title: Control retina C2 replicate2

city: Bangalore

first: Vishnu

last: Suresh Babu

state: Karnataka

address: NH Health city, Bommasandra

department: Narayana Nethralaya Foundation

country: India

institute: GROW Research Laboratory

description: mRNA expressions in tumors

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Pediatric Control retina

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from 9 Rb tumors and 2 control pediatric retina samples using Agilent Absolutely RNA miRNA kit (cat# 400814) according to the manufacturer’s instructions. Twenty-five nanograms of RNA from Rb tumors and control pediatric retina samples were labeled with Cy3 dye using an Agilent Low Input Quick Amp Labeling Kit

treatment_protocol: The study was conducted by the Declaration of Helsinki principles under a protocol approved by the institutional ethics committee of Narayana Nethralaya (EC Ref no: C/2013/03/02). Informed written consents were received from all parents before inclusion in the study. Histology confirmed Rb tumors (n=9) comprising of Group E and Group D of the age range 0.2 -4years and pediatric controls (n=2) of the age range (0.2-0.3 years) were used for the microarray

value: Pediatric Retina


title: Pre-intervention monocyte genomic DNA methylation for participant 30-15

status: Public on Jul 18 2022

type: genomic

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

country: USA

institute: University of Hawaii at Manoa

description: Diabetic participant total monocytes

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina procedures.

scan_protocol: Imaging was performed using Illumina iScan using recommended settings

data_processing: Raw IDAT files were processed using RnBeads version 0.99.18 in R studio (3.1.2)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood mononuclear cells were subjected to magnetic bead enrichment via negative selection for CD14+ (without CD16 depletion) to enrich for monocytes. Monocytes were isolated for genomic DNA using Qiagen AllPrep DNA/RNA Universal Kit following stanard protocols

tag: participant

tag: gender

value: Male

tag: ethnicity

value: Native Hawaiian

tag: disease status

value: Diabetic

tag: cell type

value: Monocyte


title: S2_RTnTag_H3K27me3_n5_(211004_NK_dm_1015)

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RT&Tag for H3K27me3 in S2 cells, replicate 5

library_source: transcriptomic

data_processing: 1. We used trim-galore 0.6.4_dev with parameters "-q 20 --length 20" to trim adapters from 50bp single-end reads. 2. We used hisat2 2.1.0 with parameters "--max-intronlen 5000" to map the trimmed reads to the reference sequence for Drosophilia melanogaster, dm6 from UCSC. 3. We used deepTools 3.3.1 bedCoverage to with parameters "--normalizeUsing CPM" to make bigwig files (Supplementary file .bw).

molecule: total RNA

organism: Drosophila melanogaster

source_name: RT&Tag

tag: antibody

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: Post-intervention monocyte genomic DNA methylation for participant 30-01

description: Diabetic participant total monocytes


title: HCAEC_4 (RNASeq)

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode. to human genome hg38 using the combined transcript models from Ensembl and FANTOM5.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -t CDS -g gene_id -O -s 2 -J -T 8 -R -G Homo_sapiens.GRCh38.dna.primary_assembly.fa -a ensemble_hg38_fCAT_V3.gtf.
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: untreated human coronary artery endothelial cells

growth_protocol: Fibroblasts, hepatocytes, hESCs and endothelial cells were grown to 90% confluence in a 10cm culture dish, while vascular smooth muscle cells (VSMC) were pooled from 5 wells of a 6-well culture plate at baseline conditions in basal M231 medium (M-231-500) for 24h, and pelleted before snap-freezing in liquid nitrogen and stored at -80°C prior to lysis for Ribo-Seq.

extract_protocol:
Total RNA was extracted from either HSCs or HLFs using Trizol (Invitrogen) followed by Purelink RNA mini kit (Invitrogen) purification.
Illumina Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol: Cells were either untreated, treated with TGF-beta with or without anti-IL11 or anti-IgG antibody or IL-11 alone as described above

tag: treatment

value: untreated

tag: fraction

value: polyA mRNA


title: Fibroblast_21 (RNASeq)

source_name: untreated normal human fibroblast

value: fibroblast


title: Post-intervention monocyte genomic DNA methylation for participant 30-02

description: Diabetic participant total monocytes

value: Female


title: Control retina C2 replicate3

type: RNA

description: mRNA expressions in tumors

tag: tissue


title: S2_RTnTag_HS_IgG_n1_(211004_NK_dm_993)

description: RT&Tag for IgG in S2 cell, heat shock, replicate 1

value: IgG Abcam cat# ab172730

value: heat shock


title: Pre-intervention monocyte genomic DNA methylation for participant 30-04

description: Diabetic participant total monocytes


title: Control retina C2 replicate1

description: mRNA expressions in tumors


title: CTRL4 [methylation]

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

country: France

hyb_protocol: Manufacturer protocol

scan_protocol: Manufacturer protocol

data_processing:
Analysis of DNA methylation data was performed with the R ChAMP package. Probe with a detection P value <= 0.01 and with a beadcount less than 3 have been discarded. The beta values were normalized with the BMIQ method, and the batch effect was corrected with the ComBat method.
normalized data: Average Beta

source_name: Heart

label_protocol: Manufacturer protocol

extract_protocol: Tissue : DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California). Blood : Blood (5 to 15 ml of blood)  was  collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).

tag: group

value: non-chagasic control

value: Left ventricular wall


title: CTRL5 [methylation]

description: DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).


title: S2_RTnTag_H3K27me3_n3_(211004_NK_dm_1023)

description: RT&Tag for H3K27me3 in S2 cells, replicate 3


title: Pre-intervention monocyte genomic DNA methylation for participant 30-05

description: Diabetic participant total monocytes


title: Fibroblast_29 (RNASeq)

source_name: IL11 treated normal human fibroblast

value: IL11 stimulated


title: Fibroblast_34 (RNASeq)

source_name: TGF-beta + anti-IL-11 antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IL11 antibody treatment


title: S2_RTnTag_H3K27me3_n4_(211004_NK_dm_1046)

description: RT&Tag for H3K27me3 in S2 cells, replicate 4


title: CTRL6 [methylation]


title: Pre-intervention monocyte genomic DNA methylation for participant 30-12

description: Diabetic participant total monocytes


title: Fibroblast_24 (RNASeq)

source_name: TGF-beta treated normal human fibroblast

value: TGF-B stimulated


title: Control retina C1 replicate2

description: mRNA expressions in tumors

value: Pediatric Retina


title: Fibroblast_41 (RNASeq)

source_name: TGF-beta + anti-Ig-G antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IgG antibody treatment


title: Fibroblast_35 (RNASeq)


title: Pre-intervention monocyte genomic DNA methylation for participant 30-03

description: Diabetic participant total monocytes

value: Male

value: Native Hawaiian

value: Diabetic


title: Control retina C1 replicate3

description: mRNA expressions in tumors


title: S2_RTnTag_H3K27me3_n2_(210820_NK_dm_910)

description: RT&Tag for H3K27me3 in S2 cells, replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: Pre-intervention monocyte genomic DNA methylation for participant 30-02

description: Diabetic participant total monocytes

value: Monocyte


title: S2_RTnTag_controlRNAi_m6A_n1_(211004_NK_dm_1066)

description: RT&Tag for m6A in S2 cells treated with control RNAi, replicate 1

value: m6A Megabase cat# AP60500

value: control RNAi


title: CTRL1 [methylation]


title: S2_RTnTag_controlRNAi_IgG_n2_(211227_NK_dm_1160)

description: RT&Tag for IgG control in S2 cells treated with control RNAi, replicate 2

value: IgG Abcam cat# ab172730


title: MC3T3-E1 Day14 LAMZ+ Rep2

city: Tokyo

first: Takehito

last: Ono

address: Yushima, 1-5-45

department: Department of Cell Signaling

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Data were acquired on an Ion Proton (Thermo Fisher).
Data were analyzed using CLC Genomics Workbench (CLC).  Procedures were as follows.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
k-means clustering and gene ontology enrichment analysis were performed using an online tool, iDEP.91.
Genome_build: mm10
Supplementary_files_format_and_content: Tabbed text file with genes and their expression of each sample

organism: Mus musculus

source_name: MC3T3-E1 cells

growth_protocol: Alpha-MEM containing 10% FBS, 50 mg mL–1 ascorbic acid, 10 nM dexamethasone and 10 mM β–glycerophosphate

extract_protocol:
RNA was extracted using Maxwell 16 LEV simplyRNA Tissue Kit (Promega).
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: DMSO (vehicle) or 1 uM LAMZ was added to the medium above

tag: day of culture

tag: stimulation

value: LAMZ

tag: replicate

value: MC3T3-E1 cells


title: S2_RTnTag_controlRNAi_m6A_n2_(211227_NK_dm_1161)

description: RT&Tag for m6A in S2 cells treated with control RNAi, replicate 2


title: Pre-intervention monocyte genomic DNA methylation for participant 30-01

description: Diabetic participant total monocytes


title: S2_RTnTag_H3K27me3_n1_(210820_NK_dm_890)

description: RT&Tag for H3K27me3 in S2 cells, replicate 1


title: Control retina C1 replicate1

description: mRNA expressions in tumors

value: Female


title: Fibroblast_32 (RNASeq)

value: fibroblast

value: polyA mRNA


title: S2_RTnTag_controlRNAi_IgG_n1_(211004_NK_dm_1065)

description: RT&Tag for IgG control in S2 cells treated with control RNAi, replicate 1


title: MC3T3-E1 Day14 LAMZ+ Rep1


title: Fibroblast_30 (RNASeq)

value: untreated


title: Fibroblast_25 (RNASeq)

value: TGF-B stimulated and anti-IL11 antibody treatment


title: CTRL2 [methylation]

value: non-chagasic control

value: Left ventricular wall


title: Fibroblast_47 (RNASeq)


title: Fibroblast_31 (RNASeq)

value: IL11 stimulated


title: S2_CUTnTag_RNAPolII_n2_(210831_NK_dm_980)

description: CUT&Tag for RNA PolII in S2 cells, replicate 2

library_source: genomic

data_processing: 1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence for Drosophilia melanogaster, dm6 from UCSC. 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments.  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUT&Tag

value: RNA polymerase II Abcam cat# ab817


title: Retinoblastoma tumor P9 replicate1

description: mRNA expressions in tumors

source_name: Retinoblastoma tumor

value: Tumor

value: Male


title: Retinoblastoma tumor P9 replicate2

description: mRNA expressions in tumors


title: MC3T3-E1 Day7 LAMZ+ Rep2


title: Retinoblastoma tumor P9 replicate3

description: mRNA expressions in tumors


title: MC3T3-E1 Day14 LAMZ- Rep2

value: DMSO


title: S2_CUTnTag_RNAPolII_n1_(210810_NK_dm_944)

description: CUT&Tag for RNA PolII in S2 cells, replicate 1

value: S2 cell line


title: Retinoblastoma tumor P8 replicate2

description: mRNA expressions in tumors


title: S2_CUTnTag_RNAPolII_HS_n1_(210810_NK_dm_948)

description: CUT&Tag for RNA PolII in S2 cells, heat shock, replicate 1

value: heat shock


title: Fibroblast_22 (RNASeq)


title: Fibroblast_48 (RNASeq)


title: MC3T3-E1 Day7 LAMZ+ Rep1


title: HA, resting Bcells, rep2

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) with the options ‘-p 40 --very-sensitive --end-to-end --no-unal --phred33’. For analysis at repetitive elements, multimapping reads where kept but only the best alignment was reported. For reads with multiple equally good alignments, a single alignment was selected for reporting using a pseudo-random number generator. High quality-mapped reads, that we considered as mapping uniquely, were identified with samtools v1.15 (Danecek et al., 2021) using ‘samtools view -q 30’. SAM files containing either all reads or only unique reads were filtered using bedtools v2.30.0 (Quinlan and Hall, 2010) to exclude reads overlapping with the mm10 blacklist (Amemiya et al., 2019; Consortium, 2012). Duplicates were removed with the “Picard Toolkit.” from the Broad Institute (GitHub Repository: https://broadinstitute.github.io/picard/) using ‘java -jar picard.jar MarkDuplicates’. BigWig files were generated using deeptools v3.5.1 (Ramirez et al., 2016) using the RPKM normalization method and visualized on the IGV browser (Robinson et al., 2011).
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus

source_name: Spleen

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were used immediately after isolation.
libraries were generated using Thruplex DNA-seq Kit from Takara according to manufactures’ instructions.

