title: Kidney,DD0-3,WT

tag: strain


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, ChIP-H3K27ac, rep2

status: Public on Jun 03 2024

type: SRA

city: Houston

first: Hsiao-Chi

last: Chen

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.6).
Reads were mapped to the mouse genome mm10 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
MACS2 was used for histone serotonylation and findPeaks command in histone (for H3K27ac and H3K27me3) were used to filter ChIP peaks enriched over Input control
Annotation of enriched peaks was performed using annotatePeaks with mm10 assembly
Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Assembly: mm10
Supplementary files format and content: bw

molecule: genomic DNA

organism: Mus musculus

source_name: mouse ZFTA-RELA ependymoma tumor

extract_protocol:
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012). 10 ng of DNA was used as starting material. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and quality assessed using a Standard Sensivity NGS Fragment Analysis Kit.

tag: cell type

value: mouse ZFTA-RELA ependymoma tumor

tag: genotype

value: human variant ETV5 overexpression

tag: chip antibody

value: anti-H3K27ac, Abcam #ab4729


title: Kidney,DD0-4,WT

city: Shanghai

first: Renrui

address: No. 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter:--phred33 --length 50 --stringency 3 --paired)
Trimmed sequence reads were mapped to GrCM38/mm10 using  HISAT2 (parameters-  -t -p 8 --dta --rna-strandness RF)
Read count extraction and normalization were performed using Samtools (parameters view -b -q 60) and featureCounts(parameters -T 16 -p -s 2)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

source_name: Kidney

extract_protocol:
We extracted total RNA from tissue samples using Trizol (Invitrogen). After separating the RNA, DNA, and protein layers with chloroform, we precipitated the RNA using a standard isopropanol/ethanol procedure. The resulting RNA pellet was washed, and then resuspended in RNase-free water.
We assessed the quantity and quality of the total RNA using the Qubit RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). For RNA-seq library construction, we followed the Illumina TruSeq Total RNA stranded protocol.

tag: tissue

value: Kidney

value: WT

tag: time point


title: Aedes aegypti, Naïve-infected, Day2, Rep1

city: Taipei

first: Yu-Ning

last: Huang

address: No.1 Jen Ai road section 1

department: Biochemistry and molecular biology

country: Taiwan

institute: National Taiwan University

data_processing:
The bcl2fastq conversion software v2.20 was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic v0.36 with a sliding-window approach (parameter: Q20)
Trimmed sequence reads were aligned to AaegL5.0 using HISAT2
Cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline were used to perform differential expression analysis.
Assembly: AaegL5.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Aedes aegypti

source_name: Higgs

growth_protocol: The mosquitoes were kept in 75%–80% humidity at 28℃ and were given 10% sucrose. Light and dark periods were 12:12 h.

extract_protocol:
RNA was harvested using RNA extraction kit (ZYMO Research, catalog E1011-A). Five ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent's SureSelect Strand-Specific RNA Library Preparation Kit.

treatment_protocol:
The female mosquitoes at 7 to 14 days post eclosion were used for the experiments. The mice were tail-vein injected with DENV TW-2015 or PBS as naïve infection. After 3-4 days, the female mosquitoes were feed with DENV- or naïve- infected mice.
After taking the blood meal, the mosquitoes were supplied with 10% sucrose until whole body harvesting for RNA-seq.

value: Higgs

tag: treatment

value: Naïve infection

tag: time

value: Day 2


title: 30-W1: Patient 29 Early Wound

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Our processing pipeline consists of the following elements: (1) base calls generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 26 (GRCh38.p10) using STAR (v2.5.3a).
Counts per gene were generated using the Bioconductor Rsubread package version 1.32.4, using the inbuilt hg38 gene annotations
Genes were filtered using the Bioconductor edgeR package version 3.24.3, using the filterByExpr function to remove unexpressed or unreliable genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table containing raw gene counts per sample. Column names correspond to the raw file names and the row names correspond to the NCBI Gene ID

organism: Homo sapiens

source_name: Skin

extract_protocol:
RNA was isolated from 108 human samples comprising of uninjured skin (n=26), acute burn wounds (n=54), and hypertrophic scars (HTS) (n=30). Frozen tissue was pulverized using mortar and pestle in liquid nitrogen to maintain temperature during processing. Total RNA, including small RNAs such as microRNAs, non-coding RNA, messenger RNA, and ribosomal RNA was isolated using the MagMAX™ mirVana™ Total RNA Isolation Kit (Applied Biosystems) followed by DNAse digestion on Purelink RNA mini kit spin columns (Thermo Fisher Scientific).
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103). All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput. Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474). Samples where adapter dimers constitute more than 4% of the electropherogram area are failed prior to sequencing. Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized. Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Samples were collected from patients admitted to the UW Medicine Regional Burn Center and undergoing an operation for burn injury from 2002 to 2018. Samples consisted of discarded burn wounds, scars, and donor skin that were stored as part of an IRB exempt human tissue repository. All samples were de-identified upon collection. Specific to the wound samples, when able, samples were collected at periphery of the burn wound to include the epithelial edge where the transition from wound to normal tissue exists as previously described.[8] Tissue samples were minced and placed in cryogenic vials for either snap freezing in liquid nitrogen within 20 minutes of collection or placement in RNALater (Invitrogen, Carlsbad, CA) and stored in 4°C overnight to allow the solution to penetrate the tissue. All samples were transferred to -80°C for long term storage.

tag: subject

value: Patient 29

value: Skin

tag: wound type

value: Early Wound

tag: days since injury

tag: age

tag: Sex

value: male

tag: hispanic

value: no

tag: race

value: native american

tag: burn type

value: flame

value: wound

tag: location

value: back


title: mouse ZFTA-RELA ependymoma tumor, ChIP-5HTH3, rep2

value: mouse ZFTA-RELA ependymoma tumor

value: control

value: anti-H3K4me3Q5ser, EMD #ABE2580


title: Kidney,DD0-2,WT

value: Kidney

tag: strain


title: Aedes aegypti, Naïve-infected, Day7, Rep3

value: Day 7


title: 17-S: Patient 16 Normal scar

value: Patient 16

value: Normal scar

value: female

value: yes

value: hispanic

value: contact

value: scar

value: hand


title: Aedes aegypti, Naïve-infected, Day1, Rep3

value: Higgs

value: Naïve infection

value: Day 1


title: 16-D: Patient 15 Normal skin

value: Patient 15

value: Skin

value: Normal skin

value: male

value: unknown

value: white

value: flash

value: uninjured


title: 18-S: Patient 17 HTS

value: Patient 17

value: HTS

value: asian

value: flame

value: neck


title: Aedes aegypti, Dengue-infected, Day7, Rep3

value: Day 7


title: mouse ZFTA-RELA ependymoma tumor, input (for 5HTH3), rep2

tag: cell type

value: mouse ZFTA-RELA ependymoma tumor

value: control


title: 14-S: Patient 14 Normal scar

value: Patient 14

value: Normal scar

value: female

value: black

value: scar

value: upper extremity


title: Aedes aegypti, Dengue-infected, Day7, Rep2

value: Higgs

value: Dengue infection


title: Liver,DD20-2,WT

source_name: Liver

value: Liver

tag: genotype

value: WT


title: Liver,DD20-4,WT


title: Kidney,DD0-1,WT

value: Kidney


title: 13-W: Patient 13 Late wound

value: Patient 13

value: Skin

value: Late wound

value: male

value: yes

value: hispanic

value: chemical

value: wound

value: lower extremity


title: mouse ZFTA-RELA ependymoma tumor, input (for 5HTH3), rep1

value: mouse ZFTA-RELA ependymoma tumor

value: control

tag: chip antibody


title: Aedes aegypti, Dengue-infected, Day7, Rep1

value: Day 7


title: mouse ZFTA-RELA ependymoma tumor, NPY overexpression rep3

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.6).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.3).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values

molecule: polyA RNA

source_name: ZFTA-RELA ependymoma

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (Qiagen, 74106)
cDNA synthesis and library construction with 6-bp single indices were done from 300 ng total RNA using TruSeq Stranded mRNA kit (Illumina, RS-122-2101).
A final library dilution of 1.3 pM was subjected to paired-end sequencing.

value: ZFTA-RELA ependymoma

value: ZFTA-RELA, human variant NPY overexpression


title: Aedes aegypti, Naïve-infected, Day1, Rep2

value: Higgs

value: Naïve infection

value: Day 1


title: Aedes aegypti, Naïve-infected, Day1, Rep1


title: Liver,DD20-3,WT

tag: tissue

value: Liver

value: WT


title: 12-W: Patient 12 Early Wound

value: Patient 12

value: Skin

value: Early Wound

value: unknown

value: white

value: upper extremity


title: mouse ZFTA-RELA ependymoma tumor, input (for 5HTH3), rep3


title: Aedes aegypti, Dengue-infected, Day2, Rep3

value: Dengue infection

value: Day 2


title: mouse ZFTA-RELA ependymoma tumor, NPY overexpression rep2


title: mouse ZFTA-RELA ependymoma tumor, NPY overexpression rep1


title: Liver,DD20-1,WT

tag: time point


title: mouse ZFTA-RELA ependymoma tumor, ChIP-5HTH3, rep1

value: mouse ZFTA-RELA ependymoma tumor

value: control

value: anti-H3K4me3Q5ser, EMD #ABE2580


title: Liver,DD16-4,WT


title: Liver,DD16-3,WT


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression rep3

value: ZFTA-RELA ependymoma

value: ZFTA-RELA, human variant ETV5 overexpression


title: Aedes aegypti, Dengue-infected, Day2, Rep1

value: Higgs

tag: treatment


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression rep2


title: Liver,DD16-2,WT


title: Aedes aegypti, Dengue-infected, Day1, Rep3

tag: time

value: Day 1


title: Liver,DD16-1,WT

value: Liver


title: Liver,DD12-4,WT

value: WT


title: mouse ZFTA-RELA ependymoma tumor, rep3

value: ZFTA-RELA


title: Aedes aegypti, Dengue-infected, Day1, Rep2


title: mouse ZFTA-RELA ependymoma tumor, rep2


title: Gypsy Moth Strain RM, Day 5, Replicate 2

city: Quebec City

first: Christopher

middle: Ian

last: Keeling

state: QC

address: 1055 rue du PEPS

department: Canadian Forest Service

country: Canada

institute: Natural Resources Canada

data_processing:
Sequencing reads were assessed for quality with FastQC (v0.11.5) (Andrews, 2019).
Sequences were trimmed for adapters, quality, and minimum length with Trimmomatic (v0.36) (Bolger et al., 2014).
The existing annotations from the draft genome were augmented by merging them with the read mapping information from all samples using StringTie prior to counting reads at each locus with featureCounts (v2.0.0, counting gene_id meta-features) (Liao et al., 2014).
Statistical analyses were conducted with the DESeq2 package (v1.28.1) (Love et al., 2014) in R (v4.0.2) (R Core Team, 2020), using the apeglm package (v1.10.0) (Zhu et al., 2019) for shrinkage estimation.
Data in this GEO submission report the normalized counts after variance stabilizing transformation with vst(fitType='local') within DESeq2.
Genome_build: lda.genome.v0.3.fasta available here: https://doi.org/10.17605/OSF.IO/UNZ2V
Supplementary_files_format_and_content: PROJECT_Cusson_pupae_flight_vst_counts.txt: Normalized count data after variance-stabilizing transformation.
Supplementary_files_format_and_content: The 'PROJECT_Cusson_pupae_flight_representative_transcripts.fa' contains a representative transcript sequence for each locus in the genome for which gene-level expression levels are reported. The best representative at each locus was chosen based upon the highest expression of the various splice variants from StringTie, counting transcript_id meta-features.

