title: MO0016b +RACIN

city: Epalinges

first: Raphael

last: Genolet

address: Biopole 3, Chemin des Boveresses 155

department: Departement d'oncologie UNIL-CHUV

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

description: beta TCR repertoire

data_processing:
Deep sequencing of the TCR alpha and beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Genome_build: IMGT data base was used to identifiy TCR
Supplementary_files_format_and_content: txt files containing the list of TCR and their frequencies

source_name: peripheral blood mononuclear cell (PBMC)

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction
Libraries were prepare using targeted TCR amplification (Bobisse et al, Nat Commun. 2018 Mar 15;9(1):1092.
TCRseq

value: PBMC

tag: Sex

value: male

tag: tumor type

value: prostate

tag: radiotherapy

value: 1 Gy


title: LNCaP ENZ 168hrs [scRNA-seq]

status: Public on Aug 16 2021

type: SRA

city: London

first: Paolo

last: Cremaschi

state: Non-US

address: 72 Huntley Street

department: Oncology

country: United Kingdom

institute: UCL Cancer Institute

library_source: transcriptomic

data_processing:
Samples were pre-processed, aligned, and processed to gene-cell count matrices with Drop-seq tools v2.3.0 using default parameters and with the expectation that each sample contained 1000 cells (Macosko et al., 2015). We utilized the human reference genome version GRCh38, along with Gencode annotations version 33.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP cells

growth_protocol: LNCaP cells were cultured in RPMI 1640 (Sigma R0883) supplemented with 10% FBS (Sigma F7524), 2 mM Alanyl-glutamine (Sigma G8541), 1 mM sodium pyruvate (Merck TMS-005-C), 2.5 g/L glucose (Sigma G8769), and 1x Antibiotic-Antimycotic (Gibco, 15240062) in a humidified 37°C incubator with 5% CO2. VCaP cells were cultured in DMEM (Gibco) supplemented with 10% FBS in a humidified 37°C incubator with 5% CO2.

extract_protocol:
Cells were trypsinized with TrypLETM Express Enzyme (ThermoFisher Scientific, #12604021), spun down (5 min at 300xg) and washed with 0.1% BSA-PBS. After pelleting, the cells were resuspended in plain PBS and passed through a 40-micron filter. The number of viable cells was estimated with the use of trypan blue staining and Fuchs-Rosenthal hemocytometer chamber. The concentration of cells was brought down to 3x105 cells/mL in 0.1% BSA-PBS. For single-cell encapsulation, single-cell suspension, beads in lysis buffer and oil were connected with the loops and tubing to the Mitos P pumps and run through the glass microfluidic chip at the following flow rates: 100μL/min (Oil channel), 20μL/min (Bead channel); 350 mbar (Cell channel). Droplets were separated by centrifugation and beads counted with the use of Fuchs-Rosenthal hemocytometer chamber and up to 90000 beads were collected into one tube for Reverse Transcription reaction, exonuclease treatment, and amplification of cDNA library according to the original protocol (Macosko et al., 2015). Tagmentation of cDNA was performed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1024). The PCR product was cleaned-up with AMPure XP beads and eluted in 10μL H2O.
Samples were prepared with Drop-seq (Macosko et al., 2015) using the Dolomite cell encapsulation system (Dolomite Bio).

treatment_protocol: Cells were seeded into 5 cm culture plate dishes and allowed to settle before exposure to 10 µM enzalutamide or DMSO vehicle control (0.1%) for 48 h or 168 h.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cell line

tag: enzalutamide sensitivity

value: sensitive

tag: treatment

value: 10µM enzalutamide for 168 hours


title: SC_S312_HFD2

city: Berkeley

first: Karthik

last: Shekhar

state: CA

address: 101D Gilman Hall

country: USA

institute: University of California, Berkeley

data_processing:
Samples were aligned to the transcriptome using Bowtie2 and gene expression was quantified using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Txt files including the gene expression matrix

organism: Mus musculus

source_name: Mouse small intestine stem cells

extract_protocol:
Lgr5+ cells were extracted from mice either fed a control diet or high fat diet using FACS
Smart-seq2 (Picelli et al., 2014)