value: Spleen

value: resting B cells

tag: genotype

tag: chip antibody


title: Retinoblastoma tumor P8 replicate1

description: mRNA expressions in tumors


title: MC3T3-E1 Day7 LAMZ- Rep1

value: MC3T3-E1 cells


title: Retinoblastoma tumor P7 replicate3

description: mRNA expressions in tumors

value: Female


title: MC3T3-E1 Day7 LAMZ- Rep2


title: Retinoblastoma tumor P8 replicate3

description: mRNA expressions in tumors


title: Retinoblastoma tumor P7 replicate2

description: mRNA expressions in tumors


title: MC3T3-E1 Day14 LAMZ- Rep1


title: Fibroblast_27 (RNASeq)

value: fibroblast


title: S2_CUTnTag_MSL2_n2_(201005_NK_dm_115)

description: CUT&Tag for MSL2 in S2 cells, replicate 2

value: MSL2 gift from Mitzi Kuroda


title: Retinoblastoma tumor P7 replicate1

description: mRNA expressions in tumors


title: S2_CUTnTag_METTL3_n2_(210831_NK_dm_979)

description: CUT&Tag for METTL3 in S2 cells, replicate 1

value: METTL3 Proteintech cat# 15073-1-AP


title: Fibroblast_51 (RNASeq)

value: untreated

value: polyA mRNA


title: S2_CUTnTag_MSL2_n1_(201005_NK_dm_113)

description: CUT&Tag for MSL2 in S2 cells, replicate 1


title: Fibroblast_43 (RNASeq)


title: Fibroblast_39 (RNASeq)

value: TGF-B stimulated


title: S2_CUTnTag_METTL3_n1_(210810_NK_dm_942)

description: CUT&Tag for METTL3 in S2 cells, replicate 2


title: S2_CUTnTag_METTL3_n3_(210628_NK_dm_786)

description: CUT&Tag for METTL3 in S2 cells, replicate 3


title: Retinoblastoma tumor P6 replicate2

description: mRNA expressions in tumors


title: HA, resting Bcells, rep1


title: Fibroblast_38 (RNASeq)

value: IL11 stimulated


title: Fibroblast_45 (RNASeq)

value: TGF-B stimulated and anti-IL11 antibody treatment


title: WT, resting Bcells, rep2


title: Fibroblast_36 (RNASeq)


title: WT, resting Bcells, rep1


title: S2_CUTnTag_METTL3_HS_n1_(210810_NK_dm_946)

description: CUT&Tag for METTL3 in S2 cells, heat shock, replicate 1


title: S2_CUTnTag_IgG_n3_(210628_NK_dm_785)

description: CUT&Tag for IgG in S2 cells, replicate 3

value: IgG Abcam cat# ab172730


title: Retinoblastoma tumor P5 replicate3

description: mRNA expressions in tumors

value: Tumor

value: Male


title: Retinoblastoma tumor P6 replicate1

description: mRNA expressions in tumors


title: S2_CUTnTag_IgG_n2_(210831_NK_dm_978)

description: CUT&Tag for IgG in S2 cells, replicate 2

value: S2 cell line


title: CTRL3 [methylation]

description: DNAs, extracted from whole tissue, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).

value: non-chagasic control

value: Left ventricular wall


title: S2_CUTnTag_IgG_n1_(210810_NK_dm_941)

description: CUT&Tag for IgG in S2 cells, replicate 1


title: S2_CUTnTag_METTL3_HS_n2_(210831_NK_dm_982)

description: CUT&Tag for METTL3 in S2 cells, heat shock, replicate 2

value: heat shock


title: Fibroblast_44 (RNASeq)


title: Fibroblast_28 (RNASeq)


title: Fibroblast_50 (RNASeq)


title: Fibroblast_49 (RNASeq)


title: S2_CUTnTag_IgG_HS_n2_(210831_NK_dm_981)

description: CUT&Tag for IgG in S2 cells, heat shock, replicate 2


title: Retinoblastoma tumor P5 replicate1

description: mRNA expressions in tumors


title: Fibroblast_46 (RNASeq)

value: TGF-B stimulated and anti-IgG antibody treatment


title: Retinoblastoma tumor P6 replicate3

description: mRNA expressions in tumors

value: Female


title: mcu123_03_20-d-old roots, rep3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Aragene1_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

organism: Arabidopsis thaliana

source_name: mcu123_20d-old roots

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Seedlings were cultured under sterile conditions on a mesh in sterile hydroponics boxes (Phytatray II; Sigma-Aldrich, Darmstadt, Germany) filled with 150 mL half-strength MS medium supplemented with 0.1% (w/v) sucrose and 0.05% (w/v) MES, pH 5.8 (KOH). Seedling culture was performed in growth cupboards set to long day conditions (16 h at 21°C and 90 mE m-2 s-1, 8 h at 17°C and darkness).

extract_protocol: Total RNA from pooled roots of 20-d-old seedlings grown in hydroponics was exctracted using the NucleoSpin® RNA Plant kit and treated with DNase I (both from Macherey-Nagel, Düren, Germany), according to the manufacturers' instructions.

treatment_protocol: 20-d-old roots were separated from the shoot with a sharp blade, immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

tag: genotype/variation

value: MCU triple knockout

value: 20-d-old roots


title: mcu123_05_20-d-old roots, rep5


title: Retinoblastoma tumor P4 replicate3

description: mRNA expressions in tumors


title: S2_CUTnTag_IgG_HS_n1_(210810_NK_dm_945)

description: CUT&Tag for IgG in S2 cells, heat shock, replicate 1


title: Retinoblastoma tumor P5 replicate2

description: mRNA expressions in tumors


title: Col-0_05_20-d-old roots, rep5

source_name: Col-0_20d-old roots

value: wild type


title: mcu123_02_20-d-old roots, rep2


title: mcu123_04_20-d-old roots, rep4


title: S2_CUTnTag_RNAPolII_HS_n2_(210831_NK_dm_983)

description: CUT&Tag for RNA PolII in S2 cells, heat shock, replicate 2

value: RNA polymerase II Abcam cat# ab817


title: Retinoblastoma tumor P3 replicate2

description: mRNA expressions in tumors


title: Retinoblastoma tumor P4 replicate1

description: mRNA expressions in tumors


title: Col-0_04_20-d-old roots, rep4


title: mcu123_01_20-d-old roots, rep1


title: Fibroblast_37 (RNASeq)

value: fibroblast

value: polyA mRNA


title: Retinoblastoma tumor P3 replicate1

description: mRNA expressions in tumors


title: S2_CUTnTag_H4K16ac_(200122_KA_DmEc_1422_H4K16ac)

description: CUT&Tag for H4K16ac in S2 cells, replicate 2

value: H4K16ac Abcam cat# ab109463


title: Retinoblastoma tumor P4 replicate2

description: mRNA expressions in tumors


title: Retinoblastoma tumor P2 replicate3

description: mRNA expressions in tumors


title: S2_CUTnTag_H3K36me3_(200122_KA_DmEc_1417_K36me3)

description: CUT&Tag for H3K36me3 in S2 cells

value: H3K36me3 ThermoFisher cat# Thermo Thermo MA5-24687


title: Retinoblastoma tumor P2 replicate2

description: mRNA expressions in tumors


title: Fibroblast_26 (RNASeq)

value: untreated


title: Retinoblastoma tumor P3 replicate3

description: mRNA expressions in tumors

value: Tumor


title: Fat_2 (RNASeq)

source_name: untreated normal human fat tissue

value: fat


title: Fibroblast_33 (RNASeq)

value: TGF-B stimulated


title: Fibroblast_42 (RNASeq)


title: S2_CUTnTag_H3K4me3_(200122_KA_DmEc_1414_K4me3)

description: CUT&Tag for H3K4me3 in S2 cells

value: H3K4me3 ThermoFisher cat# Thermo 711958

value: S2 cell line


title: S2_CUTnTag_H3K27me3_n2_(200709_NK_Dm_10)

description: CUT&Tag for H3K27me3 in S2 cells, replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733


title: naïve XH001 passage 6 time 6 rep 2

first: Jeffrey

middle: S

last: McLean

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software
The paired end reads were trimmed of low-quality sequence at a quality cutoff of 30 using BBduk 38.37 in Geneious prime 2020.0.5
Trimmed sequences were mapped to a reference database containing XH001 and TM7x reference sequences using Geneious prime with the default settings.
For expression ratios and false discovery rates XH001 and TM7x data were analyzed separately via the Degust website using voom/limma with a significance cutoff of FDR 0.05
Genome_build: NZ_CP007496.1, LLVT00000000.1
Supplementary_files_format_and_content: Spread sheet with mapped reads for all samples as well as expression ratios and false discovery rates for the analyzed comparisons

organism: Schaalia odontolytica

source_name: in vitro culture

growth_protocol: Naive XH001 (XH001n) monoculture and XH001/TM7x coculture were both grown in Bacto Brain Heart Infusion medium at 37 °C in microaerophilic chamber (2% O2, 5% CO2, balanced with N2). Samples were grown for 24 hours and then passaged by sub-culturing to 0.1 OD600 then grown for 24 hours. Cultures were passaged 6 times.

extract_protocol:
Cell pellets were resuspended in cold PBS buffer and beaten with glass beads 3 times for 30 seconds with 30 second breaks at 6 m/s speed. Total RNA was isolated using the High Pure RNA isolation kit. Isolated RNA was cleaned and concentrated with Zymo Research RNA clean & concentrator kit following kit protocol. DNA was removed using the Ambion TURBO DNA-free kit. rRNA was depleted with Ribo-Zero.
RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit

tag: strain

tag: time

value: passage 6 time 6


title: naïve XH001 passage 6 time 6 rep 3


title: Fat_1 (RNASeq)


title: naïve XH001 passage 6 time 6 rep 1


title: cth2Δ Ribo-seq, old, replicate 2

city: Boston

first: Vyacheslav

last: Labunskyy

state: MA

address: 609 Albany St

department: Department of Dermatology

institute: Boston University School of Medicine

data_processing:
De-multiplexing and base-calling was performed by Harvard University Bauer Center Sequencing Core
Sequence reads were trimmed for 3' adaptor sequence with cutadapt v.3.4
rRNA sequences were removed using alignment with bowtie v1.1.2
Sequence reads were mapped to the yeast genome with STAR 2.7.9a
Quantitation of reads was performed with Rsubread v.1.22.2
Genome_build: R64-2-1
Supplementary_files_format_and_content: Tab-delimited txt files with 3 columns: 1. SGD ORF name, 2. transcript length, 3. counts

