1 ChIP-seq_clr4

value: chip_antibody:anti-RNA Pol II (Biolegend 904001)


title: 02-02_Epe1-Flag_WT


title: SAM_650_RNA-seq


title: COG9 Relapse


title: WI38_SENESCENCE_TRANSCRIPTOME_RAS_D00_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_T0_REP1

value: DNA Damage-Induced Senescence


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_T0_REP2


title: COG9 Diagnosis


title: 01-17_Rpb1 ChIP-seq_dcr1 ubc4-1

value: dcr1delta ubc4-1


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_T0_REP3


title: 01-16_Rpb1 ChIP-seq_dcr1


title: SAM_626_RNA-seq


title: 01-15_Rpb1 ChIP-seq_cul4-1


title: COG8 Remission bulk


title: COG8 Remission cd19 enriched


title: 01-14_Rpb1 ChIP-seq_ubc4-1


title: COG8 Relapse


title: SAM_595_RNA-seq


title: 01-13_Rpb1 ChIP-seq_WT


title: COG8 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_48H_REP3

source_name: WI38, DDIS, D02


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_48H_REP1


title: SAM_575_RNA-seq


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_24H_REP3

source_name: WI38, DDIS, D01


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_336H_REP5


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_48H_REP2


title: COG7 Remission cd19 enriched


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_336H_REP4


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_24H_REP2


title: 01-10_H3K9me3 ChIP-seq_dcr1


title: SAM_571_RNA-seq


title: 01-12_H3K9me3 ChIP-seq_clr4


title: COG7 Remission bulk


title: COG7 Relapse


title: SAM_637_RNA-seq


title: SAM_573_RNA-seq


title: COG7 Diagnosis


title: SAM_569_RNA-seq


title: 01-09_H3K9me3 ChIP-seq_cul4-1


title: SAM_599_RNA-seq


title: 01-08_H3K9me3 ChIP-seq_ubc4-1


title: COG6 Remission cd19 enriched


title: 01-11_H3K9me3 ChIP-seq_dcr1 ubc4-1


title: 01-07_H3K9me3 ChIP-seq_WT


title: SAM_531_RNA-seq


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_240H_REP4

source_name: WI38, DDIS, D10


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_240H_REP5


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_168H_REP5


title: SAM_527_RNA-seq


title: 01-06_H3K9me2 ChIP-seq_clr4


title: COG6 Relapse


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_168H_REP4


title: SAM_517_RNA-seq


title: 01-05_H3K9me2 ChIP-seq_dcr1 ubc4-1


title: COG6 Diagnosis


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_24H_REP1


title: SAM_566_RNA-seq


title: COG5 Remission cd19 enriched


title: 01-04_H3K9me2 ChIP-seq_dcr1


title: SAM_513_RNA-seq


title: SAM_510_RNA-seq


title: 01-03_H3K9me2 ChIP-seq_cul4-1


title: 01-02_H3K9me2 ChIP-seq_ubc4-1


title: COG6 Remission bulk


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_168H_REP2


title: SAM_482_RNA-seq


title: COG5 Remission bulk


title: COG5 Relapse


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_168H_REP1


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_T0_REP2

source_name: SkMC, RASOIS, D00

value: SkMC

value: RAS-Oncogene Induced Senescence


title: SAM_464_RNA-seq


title: COG5 Diagnosis


title: iscWAT_old_Rep4

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads were aligned  with STAR Mapper v2.7.8a using Ensembl gene annotations.
Count files were created using STAR counts.
Assembly: Monodelphis domestica reference genome (ASM229v1) using Ensembl gene annotations.
Supplementary files format and content: csv countfiles, raw reads, Ensembl Gene Annotation

organism: Monodelphis domestica

source_name: interscapular adipose tissue

extract_protocol:
RNA was extracted from three different adipose tissue depots (anterior subcutanous, inguinal, interscapular) using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
Paired-end: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Single-end: Libraries were prepared by isolating total RNA from fat tissue homogenized in TRIzol reagent. Total RNA was converted to cDNA and then to sequencing-ready barcoded Illumina libraries with the NUGEN complete RNAseq kit