tag: diet

value: HFD


title: MO0016a +RACIN

country: Switzerland

description: alpha TCR repertoire


title: SC_S311_HFD2


title: SC_S313_HFD2


title: MO0015b -RACIN

description: beta TCR repertoire

value: before treatment


title: MO0015a -RACIN

description: alpha TCR repertoire


title: SC_S309_HFD2


title: SC_S310_HFD2


title: MO0014b +RACIN

description: beta TCR repertoire

value: gallbladder


title: SC_S30_Control1

value: control


title: MO0014a +RACIN

description: alpha TCR repertoire


title: MO0013b -RACIN

description: beta TCR repertoire


title: SC_S308_HFD2


title: MO0013a -RACIN

description: alpha TCR repertoire


title: SC_S315_HFD2


title: SC_S319_HFD2


title: MO0012b +RACIN

description: beta TCR repertoire

value: female

value: ovary


title: SC_S306_HFD2


title: MO0011a -RACIN

description: alpha TCR repertoire


title: MO0012a +RACIN

description: alpha TCR repertoire


title: MO0011b -RACIN

description: beta TCR repertoire


title: SC_S305_HFD2


title: MO0010b +RACIN

description: beta TCR repertoire


title: MO0009b -RACIN

description: beta TCR repertoire


title: SC_S304_HFD2


title: SC_S301_HFD2


title: SC_S2_Control1


title: MO0008b +RACIN

description: beta TCR repertoire

value: recto-sigm ADC


title: SC_S302_HFD2


title: MO0009a -RACIN

description: alpha TCR repertoire


title: SC_S303_HFD2


title: SC_S299_HFD2


title: SC_S307_HFD2


title: MO0007a -RACIN

description: alpha TCR repertoire


title: SC_S29_Control1


title: SC_S296_HFD2


title: MO0005b -RACIN

description: beta TCR repertoire


title: MO0008a +RACIN

description: alpha TCR repertoire


title: MO0010a +RACIN

description: alpha TCR repertoire


title: SC_S293_HFD2


title: SC_S300_HFD2


title: SC_S292_HFD2


title: SC_S298_HFD2


title: MO0004a +RACIN

description: alpha TCR repertoire


title: MO0006a +RACIN

description: alpha TCR repertoire


title: MO0006b +RACIN

description: beta TCR repertoire


title: SC_S297_HFD2


title: SC_S290_HFD2


title: SC_S295_HFD2


title: SC_S294_HFD2


title: MO0005a -RACIN

description: alpha TCR repertoire


title: input DNA

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

library_source: genomic

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

molecule: genomic DNA

source_name: MCF-7 cells

extract_protocol:
For ChIP-seq, the crosslinked protein-DNA complex was extracted from the sonicated nuclei and isolated with antibody. For Repli-seq, EdU incorporated nascent DNA was sonicated and enriched with streptavidin magnetic beads. For extrachromosomal DNA sequencing, extrachromosomal DNA was purified from the nuclei treated with ATP-dependent exonuclease to remove linear genomic DNA.
Enriched DNA for ChIP-seq, Repli-seq or extrachromosomal DNA sequencing was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Sequencing adaptors were ligated to the DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by Qubit 2.0 and subjected to HiSeq X Ten or HiSeq 2500 sequencing according to the manufacturer’s instructions.

tag: genotype/variation

value: wildtype

value: Breast cancer cells

tag: antibodies


title: MO0004b +RACIN

description: beta TCR repertoire

value: PBMC


title: TRPS1_ChIPSeq

value: TRPS1 (Abcam, ab209664)


title: SC_S291_HFD2


title: SC_S286_HFD1


title: SC_S28_Control1


title: DelMut.SE

city: Worcester

first: Y.

middle: Tony

last: Ip

state: Massachusetts

address: 373 Plantation Street, Ste 109

department: Molcular Medicine

institute: University of Massachusetts Medical School

description: Hinfp2-DelMut, Rep1

data_processing:
# Gene Expression Analysis
Both paired-end (PE) and single-end (SE) reads were aligned to Drosophila Melanogaster genome Drosophila_melanogaster.BDGP6.22.dna.toplevel.fa, with STAR_2.5.3a 1. The alignment was guided by EMSEMBL2 annotation Drosophila_melanogaster.BDGP6.22.96.gtf. Multi-mapping of up to 200 locations and maximum percentage of mismatch 5% were allowed. Out of the many mapped locations of the multi-mapped reads, only one location is picked randomly to allow for the quantification of multi-copy genes, such as histone genes.
Aligned exon fragments/reads were counted toward gene expression with featureCounts_1.5.2 3. Parameters of STAR and featureCount were set so that multi-mapped fragments/reads can be counted once for each fragment/read. Then fragment/read counts for histone genes were aggregated by summing up counts for the many copies of the same gene on the genome.
RPKM and TPM calculated with R package scater
# Transposable Element Analysis
First 12nt of sequences were trimmed from SE-RNAseq reads, and first 14nt were trimmed from PE-RNAseq reads. Then trimmed reads were mapped to 175 sequences of transposon elements (TE, dm6.transposon.fa) with bowtie21 (parameters: -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local -k 1 --seed 1), which allows multiple mapping, and randomly assigned multiple mapped reads to one of the best matches2. Then mapping results were quantified with featureCounts3. Expression quantification of TE were combined with the count table of regular genes in RNAseq data analysis for more robust normalization. Differential expression (DE) analysis was performed with  DESeq24. Within DE analysis, 'ashr' was used to create log2FoldChange (LFC) shrinkage for each comparison5. Significant DE TE were filtered with the criteria FDR < 0.05 and |LFC| > 1.  The heatmap was created with ComplexHeatmap6, using z-scores converted from TPM.
Genome_build: BDGP6
Supplementary_files_format_and_content: Excel tables; Annotated with BDGP6.22.96