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Wild-type (MEP strain UCC8773) and cth2△ (UCC8773 derivative) cells were grown to OD(600)=0.2 in 20 mL YPD containing nourseothricin (100 ug/mL) and hygromycin B (300 ug/mL). For each strain, 300x106 cells were labeled with biotin EZ-Link Sulfo-NHS-LC-Biotin (5 mg/mL) for 30 min at room temperature. 1.5x10^8 labeled cells were added to 700 mL of cold YPD medium containing 1 uM 17β-estradiol and grown at 30C for 20 h. Then 300 mL of fresh YPD medium containing 1 uM 17β-estradiol was added, and cells were incubated for an additional 10 h (total 30 h incubation time). These cells were used to isolate replicatively aged (OLD) cells. For isolation of young (YNG) samples, cells were labeled with biotin and cultured under the same conditions for 2 h, allowing direct comparison between young and old cells. Repilcatively aged and young cells were isolated using Dynabeads Biotin Binder magnetic beads and flesh frozen in liquid nitrogen. At least 100x10^6 cells were used to make each of the RNA-seq and ribosome profiling libraries.

extract_protocol:
Lysates were subjected to ribosome footprinting by RNAse I treatment. After sucrose density gradient fractionation ribosome-protected fragments were purified from 80S peak fractions. In parallel, mRNA was isolated with Dynabeads mRNA Purification Kit (Life technologies) and subjected to alkaline hydrolysis. Fragments of 50-75 nt were used for library preparation.
The RNA-seq and Ribo-seq libraries were prepared using ARTseq Ribosome Profiling kit (Illumina)

treatment_protocol: Yeast extracts were prepared by cryogrinding with BioSpec cryomill. Extracts were resuspended in buffer containging cycloheximide, and aliquots of cell lysates were used for footprint extraction and isolation of total RNA.

value: cth2<delta> (UCC8773 derivative)

tag: age

value: old

tag: library type

value: ribosome profiling


title: ES_1 (RNASeq)

source_name: untreated human embryonic stem cells

value: embryonic stem cells


title: Col-0_03_20-d-old roots, rep3

value: wild type

value: 20-d-old roots


title: S2_CUTnTag_GAF_(200122_KA_DmEc_1428_174)

description: CUT&Tag for GAF in S2 cells

value: GAF gift from Giovanni Cavalli


title: cth2Δ Ribo-seq, old, replicate 1


title: Col-0_02_20-d-old roots, rep2


title: ES_2 (RNASeq)

value: polyA mRNA


title: Col-0_01_20-d-old roots, rep1


title: Retinoblastoma tumor P1 replicate1

description: mRNA expressions in tumors

tag: gender

value: Male


title: Retinoblastoma tumor P2 replicate1

description: mRNA expressions in tumors

value: Female


title: Retinoblastoma tumor P1 replicate2

description: mRNA expressions in tumors

value: Tumor


title: naïve XH001 passage 4 time 15 rep 2

value: untreated

value: passage 4 time 15


title: cth2Δ Ribo-seq, young, replicate 2

value: young


title: Retinoblastoma tumor P1 replicate3

description: mRNA expressions in tumors


title: Brain_1 (RNASeq)

source_name: untreated normal human brain tissue

value: brain


title: naïve XH001 passage 4 time 10 rep 2

value: passage 4 time 10


title: cth2Δ RNA-seq, old, replicate 1

value: RNA-seq


title: cth2Δ RNA-seq, young, replicate 2

value: cth2<delta> (UCC8773 derivative)


title: cth2Δ Ribo-seq, young, replicate 1


title: naïve XH001 passage 4 time 15 rep 3


title: VSMC_8 (RiboSeq)

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:20:0.5 MINLEN:20. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed Ribo-seq reads were aligned using Bowtie2 to sequences present on RNACentral (release 5.0) database, a database of known rRNA, mtRNA and tRNA sequences. All aligned rRNA, mtRNA and tRNA sequences were considered contaminance and were discarded.
Unaligned reads were then aligned using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode to human genome hg38 using the combined transcript models from Ensembl and FANTOM5.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -t CDS -g gene_id -O -s 1 -J -T 16 -R -G Homo_sapiens.GRCh38.dna.primary_assembly.fa -a ensemble_hg38_fCAT_V3.gtf.
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: untreated normal human vascular smooth muscle cells

extract_protocol:
For brain and adipose tissue, 80-100mg of tissue were placed in chilled tubes containing zirconia beads and 1 mL cold lysis buffer supplemented with 0.1 mg/mL cycloheximide (formulation as in TruSeq® Ribo Profile Mammalian Kit, RPHMR12126, Illumina) and lysed using the Magnalyser machine (Roche) in pulses of 20s at 6000g so that the sample would remain cold. While for fibroblasts, hepatocytes, hESCs, endothelial and VSMC cells, cell lysis occurred in presence of 0.1 mg/mL cycloheximide in 1ml cold lysis buffer as formulated above.
Illumina TruSeq® Ribo Profile Mammalian Kit
Ribosome profiling

tag: cell type

value: VSMC

value: ribosome-protected mRNA fragments


title: S2_CUTnTag_H3K27me3_n1_(200709_NK_Dm_9)

description: CUT&Tag for H3K27me3 in S2 cells, replicate 1

tag: antibody

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: naïve XH001 passage 4 time 10 rep 1

tag: treatment


title: naïve XH001 passage 4 time 6 rep 3

value: passage 4 time 6


title: cth2Δ RNA-seq, young, replicate 1


title: naïve XH001 passage 4 time 6 rep 2


title: VSMC_6 (RiboSeq)

tag: fraction


title: VSMC_7 (RiboSeq)


title: wild-type Ribo-seq, old, replicate 2

value: wild-type (MEP strain UCC8773)

value: old

value: ribosome profiling


title: Brain_4 (RNASeq)

tag: tissue

value: polyA mRNA


title: wild-type Ribo-seq, old, replicate 1


title: naïve XH001 passage 4 time 15 rep 1


title: VSMC_4 (RiboSeq)


title: VSMC_5 (RiboSeq)


title: naïve XH001 passage 4 time 10 rep 3


title: wild-type Ribo-seq, young, replicate 1


title: naïve XH001 passage 0 time 6 rep 2

value: passage 0 time 6


title: wild-type Ribo-seq, young, replicate 2


title: VSMC_2 (RiboSeq)

value: untreated


title: wild-type RNA-seq, old, replicate 2


title: wild-type RNA-seq, young, replicate 2


title: wild-type RNA-seq, old, replicate 1


title: naïve XH001 passage 0 time 6 rep 3


title: VSMC_10 (RiboSeq)


title: naïve XH001 passage 0 time 6 rep 1


title: 16_CTRL_2_S16

city: Newcastle Upon Tyne

first: Christopher

middle: J

last: Stewart

address: Medical School, Framlington Place

department: Translational and Clinical research institute

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were quantified to Gencode (rel40) using Salmon (v 0.13.1)
Transcript level counts were aggrgated to the gene level using tximport.
Data was analysed using Deseq2
Assembly: GRCh38.p13, Ensembl release 100
Supplementary files format and content: txt files with transcript-level counts

molecule: polyA RNA

source_name: Enteroid monolayer

growth_protocol: Growth in 3D using complete media growth factor positive (high wnt) and after forming confluent 2D monolayers was changed to differentiation media

extract_protocol:
RNA from culture samples was prepared using QIAGEN RNeasy Mini Kit following the manufacturer’s instruction. Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
Total RNA-Seq libraries were prepared for differential gene expression analysis using the SMART-Seq® Stranded Kit [Takara] following manufacturer’s instructions.

value: Intestinal derived organoids

tag: passages

tag: line

value: Preterm

value: control


title: 17_CTRL_3_S17


title: naïve XH001 passage 4 time 6 rep 1


title: VSMC_11 (RiboSeq)


title: VSMC_1 (RiboSeq)


title: wild-type RNA-seq, young, replicate 1

value: young


title: 15_CTRL_1_S15


title: KO1

city: 武汉

first: Ran

last: An

state: 湖北

address: 中国湖北武汉

country: China

institute: 武汉大学

data_processing:
Illumina Casava1.7
1) Use the Cutadapt (V1.15) to remove the sequence with the connector at the 3 'end;2) Reads with average mass fraction lower than Q20 were removed
HISAT2 v2.0.5
Read count extraction using HTSeq(0.9.1) and normalization were performed using FPKM
Assembly: GRCm39
Supplementary files format and content: The table file contains the name, FPKM, and Count values for each gene

source_name: Colon

extract_protocol:
RNA was harvested using Invitrogen TRIzol reagent.  Great than or equal to 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina Kit following manufacturer's protocols.

value: Colon

value: lamina propria myeloid cells

value: Usp2 defficient

value: 3% DSS treated for 5 days followed by water treated for 3 days


title: 14_CT5_3_S14

value: Community Type 5


title: HUVEC_3 (RiboSeq)

source_name: untreated normal human umbilical vein endothelial cells

value: HUVEC

value: ribosome-protected mRNA fragments


title: VSMC_3 (RiboSeq)

value: VSMC


title: HUVEC_1 (RiboSeq)


title: HUVEC_2 (RiboSeq)


title: 13_CT5_1_S13


title: 10_CT4_1_S10

value: Community Type 4


title: Hepatocytes_4 (RiboSeq)

source_name: untreated normal human hepatocytes

value: Hepatocytes


title: WT1

value: Usp2 sufficient


title: Hepatocytes_5 (RiboSeq)


title: Hepatocytes_2 (RiboSeq)


title: Hepatocytes_3 (RiboSeq)


title: 9_CT3_3_S9

value: Community Type 3


title: 8_CT3_2_S8


title: 12_CT4_3_S12


title: 11_CT4_2_S11


title: 7_CT3_1_S7


title: VSMC_9 (RiboSeq)

value: untreated


title: HCAEC_5 (RiboSeq)

source_name: untreated human coronary artery endothelial cells

value: HCAEC


title: KO+ lacripep bio rep 4

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

data_processing:
Quality control metrics were performed on raw sequencing reads using fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene
Assembly: mm10
Supplementary files format and content: Excel file that contains matrix of raw counts of all samples (5 WT, 5 KO, 5 KO+PBS, 5 KO+lacripep)

source_name: Cornea

extract_protocol:
Total RNA was collected  and purified using RNAaqueous and DNase reagents according to the manufacturer’s instructions (Ambion, Houston, TX, USA)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Cornea

value: Aire KO

value: Lacripep


title: KO+ PBS bio rep 5

value: PBS


title: KO+ lacripep bio rep 2


title: KO+ lacripep bio rep 3


title: 6_CT2_3_S6

value: Intestinal derived organoids

value: Preterm

value: Community Type 2


title: KO+ PBS bio rep 4


title: Hepatocytes_1 (RiboSeq)


title: 4_CT2_1_S4


title: HCAEC_3 (RiboSeq)


title: 5_CT2_2_S5


title: KO+ PBS bio rep 2


title: KO+ PBS bio rep 3


title: KO+ lacripep bio rep 1


title: 3_CT1_3_S3

value: Community Type 1


title: WT2

value: Colon

value: lamina propria myeloid cells

value: 3% DSS treated for 5 days followed by water treated for 3 days


title: HCAEC_2 (RiboSeq)

value: ribosome-protected mRNA fragments


title: HCAEC_1 (RiboSeq)


title: HCAEC_4 (RiboSeq)


title: KO2

value: Usp2 defficient


title: 2_CT1_2_S2


title: KO 6wk bio rep 4


title: RNA-seq_wk6phleo2

city: Hobart

first: Kate

last: Brettingham-Moore

state: Tasmania

address: 17 Liverpool Street

department: School of Medicine

country: Australia

institute: University of Tasmania

data_processing:
cleaned sequence reads were then aligned against the Homo sapiens  genome (Build version HG38). The STAR aligner (v2.5.3a) was used to map  reads to the genomic sequences.
Counts were summarised at gene level using the featureCounts v1.5.3 utility of the  subread package (http://subread.sourceforge.net/).
transcripts were assembled with the Stringtie tool v1.3.3  (http://ccb.jhu.edu/software/stringtie/) utilising the reads alignment with hg38  and reference annotation based assembly option (RABT)
edgeR (version 3.22.3) was used to perform differential expression analysis.  (https://bioconductor.org/packages/release/bioc/html/edgeR.html) using R  3.5.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 22Rv1 prostate cancer cells grown in culture for 6 weeks and exposed to daily DNA damage, biological replicate 2

growth_protocol: 22Rv1 cells were cultured in RPMI medium supplemented with 10% FBS and 100 units/ml penicillin and 100 micrograms/ml streptomycin. Cells were maintained at a density of 30 to 90% confluency.