organism: Lymantria dispar asiatica

source_name: Gypsy Moth Strain RM_Day 5

growth_protocol: Eggs from laboratory colonies were held at 5±1°C and ~100% RH with L:D of 16:8 for 144 days to ensure that diapause requirements were met. All eggs produced by 100 individual females from each geographic population (CT 32nd lab generation and RM 34th lab generation) were mixed together, as is the normal process for maintaining these colonies. From the pool of mixed eggs, packets of about 500 eggs were made. Eggs were incubated at 25±1°C and 60% RH with L:D of 16:8 to initiate hatch.

extract_protocol:
Samples were homogenized individually in Trizol reagent (Ambion, Life Technologies; 4 to 7 mL depending on the size of the pupa) using 15 mL disposable tissue grinders (VWR, Cat.47732-446). For each sample, 500 µL of the homogenate was transferred to a 1.5 mL microfuge tube, to which another 500 µL of Trizol was added. The tubes were then centrifuged for 4 min at 17,000 x g to pellet debris. 400 µL of the supernatant was subsequently used for RNA extraction using the Direct-zol RNA miniprep kit (Zymo Research). RNAs were eluted using 50 µL of water, quantified using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific Inc.) and assessed for quality using a 2100 Bioanalyzer system (Agilent).
RNASeq libraries and Ion Proton sequencing were performed at the Genomic Analysis Platform of the Institute of Integrative and Systems Biology (Laval University, Quebec, QC, Canada) using the NEBNext Ultra II directional RNA library prep kit (New England BioLabs) with the NEBNext Poly (A) mRNA magnetic isolation module. Ion Proton sequencing was performed on an Ion Chef with a P1 chip according to manufacturer's instructions.

treatment_protocol: Larvae were reared in cohorts of 6 at 25±1°C and 60% RH with L:D of 16:8, using methods previously described (Keena 1996). The high wheat germ artificial diet (Bell et al. 1091) was optimized for the individual populations using Wesson salt mix without iron and by adding 0.21 g (RM population) or 0.13 g (CT population) amorphous FePO4/L of diet. Pupae were harvested daily and separated according to sex.

value: RM

value: female

tag: sampling timepoint (day)


title: Aedes aegypti, Dengue-infected, Day1, Rep1


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression rep1


title: Aedes aegypti, Dengue-infected, Day2, Rep2


title: Liver,DD12-3,WT


title: Gypsy Moth Strain RM, Day 11, Replicate 3

source_name: Gypsy Moth Strain RM_Day 11


title: mouse ZFTA-RELA ependymoma tumor, rep1


title: mouse non-tumor cortex tissue, rep3

source_name: cortex

value: cortex

value: wild-type


title: Liver,DD12-1,WT


title: Gypsy Moth Strain RM, Day 5, Replicate 1


title: mouse non-tumor cortex tissue, rep2


title: Gypsy Moth Strain RM, Day 11, Replicate 2


title: Liver,DD8-4,WT


title: Liver,DD8-3,WT


title: Liver,DD12-2,WT


title: Liver,DD8-2,WT


title: mouse non-tumor cortex tissue, rep1


title: WT cells, 24h stimulated, rep2

city: San Diego

first: Bryan

last: McDonald

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto"
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig

source_name: WT

extract_protocol:
Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.

tag: cell line

value: 24h stimulated


title: WT cells, 24h stimulated, rep1


title: Gypsy Moth Strain RM, Day 11, Replicate 1


title: WT cells, 1h stimulated, rep2

value: 1h stimulated


title: Liver,DD8-1,WT


title: Liver,DD4-4,WT


title: Gypsy Moth Strain RM, Day 8, Replicate 3

source_name: Gypsy Moth Strain RM_Day 8


title: WT cells, 1h stimulated, rep1


title: Gypsy Moth Strain RM, Day 3, Replicate 3

source_name: Gypsy Moth Strain RM_Day 3


title: Liver,DD4-3,WT


title: WT cells, Naïve, rep2

value: Naive


title: Gypsy Moth Strain RM, Day 3, Replicate 2


title: Liver,DD4-2,WT


title: Gypsy Moth Strain RM, Day 8, Replicate 2


title: Liver,DD4-1,WT


title: WT cells, Naïve, rep1


title: Gypsy Moth Strain RM, Day 3, Replicate 1


title: Gypsy Moth Strain RM, Day 1, Replicate 2

source_name: Gypsy Moth Strain RM_Day 1


title: Liver,DD0-3,WT


title: Gypsy Moth Strain RM, Day 1, Replicate 3


title: Gypsy Moth Strain RM, Day 8, Replicate 1


title: control_Lats2-2_12w

city: Münster

first: Paul-Georg

last: Majev

address: Röntgenstraße 20

department: Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

library_source: transcriptomic single cell

data_processing:
Read pre-processing using cutadapt version 3.5
Read alignment and feature counting using STARsolo version 2.7.10a
Assembly: mm39
Supplementary files format and content: Feature count matrices were generated using STARsolo and are present in mtx format with annotations present in tsv format

source_name: mouse long bone

extract_protocol: 10x genomics Chromium V3

value: post natal week 12

value: untreated

value: bone


title: cKO_Lats2-2_12w

value: conditional Lats2 KO


title: Liver,DD0-2,WT


title: Liver,DD0-1,WT


title: Gypsy Moth Strain RM, Day 1, Replicate 1


title: Spt3/7-degron yeast, minus auxin treatment (negative control)

status: Public on Jun 02 2024

first: Jeremy

middle: Aspin

last: Schofield

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
The CellRanger count pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was performed on Fastq cells using a custom 3'-end S. cerevisiae annotation (derived from Roy and Chanfreau, 2020, PMID: 31128237) to generate a barcode, feature and matrix files.
Assembly: SacCer3
Supplementary files format and content: Tab-separated values files and matrix files

organism: Saccharomyces cerevisiae

source_name: Spt3/7-degron (SHY1176)

growth_protocol: Saturated overnight cultures of yeast cells were diluted in fresh YPD media at an initial OD of 0.2. Cells were then cultured at 30°C to mid-log phase (OD ~0.8).

extract_protocol:
Fixed cells were incubated on ice for 15min, then pelleted and washed twice with ice cold PBS + 0.01% BSA. Cells were resuspended in 400ul PBS + 0.01% BSA, and the cell suspension was added to 1mL of alkylation buffer, followed by a 45min incubation at 45°C with occasional inversion. Cells were pelleted and washed twice with PBS + 0.01% BSA + 10mM DTT, then washed once with 1M sorbitol + 0.01% BSA. Cells were then resuspended in 900ul spheroplasting buffer, and 100ul of 100mg/ml Zymolyase 100T was added. Cells were spheroplasted for ~30min at 30°C with occasional inversion. The spheroplasting mixture was filtered through a MACS SmartStrainer, and spheroplasts were pelleted then washed twice in 1M sorbitol + 0.01% BSA. Spheroplasts were counted immediately prior to GEM generation using a hemocytometer.
The Chromium Next GEM Single Cell 3ʹ Kit (10x Genomics, V3.1) protocol was performed according to manufacturer's instructions. Briefly, GEMs containing Gel Beads decorated with poly(dT) capture sequences (including Illumina TruSeq Read 1 sequence, 10x Cell barcode, and UMI) were prepared. GEMs were combined with prepared yeast spheroplasts, resulting in lysis of the spheroplasts in droplets and capture of PolyA-containing RNA on Gel Beads. Captured RNAs were reverse transcribed, GEMs were broken and pooled, and cDNA was amplified resulting in the installation of i5 and i7 sample indexes. Prepared paired-end libraries were sequenced on an Illumina NextSeq 2000 instrument using P3 reagents, with read configuration of 28nt for R1 to identify cell barcode and UMIs, and 125nt for R2 to sequence the captured mRNA.

treatment_protocol: For timecourse studies, WT yeast cells (BY4705) at mid-log phase were treated with 5 mM 4-TU (5mM) for 5min, 10min, or 15min or left untreated (DMSO only). Immediately following 4-TU treatment, cells were placed on ice and 2 volumes of ice-cold PBS was added to the culture. Cells were pelleted at 4°C and washed with ice cold PBS + 0.01% BSA. Cells were again pelleted and resuspended in 1mL 1ml PBS + 0.01% BSA. Cells were fixed by continuous gentle vortexing while adding ice cold methanol dropwise to a final concentration of 80%. Cells were incubated on ice for 15min, at which point fixed cells were stored overnight at –20°C. Coactivator depletion studies were performed in Med15-degron (SHY1055) or Spt3/7-degron (SHY1176) strains. Prior to 4-TU labeling for 10min, cells were treated with either 500uM auxin (3-indoleacetic acid) in DMSO or DMSO alone as a negative control, and the remainder of the above protocol was performed.