organism: Drosophila melanogaster

source_name: Adult pharate male

extract_protocol:
Around 50 guts were isolated in cold RNAase free water. Total RNA was extracted from each sample using Tri-reagents (Sigma). The quality of RNA was measured in Agilant bio-analyzer. The qulified RNA of each sample send to BGI for making library preparation and sequencing on BGISeq-500 platform.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo- attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification and  quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: tissue

value: Gut with malpighian tubules

tag: developmental stage

value: pharate adult

tag: gender

value: male

tag: genotype


title: SC_S289_HFD2


title: SC_S282_HFD1


title: SC_S285_HFD1


title: MO0007b -RACIN

description: beta TCR repertoire


title: Rescue by His1 OE

description: processed data file: gene_TE.DE.RNAseq.log2FC.csv

data_processing:
The raw sequencing data were first quality filtered with Trimmomatic (0.39)(Bolger et al., 2014
mapped to the corresponding rRNA(fruit fly, mouse or human) references with Bowtie2 (2.3.5)(Langmead and Salzberg, 2013).
The unmapped reads were thenused as cleaned reads for the downstream mapping and quantification analysis.To quantify the readcount of genes and transposable element (TE), the cleaned reads were mapped to the reference separately.
For genes, reads were mapped to the corresponding whole genome (dm6 for fruit fly, mm10 for mouse, and hg38 for human) using STAR (2.5.3a) (Dobin and Gingeras, 2015)with default parameters. For TEs, reference sequencesand annotationsof each species were first extracted from RepBase (Jurka et al., 2005), first12nt were trimmed from single-end reads, and first 14nt were trimmed from pair-end readsusing FASTX-Toolkit (0.0.14)(http://hannonlab.cshl.edu/fastx_toolkit/index.html).
The trimmed reads were then mapped to corresponding TE referencesusingBowtie2(Langmead and Salzberg, 2013)with parameters: -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local -k 1 --seed 1(Lerat et al., 2017).Subreads:featureCounts (1.6.2)(Liao et al., 2014)was used to obtain the read count of each gene and TE. Normalization and differentially geneexpression analysis was then performed using DESeq2 (Love et al., 2014)for the multi-replicate datasets, edgeR (3.28.1) (Robinson et al., 2010)for non-replicate datasets
Genome_build: dm6
Supplementary_files_format_and_content: csv format; raw gene count, DE analysis p-value and LFC

source_name: Intestinal cells

value: Rescue by His1 OE

value: Intestine

tag: condition

value: adult


title: Rescue by Hinfp OE

value: Rescue by Hinfp OE


title: DelMut.PE

description: Hinfp2-DelMut, Rep2


title: PointMut.SE

description: Hinfp3-PointMut, Rep1


title: SC_S284_HFD1

value: HFD


title: FRT19A Control

value: Control


title: W1118.CTRL.SE

description: W1118-Control, Rep1


title: W1118.CTRL.PE

description: W1118-Control, Rep2


title: FRT19A.CTRL.PE

description: FRT19A-Control, Rep2


title: SC_S283_HFD1


title: FRT19A.CTRL.SE

description: FRT19A-Control, Rep1


title: PointMut.PE

description: Hinfp3-PointMut, Rep2


title: SC_S278_HFD1


title: SC_S277_HFD1


title: SC_S280_HFD1


title: SC_S281_HFD1


title: Hinfp2 mutant M2

value: mutant


title: SC_S27_Control1

value: control


title: plate7

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

data_processing:
Fastq files were obtained from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Quality control was performed to remove poor quality cells. Cells with less than 250 genes detected were removed. We further excluded cells with values below 3 median absolute deviations (MADs) from the median for UMI counts, for the number of genes detected, or for ERCC accuracy, and cells with values above 3 MADs from the median for ERCC transcript percentage.
Genome_build: GRCm38 with additional artificial chromosomes for 92 ERCC spike-in genes.
Supplementary_files_format_and_content: m_cDC1_UMI.csv: Comma-separated text file containing gene UMI counts.
Supplementary_files_format_and_content: Ghislat_GEO_metadata.csv: Comma-separated text file containing additional cell-specific metadata (index sorting parameters) for each filtered cell identified by a UniqueCellID.