extract_protocol:
RNA was extracted using TRI reagent®.  RNA samples underwent clean-up using the RNeasy Plus Micro Kit (50) (Qiagen, USA) following the manufacturer’s instructions
Illumina's TruSeq stranded RNA sample preparation protocol

treatment_protocol: 1 microgram per ml phleomycin added to 22Rv1 cell culture daily (week days only) for a period of 6 weeks; cells were also left untreated and DNA harvested at day 0 or the end of week 6 (age matched)

value: prostate

tag: cell line

value: prostate carcinoma epithelial cell

value: WT

value: Daily DNA damage with 1ug/ml phleomycin

value: 6 weeks


title: KO 6wk bio rep 3

value: Cornea

value: Aire KO

value: untreated


title: HA_EC_3 (RiboSeq)

source_name: untreated human aortic endothelial cells


title: HA_EC_2 (RiboSeq)


title: KO+ PBS bio rep 1

value: PBS


title: WT 6wk bio rep5


title: KO 6wk bio rep 1


title: HA_EC_5 (RiboSeq)


title: HA_EC_4 (RiboSeq)


title: 1_CT1_1_S1

value: Intestinal derived organoids

value: Preterm


title: KO 6wk bio rep 2


title: HA_EC_6 (RiboSeq)


title: Fibroblast_49 (RiboSeq)

source_name: untreated normal human fibroblast

value: Fibroblast


title: Fibroblast_50 (RiboSeq)

source_name: IL11 treated normal human fibroblast

value: IL11 stimulated


title: KO 6wk bio rep 5


title: RNA-seq_wk6phleo1

source_name: 22Rv1 prostate cancer cells grown in culture for 6 weeks and exposed to daily DNA damage, biological replicate 1

value: Daily DNA damage with 1ug/phleomycin


title: RNA-seq_wk6control2

source_name: 22Rv1 prostate cancer cells grown in culture for 6 weeks, biological replicate 2


title: Fibroblast_48 (RiboSeq)


title: Fibroblast_47 (RiboSeq)


title: Fibroblast_51 (RiboSeq)


title: U2OS_c16-4_2 [U2OS_c16-4_2_08-26-2021_S11_R1_001]

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
Assembly: hg38
Supplementary files format and content: htseq counts tables provide normalized count estimates of uniquely mapped RNAseq reads

growth_protocol: Cells were grown at 37°C and 5% CO2 according to manufacturer's guidelines

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization
Lexogen 3' QuantSeq FWD for Illumina

treatment_protocol: See sample section

value: osteosarcoma cancer cell line

value: siHAPSTR1 hairpin 4


title: db-LRG1-10w-2.S22

city: New York

first: Chan Hee

last: Choi

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
NovaSeq Control Software v.1.7.0 used to generate 50 base-pair paired-end reads
Reads were trimmed with Cutadapt, aligned to GRCm38/mm10 reference genome using STAR, and quantified using featureCounts.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited matrix file ("db_counts.matrix") contains counts for each sample in columns

source_name: db/db eWAT, AAV8-LRG1-FL, week 10

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols

value: eWAT

value: week 10


title: WT 6wk bio rep3


title: RNA-seq_wk6control1

source_name: 22Rv1 prostate cancer cells grown in culture for 6 weeks, biological replicate 1

value: prostate

value: prostate carcinoma epithelial cell


title: RNA-seq_control 1

source_name: untreated 22Rv1 prostate cancer cells, biological replicate 1

value: WT


title: Fibroblast_45 (RiboSeq)

source_name: TGF-beta + anti-IL-11 antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IL11 antibody treatment

value: ribosome-protected mRNA fragments


title: HA_EC_1 (RiboSeq)


title: U2OS_NT_3 [U2OS_NT_3_08-26-2021_S3_R1_001]

value: siNT


title: U2OS_c16-3_3 [U2OS_c16-3_3_08-26-2021_S9_R1_001]

value: siHAPSTR1 hairpin 3


title: WT 6wk bio rep1

value: Cornea

value: untreated


title: db-LRG1-10w-4.S24


title: RNA-seq_control 2

source_name: untreated 22Rv1 prostate cancer cells, biological replicate 2


title: U2OS_NT_1 [U2OS_NT_1_08-26-2021_S1_R1_001]


title: WT 6wk bio rep4


title: WT 6wk bio rep2


title: Fibroblast_52 (RiboSeq)


title: db-LRG1-10w-3.S23


title: U2OS_c16-4_1 [U2OS_c16-4_1_08-26-2021_S10_R1_001]


title: U2OS_c16-1_3 [U2OS_c16-1_3_08-26-2021_S6_R1_001]

value: siHAPSTR1 hairpin 1


title: Fibroblast_42 (RiboSeq)

value: Fibroblast


title: db-eGFP-10w-4.S20

source_name: db/db eWAT, AAV8-eGFP control, week 10


title: Fibroblast_46 (RiboSeq)

source_name: TGF-beta + anti-Ig-G antibody treated normal human fibroblast

value: TGF-B stimulated and anti-IgG antibody treatment


title: U2OS_c16-3_2 [U2OS_c16-3_2_08-26-2021_S8_R1_001]


title: db-LRG1-7w-4.S16

source_name: db/db eWAT, AAV8-LRG1-FL, week 7

value: week 7


title: U2OS_NT_2 [U2OS_NT_2_08-26-2021_S2_R1_001]

value: osteosarcoma cancer cell line


title: Fibroblast_41 (RiboSeq)


title: db-LRG1-10w-1.S21


title: db-eGFP-10w-1.S17


title: db-eGFP-10w-3.S19


title: U2OS_c16-4_3 [U2OS_c16-4_3_08-26-2021_S12_R1_001]

value: siHAPSTR1 hairpin 4


title: U2OS_c16-3_1 [U2OS_c16-3_1_08-26-2021_S7_R1_001]


title: db-eGFP-10w-2.S18

value: eWAT


title: U2OS_c16-1_1 [U2OS_c16-1_1_08-26-2021_S4_R1_001]


title: U2OS_c16-1_2 [U2OS_c16-1_2_08-26-2021_S5_R1_001]


title: Fibroblast_44 (RiboSeq)

source_name: TGF-beta treated normal human fibroblast

value: TGF-B stimulated


title: Fibroblast_43 (RiboSeq)

value: IL11 stimulated


title: Fibroblast_40 (RiboSeq)


title: Fibroblast_37 (RiboSeq)


title: 293T-siNT_C16oe_2 [293T-siNT_C16oe_2_08-26-2021_S100_R1_001]

value: immortalized embryonic kidney cell line

value: HAPSTR1 overexpression in siNT background


title: db-LRG1-7w-2.S14


title: Fibroblast_35 (RiboSeq)


title: Fibroblast_38 (RiboSeq)


title: db-eGFP-7w-2.S10

source_name: db/db eWAT, AAV8-eGFP control, week 7


title: Fibroblast_34 (RiboSeq)


title: db-eGFP-7w-4.S12


title: 293T-siNT_GFPoe_2 [293T-siNT_GFPoe_2_08-26-2021_S98_R1_001]

value: GFP overexpression in siNT background


title: Fasted_APAP_2

city: Shanghai

first: Zhijie

last: Li

state: Other

address: Haike Road 230

institute: ShanghaiTech University

description:
RNA-seq method
APAP_PBS_counts.xlsx

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2
Read count extraction and normalization were performed using featurecount
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: liver

extract_protocol:
RNA was extracted using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ILLUMINA total RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For TAA-induced ALF model, all male mice (8-9 weeks old) were injected intraperitoneally with 200 mg/kg of TAA. For APAP-induced ALF model, all male mice (8-9 weeks old) were fasted overnight and injected intragastriclly with 500 mg/kg of APAP. Fasting was maintained for 6 h after APAP treatment. The same volume of sterilized PBS was injected into fed or fasted mice as a control group for TAA or APAP-induced ALF, respectively.

value: liver

value: WT


title: 293T-siNT_GFPoe_1 [293T-siNT_GFPoe_1_08-26-2021_S97_R1_001]


title: db-LRG1-7w-1.S13


title: 293T-siNT_C16oe_1 [293T-siNT_C16oe_1_08-26-2021_S99_R1_001]


title: Fibroblast_39 (RiboSeq)

value: ribosome-protected mRNA fragments


title: Fibroblast_32 (RiboSeq)


title: Fibroblast_33 (RiboSeq)

value: TGF-B stimulated and anti-IL11 antibody treatment


title: Fibroblast_36 (RiboSeq)

value: untreated


title: 293T-siHUWE1_GFPoe_2 [293T-siHUWE1_GFPoe_2_08-26-2021_S102_R1_001]

value: GFP overexpression in siHUWE1 background


title: db-eGFP-7w-3.S11


title: 231_VEH_C16Hu1_3 [D48_231_VEH_C16Hu1_3]

value: breat cancer cell line


title: Fibroblast_31 (RiboSeq)

value: Fibroblast


title: 293T-siHUWE1_C16oe_1 [293T-siHUWE1_C16oe_1_08-26-2021_S103_R1_001]

value: HAPSTR1 overexpression in siHUWE1 background


title: Fasted_PBS_1

description:
RNA-seq method
APAP_PBS_counts.xlsx


title: Fibroblast_29 (RiboSeq)


title: 231_VEH_C16Hu1_2 [D47_231_VEH_C16Hu1_2]


title: db-LRG1-7w-3.S15

value: week 7


title: 231_VEH_C16Hu1_1 [D46_231_VEH_C16Hu1_1]


title: Fasted_APAP_1

description:
RNA-seq method
APAP_PBS_counts.xlsx


title: db-eGFP-7w-1.S9


title: 231_VEH_NTHu1_3 [D45_231_VEH_NTHu1_3]


title: Fibroblast_28 (RiboSeq)


title: Intestine_ec 1

first: Ophir

last: klein

address: 505 Parnassus Ave

institute: UCSF

description:
10x Chromium single cell data
mix of 1 male + 1 female

data_processing:
10x genomics cellranger mkfastq which internally used Illumina bcl2fastq2.20v is used to obtain fastq files
cellranger count is used to produce the gene matrix files from the obtained fastqs
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Endothelial cells from wild-type mice

extract_protocol: 10x libraries were prepared for sequencing using standard 10x genomics protocols

treatment_protocol: Endothelial cells from small intestine blood vessels were FACs sorted as CD31+, CD45neg, EPCAMneg, PODOPLANIN Neg, and lymphatic endothelial cells were sorted as CD31+, CD45neg, EPCAMneg, PODOPLANIN+.

value: small intestine

tag: cell state

value: homeostasis

value: FACS sorted cells blood and lymphatic endothelial

value: Wild-type

tag: background strain

tag: Sex

value: pooled male and female


title: 231_VEH_NTHu1_2 [D44_231_VEH_NTHu1_2]

tag: genotype


title: Fibroblast_27 (RiboSeq)

value: IL11 stimulated


title: Fibroblast_26 (RiboSeq)


title: 231_VEH_NTHu1_1 [D43_231_VEH_NTHu1_1]


title: Fasted_PBS_2

description:
RNA-seq method
APAP_PBS_counts.xlsx


title: 293T-siHUWE1_GFPoe_1 [293T-siHUWE1_GFPoe_1_08-26-2021_S101_R1_001]

value: immortalized embryonic kidney cell line


title: Fibroblast_25 (RiboSeq)

value: TGF-B stimulated and anti-IgG antibody treatment


title: Control mice after 5FU experiment 2

description:
10x Chromium single cell data
CTRL_2

source_name: small intestine

treatment_protocol: Control and knock-out mice that underwent tamoxifen gavage, were injected on three consecutive days with 5FU (75 mg/kg). Mice were sacrificed at day 3 after the last injection of 5FU, small intestines isolated, and crypt epithelial cells, epithelial cells, lympphatic endothelial cells, blood endothelial cells and mesenchymal cells enriched by FACS.