value: Spt3/7-degron (SHY1176)

value: DMSO (30min), 5mM 4-TU (10min)


title: Med15-degron yeast, minus auxin treatment (negative control)

source_name: Med15-degron (SHY1055)

value: Med15-degron (SHY1055)


title: Spt3/7-degron yeast, plus auxin treatment


title: control_Lats2-1_12w

value: control


title: Gypsy Moth Strain RM, Day 5, Replicate 3


title: Liver,DD0-4,WT

value: Liver

value: WT


title: WT yeast, 15 minute 4-TU treatment

value: 5mM 4-TU (15min)


title: WT yeast, 10 minute 4-TU treatment

value: 5mM 4-TU (10min)


title: Med15-degron yeast, plus auxin treatment


title: WT yeast, 5 minute 4-TU treatment

value: 5mM 4-TU (5min)


title: WT yeast, DMSO treatment (negative control)

value: none (DMSO)


title: MRC5_ZFAS1 overexpression, UV_12H, Ser2P

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v3.36, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Burrows-Wheeler Aligner (BWA-v0.7.12), only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequence fragments, renormalized and reformatted in the bigWig file format.
Peaks were called using MACS v1.4.2 with the significance cut-off q-value <=0.01.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v1.4.2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

growth_protocol: DMEM, 10% fetal bovine serum,  1 x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes, after quenching and cell lysis, chromatin was sonicated using an ice-water bath-embedded Bioruptor sonication system.
1 ng of ChIPed DNA and Input DNA samples were used for library construction by standard ChIP-Seq library preparation techniques (NEBNext® Ultra™ DNA Library prep kit, NEB, #E7103) and sequenced under Illumina NovaSeq 6000 system.

treatment_protocol: Cells were irradiated by 10 J/m2 UV-C and recovered for the indicated time prior to extraction.

value: Human lung fibroblast

value: 10 J/m2 UV-C, recovered for 12hr

value: RNAPII CTD-Ser2P (Millipore, 04-1571)


title: genomic DNA, U251, DMSO, 2

type: genomic

city: Los Angeles

first: Thomas

middle: Jasper

last: Lai

address: Gonda Room 1554 695 Charles E. Young Dr.

department: Neurosurgery

institute: University of California; Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Human MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: scans were analyzed in R using the minfi R package (version 1.44.0)

label: Cy3, Cy5

source_name: immortalized glioma cell line

label_protocol: Standard Illumina protocol

growth_protocol: Primary GS lines were cultured in serum free media as spheres. U251 cells cultured in 10% FBS in DMEM as adherent cells.

extract_protocol: Genomic DNA was isolated using Quick DNA/RNA Miniprep Kit according to manufacturer’s protocol (Zymo Research) and bisulfite converted using the EZ Methylation Gold Kit (Zymo Research).

treatment_protocol: GS cells treated with 0.5-uM DAC 4 days a week for 3 weeks. U-251 cells cultured with 1-uM DAC for 2 or 4 days for one week.

tag: diagnosis

value: immortalized GBM


title: cKO_Lats2-1_12w

tag: age

value: post natal week 12


title: MRC5_ZFAS1 overexpression, UV_12H, input


title: MRC5_ZFAS1 overexpression, UV_12H, Ser5P

value: RNAPII CTD-Ser5P (Millipore, 04-1572)


title: genomic DNA, U251, DMSO, 1


title: MRC5_ZFAS1 overexpression, UV_3H, Ser5P

value: 10 J/m2 UV-C, recovered for 3hr


title: MRC5_ZFAS1 overexpression, UV_3H, Ser2P


title: MRC5_ZFAS1 overexpression, UV_6H, Ser5P

value: 10 J/m2 UV-C, recovered for 6hr


title: MRC5_ZFAS1 overexpression, CTD Ser2P

value: untreated


title: MRC5_ZFAS1 overexpression, UV_3H, input


title: MRC5_ZFAS1 overexpression, CTD Ser5P


title: MRC5_WT, UV, H3.3 [H3_UV_IP]

treatment_protocol: Cells were irradiated by 10 J/m2 UV-C and recovered for 3 hrs prior to extraction.

value: 10 J/m2 UV-C irradiation


title: MRC5_ZFAS1 overexpression, UV_6H, input


title: MRC5_ZFAS1 overexpression, input


title: genomic DNA, U251, DAC, 2d, 1


title: MRC5_WT, input [H3_in]


title: genomic DNA, U251, DAC, 4d, 2


title: MRC5_KD, UV, 40 minutes, GRO-seq

data_processing:
single-ended reads were aligned to the hg38 genome assembly using BWA v0.5.9.
Bam files were sorted and indexed using SAMtools.
Assembly: hg38
Supplementary files format and content: excel file include raw counts for each sample

molecule: nuclear RNA

extract_protocol:
Transcription-competent nuclei were extracted using the Nuclei Isolation Kit. Nuclear Run-On reactions were carried out by adding of Run-On Buffer and incubated for 5 minutes. Br-UTP run-on labeled RNA was isolated using anti-Br-UTP coupled agarose beads. RNA was eluated and purified by phenol-chloroform.
The purified RNA was used for the preparation of strand-specific RNA libraries using the TruSeq Stranded Total RNA LT sample Prep Kit, and sequenced under Illumina NovaSeq 6000 system as single-ended 50 bp reads.

treatment_protocol:
Cells were incubated with 100 μM DRB for 3.5 hr.
Cells were irradiated by 10 J/m2 UV-C and recovered for 10 minutes or 40 minutes prior to extraction.

value: 40 minutes


title: genomic DNA, GS243, DMSO, 1

source_name: primary gliomasphere

value: IDHwt Glioblastoma


title: MRC5_ZFAS1 overexpression, UV_6H, Ser2P


title: MRC5_WT, UV, input [H3_UV_in]


title: genomic DNA, U251, DAC, 4d, 1


title: MRC5_KD, UV, 10 minutes, GRO-seq

value: 10 minutes


title: MRC5_KD, no UV, 40 minutes, GRO-seq


title: MRC5_WT, UV, 40 minutes, GRO-seq


title: MRC5_WT, UV, 10 minutes, GRO-seq


title: genomic DNA, GS277, DMSO, 1


title: MRC5_WT, no UV, 40 minutes, GRO-seq


title: genomic DNA, GS351, DAC, 1


title: genomic DNA, GS025, DAC, 1


title: genomic DNA, GS277, DAC, 1


title: MRC5_WT, no UV, 10 minutes, GRO-seq


title: MRC5_KD, UV, input


title: MRC5_KD, CDK9

value: CDK9 (Abcam, ab239364)


title: genomic DNA, U251, DAC, 4d, 3


title: MRC5_KD, input


title: MRC5_WT, UV, input


title: MRC5_WT, CDK9


title: MRC5_WT, input


title: MRC5_KD, UV, CDK9


title: MRC5_WT, UV, CDK9


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep3, input

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

country: Switzerland

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

data_processing:
Raw reads were trimmed to remove reads shorter than 99 base pairs and crop reads exceeding 101 bp (trimmomatic v.0.39), then aligned (bwa mem v.0.7.17-r1188) to the human reference genome build GCA hg38 lacking chrY but including non-canonical contigs. Alignments were filtered to exclude reads with mapping quality scores below 30 (bedtools v.2.29.2), PCR and optical duplicates (Picard MarkDuplicates, v.2.23.8), ENCODE-blacklisted regions, non-canonical contigs, and unmapped or secondary alignments (and for paired-end top-up reads, unpaired reads) (samtools v.1.7).
Filtered alignments were used to call peaks (macs2 v.2.2.7.1) from treatment (IP) over input control tagAlign files, where input control replicates were pooled together for all replicates and, following the ENCODE ChIP-seq processing guidelines, subsampled to 200 million reads for the H3K27ac ChIP-seq assays from wildtype cells.
Peaks were called with default parameters of macs2 using a cutoff p-value of 1e-2; broad peaks were called for H3K4me1 and narrow peaks for H3K27ac ChIP-seq. Peaks were used to verify replicabiity with idr (v.2.0.4.2). Only robust peaks (those shared across at least two of three biological duplicates) were retained in downstream analyses. The top quartile of robust peaks were determined by rank ordering peaks by signal strength. Fold enrichment (bigWig) tracks were generated of IP signal over input control.
Assembly: hg38
Supplementary files format and content: BED files: gzipped broadPeak (for H3K4me1) or narrowPeak (for H3K27ac) for each biological replicate.
Supplementary files format and content: bigWig files: Fold change (IP over IN) for each biological replicate.

growth_protocol: Low glucose DMEM, 10% fetal calf serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Non-UV or 3h-post UV cells were crosslinked with 1% formaldehyde for 10 minutes. Quenching and lysis was followed by sonication (BioRuptor Plus) for 20 cycles (30 sec on/off).
To remove UV-induced DNA lesions with the potential to inhibit sequencing, immunoprecipitated, de-crosslinked fragments were incubated with PreCR Repair mix (New England BioLabs, M0309) for 15 min at 37°C, then re-purified, quantified by Qubit (Invitrogen, Q33238) and sent to the Functional Genomics Center Zurich for final library preparation with the NEB Next Ultra Kit (New England BioLabs, E7645). Libraries were sequenced as 100 bp single-end reads on the NovaSeq 6000.

treatment_protocol: Cells grown to 80-90% confluency were left untreated (non-UV) or were UV-C irradiated at 20 J/m2 and left to recover for 3h.

value: ASH1L knockout

value: 3h post UV

tag: antibody

value: none (input control)


title: genomic DNA, GS025, DMSO, 1


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep2, input


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep3

value: H3K27ac (Abcam, ab4729)