molecule: polyA RNA

source_name: YUMM1.7 tumor grown in a female mouse

growth_protocol: 1x10^6 YUMM1.7 cells were injected s.c. in 100µl endotoxin-free PBS on the right flank of recipient mice.

extract_protocol:
Single cells were FACS sorted into ice-cold 96-well PCR plates (Thermofisher) containing 2 µl lysis mix per well. The lysis mix contained 0.5 µl 0.4% (v/v) Triton X-100 (Sigma-Aldrich), 0.05 µl 40 U/µl RnaseOUT (Thermofisher), 0.08 µl 25 mM dNTP mix (Thermofisher), 0.5 µl 10 µM (dT)30_Smarter primer (Supplementary file), 0.05 µl 0.5 pg/µl External RNA Controls Consortium (ERCC) spike-ins mix (Thermofisher), and 0.82 µl PCR-grade H20 (Qiagen). Immediately after cell sorting, each plate was covered with adhesive film (Thermofisher), briefly spun down in a benchtop plate centrifuge, and frozen on dry ice. Plates containing single cells in lysis mix were stored at -80°C and shipped on dry ice (only T cells) until further processing. The plate containing single cells in lysis mix was thawed on ice, briefly spun down in a benchtop plate centrifuge, and incubated in a thermal cycler for 3 minutes at 72°C (lid temperature 72°C). Immediately after, the plate was placed back on ice and 3 µl RT mastermix was added to each well. The RT mastermix contained 0.25 µl 200 U/µl SuperScript II (Thermofisher), 0.25 µl 40 U/µl RnaseOUT (Thermofisher), and 2.5 µl 2x RT mastermix. The 2x RT mastermix contained 1 µl 5x SuperScript II buffer (Thermofisher), 0.25 µl 100 mM DTT (Thermofisher), 1 µl 5 M betaine (Sigma-Aldrich), 0.03 µl 1 M MgCl2 (Sigma-Aldrich), 0.125 µl 100 µM well-specific template switching oligonucleotide TSO_BCx_UMI5_TATA (Table S3 and Table S4), and 0.095 µl PCR-grade H2O (Qiagen). Reverse transcription was performed in a thermal cycler (lid temperature 70°C) by 90 min at 42°C, followed by 10 cycles of 2 min at 50°C and 2 min at 42°C, then 15 min at 70°C. Plates with single-cell cDNA were stored at -20°C until further processing. For cDNA amplification, 7.5 µl LD-PCR mastermix were added to each well. The LD-PCR mastermix contained 6.25 µl 2x KAPA HiFi HotStart ReadyMix (Roche Diagnostics), 0.125 µl 20:µM PCR_Satija forward primer (Supplementary file), 0.125 µl 20 µM SmarterR reverse primer (Supplementary file), and 1 µl PCR-grade H2O (Qiagen). The amplification was performed in a thermal cycler (lid temperature 98°C) by 3 min at 98°C, followed by 22 cycles of 15 sec at 98°C, 20 sec at 67°C, 6 min at 72°C, then a final elongation for 5 min at 72°C. Plates with amplified single-cell cDNA were stored at -20°C until further processing.
For library preparation, 5 µl amplified cDNA from each well of a 96-well plate were pooled and completed to 500 µl with PCR-grade H2O (Qiagen). Two rounds of 0.6X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene) cleaning were used to purify 100 µl pooled cDNA with final elution in 15 µl PCR-grade H2O (Qiagen). After quantification with Qubit dsDNA HS assay (Thermofisher), 800 pg purified cDNA pool were processed with the Nextera XT DNA sample Preparation kit (Illumina), according to the manufacturer’s instructions with modifications to enrich 5’-ends of tagmented cDNA during library PCR. After tagmentation and neutralization, 25 µl tagmented cDNA was amplified with 15 µl Nextera PCR Mastermix, 5 µl Nextera i5 primer (S5xx, Illumina), and 5 µl of a custom i7 primer mix (0.5 µM i7_BCx + 10 µM i7_primer, Supplementary file). The amplification was performed in a thermal cycler (lid temperature 72°C) by 3 min at 72°C, 30 sec at 95°C, followed by 12 cycles of 10 sec at 95°C, 30 sec at 55°C, 30 sec at 72°C, then a final elongation for 5 min at 72°C. The resulting library was purified with 0.8X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene).
Libraries generated from multiple 96-well plates of single cells and carrying distinct i7 barcodes were pooled for sequencing on an Illumina NextSeq550 platform, with High Output 75 cycles flow cells, targeting 5x10^5 reads per cell in paired-end single-index mode with the 14 different barcode primers (supplementary file) and cycles: Read1 (Read1_SP, 67 cycles), Read i7 (i7_SP, 8 cycles), Read2 (Read2_SP, 16 cycles).