tag: condition

value: day 3 after 3 5FU injections

value: FACS sorted cells, mix of epithelial, endothelial and mesenchymal cells

value: Prox1 creert2 fl/fl mice


title: 231_VEH_NTC16_3 [D42_231_VEH_NTC16_3]


title: Rspo3 knock out mice 5FU experiment 2

description:
10x Chromium single cell data
KO_2


title: Fibroblast_24 (RiboSeq)

value: TGF-B stimulated and anti-IL11 antibody treatment

value: ribosome-protected mRNA fragments


title: 293T-siHUWE1_C16oe_2 [293T-siHUWE1_C16oe_2_08-26-2021_S104_R1_001]


title: Control mice after 5FU experiment 1

description:
10x Chromium single cell data
CTRL_1

value: FACS sorted cells,mix of epithelial, endothelial and mesenchymal cells

value: Rspo3 fl/fl mice


title: 231_VEH_NTC16_2 [D41_231_VEH_NTC16_2]

value: breat cancer cell line


title: Fibroblast_30 (RiboSeq)

source_name: untreated normal human fibroblast

value: Fibroblast

value: untreated


title: 231_VEH_NTC16_1 [D40_231_VEH_NTC16_1]


title: Fibroblast_21 (RiboSeq)


title: Fibroblast_22 (RiboSeq)

source_name: IL11 treated normal human fibroblast


title: Rspo3 knock out mice 5FU experiment 1

description:
10x Chromium single cell data
KO_1

value: small intestine


title: male_proximal sciatic_nerve stump_rep_3

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic (Version 0.39)
Transcript-level quantification was performed using Salmon (Version 1.5.2) in quasi-mapping mode using the Gencode mouse genome. To correct for systematic biases commonly present in RNA-seq data, both -seqBias and -gcBias features were used.
RNA-seq quantification data quality was assessed using MultiQC (Version 1.9).
Genome_build: GENCODE M27 (05.05.21)
Supplementary_files_format_and_content: Salmon quant.sf format consisting Entrez IDs, Length, EffectiveLength, abundance measurements (TPM) and number of reads mapping to each transcript (NumReads)

source_name: left sciatic nerve, proxomal stump

growth_protocol: Female and male C57BL6/J mice (6-8 weeks old, Jackson Labs) were randomly assigned to groups (n =6/group). The mice were housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle, and free access to food and water.

extract_protocol:
Tissues were submerged in 500 µl RNAlater Stabilization Solution to preserve RNA integrity, placed at 4C overnight, then transferred for storage at -20C.
RNA purification. Tissues from 2 animals were pooled to obtain at least 500 ng of total RNAs. Tissues were transferred in Trizol solution and disrupted by mechanical homogenization. Total RNAs were purified using RNeasy RNA purification reagents. RNA concentrations and quality were determined using Nanodrop absorbance ratios at 260/280nm and 260/230nm. RNA integrity was determined using Agilent Bioanalyzer Nano RNA chip. 500 ng of total RNA samples (3 replicates/group) with RIN≥7.0 were used for RNA-seq.
RNA-seq. mRNA libraries were generated following TruSeq Stranded mRNA library preparation protocol (Illumina). In brief, the Poly-A enriched mRNAs were purified using poly-T oligo coupled magnetic beads, followed by mRNA fragmentation, first and second strands synthesis, cleaning on AMPure XP beads, and 3’-adenylation. Barcoded libraries were constructed by ligation of TruSeq dual-index adapters. The quality of RNAseq libraries was validated using qPCR. Libraries were sized on Agilent Bioanalyzer DNA high sensitivity chip and normalized. RNA-seq was performed using the paired-end 100 cycle program on the NovaSeq 6000 system
Sequencing was conducted until at least 50 million paired-end reads per sample were acquired. Base calls were recorded and converted to FASTQ files containing sequencing reads and the corresponding quality scores using Illumina software.

treatment_protocol: All procedures were conducted between 8 and 12 daytime. Under isoflurane anesthesia, the left sciatic nerve was exposed at the mid-thigh level and transection (axotomy) was performed using sterile surgical scissors. The muscle was then sutured, and the skin stapled. At 24 h after surgery, proximal (to DRG) portion of the sciatic nerves was collected for RNA isolation. All animal procedures were performed in agreement with the Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: male

tag: strain

value: axotomy

tag: time point

value: 24 h post surgery


title: 231_VEH_NTNT_3 [D39_231_VEH_NTNT_3]

value: siNT/siNT


title: male_proximal sciatic_nerve stump_rep_1


title: 2_bc3_hs_5h, rep2

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

institute: Temasek Life Science Laboratory

description:
female background
2_raw_reads
P18_1

data_processing:
STAR for genome mapping
Genome_build: M. polymorpha: v3.1 & v5.1 from Marchantia.info; K. nitens: GCA_000708835.1_ASM70883v1 from NCBI
Supplementary_files_format_and_content: raw counts

organism: Marchantia polymorpha

source_name: gemmalings

growth_protocol: M. polymorpha wildtype (accession BC3 (female), Tak-2 (female) and Tak-1 (male)), MpHSFA1 overexpression lines, and mphsfa1 and mphsfb1 knockout mutants were grown on ½ x Gamborg B5 media (pH 5.5) with 1% agar under continuous light (50-60 µmol m-2s-1) at 22°C; For K. nitens, droplets of algal suspension from a fully-grown plate were plated on C-medium plates and incubated for one month under continuous light at 22°C

extract_protocol:
Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Novoseq protocols

treatment_protocol: M. polymorpha, gemmalings were grown in ½ x B5 liquid media for 7 days at continuous light and heat shocked at 37°C for 0, 1 and 5 h; K. nitens, droplets of algal suspension from a fully-grown plate were plated on C-medium plates and incubated for one month. The algal plates were then immersed into a water bath at 37°C for 2 h.

value: gemmalings

tag: age

value: BC3, WT


title: Fat_5 (RiboSeq)

first: Benjamin

last: Ng

address: 8 College Road

source_name: untreated normal human fat tissue

value: fat


title: SKBR3_VEH_C16_3 [D36_SKBR3_VEH_C16_3]


title: 2_bc3_hs_5h, rep1

description:
female background
2_raw_reads
P17_1


title: Fibroblast_23 (RiboSeq)

value: TGF-B stimulated


title: SKBR3_VEH_C16_2 [D35_SKBR3_VEH_C16_2]


title: female_proximal sciatic_nerve stump_rep_2

value: female


title: female_proximal sciatic_nerve stump_rep_3


title: 2_bc3_hs_1h, rep2

description:
female background
2_raw_reads
P16_1


title: 231_VEH_NTNT_2 [D38_231_VEH_NTNT_2]


title: Fat_3 (RiboSeq)


title: Fat_4 (RiboSeq)


title: male_left_sciatic_sham_rep_3

source_name: left sciatic nerve, whole

treatment_protocol: All procedures were conducted between 8 and 12 daytime. Under isoflurane anesthesia, the left sciatic nerve was exposed at the mid-thigh level using sterile surgical scissors without transection (sham). The muscle was then sutured, and the skin stapled. At 24 h after surgery, sciatic nerves were collected for RNA isolation. All animal procedures were performed in agreement with the Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: sham surgery


title: 2_bc3_hs_1h, rep1

description:
female background
2_raw_reads
P15_1


title: male_proximal sciatic_nerve stump_rep_2


title: male_left_sciatic_sham_rep_2


title: 2_bc3_cntr, rep2

description:
female background
2_raw_reads
P14_1


title: Intestine_ec 2

value: homeostasis

value: FACS sorted cells blood and lymphatic endothelial

value: Wild-type

value: pooled male and female


title: Fat_2 (RiboSeq)

value: ribosome-protected mRNA fragments


title: 2_bc3_cntr, rep1

description:
female background
2_raw_reads
P13_1


title: Fat_1 (RiboSeq)

value: untreated


title: SKBR3_VEH_NT_3 [D33_SKBR3_VEH_NT_3]

value: breat cancer cell line

value: siNT


title: SKBR3_VEH_NT_1 [D31_SKBR3_VEH_NT_1]


title: ES_6 (RiboSeq)

source_name: untreated human embryonic stem cells

value: ES


title: female_proximal sciatic_nerve stump_rep_1

value: axotomy

value: 24 h post surgery


title: 2_tak2_hs_5h, rep2

description:
female background
2_raw_reads
P12_1

value: gemmalings

value: Tak-2, WT


title: SKBR3_VEH_NT_2 [D32_SKBR3_VEH_NT_2]


title: SKBR3_VEH_C16_1 [D34_SKBR3_VEH_C16_1]


title: ZR75_VEH_C16_3 [D30_ZR75_VEH_C16_3]


title: female_left_sciatic_sham_rep_3


title: 2_tak2_hs_5h, rep1

description:
female background
2_raw_reads
P11_1


title: female_left_sciatic_sham_rep_2


title: ES_5 (RiboSeq)


title: ZR75_VEH_C16_2 [D29_ZR75_VEH_C16_2]


title: ES_4 (RiboSeq)


title: female_left_sciatic_sham_rep_1


title: 2_tak2_hs_1h, rep2

description:
female background
2_raw_reads
P10_1


title: 2_tak2_hs_1h, rep1

description:
female background
2_raw_reads
P9_1


title: ZR75_VEH_C16_1 [D28_ZR75_VEH_C16_1]


title: ES_3 (RiboSeq)


title: male_left_sciatic_sham_rep_1

value: male


title: ZR75_VEH_NT_3 [D27_ZR75_VEH_NT_3]


title: L-Rpa1_KO_ATAC_Rep6

city: Beijing

first: Qi

last: Yin

address: 38 Xueyuan Rd

institute: Peking University

data_processing:
For CUT&Tag, after adapters were removed, reads were aligned to mouse reference genome (mm10) using Bowtie2 with options: --end-to-end --very-sensitive –no-mixed –no-discordant –phred33 -X 700. Duplicated reads were removed. For peak calling, parameters used were macs2 callpeak -p 1e-5 -g mm -f BEDPE –keep-dup.
For RNA-seq, reads were aligned to the mouse genome (mm10) by HISAT24. Read counts were calculated by featureCounts5 and differential analysis were performed using R package DESeq26.
For ATAC-seq, after adapters were removed, reads were aligned to mouse reference genome (mm10) with random chromosome removed by Bowtie2 under the parameters –very-sensitive -X 2000. All duplicated reads, mitochondrial reads, low quality reads were removed. Peak calling was performed using MACS2 with parameters callpeak --shift -100 --extsize 200 --nomodel --SPMR -g mm
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: narrowPeak, bigWig, rna_seq_counts.txt

source_name: Liver tissue

extract_protocol:
30,000 isolated nuclei were used for ATAC-seq library preparation.
ATAC-seq library preparation was conducted with TruePrep Index Kit V2 for Illumina (TD202, Vazyme).