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep1, input


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep3, input

value: no UV


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep2, input


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep2


title: genomic DNA, GS243, DAC, 1


title: genomic DNA, GS025, DMSO, 2


title: genomic DNA, GS243, DMSO, 2


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep3, input

value: wildtype


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep2


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep1, input


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep2


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep2, input


title: genomic DNA, GS081, DMSO, 1


title: H3K27ac, U2OS ASH1L knockout cells, 3h post UV, biol rep1


title: H3K27ac, U2OS wildtype cells, no UV, biol rep3, input


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep3


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep1


title: H3K27ac, U2OS ASH1L knockout cells, no UV, biol rep1


title: genomic DNA, GS081, DAC, 1


title: H3K27ac, U2OS wildtype cells, no UV, biol rep3


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep3


title: H3K27ac, U2OS wildtype cells, no UV, biol rep2, input


title: genomic DNA, GS025, DAC, 2


title: genomic DNA, GS351, DMSO, 1


title: genomic DNA, GS243, DAC, 2


title: H3K27ac, U2OS wildtype cells, 3h post UV, biol rep1, input


title: H3K27ac, U2OS wildtype cells, no UV, biol rep1, input


title: C. difficile, Primary Intestinal Epithelial Cell (IEC) Mucus (Condition 3), Rep C

city: Chapel Hill

first: Kathleen

middle: Louise

last: Furtado

email: klfurtado@ucdavis.edu, kfurtado@unc.edu

state: NC

address: 125 Mason Farm Road

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

description: 2x150bp reads

data_processing:
Read quality assessed using FASTQC (v0.11.8).
Universal sequencing adapters removed using Trimmomatic (v0.36) in PE mode with palindromic adapter trimming. Additional parameters as follows: SLIDINGWINDOW:5:25 MAXINFO:50:0.8 LEADING:30 TRAILING:25 MINLEN:40. Adapter file available from Trimmomatic GitHub page.
Contaminating reads from human or porcine mitochondria (which may have been present in mucus sources), as well as PhiX, were removed using Fastq_screen (v0.14.0), with --aligner bowtie2 --force parameters. Contaminating genome sequence accession IDs as follows: NC_012920.1 (Homo sapiens mitochondrion), NC_000845.1 (Sus scrofa mitochondrion), NC_001422.1 (PhiX)
Read mapping performed using Bowtie2 (v2.4.1) in global mode with --very-sensitive, --dovetail, --phred33, -t, and -q parameters.
Genomic feature counting performed using Feature Aggregate Depth Utility (FADU, v1.8), a prokaryotic-specific algorithm. This step generated the processed data files uploaded herein. Default parameters used.
More details on data processing and associated code are available from GitHub: https://github.com/klfurtado/2024_Cdiff_Mucus_Paper
Assembly: FN545816.1
Supplementary files format and content: Processed data files are provided as tab-delimted .txt as the direct output from FADU. One file is uploaded per sample. First column (featureID) provides CDR20291 locus tags from Accession ID FN545816.1, with "gene-" preceeding each locus tag. Second column (uniq_len) provides the number of bases that do not overlap with other features. Third column (num_alignments) provides the number of BAM records that align to non-overlapping bases for each feature. Fourth column (counts) provides fractionalized read counts for each feature; these values were used in differential expression analysis in the above study. Fifth column provides transcript per million values; these values were used in contextualized metabolic modeling for the above study.

organism: Clostridioides difficile R20291

source_name: bacteria

growth_protocol: C. difficile grown in C. difficile minimal medium (CDMM) with or without 50 µg/mL mucus; C. difficile cultures were inoculated at a starting OD600 ~ 0.05, then grown to exponential phase (OD600 ~0.5) prior to collection.

extract_protocol:
C. difficile RNA extracted by bead beating in 1 mL TriZol, followed by addition of 200 µl chloroform. Samples centrifuged, then aqueous layers containing RNA were mixed 1:1 with 70% cold ethanol. This mixture was then applied to columns in an RNeasy kit (Qiagen) and purified using manufacturer instructions, including on-column DNase treatment with RNase-Free DNase Set (Qiagen) prior to elution.
Libraries prepared using GENEWIZ (now Azenta Life Sciences) commercial services. Library preparation included RNA quality assessment, rRNA depletion, and adapter ligation (all completed by vendor).

treatment_protocol: Prior to growth, CDMM supplemented with 50 µg/mL commercial porcine gastric mucus (PGM) or primary intestinal epithelial cell (IEC)-derived mucus

value: bacteria

value: Primary IEC Mucus


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl3, input


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl2, input


title: C. difficile, Primary Intestinal Epithelial Cell (IEC) Mucus (Condition 3), Rep A

description: 2x150bp reads


title: H3K27ac, U2OS wildtype cells, no UV, biol rep1


title: C. difficile, Commercial Porcine Gastric Mucus (PGM, Condition 2), Rep C

description: 2x150bp reads

value: Commercial PGM


title: MRC5_WT, H3.3 [H3_IP]

value: Human lung fibroblast


title: C. difficile, Primary Intestinal Epithelial Cell (IEC) Mucus (Condition 3), Rep B

description: 2x150bp reads


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl3

value: H3K4me1 (Abcam, ab8895)


title: C. difficile, No Mucus (Condition 1),  Rep C

description: 2x150bp reads

value: No Mucus


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl3, input


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl2


title: C. difficile, No Mucus (Condition 1), Rep A

description: 2x150bp reads


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl3


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl1, input


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl2, input


title: C. difficile, No Mucus (Condition 1),  Rep B

description: 2x150bp reads


title: 50_204004_RUM

city: Wanju

first: Yejee

last: Park

address: Kongjwipatjwi-ro 1500

country: South Korea

institute: National Institute of Animal Science

data_processing:
Quality of RNA-seq reads from all of the rumen tissues were checked using FastQC (v0.11.9).
Reads passed the quality control were mapped to Bos taurus genome (ARS-UCD1.2) from ENSEMBL using Hisat2 (v2.2.1).
The reads were counted using featurecount tool
The reads were nomalized using VST by DESeq2
DEGs were detacted by DESeq2 tool
Assembly: Bos taurus (ARS-UCD1.2)
Supplementary files format and content: tab-delimited text files include raw counts of genes for each sample.

organism: Bos taurus

source_name: rumen

extract_protocol:
RNA extraction using Qia 96 RNA, Qia Mini
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide

value: rumen

tag: breed

value: Hanwoo

value: 30 month


title: H3K27ac, U2OS wildtype cells, no UV, biol rep2


title: C. difficile, Commercial Porcine Gastric Mucus (PGM, Condition 2), Rep A

description: 2x150bp reads


title: 49_202013_RUM


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl1, input


title: 35_192027_RUM


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl2


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep3


title: H3K4me1, U2OS ASH1L knockout cells, no UV, biol repl1


title: 36_192028_RUM


title: C. difficile, Commercial Porcine Gastric Mucus (PGM, Condition 2), Rep B

description: 2x150bp reads


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep3, input


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep1, input


title: 33_192022_RUM


title: H3K4me1, U2OS ASH1L knockout cells, 3h post UV, biol repl1


title: 56_202041_RUM

value: 26 month


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep2


title: MRC5_KD, no UV, 10 minutes, GRO-seq

value: untreated

value: 10 minutes


title: 34_192029_RUM


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep1

value: 3h post UV


title: H3K4me1, U2OS wildtype cells, 3h post UV, biol rep2, input

value: none (input control)


title: 25_192025_RUM


title: 42_202003_RUM


title: 23_192030_RUM


title: H3K4me1, U2OS wildtype cells, no UV, biol rep3, input


title: 41_202021_RUM


title: H3K4me1, U2OS wildtype cells, no UV, biol rep2, input


title: H3K4me1, U2OS wildtype cells, no UV, biol rep3


title: 24_192024_RUM


title: 32_192034_RUM


title: CPDs, U2OS ASH1L knockout cells, 3h post UV (paired-end)

data_processing:
Raw reads were trimmed and adapters removed with bbduk (bbmap v.38.90) followed by alignment (bwa mem v.0.7.17-r1188) to the human reference genome build GCA hg38 lacking chrY but including non-canonical contigs.  Alignments were merged across technical replicates.
Alignments were filtered to remove PCR and optical duplicates, ENCODE-blacklisted regions, and non-canonical contigs. Only alignments with mapping quality scores of at least 20 were retained (samtools v.1.7; bedtools v.2.29.2).
The dinucleotide sequences immediately upstream of each read were extracted from the opposite strand and filtered to retain only dipyrimidines.
Assembly: hg38
Supplementary files format and content: BED files are provided of genome-wide CPD positions, fltered to include only di-pyrimidine sequences.
Library strategy: High-sensitivity DNA damage-seq

extract_protocol:
UV-C-irradiated DNA was extracted with the QIAamp DNA Mini kit (Qiagen). As naked DNA controls, genomic DNA extracted with the same kit was also subjected to UV-C irradiation and thereafter immediately subjected to the damage-seq assay. DNA was fragmented to around 400 bp average length by sonication (Q800 sonicator, Qsonica; 20% amplitude for 3 min, 2 sec on/5 sec off).
Sonicated fragments were size selected with beads (AMPure XP, Beckman Coulter) to remove fragments below 200 bp, end repaired and ligated to the first of two indexed Illumina adapters with the NEB Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)), pulled down with anti-CPD antibody (TMD2, Cosmo Bio), and subjected to subtractive hybridization with salmon sperm DNA (Thermo Fisher Scientific, AM9680) to remove non-CPD-containing fragments. DNA was re-extracted by phenol-chloroform extraction and  primer extended with NEBNext Ultra II Q5 polymerase until the damage site, ligated to the second Illumina adapter, and PCR amplified. All libraries were sequenced on the NovaSeq 6000 (Illumina). The 0 h and 3 h cellular damage-seq experiments were first sequenced as 100 bp single-end reads and subsequently, to obtain higher coverage, as 150 bp paired-end reads. The naked DNA controls and the replication experiment were sequenced as 100 bp single-end reads.

treatment_protocol: Cells grown to 80-90% confluency were UV-C irradiated at 20 J/m2, harvested immediately (0h timepoints), or left to recover for 3h.

value: ASH1L knockout

value: CPD (Cosmo Bio, TMD2)


title: H3K4me1, U2OS wildtype cells, no UV, biol rep1, input

value: wildtype

value: no UV


title: 45_202040_RUM

value: 22 month


title: H3K4me1, U2OS wildtype cells, no UV, biol rep1


title: H3K4me1, U2OS wildtype cells, no UV, biol rep2


title: CPDs, U2OS ASH1L kncokout cells, 0h post UV, naked DNA control

value: 0h post UV


title: 46_202029_RUM


title: 16_192031_RUM


title: CPDs, U2OS ASH1L knockout cells, 3h post UV


title: 15_192019_RUM


title: CPDs, U2OS ASH1L knockout cells, 0h post UV


title: CPDs, U2OS ASH1L knockout cells, 0h post UV (paired-end)


title: CPDs, U2OS wildtype cells, 3h post UV (paired-end)


title: 51_212011_RUM

value: 18 month


title: 53_212001_RUM


title: CPDs, U2OS wildtype cells, 3h post UV


title: 38_202034_RUM


title: CPDs, U2OS wildtype cells, 0h post UV, naked DNA control


title: CPDs, U2OS wildtype cells, 0h post UV, biol repl experiment


title: CPDs, U2OS wildtype cells, 0h post UV (paired-end)


title: 12_192026_RUM


title: 29_202018_RUM


title: 20_202005_RUM


title: siNC_3

city: Urumqi

first: Yongkang

address: 91 Tianchi Road, Tianshan District, Urumqi, Xinjiang

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

data_processing:
Raw reads containing more than 2-N bases were first discarded. The adaptors and low-quality bases were then trimmed from the raw sequencing reads using FASTX-Toolkit (Version 0.0.13).
Short reads less than 16 nt were also removed. The obtained clean reads were aligned to the GRch38 genome by tophat2 allowing four mismatches.
The uniquely mapped reads were used for gene reads number counting and fragments per kilobase of transcript per million fragments mapped (FPKM) calculation
Assembly: GRch38 genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: KYSE150 cells

growth_protocol: The KYSE150 cell line (Procell Life Science & Technology Co., Ltd., China) was cultured at 37 °C with 5% CO2 in RPMI1640 with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation using KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01), and fragmented mRNAs were converted into double-strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). After the purification of ligation product and size fractioning to 300–500 bps, the ligated products were amplified, purified, quantified, and stored at −80 °C before sequencing. For strand-specific sequencing, the strand marked with dUTP (second cDNA strand) was not amplified.
For high-throughput sequencing, the libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: SiRNA transfection of the cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s protocol. Transfected cells were harvested after 48 h for quantitative reverse-transcription polymerase chain reaction (RT-qPCR) and Western blot analysis.