treatment_protocol: Tumors were minced and digested in RPMI 1640, 1 mg/ml collagenase II (Sigma -Aldrich), 50 µg/ml DNaseI (Roche), and 0.1% (wt/vol) BSA for 30 min at 37°C with 750 rpm agitation. Cell suspensions were subsequently passed through a 70-µm cell strainer (BD Biosciences) and collected by centrifugation.

tag: mouse genotype

value: Tumor

tag: experiment

tag: plate


title: SC_S270_HFD1


title: SC_S275_HFD1


title: SC_S271_HFD1


title: SC_S26_Control1


title: SC_S268_HFD1


title: SC_S274_HFD1


title: plate9


title: plate8


title: H3K27me3 500 cell [CUT&RUN]

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38) with bowtie2 (version 2.2.1)
Parameter for bowtie2 mapping were: --dovetail --phred33
Samtools (version 1.9) was used to convert SAM files to BAM files
Peaks was called using MACS2 (version 2.1.2)
Parameters used for MACS2 peak calling: --broad --pvalue 0.01 (for the 10k cell) or --pvalue --0.01 (for the 500 cell sample)
Deeptools (version 3.5.1) was used to convert BAM to bigWig
Parameters used for deeptools BAM to BigWig conversion: bamCoverage --bam ${bamDir} -o ${outDir} --normalizeUsing None --effectiveGenomeSize 2150570000 --extendReads --ignoreForNormalization chrX --binSize 10
Genome_build: mm10
Supplementary_files_format_and_content: BED: Peaks called by MACS2, bigWig: Coverage tracks from deeptools bamCompare. Annotated BED: Annotated BED from from ChIPpeakAnno

extract_protocol:
E10.5 yolk sac erythro-myeloid progenitors were prepared for CUT&RUN using the CUT&RUN kit from Cell Signaling Technologies with Rabbit (DA1E) mAb IgG XP® isotype control (Cell Signaling Technologies) and anti-H3K27me3 (07-449, Merck MilliPore).
DNA libraries were pre-amplified using 17 (500 EMPs) or 16 (15,000 EMPs) cycles of PCR. DNA libraries were prepared using Nextera XT (Illumina). Samples were sequenced using the Illumina NextSeq 550 (500 EMPs) and NovaSeq XP (15,000 EMPs) platform, generating 76 bp (500 EMPs) and 59 bp (15,000 EMPs) paired-end reads.

tag: strain

value: Ezh2fl/fl; Tie2-Cre+/+  Wild type

value: yolk sac


title: IgG 500 cell  [CUT&RUN]

source_name: E10.5 yolk sac erythro-myeloid progenitors


title: SC_S267_HFD1


title: SC_S273_HFD1


title: SC_S272_HFD1


title: plate16


title: plate14


title: SC_S266_HFD1


title: plate3


title: plate13


title: SC_S265_HFD1


title: SC_S269_HFD1


title: SC_S279_HFD1


title: plate11


title: SC_S263_HFD1


title: plate15


title: plate10


title: plate12


title: plate6


title: SC_S25_Control1


title: plate4


title: plate5


title: ZT1S1

type: RNA

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.