value: interscapular adipose tissue

value: 10 weeks

value: m

tag: animal id

tag: developmental stage

value: old


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_T0_REP2_BIS


title: WI38_SENESCENCE_TRANSCRIPTOME_ETOPOSIDE_168H_REP3


title: COG4 Remission bulk

value: leukemia


title: iscWAT_old_Rep3


title: SAM_446_RNA-seq

value: female

value: Non-muscle invasive bladder cancer (NMIBC)

value: yes


title: SAM_454_RNA-seq

value: no


title: COG4 Relapse


title: iscWAT_old_Rep2

value: f


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_96H_REP1

source_name: SkMC, RASOIS, D04


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_T0_REP1


title: iscWAT_young_Rep4

value: 6 weeks

value: young


title: SAM_433_RNA-seq

value: male


title: COG19 Remission cd19 enriched


title: iscWAT_old_Rep1


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_96H_REP2


title: SAM_425_RNA-seq


title: COG4 Diagnosis


title: COG4 Remission cd19 enriched


title: iscWAT_young_Rep3


title: SAM_437_RNA-seq


title: SAM_455_RNA-seq


title: iscWAT_young_Rep2


title: COG19 Relapse


title: 01-01_H3K9me2 ChIP-seq_WT

value: yeast cells

value: WT


title: iscWAT_young_Rep1


title: SAM_395_RNA-seq


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_48H_REP1

source_name: SkMC, RASOIS, D02

value: SkMC


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_48H_REP2

value: RAS-Oncogene Induced Senescence


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_432H_REP1

source_name: SkMC, RASOIS, D18


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_432H_REP2


title: COG19 Diagnosis


title: SAM_391_RNA-seq


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_336H_REP2_BIS

source_name: SkMC, RASOIS, D14


title: COG19 Remission bulk


title: SAM_408_RNA-seq


title: COG17 Remission bulk


title: SAM_375_RNA-seq


title: SAM_370_RNA-seq


title: Ribo_CQC-2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: SacCer3
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

growth_protocol: SC medium

extract_protocol:
The cells were filtered using 0.45µm MCE membrane and lysed in lysis buffer using the beads shocker.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion by riboPOOL for Saccharomyces cerevisiae (siTOOLs), reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, SEQuoia Express Stranded RNA Library Prep Kit (Bio-Rad).

tag: isolates

value: CQC

value: Wild type


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_240H_REP2

source_name: SkMC, RASOIS, D10


title: scRNAseq_CD31_P8MI_1

city: Houston

first: Jong

middle: H

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: snRNA

library_source: transcriptomic single cell

data_processing:
scRNA-seq: The 10x Genomics Cell Ranger software (cellranger 3.0.1,www.10xgenomics.com) was used to handle raw sequencing data. Fastq files were aligned to the mouse mm10 genome. A pre-mRNA version of the reference genome was provided for gene count quantification with the Cellranger count function.
CellBender v0.1.0 was used to remove background from the Cellranger output with the remove-background module in default settings.
The h5 expression matrices from each data source were then imported into Seurat 3 for downstream processing and annotation to account for source-specific quality differences (Stuart et al, 2019).
Single cells were filtered for UMI (unique molecular identifiers) counts with a minimum of 500 and a maximum of 25,000 per cell. We also imposed a cutoff of 0.5% for mitochondrial reads and a cutoff of 0.25% for doublet score.
Seurat toolkit version v.4.0 in R v.3.8 was used to perform downstream analyses. The processed UMI count matrices of filtered cells were normalized with the Seurat function SCTransform to regress out additional variation.
The FindVariableFeatures function was used to calculate the top 5,000 most variable features for each sequenced library. The Seurat function FindIntegrationAnchors was used to find mutual nearest neighbors across subsets. Seurat’s IntegrateData function was used to construct an integrated matrix for each cell with a correction vector (based on anchor and similarity scores). The integrated data were scaled and the principal components were calculated (n = 50). Dimensional reduction (UMAP) and clustering were used to identify clusters (dimensions = 20, cluster resolution = 1.5).
Assembly: mm10
Supplementary files format and content: 10x output