value: KYSE150 cells

value: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a control gene


title: 28_202002_RUM

value: rumen


title: siNC_2


title: 58_212021_RUM

value: Hanwoo

value: 14 month


title: 11_192021_RUM


title: 43_212005_RUM


title: siNC_1


title: 44_212002_RUM


title: siALDH18A1_2

value: ALDH18A1 knockdown


title: 40_202030_RUM


title: 27_202039_RUM


title: 19_202020_RUM


title: siALDH18A1_1


title: CPDs, U2OS wildtype cells, 0h post UV


title: 26_202043_RUM


title: siALDH18A1_3


title: 57_212012_RUM


title: 14_202017_RUM


title: Input_1

data_processing:
After the reads were aligned onto the genome with TopHat2, only uniquely mapped reads were used for the following analysis. The “ABLIRC” strategy was applied to identify the binding regions of ALDH18A1 on genome.
For each gene, computational simulation was used to randomly generated reads with the same number and lengths as the reads in peaks. The output reads were further mapped to the same genes to generate random max peak height from the overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (P-value < 0.05) were selected.
The target genes of IP were finally determined from the peaks and the binding motifs of IP protein with the HOMER software.
Assembly: GRch38 genome
Supplementary files format and content: tab-delimited text files include peak information for each group.

growth_protocol: KYSE150 cells were irradiated once for 400 mJ/cm2, lysed in ice-cold wash buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 200 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Roche), and incubated on ice for 30 min.

extract_protocol:
Clear cell lysate was obtained by centrifugation at 10,000 rpm and 4 °C for 10 min. RQ I (Promega, 1U/μL) was added to a final concentration of 1 U/μL, and the sample was incubated in a water bath for 30 min at 37 °C. A stop solution was immediately added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 x g and 4 °C for 20 min to remove cell debris. The RNA was then digested using MNase (Thermo Scientific)
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) in accordance with the manufacturer’s procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to Illumina NovaSeq system for 150 nt paired-end sequencing.

treatment_protocol: For immunoprecipitation, the supernatant was incubated overnight at 4 °C with 10 μL of ALDH18A1-antibody (proteintech: 17719-1-AP) and control IgG-antibody (CST: 2729). The immunuprecipitates were further incubated with protein A/G Dynabeads (Thermo Scientific) for 2 h at 4 °C. After the magnet was applied and the supernatants were removed, the beads were sequentially washed twice with lysis buffer, high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), and PNK buffer (50 mM Tris, 20 mM EGTA and 0.5% NP-40). The beads were resuspended in the elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS), and the suspension was incubated for 20 min in a heat block at 70 °C to release the immunoprecipitated RBP with crosslinked RNA and vortex. The magnetic beads on the separator were removed, and the supernatant was transferred to a clean 1.5 mL microfuge tube. Proteinase K (Roche) was added into the 1% input (without immunoprecipitation) and immunoprecipitated RBP with crosslinked RNA at a final concentration of 1.2 mg/mL. The sample was incubated for 120 min at 55 °C. The RNA was purified with Trizol reagent (Life technologies).

tag: fraction

value: Input


title: Input_2


title: DS sample 19, cortex (total RNA)

city: Genova

first: Laura

last: Cancedda

state: Genova

address: Via Morego, 30

department: Brain Development and Disease

country: Italy

institute: Italian Institute of Technology

description:
Ds19
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

data_processing:
fastq files were mapped using STAR v2.7.3a aligner to Homo sapiens GRCh38/hg38 ensembl version 99 genome using two-pass method.
In the first pass mapping, each file was mapped to the reference genome with 1pass mapping parameters.
Then, the mapped spliced junctions for each sample were extracted and concatenated. The junctions originating from mitochondrial genes were filtered out.
A new index was created based on the concatenated splice junctions, and then the 2pass mapping was performed on the 1pass mapped files. The output of the 2pass mapping consisted of bam files and reads per gene information for each sample.
These were the raw counts to be used for further analysis.
For the transcript quantitation, the files were processed using RSEM and the count matrix was used to perform differential expression analysis using EBSeq.
Assembly: hg38 version 99 (Ensembl)
Supplementary files format and content: tab-delimited raw counts text file contains Ensembl ID as the row names and the sample ID as columns with values indicating raw counts obtained from STAR aligner.
Supplementary files format and content: tab-delimited cpm text file contains Ensembl ID as the row names and the sample ID  as columns with counts per million values obtained after performing PCA analysis and before differential expression analysis using EdgeR.
Supplementary files format and content: tab-delimited raw counts text file contains Ensembl transcript ID as the row names and the sample ID as columns with values indicating raw counts obtained from RSEM

source_name: Cortex

extract_protocol:
Briefly, RNA was extracted from 50 mg of crushed tissue lysated with 1 mL of QIAzol reagent (Qiagen) and the help of stainless steel beads in a TissueLyzer apparatus (Qiagen) at 20Hz for 2 minutes at room temperature. RNA was purified on miRNeasy spin columns (Qiagen). RNA samples were initially quantified at 260 nm with an ND1000 Nanodrop spectrophotometer (Thermo Scientific). RNA purity was also determined by absorbance at 280 and 230 nm. All samples showed A260/280 and A260/230 ratios greater than 1.9. RNA quality and integrity were verified by microfluidic assay with Agilent 2100 Bioanalyzer. The RNA integrity number (RIN) ranged between 2.1 and 7.3. For library preparation the RNA concentration was measured with Qubit 4 Fluorometer (Thermo Fisher Scientific).
500 ng RNA was used to prepare sample libraries. Briefly, Illumina’s TruSeq stranded total RNA library preparation kit was used following manufacturer’s instructions. All the sample libraries were then quantitated on Agilent 2100 Bioanalyzer. The size in bp and concentration of the peak corresponding to the amplified products were used for normalizing the library inputs. The normalized libraries were then multiplexed and loaded onto the Illumina flow cell. Paired-end sequencing for 100 bp each was performed on Illumina NovaSeq 6000 system with 100 million reads/sample.

value: Cortex

tag: condition

value: Down syndrome

tag: Sex

value: male

tag: race

value: white


title: 54_214031_RUM

value: 12 month


title: 13_202012_RUM


title: ALDH18A1_IP_1

value: IP


title: 52_214027_RUM


title: DS sample 18, cortex (total RNA)

description:
Ds18
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: black


title: 39_212006_RUM


title: DS sample 17, cortex (total RNA)

description:
Ds17
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: 22_202037_RUM


title: DS sample 16, cortex (total RNA)

description:
Ds16
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: female


title: 37_212008_RUM


title: DS sample 15, cortex (total RNA)

description:
Ds15
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: ALDH18A1_IP_2


title: 21_202044_RUM


title: 10_202001_RUM


title: DS sample 13, cortex (total RNA)

description:
Ds13
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: 9_202009_RUM


title: DS sample 14, cortex (total RNA)

description:
Ds14
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: DS sample 12, cortex (total RNA)

description:
Ds12
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: 4_192032_RUM


title: DS sample 9, hippocampus (total RNA)

description:
Ds9
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

source_name: Hippocampus

value: Hippocampus


title: DS sample 11, cortex (total RNA)

description:
Ds11
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: DS sample 8, hippocampus (total RNA)

description:
Ds8
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 3_192018_RUM


title: DS sample 10, cortex (total RNA)

description:
Ds10
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: 48_214039_RUM

value: 10 month


title: 31_212003_RUM


title: 47_212019_RUM


title: DS sample 7, hippocampus (total RNA)

description:
Ds7
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 2_192033_RUM


title: DS sample 5, hippocampus (total RNA)

description:
Ds5
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: Asian


title: DS sample 3, hippocampus (total RNA)

description:
Ds3
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 7_204006_RUM


title: DS sample 6, hippocampus (total RNA)

description:
Ds6
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 8_204011_RUM


title: 68_224063_RUM

value: 6 month


title: DS sample 2, hippocampus (total RNA)

description:
Ds2
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 1_192017_RUM

value: rumen


title: DS sample 4, hippocampus (total RNA)

description:
Ds4
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: 66_224045_RUM

value: Hanwoo


title: Control sample 22, cortex (total RNA)

description:
C22
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: Control


title: 65_224042_RUM


title: 18_202033_RUM


title: 17_202036_RUM


title: Control sample 20, cortex (total RNA)

description:
C20
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: Control sample 23, cortex (total RNA)

description:
C23
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: Control sample 18, cortex (total RNA)

description:
C18
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: greater omental adipose tissue, replicate 1, scRNAseq

city: Taigu

first: Ruiwen

last: Fan

address: Mingxian South Road 1

institute: Shanxi Agricultural University

description:
Go_YM03
10×Genomics

data_processing:
Sample collection and preparation for single-cell sequencing,Single-cell capture preparation and sequencing,scRNA-seq computational analyss,Cell Ranger v5.0.1(https://support.10xgenomics.com/single- cell-gene-expression/software/downloads/latest),Seurat v3.2.0(https://satijalab.org/seurat/),CellPhoneDB v2.1.4(https://www.cellphonedb.org),iTALK v0.1.0(https://github.com/Coolgenome/iTALK)
Assembly: GCF_002263795.2_ARS-UCD1.3
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adipose tissue

extract_protocol:
The approximately 100mg liquid nitrogen frozen tissue was ground onto ice and 2 mL of pre-cooled Homogeniza Buffer was added, which was put for 3-5 minutes until the cell nucleus were fully released under the microscope. The tissue homogenate was filtered using 70 µ m and 40 µ m filters, and centrifugated at 500g at 4 ℃ for 5 minutes. Discarding the supernatant and washing twice with 1 mL Wash Buffer, the precipitate was resuspended with an appropriate volume of Blocking Buffer, mixed well and observed the background in the nucleus suspension under the microscope. If the suspension background was clean, it could be directly counted and the cellular ornuclei suspensionwasstainedwith 0.4% trypan blue to assess cell viability under microscope. Cells with greater than 80% viability were qualified for library construction process.
The single-cell suspension was partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs were reversely transcribed into cDNAs, configured for breaking GEMs, which were purified for PCR. The cDNAs were subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand, which were subjected to adaptor ligation and PCR. Basing on the requirements of good library quality, single-stranded PCR products were produced via denaturation and then circularized to get single-stranded cyclized products. The uncyclized linear DNA molecules were digested. Single-stranded circle DNA molecules were replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contains multiple copies of DNA was generated.