tag: genotype/variation

value: L-Rpa1 KO

value: Liver


title: ES_2 (RiboSeq)

institute: Duke-National University of Singapore Medical School

tag: cell type


title: ES_1 (RiboSeq)


title: 2_tak2_cntr, rep2

description:
female background
2_raw_reads
P8_1


title: ZR75_VEH_NT_2 [D26_ZR75_VEH_NT_2]


title: 2_tak2_cntr, rep1

description:
female background
2_raw_reads
P7_1


title: Brain_5 (RiboSeq)

source_name: untreated normal human brain tissue

value: Brain


title: ZR75_VEH_NT_1 [D25_ZR75_VEH_NT_1]


title: Brain_4 (RiboSeq)


title: 231_SS_C16_3 [D24_231_SS_C16_3]

value: serum starvation 0% FBS


title: L-Rpa1_KO_ATAC_Rep5


title: 2_tak1_hs_5h, rep2

description:
male background
2_raw_reads
P6_1

value: Tak-1, WT


title: L-Rpa1_KO_ATAC_Rep2


title: L-Rpa1_KO_ATAC_Rep1


title: 231_VEH_NTNT_1 [D37_231_VEH_NTNT_1]

value: siNT/siNT


title: Brain_3 (RiboSeq)


title: 2_tak1_hs_1h, rep2

description:
male background
2_raw_reads
P4_1


title: L-Rpa1_KO_ATAC_Rep3


title: Brain_2 (RiboSeq)


title: 231_SS_C16_2 [D23_231_SS_C16_2]


title: Brain_1 (RiboSeq)


title: L-Rpa1_WT_ATAC_Rep5

value: L-Rpa1 WT


title: 2_tak1_hs_1h, rep1

description:
male background
2_raw_reads
P3_1


title: 231_SS_NT_3 [D21_231_SS_NT_3]


title: L-Rpa1_KO_ATAC_Rep4


title: 231_SS_C16_1 [D22_231_SS_C16_1]


title: L-Rpa1_WT_ATAC_Rep4


title: 2_tak1_cntr, rep1

description:
male background
2_raw_reads
P1_1


title: 231_SS_NT_1 [D19_231_SS_NT_1]


title: PLC.3ug [S2]

city: Maebashi

first: Dolgormaa

last: Gantumur

state: Select a State or Province

address: 3-39-22 Showamachi

institute: Gunma University

data_processing:
Sequenced reads were mapped to hg19 using BWA. Unmapped reads are then mapped to hg19 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr (Nucleic Acids Res. 2015 Apr 30;43(8)).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

growth_protocol: PLC/PRF/5 cells were seeded in 10-cm dishes and grown to 70%–80% confluency at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags.

treatment_protocol: When cells are 70% - 80% confluency, medium were changed to supplemented or not with 3 µg/ml M2BPGi and incubated for 6 hours 37°C in a humidified incubator with 5% CO2. The cells were collected and washed with PBS, snap-frozen in nitrogen, and stored at −80°C until use.

value: Human Hepatoma cell line

value: 3 µg/ml M2BPGi for 6hrs


title: PLC.0ug [S1]

value: none (control)


title: 2_tak1_cntr, rep2

description:
male background
2_raw_reads
P2_1


title: 2_tak1_hs_5h, rep1

description:
male background
2_raw_reads
P5_1


title: 1_hsfa1yox_bc3_cntr, rep2

description:
female background
1_raw_reads
S4_1


title: L-Rpa1_WT_ATAC_Rep3


title: 360 min light rep3

city: Durham

first: Miguel

last: de Lucas

state: Durham

address: South Road

department: Biosciences

institute: Durham University

description:
5 day old seedlings grown in the dark and  treated with 360min of light
Normalized_gene_level_counts.csv

data_processing:
Sequencing on Illumina HiSeq 2500 at 50 bp SR.
Quality filtering was conducted using the method described by (Toal et al., 2018, G3 8(12), 3841-3855).
Reads were mapped to the AtRTD2-QUASI transcriptome (Zhang et al., 2017, Nucleic Acids Research 45(9), 5061-5073) using Kallisto. Kallisto was run with the following parameters: Defaut k-mer size of 31 bp, and with the additional options: -b 30 --single -l 187 -s 81
Gene-level counts were obtained from the kallisto "abudance.tsv" output files using tximport version 1.12.3. The following parameters were used: type = "kallisto", countsFromAbundance = "lengthScaledTPM"
Gene-level counts were normalized between replicates using DESeq version 1.36.0.
A dispersion value (theta) is required to run maSigPro with RNA-seq data. Therefore, EdgeR version 3.26.8 was used to determine this value. Theta was defined as being 1/common.dispersion, which is an output of the estimateDisp() function.
Genes were filtered. Genes for which two or more of the biological replicates had a count value of "0" at any time point were removed from the analysis.
maSigPro version 1.56.0 was used to identify gene expression patterns and to group genes into clusters. The following parameters were used: design matrix = 5 degrees of freedom; For the p.vector() function: Q = 0.01, MT.adjust = "BH", counts = TRUE, theta = 2.814765. For the T.fit() function: step.method = "backward", alfa = 0.01. For the sigs() functinon: rsq = 0.5, vars = "all". For the see.genes() function: cluster.method = "hclust", cluster.data = 1, k = 5.
Genome_build: AtRTD2-QUASI (Zhang et al., 2017, Nucleic Acids Research 45(9), 5061-6073) was used as the reference transcriptome.
Supplementary_files_format_and_content: Files ending in _abundance.tsv are tab-separated values files containing raw kallisto outputs. One file per replicate/condition is included. These files contain the length, effective length, estimated counts, and tpm values for each transcript isoform in the AtRTD2-QUASI transcriptome.
Supplementary_files_format_and_content: Normalized_gene_level_counts.csv is a comma-separated values file containing gene-level count values for all genes in all conditions/replicates, normalized with DESeq.

source_name: 5-day-old whole seedlings

growth_protocol: Arabidopsis seedlings (Col-0) were grown at 21˚C, in constant darkness, for 5 days following germination induction in 1% MS medium without sucrose.

extract_protocol: As previously described by Townsley, B. T., Covington, M. F., Ichihashi, Y., Zumstein, K. & Sinha, N. R. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Frontiers in plant science 6, (2015).

treatment_protocol: Tissue from dark-grown seedlings was collected in a dark room under green light. Remaining seedlings were then exposed to 200 µmol m-2 s-1 white light for different lengths of time: 15, 30, 60, 150, and 360 min.

tag: ecotype

value: whole seedling

tag: duration of white light exposure

value: 360 min


title: 231_CoCl2_C16_3 [D18_231_CoCl2_C16_3]

value: breat cancer cell line

tag: treatment

value: CoCl2 250 μM


title: L-Rpa1_WT_ATAC_Rep2

tag: tissue


title: 231_CoCl2_C16_2 [D17_231_CoCl2_C16_2]


title: 360 min light rep2


title: 1_hsfa1xox_bc3_cntr, rep2

description:
female background
1_raw_reads
S2_1

value: gemmalings

value: HSFA1X, ox


title: 231_CoCl2_C16_1 [D16_231_CoCl2_C16_1]


title: L-Rpa1_WT_ATAC_Rep1


title: 1_hsfa1yox_bc3_cntr, rep1

description:
female background
1_raw_reads
S3_1


title: 231_SS_NT_2 [D20_231_SS_NT_2]

value: siNT


title: L-Rpa1_WT_ATAC_Rep6


title: 231_CoCl2_NT_3 [D15_231_CoCl2_NT_3]


title: 150 min light rep3

description:
5 day old seedlings grown in the dark and  treated with 150min of light
Normalized_gene_level_counts.csv

value: 150 min


title: 1_hsfa1yox_tak1_cntr, rep2

description:
male background
1_raw_reads
S8_1


title: 231_CoCl2_NT_2 [D14_231_CoCl2_NT_2]


title: 360 min light rep1


title: 1_hsfa1xox_bc3_cntr, rep1

description:
female background
1_raw_reads
S1_1


title: 150 min light rep2


title: L-Rpa1_WT - IgG_mouse_rep1

data_processing:
Library strategy: CUT&Tag
For CUT&Tag, after adapters were removed, reads were aligned to mouse reference genome (mm10) using Bowtie2 with options: --end-to-end --very-sensitive –no-mixed –no-discordant –phred33 -X 700. Duplicated reads were removed. For peak calling, parameters used were macs2 callpeak -p 1e-5 -g mm -f BEDPE –keep-dup.
For RNA-seq, reads were aligned to the mouse genome (mm10) by HISAT24. Read counts were calculated by featureCounts5 and differential analysis were performed using R package DESeq26.
For ATAC-seq, after adapters were removed, reads were aligned to mouse reference genome (mm10) with random chromosome removed by Bowtie2 under the parameters –very-sensitive -X 2000. All duplicated reads, mitochondrial reads, low quality reads were removed. Peak calling was performed using MACS2 with parameters callpeak --shift -100 --extsize 200 --nomodel --SPMR -g mm
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: narrowPeak, bigWig, rna_seq_counts.txt

extract_protocol:
100,000 isolated nuclei were used for CUT&Tag library preparation.
Libraries were prepared according to NovoNGS® CUT&Tag2.0 High-Sensitivity Kit (for Illumina®) (N259-YH01, Novoprotein Scientific Inc.)

value: Liver

tag: cut&tag antibody

value: Normal mouse IgG (Santa, SC-2025)


title: 150 min light rep1


title: 231_CoCl2_NT_1 [D13_231_CoCl2_NT_1]


title: 1_hsfa1yox_tak1_cntr, rep1

description:
male background
1_raw_reads
S7_1


title: L-Rpa1_KO - PPA1_rep1

value: L-Rpa1 KO

value: RPA1 (Homemade, this paper)


title: L-Rpa1_WT - PPA1_rep1


title: Fat_6 (RiboSeq)

city: Singapore

value: fat

value: untreated

tag: fraction

value: ribosome-protected mRNA fragments


title: 60 min light rep3

description:
5 day old seedlings grown in the dark and  treated with 60min of light
Normalized_gene_level_counts.csv

value: 60 min


title: 1_hsfa1xox_tak1_cntr, rep1

description:
male background
1_raw_reads
S5_1


title: 60 min light rep2


title: 231_CPA_C16_3 [D12_231_CPA_C16_3]

tag: cell line

value: Cyclophosphamide 100 μM


title: L-Rpa1_KO - PPARα_rep3

value: PPARalpha (Novus, NB600-636)


title: L-Rpa1_WT - IgG_rabbit_rep1

value: L-Rpa1 WT

value: Normal rabbit IgG (Santa, SC-2027)


title: 231_CPA_C16_2 [D11_231_CPA_C16_2]

value: breat cancer cell line


title: 231_CPA_C16_1 [D10_231_CPA_C16_1]


title: L-Rpa1_KO - PPARα_rep1


title: L-Rpa1_KO - PPARα_rep2


title: 231_CPA_NT_3 [D9_231_CPA_NT_3]


title: 1_hsfa1xox_tak1_cntr, rep2

description:
male background
1_raw_reads
S6_1

value: gemmalings


title: 60 min light rep1

value: whole seedling


title: 231_CPA_NT_2 [D8_231_CPA_NT_2]

value: siNT


title: 30 min light rep3

description:
5 day old seedlings grown in the dark and  treated with 30min of light
Normalized_gene_level_counts.csv

value: 30 min


title: 1_hsfa1x_hs, rep1

description:
female background
1_raw_reads
S15_1

value: hsfa1x, ox


title: L-Rpa1_WT - PPARα_rep3

value: Liver


title: 30 min light rep1


title: 1_bc3_hs, rep2

description:
female background
1_raw_reads
S21_1

value: BC3, WT


title: 231_VEH_C16_3 [D6_231_VEH_C16_3]

value: 0.1% DMSO


title: 30 min light rep2


title: 15 min light rep3

description:
5 day old seedlings grown in the dark and  treated with 15min of light
Normalized_gene_level_counts.csv