data_processing: The reference miRNA for normalization was selected using the NormiRazor. Based on the assumption that no single miRNA is suitable as a reference in serum miRNA qPCR profiling experiments30, we found that the most stable reference was the average expression level of two miRNAs (miR-142-5p and miR-23b-3p). Differentially expressed miRNAs were shortlisted on the basis of univariate, Benjamini-Hochberg adjusted, p values. Then, the expression levels of selected miRNAs were validated using the miRCURY LNA miRNA Custom PCR Panels (QIAGEN, Hilden, Germany). Selection of miRNAs for this part of the study was based on three criteria: expression in at least two thirds of samples, fold change greater than 1.5 or smaller than 0.67 and Benjamini-Hochberg adjusted p values <0.25. The normalization was performed using the formula ∆Ct = Ct(reference) - Ct(miRNA of interest), which provides a higher value for higher miRNA expression, facilitating its use and interpretation as a biomarker. Quantitative Real-Time PCR (qPCR) was performed in duplicates using the miRCURY LNA SYBR Green system (QIAGEN, Hilden, Germany) in a 96-well format. Undetectable expression (negative result) was reported if expression was not detected >37 PCR cycles. UniSp2, UniSp4, and UniSp5 were used as RNA isolation spike-in controls and UniSp6 was used as cDNA synthesis spike-in control.

label: miRCURY LNA SYBR Green

source_name: serum

label_protocol: cDNA synthesis was performed using miRCURY LNA RT Kit (QIAGEN, Hilden, Germany). We used real-time PCR arrays with locked nucleic acid-containing primers (miRCURY LNA miRNA miRNome PCR Panels; QIAGEN, Hilden, Germany) for serum profiling

extract_protocol: total RNA was isolated from 200 μL serum samples using miRCURY RNA Isolation kit (QIAGEN, Hilden, Germany)