value: adipose tissue

tag: tissue type

value: greater omental adipose tissue

value: Mongolian Cattle


title: 62_222009_RUM


title: 63_222010_RUM


title: 64_224033_RUM


title: DS sample 1, hippocampus (total RNA)

description:
Ds1
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: Down syndrome


title: Control sample 19, cortex (total RNA)

description:
C19
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: Cortex

value: male


title: Control sample 16, cortex (total RNA)

description:
C16
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: white


title: satcutaneous adipose tissue, replicate 1, scRNAseq

description:
Sat_MF02
10×Genomics

value: satcutaneous adipose tissue


title: satcutaneous adipose tissue, replicate 3, scRNAseq

description:
Sat_YF01
10×Genomics


title: satcutaneous adipose tissue, replicate 2, scRNAseq

description:
Sat_YM03
10×Genomics


title: Control sample 15, cortex (total RNA)

description:
C15
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: Control sample 14, cortex (total RNA)

description:
C14
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: Control sample 13, cortex (total RNA)

description:
C13
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: Hispanic or Latino


title: Control sample 11, hippocampus (total RNA)

description:
C11
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: female


title: Control sample 21, cortex (total RNA)

description:
C21
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt

value: black


title: Control sample 12, cortex (total RNA)

description:
C12
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: T9

city: Glasgow

first: Max

last: Bone

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland institute

data_processing:
RNA sequencing raw read data was analysed using the nf-core/rnaseq pipeline
Sequencing reads were mapped to human genome assembly GRCh38 genome assembly  using STAR aligner
Assembly: HG38
Supplementary files format and content: tab deliminated text files with raw counts for each sample

source_name: Cell line

extract_protocol:
RNA was isolated using the Qiagen RNeasy Micro Kit as per the manufacturers protocol
TruSeq Stranded Total RNA protocol (part no. 15031048 Rev. D April 2013) was used to generate sequencing libraries from 500ng-1ug total RNA.

value: Cell line

tag: cell type

value: patient-derived cSCC cell line


title: T8


title: 55_202031_RUM

value: 26 month


title: T2


title: Control sample 10, hippocampus (total RNA)

description:
C10
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: Hippocampus


title: T11


title: Control sample 8, hippocampus (total RNA)

description:
C8
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: T10


title: Control sample 9, hippocampus (total RNA)

description:
C9
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: Control sample 17, cortex (total RNA)

description:
C17
raw_counts_human_cortex_matrix_coding.txt
cpm_human_cortex_coding_after_PCA.txt
human_cortex_filt_isoform.matrix.txt


title: perirenal adipose tissue, replicate 1, scRNAseq

description:
Pf_MM03
10×Genomics

value: perirenal adipose tissue


title: Control sample 6, hippocampus (total RNA)

description:
C6
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: Control


title: MET4


title: MET2


title: MET1


title: IC8


title: Control sample 5, hippocampus (total RNA)

description:
C5
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: Control sample 4, hippocampus (total RNA)

description:
C4
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: Control sample 3, hippocampus (total RNA)

description:
C3
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: Control sample 2, hippocampus (total RNA)

description:
C2
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: IC1


title: DS sample 19, cortex (small RNA)

description:
Ds19
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

data_processing:
fastq files were first trimmed to remove the adapter sequence using the cutadapt v1.16 and then additional 4 nucleotides were trimmed from each end.
The trimmed fastq files were mapped using miRge2.0 onto the miRBase.
Subsequently, the counts were obtained for each miRNA, and they were used to perform differential expression analysis with edgeR package.
Assembly: human small RNA gtf file from miRBase
Supplementary files format and content: tab-delimited raw counts text file contains miRNA id as the row names and the sample ID as columns with values indicating raw counts
Supplementary files format and content: tab-delimited cpm text file contains miRNA ID as the row names and the sample ID  as columns with counts per million values obtained after performing PCA analysis and before differential expression analysis using EdgeR.

extract_protocol:
Briefly, RNA was extracted from 50 mg of crushed tissue lysated with 1 mL of QIAzol reagent (Qiagen) and the help of stainless steel beads in a TissueLyzer apparatus (Qiagen) at 20Hz for 2 minutes at room temperature. RNA was purified on miRNeasy spin columns (Qiagen). RNA samples were initially quantified at 260 nm with an ND1000 Nanodrop spectrophotometer (Thermo Scientific). RNA purity was also determined by absorbance at 280 and 230 nm. All samples showed A260/280 and A260/230 ratios greater than 1.9. RNA quality and integrity were verified by microfluidic assay with Agilent 2100 Bioanalyzer. The RNA integrity number (RIN) ranged between 2.1 and 7.3. For library preparation the RNA concentration was measured with Qubit 4 Fluorometer (Thermo Fisher Scientific).
500 ng RNA was used to prepare sample libraries. Briefly,Perkin Elmer Nextflex library preparation kit v3 was used following manufacturer’s instructions. All the sample libraries were then quantitated on Agilent 2100 Bioanalyzer. The size in bp and concentration of the peak corresponding to the amplified products were used for normalizing the library inputs. The normalized libraries were then multiplexed and loaded onto the Illumina flow cell. Single-end sequencing for 75 bp each was performed on Illumina NovaSeq 6000 system with 10 million reads/sample.


title: DS sample 18, cortex (small RNA)

description:
Ds18
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: IC18


title: Control sample 1, hippocampus (total RNA)

description:
C1
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt


title: DS sample 17, cortex (small RNA)

description:
Ds17
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: IC19


title: #200_osteo_d7

city: Davos Platz

first: Martin

middle: J

last: Stoddart

address: Clavadelerstrasse 8

institute: AO Research Institute Davos

description: 75 nt read length

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina, San Diego, CA). FASTQ data were checked using the FastQC tool.
Cutadapt (1.11) was used to extract information of adapter and UMI in raw reads, and output from Cutadapt was used to remove adapter sequences and to collapse reads by UMI with a Qiagen in-house script.
Bowtie2 (2.2.2) was used to map the reads against the mirbase20 (reference genome: GRCh37).
The differential expression of miRNAs was analysed using the R package EdgeR. TMM values are used for DE analysis
Assembly: GRCh37
Supplementary files format and content: xlsx files containing data about differentially expressed miRNA between groups, including Log2FC, logCPM, Pvalue, FDR, average TMM values, and individual TMM values.

source_name: Conditioned medium

growth_protocol: BMSCs were seeded at an initial cell density of 3x103 cells/cm2 and cultured in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol:
miRNeasy Serum/Plasma Kit
QIAseq miRNA Library Prep kit

treatment_protocol: For osteogenic differentiation, cells were seeded at a density of 1.5x104 cells/cm2 . After overnight cell attachment the medium was changed: control (CRL) samples were kept in DMEM 1g/l glucose, 10% MSC-qualified FBS, 100 U/mL penicillin and 100 μg/mL streptomycin. Osteogenic differentiation was induced by the addition of 50 µg/mL ascorbic acid 2-phosphate, 5 mM β-glycerol phosphate and 10 nM dexamethasone to the control medium. Conditioned medium was generated with FBS-free DMEM culture medium. Two days before collection, medium was removed, and the cells were washed 3 times with PBS to remove any FBS residue before adding 1/3 of the standard volume with respective medium without FBS. After a 48h incubation in FBS-free culture conditions, the medium was collected in low protein binding tubes and replaced with standard volume of FBS-containing medium. To remove cell debris, the collected conditioned medium was centrifuged at 2'000 x g for 30 min, transferred in new tubes and snap frozen in liquid nitrogen before being stored at -80°C. This procedure was done in total for two timepoints during osteogenic culture condition. Day 7 and day 14 conditioned medium samples were generated and used for RNA sequencing and qPCR analysis are described in following sections.

value: Conditioned medium

value: Primary human mesenchymal stromal cells from bone marrow (vertebra) (BMSCs)

value: Osteogenic differentiation, day 7


title: #200_osteo_d14

description: 75 nt read length

value: Osteogenic differentiation, day 14


title: DS sample 16, cortex (small RNA)

description:
Ds16
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: Cortex

value: Down syndrome


title: Control sample 7, hippocampus (total RNA)

description:
C7
raw_counts_human_hippo_matrix_coding.txt
cpm_human_hippo_coding_after_PCA.txt
human_hippo_filt_isoform.matrix.txt

value: male


title: PM1


title: DS sample 15, cortex (small RNA)

description:
Ds15
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: #200_control_d14

description: 75 nt read length

value: Undifferentiated control, day 14


title: #200_control_d7

description: 75 nt read length

value: Undifferentiated control, day 7


title: DS sample 14, cortex (small RNA)

description:
Ds14
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: white


title: #191_osteo_d14

description: 75 nt read length


title: DS sample 13, cortex (small RNA)

description:
Ds13
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: female


title: DS sample 12, cortex (small RNA)

description:
Ds12
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: #191_osteo_d7

description: 75 nt read length


title: IC1MET

value: Cell line


title: #191_control_d14

description: 75 nt read length


title: DS sample 9, hippocampus (small RNA)

description:
Ds9
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: #191_control_d7

description: 75 nt read length


title: DS sample 8, hippocampus (small RNA)

description:
Ds8
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: #173_osteo_d14

description: 75 nt read length


title: #173_osteo_d7

description: 75 nt read length


title: IC12

value: patient-derived cSCC cell line


title: DS sample 7, hippocampus (small RNA)

description:
Ds7
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: DS sample 6, hippocampus (small RNA)

description:
Ds6
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: DS sample 5, hippocampus (small RNA)