value: 15 min


title: 1_bc3_hs, rep1

description:
female background
1_raw_reads
S13_1


title: L-Rpa1_WT - PPARα_rep2


title: 231_CPA_NT_1 [D7_231_CPA_NT_1]


title: L-Rpa1_WT - PPARα_rep1


title: 15 min light rep2


title: 231_VEH_C16_2 [D5_231_VEH_C16_2]


title: 1_hsfa1x_hs, rep2

description:
female background
1_raw_reads
S23_1


title: 1_bc3_cntr, rep2

description:
female background
1_raw_reads
S17_1


title: L-Rpa1_KO - Pol II_rep2

value: L-Rpa1 KO

value: Pol II (CST, 2629)


title: 1_hsfa1x_cntr, rep2

description:
female background
1_raw_reads
S19_1


title: 231_VEH_C16_1 [D4_231_VEH_C16_1]


title: L-Rpa1_KO - Pol II_rep1


title: dark-grown seedlings rep3

description:
5 day old seedlings grown in the dark
Normalized_gene_level_counts.csv

value: no light exposure


title: 1_bc3_cntr, rep1

description:
female background
1_raw_reads
S9_1


title: dark-grown seedlings rep2


title: 231_VEH_NT_3 [D3_231_VEH_NT_3]


title: 231_VEH_NT_2 [D2_231_VEH_NT_2]


title: 1_hsfb1_hs, rep2

description:
male background
1_raw_reads
S28_1

value: hsfb1, ko


title: dark-grown seedlings rep1


title: L-Rpa1_KO - Pol II_rep3


title: L-Rpa1_WT - Pol II_rep3


title: 1_hsfb1_hs, rep1

description:
male background
1_raw_reads
S26_1


title: 1_hsfb1_cntr, rep2

description:
male background
1_raw_reads
S27_1


title: WT-infected blood at 24 h _rep2

city: Suita

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: WT-infected mouse blood at 24 h after infection_rep2

data_processing:
Libraries were sequenced using Illumina HiSeq 2500 systems, with 75 bp single-end reads obtained.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNA was extracted from the blood using PureLink Total RNA Blood Purification Kit and DNase I, Amplification Grade (Thermo Fisher Science). RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)
according to the manufacturer’s instructions. An Illumina library was
prepared using a Nextera XT DNA Library Prep Kit (Illumina) according
to SMARTer kit instructions. Libraries were sequenced using Illumina HiSeq 2500 systems, with 75 bp single-end reads obtained.

treatment_protocol: Mouse whole blood at 12 h, 24 h and 36 h after intravenously infection was obtained by cardiac puncture after lethal intraperitoneal injection of sodium pentobarbital. Heparin was added to the blood at a final concentration of 30 units/mL.

tag: agent

value: WT-infected


title: Trisomy21, scRNAseq

city: Madison

first: Anita

last: Bhattacharyya

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin - Madison

library_source: transcriptomic single cell

data_processing:
Raw read quality was confirmed with FastQC Processing.
Cell Ranger mkfastq was used to demultiplex the raw read files in to FastQ files.
The FastQ files were then passed on to Cell Ranger count for alignment, filtering, barcode counting  and UMI counting.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC-derived progenitor

extract_protocol:
RNA was isolated from progenitors using the ZYMO Research Direct-Zol RNA Miniprep plus  kit
10x Genomics library preparation

value: iPSC-derived progenitor

value: WC-24-02 clone M

value: iPSC derived interneuron progenitors

value: trisomy 21


title: L-Rpa1_WT - Pol II_rep2

value: L-Rpa1 WT


title: control, scRNAseq

value: WC-24-02 clone B

value: control


title: 15 min light rep1

value: whole seedling


title: 231_VEH_NT_1 [D1_231_VEH_NT_1]

value: breat cancer cell line

value: siNT


title: WT-infected blood at 36 h _rep2

description: WT-infected mouse blood at 36 h after infection_rep2


title: L-Rpa1_KO - HNF4A_rep3

value: Liver

value: HNF4A (Abcam, ab181604)


title: 1_hsfb1_cntr, rep1

description:
male background
1_raw_reads
S25_1

value: gemmalings


title: L-Rpa1_WT - Pol II_rep1

value: Pol II (CST, 2629)


title: 1_hsfa1y_hs, rep2

description:
male background
1_raw_reads
S24_1

value: hsfa1y, ko


title: sevCCC8 [RNA-Seq]

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

description: RNA Extraction was done on frozen tissues without stimulation. Whole genome expression analysis was conducted on 8 CCC, 8 DCM and 6 control samples

data_processing:
Raw data quality was verified with FastQC (v0.11.5). Low-quality reads, Illumina adapters and reads smaller than 20 nucleotides were removed with Trimmomatic (v0.39), using default values for other options. Reads were aligned on GRCh37 (hg19) human reference genome from Ensembl using STAR (v2.5.4b), specifying that the reads are 2x150 nucleotides (paired-end). Alignment quality was checked by BAMQC (qualimap v2.2.1). Gene quantification was done with featureCounts (v2.0.0), using the exons as features and the genes as attributes
Statistical analyses were performed with R version 3.6.2. Because there is a large infiltrate of immune cells in the heart tissue, and therefore in the samples studied, genes related to immunoglobulins and T-cell receptor (TCR) were excluded of the analyses. The DESeq2 package (v1.26.0) was used for data normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Count table contain all non-normalized count for each gene, and for each sample. Normalized tables contains normalized expression for each gene and for a subset of sample, according to their phenotype.

source_name: Heart

extract_protocol:
Heart tissue samples (20–30 mg) were cleared from pericardial fat, crushed with ceramic beads (CK14, diameter 1.4 mm, Bertin) in 350 µL of RLT lysis buffer supplemented with 3.5 µL of β-mercapto-ethanol. Total RNA was extracted from biopsies using the RNeasy Mini Kit adapted with Trizol. RNA quantity and quality were measured with a 2100 BioAnalyzer (Agilent). Ribosomal RNAs were depleted and samples were prepared for sequencing according to the Illumina TruSeq RNA Preparation Kit and subjected to pairwise sequencing (2x150bp) with an Illumina HiSeq sequencer. Sequencer results were obtained as raw fastq file format.
Manufacturer protocol

value: Left ventricular wall

tag: group

value: chronic chagasic cardiomyopathy


title: 1_hsfa1y_hs, rep1

description:
male background
1_raw_reads
S16_1


title: WT-infected blood at 12 h _rep2

description: WT-infected mouse blood at 12 h after infection_rep2

value: WT-infected


title: L-Rpa1_KO - HNF4A_rep2

value: L-Rpa1 KO


title: L-Rpa1_KO - HNF4A_rep1


title: WT-infected blood at 36 h _rep1

description: WT-infected mouse blood at 36 h after infection_rep1


title: 1_hsfa1y_cntr, rep2

description:
male background
1_raw_reads
S20_1


title: L-Rpa1_WT - HNF4A_rep3


title: 1_hsfa1y_cntr, rep1

description:
male background
1_raw_reads
S12_1


title: sevCCC6 [RNA-Seq]


title: WT-infected blood at 12 h _rep1

description: WT-infected mouse blood at 12 h after infection_rep1


title: L-Rpa1_WT - HNF4A_rep2


title: PBS-infected blood at 36 h _rep2

description: PBS-infected mouse blood at 36 h after infection_rep2

value: PBS-treated


title: 1_tak1_hs, rep2

description:
male background
1_raw_reads
S22_1

value: Tak-1, WT


title: 1_tak1_hs, rep1

description:
male background
1_raw_reads
S14_1


title: L-Rpa1_WT - HNF4A_rep1

value: L-Rpa1 WT


title: sevCCC5 [RNA-Seq]


title: L-Rpa1_KO - H3K9ac_rep2


title: sevCCC4 [RNA-Seq]


title: sevCCC2 [RNA-Seq]


title: L-Rpa1_KO - H3K9ac_rep1


title: L-Rpa1_KO - H3K9ac_rep3


title: 1_tak1_cntr, rep2

description:
male background
1_raw_reads
S18_1


title: PBS-infected blood at 36 h _rep1

description: PBS-infected mouse blood at 36 h after infection_rep1


title: sevCCC3 [RNA-Seq]


title: PBS-infected blood at 24 h _rep2

description: PBS-infected mouse blood at 24 h after infection_rep2


title: 1_tak1_cntr, rep1

description:
male background
1_raw_reads
S10_1


title: PBS-infected blood at 12 h _rep2

description: PBS-infected mouse blood at 12 h after infection_rep2


title: L-Rpa1_WT - H3K9ac_rep3


title: PBS-infected blood at 24 h _rep1

description: PBS-infected mouse blood at 24 h after infection_rep1


title: DCM8 [RNA-Seq]

value: dilated cardiomyopathy


title: sevCCC1 [RNA-Seq]


title: WT, resting Bcells, rep3 (RNA-seq)

city: Bethesda

first: Joana

last: Vidigal

address: 37 Convent Dr, Room 6056

institute: NIH/NCI

data_processing:
Quantification of transposable element abundances was done using SalmonTE v0.4 (GitHub Repository: https://github.com/hyunhwan-jeong/SalmonTE) (Jeong et al., 2018) using the following options ‘SalmonTE.py quant  --reference=mm --exprtype=TPM’.
Assembly: mm10
Supplementary files format and content: TPMs of Tes

source_name: Spleen

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were used immediately after isolation.
Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing

value: Spleen

value: B cell


title: WT-infected blood at 24 h _rep1

description: WT-infected mouse blood at 24 h after infection_rep1


title: WT, resting Bcells, rep2 (RNA-seq)


title: sevCCC7 [RNA-Seq]


title: PBS-infected blood at 12 h _rep1

description: PBS-infected mouse blood at 12 h after infection_rep1


title: L-Rpa1_WT - H3K9ac_rep2


title: WT, resting Bcells, rep1 (RNA-seq)


title: DCM7 [RNA-Seq]


title: L-Rpa1_WT - H3K9ac_rep1


title: DCM6 [RNA-Seq]


title: ΔbgaA-infected blood at 36 h _rep2

description: ΔbgaA-infected mouse blood at 36 h after infection_rep2

value: deltabgaA-infected


title: siTollip+SARS-CoV-2 24 h rep3

city: guangzhou

first: shi

middle: jun

last: jie

institute: sysu

description:
TKD9
reads count

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the human genome (hg38) using Hisat2.
The gene expression level was calculated by using featureCounts.
Fold-change (FC) and p-values were calculated with DEseq2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *csv: Comma-separated text files containing read counts.

growth_protocol: Calu-3 cells were cultured in MEM (Gibco) with 1% NEAA (Gibco), 1% sodium pyruvate (Gibco) and 10% (vol/vol) fetal bovine serum (Gibco). Cells were either mock-infected or infected with SARS-CoV-2 (Accession number: MT123290), virus was allowed to adsorb at 37 °C for 1 hr with gentle rocking every 15 min before incubation at 37 °C for indicated time points. Cells were infected at different MOI and time points as indicated.

extract_protocol:
Total RNA was harvested using Trizol reagent.
Total RNA was isolated from cells using TRIzol reagent (Invitrogen), and sequencing was performed by Sangon Biotech. Sample quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer). RNA-seq libraries of polyadenylated RNA were prepared using mRNA-seq V2 Library Prep Kit and sequenced on MGISEQ-2000 platform.

treatment_protocol: Calu-3 cells transfected with siNC or siTollip were infected with SARS-CoV-2 (MOI = 0.5) for 24 h.