organism: Mus musculus

source_name: Heart

extract_protocol:
Atria and aorta were removed from the heart, and the remaining tissue was used for single cell digestion. Cells were harvested at either P5 or P12, from pools of 5 hearts subjected to MI at P1 or P8, respectively. Tissues were minced into small pieces in digestion buffer (HBSS, 1 mg/mL collagenase A) and incubated at 37ºC with agitation for 30 minutes. The suspension was triturated with a 5 mL pipette every 10 minutes. Proper digestion was verified by appearance of single cells under a microscope. The digestion was then diluted 1:1 with HBSS, and the resulting cell suspension was centrifuged at 300 rpm for 6 minutes to remove cardiomyocytes. Supernatant was passed through a 40-micron filter to remove tissue fragments and cardiomyocytes, and then centrifuged at 500 x g for 6 minutes. The cell pellet was resuspended in 1 mL of MACs buffer (PBS, 0.5 % BSA, 2 mM EDTA). The resuspended cells were centrifuged at 500 x g for 6 minutes to remove residual buffer and resuspended in a final volume of 80 uL for incubation with 20 uL of CD31 MACs beads (Miltenyi Biotech). MACs enrichment for CD31+ cells was performed according to the Miltenyi enrichment protocol. Live cells were quantified with Trypan Blue and inCyto C-Chip DHC-F01. For single-nuclei ATAC sequencing, nuclei were isolated from cells according to the 10x protocol. Live nuclei were quantified with DAPI and inCyto C-Chip DHC-F01.
scRNA-seq libraries were generated using the 10x Chromium Single Cell 3′ Library Kit v3 (10x Genomics) according to the manufacturer’s instructions. snATAC-seq libraries were generated using the 10x Chromium Single Cell ATAC Library Kit v1 according to the manufacturer’s instructions.

treatment_protocol: Mouse were subjected to MI at P1 or P8

value: Heart

tag: time

tag: enrichment

value: CD31+ enrichment

value: left anterior descending artery occlusion


title: COG17 Relapse

source_name: Leukemia cells

value: leukemia


title: Ribo_CQC-1


title: SAM_367_RNA-seq

value: Non-muscle invasive bladder cancer (NMIBC)


title: COG14 Remission cd19 enriched


title: COG17 Diagnosis


title: SAM_312_RNA-seq

value: female


title: COG17 Remission cd19 enriched


title: scRNAseq_CD31_P1MI_2

description: snRNA


title: scRNAseq_CD31_P1MI_1

description: snRNA


title: SAM_306_RNA-seq

value: no


title: COG14 Remission bulk


title: SAM_379_RNA-seq


title: Ribo_CPI-1

value: CPI


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_336H_REP1

tag: timepoint


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_240H_REP1


title: shYap-2-rep3

city: Nanjing

first: linyuan

last: peng

address: #639 Longmian Dadao, Jiangning District,Nanjing

institute: China Pharmaceutical University

data_processing:
Sequencing reads were filtered by fastp (version 0.18.0), mapped to the reference genome using HISAT2(version 2.1.0), and then assembled by Stringtie (version 1.3.4). A FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify the expression abundance and variations of each transcription region by RSEM software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: cell type

value: breast cancer

value: Knock down Yap


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_168H_REP1

source_name: SkMC, RASOIS, D07


title: SAM_259_RNA-seq

value: male


title: COG14 Relapse

tag: subject


title: MYOBLAST_SENESCENCE_TRANSCRIPTOME_RAS_168H_REP2


title: COG14 Diagnosis


title: shYap-2-rep2

tag: genotype


title: Ribo_CMP-2

value: CMP

value: yeast cells


title: shYap-2-rep1


title: SAM_223_RNA-seq


title: Ribo_CMP-1


title: shYap-1-rep3


title: SAM_208_RNA-seq


title: SAM_205_RNA-seq

value: yes


title: 8173 Diagnosis


title: Ribo_BTT-2

value: BTT


title: Ribo_CPI-2


title: 7300 Relapse


title: 8173 Relapse


title: Ribo_BTT-1


title: shYap-1-rep1


title: Ribo_BPL-1

value: BPL


title: Ribo_BPL-2

value: Wild type


title: 6787 Relapse


title: shCTRL-rep3

value: WT

value: Negative control


title: SAM_160_RNA-seq


title: 7300 Diagnosis


title: Ribo_BED-2

value: BED


title: SAM_147_RNA-seq


title: shCTRL-rep2


title: SAM_177_RNA-seq


title: shYap-1-rep2


title: 6787 Diagnosis

value: leukemia


title: Ribo_BED-1


title: shCTRL-rep1


title: SAM_141_RNA-seq

value: Non-muscle invasive bladder cancer (NMIBC)


title: SAM_144_RNA-seq