description:
Ds5
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: Asian


title: DS sample 4, hippocampus (small RNA)

description:
Ds4
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: Hippocampus


title: Fracture, Donor 8, day 19-56

description: 75 nt read length

source_name: Serum sample

value: Serum sample

value: Fracture patient, 19-56 days after injury


title: Fracture, Donor 14, day 19-56

description: 75 nt read length


title: DS sample 3, hippocampus (small RNA)

description:
Ds3
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: black


title: DS sample 10, cortex (small RNA)

description:
Ds10
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: #173_control_d7

description: 75 nt read length

value: Conditioned medium

value: Primary human mesenchymal stromal cells from bone marrow (vertebra) (BMSCs)


title: DS sample 1, hippocampus (small RNA)

description:
Ds1
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Fracture, Donor 1, day 19-56

description: 75 nt read length


title: Control sample 22, cortex (small RNA)

description:
C22
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: Control


title: Fracture, Donor 11, day 19-56

description: 75 nt read length


title: #173_control_d14

description: 75 nt read length


title: Control sample 23, cortex (small RNA)

description:
C23
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: Cortex


title: DS sample 11, cortex (small RNA)

description:
Ds11
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: Down syndrome


title: DS sample 2, hippocampus (small RNA)

description:
Ds2
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: male


title: Fracture, Donor 8, day 5-12

description: 75 nt read length

value: Fracture patient, 5-12 days after injury


title: Fracture, Donor 2, day 19-56

description: 75 nt read length


title: Control sample 21, cortex (small RNA)

description:
C21
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Fracture, Donor 1, day 5-12

description: 75 nt read length


title: Control sample 19, cortex (small RNA)

description:
C19
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Fracture, Donor 7, day 5-12 L16

description: 75 nt read length


title: Control sample 20, cortex (small RNA)

description:
C20
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Fracture, Donor 5, day 5-12

description: 75 nt read length


title: Control sample 18, cortex (small RNA)

description:
C18
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Control sample 16, cortex (small RNA)

description:
C16
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Control sample 17, cortex (small RNA)

description:
C17
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Fracture, Donor 14, day 0-3

description: 75 nt read length

value: Fracture patient, 0-3 days after injury


title: Control sample 15, cortex (small RNA)

description:
C15
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: white


title: Fracture, Donor 12, day 0-3

description: 75 nt read length


title: Fracture, Donor 9, day 19-56

description: 75 nt read length


title: Control sample 13, cortex (small RNA)

description:
C13
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: Hispanic or Latino


title: Fracture, Donor 17, day 0-3

description: 75 nt read length


title: Fracture, Donor 10, day 0-3

description: 75 nt read length


title: Fracture, Donor 11, day 0-3

description: 75 nt read length


title: Control sample 12, cortex (small RNA)

description:
C12
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt

value: female


title: Control sample 14, cortex (small RNA)

description:
C14
miRNA_counts_human_cortex.txt
cpm_miRNA_human_cortex_after_PCA.txt


title: Fracture, Donor 7, day 5-12 L27

description: 75 nt read length


title: Control sample 8, hippocampus (small RNA)

description:
C8
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Fracture, Donor 9, day 0-3

description: 75 nt read length


title: Control sample 9, hippocampus (small RNA)

description:
C9
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Fracture, Donor 2, day 0-3

description: 75 nt read length


title: Fracture, Donor 1, day 0-3

description: 75 nt read length


title: Control sample 10, hippocampus (small RNA)

description:
C10
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Control sample 7, hippocampus (small RNA)

description:
C7
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Fracture, Donor 6, day 0-3

description: 75 nt read length


title: Fracture, Donor 8, day 0-3

description: 75 nt read length


title: Control, Donor28, C

description: 75 nt read length

value: Control, healthy volunteer


title: Control sample 11, hippocampus (small RNA)

description:
C11
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Control, Donor27, C

description: 75 nt read length


title: Control sample 6, hippocampus (small RNA)

description:
C6
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: nf-ya1,Recover 2 h of mild heat stress,repeate3

city: qingdao

first: yaling

last: yang

address: Shandong University, Qingdao 266237, China;

institute: Shandong University

data_processing:
Zea_mays(Zea_mays:NCBI_GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0)
We filter out low quality, joint pollution and unknown base too high N content reads, known as the clean reads the filtered data
clean reads were aligned to the reference genome, followed by novel transcript prediction, SNP and InDel, and differentially spliced gene detection
After obtaining the new transcripts, we added the protein-coding potential transcripts to the reference sequence to form a complete reference sequence, and then calculated the gene expression level
Finally, for multiple samples, differentially expressed genes between different samples were detected according to demand, and differentially expressed genes were compared.In-depth cluster analysis and functional enrichment analysis of genes were performed
Assembly: maize B73 v5
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

organism: Zea mays

source_name: leaves

growth_protocol: Briefly, maize seeds from different lines were sown in pots (12 cm diameter × 15 cm height) containing homogeneous loam. The plants were grown under a 26 °C/22°C (day/night) temperature regimen at a photon flux density of 700 μmol m-2 s-1 with a 16 h/8 h light/dark cycle in a chamber with approximately 65% relative humidity. After germi-nation, the seedlings were watered under normal conditions.

extract_protocol:
RNA was extracted from a small sample (~0.1 g) of leaf lamina (excluding the midrib) from the middle of the first fully expanded leaf.  The sample was ground to a powder in liquid nitrogen, RNA was isolated using TRIzol reagent (Sangon Biotech, Shanghai, China), and cDNA synthesis with the RT reagent kit was performed accord-ing to the manufacturer’s protocol (DRR420, TaKaRa, Dalian, China).
total RNA was processed by mRNA enrichment or rRNA removal. For mRNA enrichment, magnetic beads with OligodT were used to enrich mRNA with polyA tail; rRNA removal: rRNA was hybridized with DNA probe, the DNA/RNA hybrid strand was selectively digested by RNaseH, and then the DNA probe was digested with DNaseI, and the desired RNA was obtained after purification. The obtained RNA was fragmented with interruption buffer, reverse transcribed with random N6 primers, and then the cDNA duplex was synthesized to form double-stranded DNA. "The resultant double-stranded DNA ends are flattened and phosphorylated at the 5 'end, forming A sticky end with an' A 'protruding from the 3' end, which is connected to a bubble-like linker with a' T 'protruding from the 3' end." The ligation products were amplified by PCR using specific primers. PCR product thermal denaturation into a single, reoccupy a bridge type primers will be single-stranded circular DNA single-strand DNA cyclization library.

treatment_protocol: During HS treatment, half of the plants were transferred to a chamber at a set temper-ature.   W22 and nf-ya1 Leaves were collected before and after 6 h of HS treatment and 2 d after recovery (0, 6 h, and R2d) and their RNA was extracted for sequencing.

value: leaves

tag: genotype

value: Recover 2 h of mild heat stress


title: Control, Donor26, C

description: 75 nt read length

tag: tissue

value: Serum sample


title: Control, Donor25, C

description: 75 nt read length


title: nf-ya1,Recover 2 h of mild heat stress,repeate2


title: Control sample 5, hippocampus (small RNA)

description:
C5
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: Hippocampus


title: nf-ya1,Recover 2 h of mild heat stress,repeate1


title: Control, Donor24, C

description: 75 nt read length


title: Control, Donor23, C

description: 75 nt read length


title: Control sample 4, hippocampus (small RNA)

description:
C4
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Control, Donor22, C

description: 75 nt read length


title: Control sample 3, hippocampus (small RNA)

description:
C3
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt

value: black


title: Control sample 2, hippocampus (small RNA)

description:
C2
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Control, Donor21, C

description: 75 nt read length


title: Control sample 1, hippocampus (small RNA)

description:
C1
miRNA_counts_human_hippo.txt
cpm_miRNA_human_hippo_after_PCA.txt


title: Exp7_DMDreporter_sno61Modified_CMC_rep1

city: Tel Aviv

first: Aldema

last: Sas-Chen

state: Israel

address: Tel Aviv University

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel Aviv University

description: Figure 5b

data_processing:
Library strategy: psi-seq
[Table S6]  alignment using STAR (V. 2.5.3a)
[Table S6]  base-calling
[Table S6]  calculation of number of read starts and coverage per base
[Table S6]  calculation of pseudouridine rate
Genome_build: [Table S6]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S2]  alignment using STAR (V. 2.5.3a)
[Table S2]  filter bam files via samtools to retain only read pairs with mapping quality=255, which fall within the expected boundaries of the PCR insert.
[Table S2]  base-calling
[Table S2]  calculation of number of read starts and coverage per base
[Table S2]  calculation of pseudouridine rate
Genome_build: [Table S2]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S5; Table S7]  alignment using STAR (V. 2.5.3a)
[Table S5; Table S7]  conduct read counting using VERSE (https://github.com/qinzhu/VERSE)
[Table S5; Table S7]  TMM normalized of VERSE output using Noiseq package in R
[Table S5; Table S7]  quantification of snoRNA expression
Genome_build: [Table S5; Table S7]  snoRNA sequences from LBME (hg18) after liftover to hg19
[Table S4]  alignment using RSEM (version 1.2.31)
[Table S4]  TMM normalized of RSEM output using Noiseq package in R
[Table S4]  quantification of snoRNA and DKC1 expression
Genome_build: [Table S4]  hg19
[Table S3]  alignment using STAR (V. 2.5.3a)
[Table S3]  base-calling
[Table S3]  calculation of number of read starts and coverage per base
[Table S3]  calculation of pseudouridine rate
Genome_build: [Table S3]  custom sequences of in vitro transcribed DNA reporters
[Figure 5b]  alignment using STAR (V. 2.5.3a)
[Figure 5b]  base-calling
[Figure 5b]  calculation of number of read starts and coverage per base
[Figure 5b]  calculation of pseudouridine rate
Genome_build: [Figure 5b]  custom sequences of DMD reporters

source_name: human cell line

growth_protocol:
[Table S6] HEK-293T cells were grown in DMEM media.
[Table S2; Table S7] HEK-293T cells were grown in DMEM media. Cells were transiently transfected with plasmids (either the library plasmid alone or divided between the library plasmid and other plasmids) using PolyJet reagent (Signagen Laboratories).
[Table S7] HEK-293T cells were grown in DMEM media.
[Table S4; Table S5] HEK-293T cells were grown in DMEM media.
[Table S3] NA. RNA was in vitro transcribed
[Figure 5b] HEK-293T cells were grown in DMEM media. Cells were transiently transfected with plasmids (either the DMD reporter and a sno61 variant) using PolyJet reagent (Signagen Laboratories).