tag: cohort

value: Validation

tag: xerostomia

value: Yes

tag: time point

value: Prior to RT


title: SC_S256_HFD1


title: SC_S264_HFD1


title: SC_S262_HFD1


title: SC_S261_HFD1


title: ZT1S4

value: After treatment completion


title: SC_S254_HFD1


title: SC_S260_HFD1


title: SC_S259_HFD1


title: SC_S258_HFD1


title: SC_S252_HFD1


title: ZT1S3

value: After 20 Gy


title: ZA1S4

value: No


title: SC_S251_HFD1


title: ZK1S3


title: SC_S250_HFD1


title: ZK1S2


title: WU1S4


title: ZA1S3


title: SC_S255_HFD1


title: ZA1S1


title: ZE1S4


title: ZK1S1


title: ZE1S3


title: ZE1S1


title: WU1S1


title: SC_S253_HFD1


title: SC_S248_HFD1


title: SC_S247_HFD1


title: WR1S4


title: SC_S24_Control1


title: SC_S257_HFD1


title: SC_S243_HFD1


title: SC_S249_HFD1


title: WU1S3


title: SC_S241_HFD1


title: SC_S246_HFD1


title: SC_S23_Control1


title: WR1S3


title: SC_S239_HFD1


title: SC_S237_HFD1


title: SC_S244_HFD1


title: WR1S1


title: SC_S245_HFD1


title: SC_S235_HFD1


title: WM1S3


title: TM1S1


title: WM1S1


title: SS1S4


title: WM1S4


title: WJ2S1


title: SS1S3


title: SC_S242_HFD1


title: SS1S1


title: SC_S232_HFD1


title: WJ2S3


title: TM1S3


title: SR1S1


title: WJ2S2


title: SR1S3


title: SM2S3


title: SC_S240_HFD1


title: SC_S233_HFD1


title: SM2S1


title: SC_S238_HFD1


title: TM1S4


title: SC_S231_HFD1


title: SS2S4


title: SS2S1


title: SC_S236_HFD1


title: SE2S4


title: SS2S3


title: SG1S3


title: SC_S234_HFD1


title: SE2S1


title: SC_S220_HFD1


title: SC_S22_Control1


title: SR1S4


title: SC_S230_HFD1


title: SC_S225_HFD1


title: SE'1S3


title: SC_S228_HFD1


title: SC_S227_HFD1


title: SC_S229_HFD1


title: SC_S226_HFD1


title: SG1S4


title: SC_S218_HFD1


title: SC_S221_HFD1


title: SG1S1


title: SC_S215_HFD1


title: SB1S4


title: SA4


title: SM2S2


title: SB1S3


title: SA1


title: SC_S213_HFD1


title: SC_S223_HFD1


title: SC_S211_HFD1


title: SC_S222_HFD1


title: SC_S216_HFD1


title: SC_S210_HFD1


title: SE2S3


title: RU1S3


title: SC_S20_Control1


title: SC_S214_HFD1


title: SC_S21_Control1


title: RJ2S4


title: SC_S207_HFD1


title: SC_S224_HFD1


title: SC_S219_HFD1


title: SE'1S4


title: SE'1S1


title: SC_S217_HFD1


title: SC_S203_HFD1


title: PS1S2


title: SB1S1


title: SC_S200_HFD1


title: SC_S212_HFD1


title: SC_S1_Control1


title: SA3


title: PK1S1


title: RU1S4


title: SC_S209_HFD1


title: RU1S1


title: RT1S4


title: RT1S3


title: PI1S3


title: SC_S208_HFD1


title: PI1S1


title: SC_S205_HFD1


title: RT1S1


title: SC_S204_HFD1


title: RJ2S3


title: RJ2S1


title: SC_S194_HFD1


title: PS1S3


title: ND1S1


title: SC_S202_HFD1


title: MM2S4


title: PK1S4


title: SC_S190_Control2


title: SC_S189_Control2


title: PI1S4


title: PS1S1


title: SC_S206_HFD1


title: SC_S201_HFD1


title: PK1S3


title: SC_S19_Control1


title: SC_S188_Control2


title: SC_S197_HFD1


title: SC_S195_HFD1


title: SC_S198_HFD1


title: SC_S185_Control2


title: SC_S186_Control2


title: ND1S4


title: SC_S184_Control2


title: ND1S3


title: LK1S3


title: SC_S183_Control2


title: SC_S199_HFD1


title: SC_S196_HFD1


title: LK1S1


title: KV1S4


title: MM2S1


title: SC_S179_Control2


title: KV1S1


title: MJ1S3


title: MM2S3


title: SC_S193_HFD1


title: SC_S18_Control1


title: SC_S178_Control2


title: KT1S2


title: LK1S2


title: MJ1S2


title: SC_S176_Control2


title: SC_S175_Control2


title: SC_S187_Control2


title: SC_S17_Control1


title: MJ1S1


title: MG2S4


title: SC_S173_Control2


title: SC_S182_Control2


title: MG2S1


title: SC_S181_Control2


title: MG2S3


title: SC_S180_Control2


title: SC_S16_Control1


title: KV1S3


title: KB3S3


title: KB3S1


title: KT1S3


title: SC_S168_Control2


title: SC_S167_Control2


title: SC_S177_Control2


title: KT1S1


title: SC_S174_Control2


title: SC_S166_Control2


title: KE3


title: KM4S3


title: SC_S165_Control2


title: KB2S1


title: SC_S171_Control2


title: SC_S170_Control2


title: KB1S2


title: KM4S4


title: KM4S1


title: KE4


title: KA1S4


title: KE1


title: KB3S2


title: SC_S172_Control2


title: KA1S1


title: SC_S169_Control2


title: KB2S3


title: HR1S4


title: HR1S3


title: SC_S156_Control2


title: KB2S2


title: H3K9me3_+Dox rep 2

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description: Merged with previous GSM4720923

data_processing:
Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignment using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Genome_build: hg19
Supplementary_files_format_and_content: WIG files with input-subtracted ChIP-Seq signal.

source_name: Breast cancer cell line

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100µg/ml streptomycin.

extract_protocol:
T47D-MTVL cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under BGI (Beijing Genomic Institution) ChIP-seq protocols, using combinatorial Probe-Anchor Synthesis (cPAS) and DNA nanoball sequencing.

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the multiple H1 variants shRNA (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxicycline treatment. To carry out experiments, Doxycycline (Sigma) was added at 2.5 µg/ml when indicated and treated for 6 days.

value: Breast cancer ductal carcinoma

tag: cell line

tag: chip antibody

value: anti-H3K9me3 (Abcam, ab8898)

tag: dox treatment

value: Treated


title: SC_S164_Control2

tag: diet


title: SC_S163_Control2


title: GW1S1


title: SC_S162_Control2


title: SC_S154_Control2


title: KB1S3


title: SC_S160_Control2


title: SC_S161_Control2


title: H1.2_WT

description: endogenous H1.2 histone protein immunoprecipitated DNA

data_processing:
Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignment using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Genome_build: hg19
Supplementary_files_format_and_content: WIG files with input-subtracted ChIP-Seq signal. Input sample is available at GSE156036.