tag: sirna

value: siTollip

tag: infection

value: SARS-CoV-2 24h


title: L-Rpa1_KO - H3K27ac_rep2

value: Liver


title: DCM5 [RNA-Seq]


title: siTollip+SARS-CoV-2 24 h rep2

description:
TKD8
reads count


title: ΔbgaA-infected blood at 24 h _rep2

description: ΔbgaA-infected mouse blood at 24 h after infection_rep2


title: DCM4 [RNA-Seq]


title: L-Rpa1_KO - H3K27ac_rep3


title: ΔbgaA-infected blood at 12 h _rep2

description: ΔbgaA-infected mouse blood at 12 h after infection_rep2


title: DCM2 [RNA-Seq]


title: L-Rpa1_WT - H3K27ac_rep3


title: DCM3 [RNA-Seq]


title: siTollip rep2

description:
TKD2
reads count

value: Mock


title: L-Rpa1_WT - H3K27ac_rep2


title: ΔbgaA-infected blood at 36 h _rep1

description: ΔbgaA-infected mouse blood at 36 h after infection_rep1


title: siTollip+SARS-CoV-2 24 h rep1

description:
TKD7
reads count


title: siTollip rep1

description:
TKD1
reads count


title: L-Rpa1_KO - H3K27ac_rep1


title: ΔbgaA-infected blood at 12 h _rep1

description: ΔbgaA-infected mouse blood at 12 h after infection_rep1


title: DCM1 [RNA-Seq]


title: L-Rpa1_WT - H3K27ac_rep1


title: L-Rpa1_KO_RNA_Seq_Rep3

description:
mRNA
rna_seq_counts.txt

extract_protocol:
Mouse liver were removed, flash frozen on liquid N2, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: siNC+SARS-CoV-2 24 h rep3

description:
NC9
reads count

value: siNC


title: L-Rpa1_KO_RNA_Seq_Rep2

description:
mRNA
rna_seq_counts.txt


title: CTRL6 [RNA-Seq]

value: non-chagasic control


title: L-Rpa1_KO - H3K4me3_rep3


title: CTRL5 [RNA-Seq]

value: Left ventricular wall


title: siNC+SARS-CoV-2 24 h rep2

description:
NC8
reads count


title: ΔbgaA-infected blood at 24 h _rep1

description: ΔbgaA-infected mouse blood at 24 h after infection_rep1


title: L-Rpa1_KO - H3K4me3_rep2


title: siTollip rep3

description:
TKD3
reads count


title: CTRL4 [RNA-Seq]

description: RNA Extraction was done on frozen tissues without stimulation. Whole genome expression analysis was conducted on 8 CCC, 8 DCM and 6 control samples


title: L-Rpa1_KO_RNA_Seq_Rep1

description:
mRNA
rna_seq_counts.txt


title: L-Rpa1_WT_RNA_Seq_Rep3

description:
mRNA
rna_seq_counts.txt


title: L-Rpa1_WT - H3K4me3_rep3


title: L-Rpa1_KO - H3K4me3_rep1


title: CTRL3 [RNA-Seq]


title: siNC rep3

description:
NC3
reads count


title: siNC rep2

description:
NC2
reads count


title: L-Rpa1_WT_RNA_Seq_Rep1

description:
mRNA
rna_seq_counts.txt


title: siNC rep1

description:
NC1
reads count


title: CTRL1 [RNA-Seq]


title: L-Rpa1_WT - H3K4me3_rep1


title: rll6-1

status: Public on Jul 17 2022

city: Nanjing

first: Xiangyu

last: Wang

address: No. 1 Weigang

institute: Nanjing agricultural university

data_processing:
Bismark version v0.22.1.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapped to TAIR10 whole genome using bowtie2 version 2.3.5.
Deduplicated reads by bismark.
methylation extracting by bismark.
Assembly: TAIR10
Supplementary files format and content: Matrix table with wig file for every sample

source_name: seeding

growth_protocol: soil,16 hour light, 8 hour dark cycle

extract_protocol:
14-day-old seeding of rll6-1 ,Col-LUC and ros1-7 plants were grown in soil
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seeding

value: Col-LUC

value: the whole plant

tag: genotype

value: 14-day-old seeding


title: SP, scRNAseq

city: Xiamen

first: Yudi

last: Hu

address: Xiangannan road

institute: Xiamen University

description: 10x Genomics

data_processing:
10X data were processed using the Cell Ranger software v3.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells (CD4+ CD25+ YFP+ and YFP- cells from Mycfl/flFoxp3Cre/WT mice) were sorted by flow cytometry into a well of a chilled 96-well plate (filled with 14 μl PBS with 0.06% BSA). Cells were encapsulated in one lane of a 10x Chromium single cell controller.
Single-cell transcriptome library is prepared with a Single Cell 3′ Reagent Kit (V2 chemistry) following standard protocol.


title: ros1-7


title: LN, scRNAseq

description: 10x Genomics

source_name: Lymphonode

value: Lymphonode


title: Col-LUC

value: wild type


title: siNC+SARS-CoV-2 24 h rep1

description:
NC7
reads count


title: CTRL2 [RNA-Seq]


title: L-Rpa1_WT_RNA_Seq_Rep2

description:
mRNA
rna_seq_counts.txt

tag: strain

value: L-Rpa1 WT


title: PDO10

city: Cambridge

first: Lena

last: Morrill Gavarró

address: Robinson Way

institute: Cancer Research UK Cambridge Institute, University of Cambridge

data_processing:
Reads were aligned to the GRCh38 genome using HISAT2
Reads were quantified using featureCounts
Assembly: GRCh38
Supplementary files format and content: Raw counts

source_name: High grade serous ovarian cancer

extract_protocol:
Extraction was performed using the DNeasy Blood & Tissue Kit (QIAGEN) according to manufacturer instructions.
Illumina TruSeq stranded mRNA kit with 12 PCR cycles.

value: High grade serous ovarian cancer

value: Organoid

value: WT

value: No treatment


title: FT8

source_name: Fallopian tube

value: Fallopian tube


title: PDO3


title: FT9


title: PDO5


title: PDO11


title: PDO1


title: L-Rpa1_WT - H3K4me3_rep2

value: Liver


title: PDO15


title: PDO2


title: PDO6


title: PDO8


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 8h wait, biol rep 2

city: Munich

first: Michael

last: Mentz

state: Bavaria

address: Marchioninistrasse 15

department: 1Department of Internal Medicine III

institute: Ludwig-Maximilians University of Munich

data_processing:
Raw sequence data was processed following the Drop-seq data pipeline as previously described (https://doi.org/10.1016/j.cell.2015.05.002)
Assembly: hg38, Ensemble release 84
Supplementary files format and content: Tab-delimited text file includes a gene expression matrix with UMI counts for 31835 unique ENSG IDs in 54 samples.

growth_protocol: OCI-Ly1 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Plus (Zymo Research, Irvine, California, USA) according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using the prime-seq protocol as previously described (dx.doi.org/10.17504/protocols.io.81wgb1pw3vpk/v2)

treatment_protocol: 1.0 x 10^6 viable cells were seeded in 1 ml growth medium. Cells were treated with IL-4 (10 ng/ml) for 20 min at 37C. After one wash in preheated PBS, cells were replated and incubated at 37C for 2 h, 4 h, and 8 h, respectively. After incubation, 10 µl cell suspension (or 10,000 cells) were transferred to a 96-well PCR tray, mixed with 100 µl Qiagen RLT buffer, and frozen at -80C.

value: B-NHL cell line carrying t(14;18)(q32;q21)

value: STAT6 D419N

value: 20min IL4, wash, 8h wait


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 7

value: STAT6 wild-type


title: 1_hsfa1x_cntr, rep1

description:
female background
1_raw_reads
S11_1

value: gemmalings

value: hsfa1x, ox


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 8h wait, biol rep 1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 2


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 8h wait, biol rep 2

value: STAT6 N421K


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 8h wait, biol rep 1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 6


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 8h wait, biol rep 3

value: STAT6 D419G


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 8h wait, biol rep 3


title: PDO7


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 8


title: FT1


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 8h wait, biol rep 3


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 4h wait, biol rep 3

value: 20min IL4, wash, 4h wait


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 9


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 8h wait, biol rep 1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 3


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 4h wait, biol rep 3


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 4


title: NSC, 3hrs, Six3_flag3

city: Cold spring harbor

first: Padmina

last: Shrestha

address: 1 bungtown road

institute: Cold spring harbor

data_processing:
Bowtie2 was used to map the reads to mm10 genome.
BamCoverage function from deepTools was used to generate bigwig files.
Henipipe wrapper tool with SEACR to generate bedfiles.
Bedops union was used to merge the bedfiles from three replicates.
Supplementary files format and content: bigwig, bedfile
Library strategy: Cut & Run

source_name: Neural stem cells

growth_protocol: Neural stem cells (NSC) were maintained in DMEM/F-12 media with N-2 media supplement, bovine serum albumin (BSA), antibiotics, epidermal growth factor (EGF) and fibroblast frowth factor 2 (FGF).

extract_protocol:
DNA was extracted using phenol/chloroform after enzymatic digestion with pA/G MNase.
DNA library was prepared using ThruPLEX DNA-Seq Kit and manufacturers protocol.

treatment_protocol: NSC media was replaced by neurobasal medium with B-27 media supplement, BSA, L-Glutamine and antibiotics.

value: Neural stem cells

value: neural differentiation (3hrs)


title: NSC, 3hrs, IgG


title: NSC, 3hrs, Six3_flag2


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 4h wait, biol rep 2


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 1


title: NSC, 3hrs, Six3_flag1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 2


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 4h wait, biol rep 2


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 8h wait, biol rep 2


title: Chd5-/- NSCs, 48hrs 2

data_processing:
Salmon was used to get transcript per milltion (TPM) counts.
Supplementary files format and content: Transcript per million (TPM) counts obrained through salmon.

source_name: Primary Neural Stem Cells

growth_protocol: Neural stem cells (NSCs) were maintained in DMEM/F-12 media supplemented with N-2 media supplement, bovine serum albumin (BSA), antibiotics, epidermal growth factor (EGF) and fibroblasat growth factor 2 (FGF) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Trizol reagent and manufacturers protocol.
RNA-seq library was prepared using TruSeq Stranded mRNA Sample Preparation Kit using manufacturers protocol.

treatment_protocol: Neural differentiation was performed by replacing the NSC media with neurobasal medium containing B-27 media supplement, BSA, L-Glutamine and antibiotics.

tag: time point

value: 48 hrs

value: Primary Neural Stem Cells

value: neural differentiation


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 7


title: PDO12

value: High grade serous ovarian cancer

value: Organoid

value: WT

value: No treatment


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 4h wait, biol rep 3

value: B-NHL cell line carrying t(14;18)(q32;q21)


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 8h wait, biol rep 5

value: 20min IL4, wash, 8h wait


title: Chd5-/- NSCs, 48hrs 3


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 3

value: STAT6 wild-type


title: Chd5-/- NSCs, 48hrs 1


title: WT NSCs, 48hrs 3


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 4h wait, biol rep 1

value: STAT6 D419N


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 6


title: WT NSCs, 48hrs 2


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 4h wait, biol rep 1


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 9


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 8


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 5


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 4h wait, biol rep 2


title: WT NSCs, 48hrs 1


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 4h wait, biol rep 1


title: Chd5-/- NSCs, 3hrs 3

value: 3 hrs


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 2h wait, biol rep 1

value: STAT6 N421K

value: 20min IL4, wash, 2h wait


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 5


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 7


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 4


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 2h wait, biol rep 1

value: STAT6 D419G


title: Chd5-/- NSCs, 3hrs 2


title: WT NSCs, 3hrs 2


title: Chd5-/- NSCs, 3hrs 1


title: WT NSCs, 3hrs 1


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 2h wait, biol rep 2


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 3


title: WT NSCs, 3hrs 3


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 6


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 8


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 2h wait, biol rep 2