extract_protocol:
[Table S6] RNA was purified using Nucleozol reagent (Macherey Nagel).
[Table S6] Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment
[Table S2; Table S7] RNA was purified using Nucleozol reagent (Macherey Nagel).
[Table S2; Table S7] Fragmentation, targeted cDNA synthesis, second adapter ligation and enrichment
[Table S7] RNA was purified using Nucleozol reagent (Macherey Nagel).
[Table S7] Column size selection (under 200nt), fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment
[Table S4; Table S5] RNA was purified using Nucleozol reagent (Macherey Nagel).
[Table S4; Table S5] Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment
[Table S3] in vitro transcribed RNA
[Table S3] cDNA synthesis, PCR enrichment
[Figure 5b] RNA was purified using Nucleozol reagent (Macherey Nagel) and treated with Ribozero (Illumina).
[Figure 5b] Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment

treatment_protocol:
[Table S6] CMC or input
[Table S2; Table S7] CMC or input
[Table S7] none
[Table S4; Table S5] CMC or input
[Table S3] CMC
[Figure 5b] CMC

tag: molecule type

value: RNA after ribo-zero treatment

tag: transfected library

value: DMD_reporter & modified sno61

value: CMC


title: Exp7_DMDreporter_sno61Modified_CMC_rep2

description: Figure 5b

tag: treatment


title: nf-ya1,Mild Heat Stress 1h,repeate1

value: Mild Heat Stress 1h


title: nf-ya1,Mild Heat Stress 1h,repeate2


title: Exp7_DMDreporter_WTsno61_CMC_rep2

description: Figure 5b

value: DMD_reporter & WT sno61


title: Control, Donor19, C

description: 75 nt read length


title: nf-ya1,control,0,repeate2

value: normal conditions


title: Exp5_totalRNA_CMC_rep1

description: Table S6

value: WT

value: total RNA

value: no plasmid


title: Exp7_DMDreporter_WTsno61_CMC_rep1

description: Figure 5b


title: nf-ya1,control,0,repeate3


title: nf-ya1,control,0,repeate1


title: Exp3_totalRNA_Pol2_siDKC1_Input

description: Table S4

data_processing:
[Table S6]  alignment using STAR (V. 2.5.3a)
[Table S6]  base-calling
[Table S6]  calculation of number of read starts and coverage per base
[Table S6]  calculation of pseudouridine rate
Genome_build: [Table S6]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S2]  alignment using STAR (V. 2.5.3a)
[Table S2]  filter bam files via samtools to retain only read pairs with mapping quality=255, which fall within the expected boundaries of the PCR insert.
[Table S2]  base-calling
[Table S2]  calculation of number of read starts and coverage per base
[Table S2]  calculation of pseudouridine rate
Genome_build: [Table S2]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S5; Table S7]  alignment using STAR (V. 2.5.3a)
[Table S5; Table S7]  conduct read counting using VERSE (https://github.com/qinzhu/VERSE)
[Table S5; Table S7]  TMM normalized of VERSE output using Noiseq package in R
[Table S5; Table S7]  quantification of snoRNA expression
Genome_build: [Table S5; Table S7]  snoRNA sequences from LBME (hg18) after liftover to hg19
[Table S4]  alignment using RSEM (version 1.2.31)
[Table S4]  TMM normalized of RSEM output using Noiseq package in R
[Table S4]  quantification of snoRNA and DKC1 expression
Genome_build: [Table S4]  hg19
[Table S3]  alignment using STAR (V. 2.5.3a)
[Table S3]  base-calling
[Table S3]  calculation of number of read starts and coverage per base
[Table S3]  calculation of pseudouridine rate
Genome_build: [Table S3]  custom sequences of in vitro transcribed DNA reporters
[Figure 5b]  alignment using STAR (V. 2.5.3a)
[Figure 5b]  base-calling
[Figure 5b]  calculation of number of read starts and coverage per base
[Figure 5b]  calculation of pseudouridine rate
Genome_build: [Figure 5b]  custom sequences of DMD reporters

value: plasmid with Pol2 promoter

value: Input


title: Exp5_totalRNA_CMC_rep2

description: Table S6


title: Exp3_totalRNA_Pol2_siDKC1_CMC

description: Table S4


title: Exp3_totalRNA_Pol2_siControl_Input

description: Table S4

value: siRNAcontrol


title: W22,Recover 2 h of mild heat stress,repeate3

value: leaves


title: Exp6_invitroReporter_psi80_CMC

description: Table S3

data_processing:
Library strategy: targeted psi-seq
[Table S6]  alignment using STAR (V. 2.5.3a)
[Table S6]  base-calling
[Table S6]  calculation of number of read starts and coverage per base
[Table S6]  calculation of pseudouridine rate
Genome_build: [Table S6]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S2]  alignment using STAR (V. 2.5.3a)
[Table S2]  filter bam files via samtools to retain only read pairs with mapping quality=255, which fall within the expected boundaries of the PCR insert.
[Table S2]  base-calling
[Table S2]  calculation of number of read starts and coverage per base
[Table S2]  calculation of pseudouridine rate
Genome_build: [Table S2]  custom sequences of synthetic constructs supplemented with rRNA sequences
[Table S5; Table S7]  alignment using STAR (V. 2.5.3a)
[Table S5; Table S7]  conduct read counting using VERSE (https://github.com/qinzhu/VERSE)
[Table S5; Table S7]  TMM normalized of VERSE output using Noiseq package in R
[Table S5; Table S7]  quantification of snoRNA expression
Genome_build: [Table S5; Table S7]  snoRNA sequences from LBME (hg18) after liftover to hg19
[Table S4]  alignment using RSEM (version 1.2.31)
[Table S4]  TMM normalized of RSEM output using Noiseq package in R
[Table S4]  quantification of snoRNA and DKC1 expression
Genome_build: [Table S4]  hg19
[Table S3]  alignment using STAR (V. 2.5.3a)
[Table S3]  base-calling
[Table S3]  calculation of number of read starts and coverage per base
[Table S3]  calculation of pseudouridine rate
Genome_build: [Table S3]  custom sequences of in vitro transcribed DNA reporters
[Figure 5b]  alignment using STAR (V. 2.5.3a)
[Figure 5b]  base-calling
[Figure 5b]  calculation of number of read starts and coverage per base
[Figure 5b]  calculation of pseudouridine rate
Genome_build: [Figure 5b]  custom sequences of DMD reporters

source_name: in vitro transcription

value: in vitro transcribed RNA from DNA reporter


title: Exp6_invitroReporter_psi40_CMC

description: Table S3


title: Control, Donor20, C

description: 75 nt read length

value: Serum sample

value: Control, healthy volunteer


title: SKF_alone_Replicate_2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
NFCore RNA Seq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Assembly: GrCH38
Supplementary files format and content: merged_gene_counts.txt
Supplementary files format and content: Read counts of all the genes expressed in each of the sample processed

organism: Rattus norvegicus

extract_protocol:
Trizol Method
As per Illumina Recommended Protocol

value: Hippocampus


title: SKF_alone_Replicate_1


title: W22,Recover 2 h of mild heat stress,repeate2

value: Recover 2 h of mild heat stress


title: Exp6_invitroReporter_psi20_CMC

description: Table S3


title: nf-ya1,Mild Heat Stress 1h,repeate3


title: Exp6_invitroReporter_psi100_CMC

description: Table S3


title: SKF_Abeta_Replicate_2


title: Exp3_Pol2_siDKC1_Input

description: Table S2

molecule: other

value: other (subset of total RNA, transcribed from plasmid)


title: Exp4_totalRNA_MCF7_Input

description: Table S7

value: total RNA (<200nt)


title: W22,Recover 2 h of mild heat stress,repeate1


title: Exp3_Pol2_siDKC1_CMC

description: Table S2

value: CMC


title: Exp6_invitroReporter_psi60_CMC

description: Table S3


title: Exp4_totalRNA_K562_Input

description: Table S7


title: Exp3_Pol2_siControl_CMC

description: Table S2


title: Exp4_totalRNA_HEK293T_Input

description: Table S7


title: CSP_SKF_Abeta_Replicate_2


title: Exp4_totalRNA_A549_Input

description: Table S7


title: W22,Mild Heat Stress 1h,repeate1

value: Mild Heat Stress 1h


title: CSP_TTK21_alone_Replicate_2


title: Exp2_Pol2_libOnlyControl_CMC

description: Table S2

value: overexpressionControl


title: W22,control,0,repeate3

value: normal conditions


title: Exp3_totalRNA_Pol2_siControl_CMC

description: Table S4; Table S6

value: total RNA


title: Exp2_totalRNA_emptyVectorControl_Input

description: Table S5


title: W22,control,0,repeate2


title: W22,Mild Heat Stress 1h,repeate2


title: Exp2_Pol2_emptyVectorControl_CMC

description: Table S2


title: Exp2_totalRNA_ACA21ACA61overexpression_Input

description: Table S5


title: CSP_TTK21_alone_Replicate_1


title: W22,control,0,repeate1


title: W22,Mild Heat Stress 1h,repeate3


title: SKF_Abeta_Replicate_1


title: CSP_TTK21_SKF_Abeta_Replicate_2


title: Exp1_Pol2_Input_rep2

description: Table S2

value: WT


title: Exp3_Pol2_siControl_Input

description: Table S2

value: plasmid with Pol2 promoter


title: CSP_TTK21_SKF_Abeta_Replicate_1


title: Exp4_Pol2_MCF7_Input

description: Table S2

value: Input


title: Exp4_Pol2_MCF7_CMC

description: Table S2; Table S7


title: CSP_SKF_Abeta_Replicate_1


title: PO_4

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

description: batch b

data_processing:
Aligned to GRCm39 by STAR aligner in standard settings
Assigned to genes by featureCounts  in standard settings excluding multi-mappers
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: hepatic tissues

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions
Poly(A) selection

treatment_protocol: Colorectal cancer was induced via implantation of CRC organoids into the cecal wall. Upon detectable metastasis, mice were subjected to 1/3 partial hepatectomy. For preoperative samples, we isolated RNA from the healthy liver of the resected lobes. Mice were then euthanized on POD 14 and RNA isolated from healthy livers after dissecting metastatic tissue

value: hepatic tissues

value: preoperative sample


title: PO_3

description: batch b


title: Exp1_Pol2_Input_rep1

description: Table S2