treatment_protocol: No treatment

value: anti-H1.2 (Abcam, ab4086)

tag: genotype/variation

value: untreated


title: SC_S15_Control1


title: SC_S158_Control2


title: KB1S1


title: HR1S1


title: SC_S157_Control2


title: GD1S1


title: GW1S4


title: H1.4_WT

description: endogenous H1.4 histone protein immunoprecipitated DNA

tag: tissue

value: anti-H1.4 (Invitrogen, 702876)


title: GW1S3


title: KA1S3


title: H3K9me3_-Dox rep 2

description: Merged with previous GSM4720922

value: Untreated


title: SC_S159_Control2

value: control


title: DJ3


title: SC_S155_Control2


title: H1X_-Dox

extract_protocol:
T47D-MTVL cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under BGI (Beijing Genomic Institution) ChIP-seq protocols, using combinatorial Probe-Anchor Synthesis (cPAS) and DNA nanoball sequencing.
ChIP-seq (DNB-seq)

value: anti-H1X (Abcam, ab31972)

tag: treatment


title: H1.5_+Dox

value: anti-H1.5 (Invitrogen, 711912)

value: Dox treatment


title: H1X_WT

description: endogenous H1X histone protein immunoprecipitated DNA


title: SC_S150_Control2


title: SC_S14_Control1


title: GD1S4

value: Validation


title: H1.5_-Dox


title: H1.4_-Dox


title: H1.2_+Dox


title: SC_S148_Control2


title: H1.5_WT

description: endogenous H1.5 histone protein immunoprecipitated DNA


title: GD1S3


title: H1.0_-Dox

value: anti-H1.0/H5 clone 3H9 (Millipore, 05-629-I)


title: H1.2_-Dox


title: H1.0_+Dox


title: Input


title: H1.0_WT

description: endogenous H1.0 histone protein immunoprecipitated DNA


title: CJ1S1

value: Prior to RT


title: deltaDbp7_Dbp7DQGD_2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Whole cell RNA from yeast

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Reads were mapped against yeast transcriptome from the SGD database (https://www.yeastgenome.org)
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

organism: Saccharomyces cerevisiae

source_name: deltaDbp7_Dbp7DQGD_whole cell RNA

growth_protocol: Yeast strains used in this study are listed in Supplementary Table S6 and were grown in Yeast Complete medium (1% yeast extract, 2% peptone/tryptone, 2% glucose or galactose or synthetic media lacking aminoacids where appropriate.

extract_protocol:
Whole cell RNA was extracted from exponentially growing yeast cells using acidic phenol and chloroform extraction
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description


title: deltaDbp7_Dbp7DQGD_3

description: Whole cell RNA from yeast


title: deltaDbp7_Dbp7DQGD_1

description: Whole cell RNA from yeast


title: DJ4

value: Yes

value: After treatment completion


title: deltaDbp7_Dbp7WT_3

description: Whole cell RNA from yeast

source_name: deltaDbp7_Dbp7WT_whole cell RNA


title: SC_S151_Control2


title: SC_S145_Control2


title: H3K9me3_+Dox rep 1


title: SC_S153_Control2


title: H3K9me3_-Dox rep 1


title: deltaDbp7_Dbp7WT_1

description: Whole cell RNA from yeast


title: SC_S144_Control2


title: H1X_+Dox


title: SC_S152_Control2


title: SC_S143_Control2


title: BZ1S1


title: SC_S146_Control2


title: WT_EV_3

description: Whole cell RNA from yeast

source_name: WT_EV_whole cell RNA


title: H1.4_+Dox


title: WT_EV_1

description: Whole cell RNA from yeast


title: CJ1S2

value: No

value: After 20 Gy


title: BK1S3


title: deltaDbp7_Dbp7WT_2

description: Whole cell RNA from yeast


title: SC_S140_Control2


title: CJ1S3


title: BA1S4


title: DJ1


title: BZ1S4


title: BZ1S3


title: SC_S147_Control2


title: rad30Δ 1G rep 2

city: Solna

first: Pei-Shang

last: Wu

address: Tomtebodavägen 16

country: Sweden

institute: Karolinska Institutet

description:
r30_1G_2
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx

data_processing:
FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control of the .fastq-files.
Adapter and poor quality read trimming was performed with cutadapt.
The RNA-seq data was mapped with the splice-aware aligner HISAT2. The mapped files were sorted using samtools and aligned to the yeast genome version SacCer3.
The mapped data was deduplicated using the MarkDuplicates tool from the Picard tool set.
The reads were counted per gene using featureCounts.
The count-files were imported into R and further analyzed using edgeR for FPKM calculations (log2, prior count = 1) and DESEQ2 for differential expression analysis.
Genome_build: SacCer3 downloaded from UCSC genome browser.
Supplementary_files_format_and_content: raw_counts.xlsx: Matrix table with raw gene counts for every gene and every sample, output from featureCounts.
Supplementary_files_format_and_content: diff_exp_r30_vs_WT.xlsx: Matrix table with 4 tabs to compare gene expression between WT and Polη-deficient cells, before and after DSB-induction in G2/M phase, output from DESEQ2 and additionally mean of log2(FPKM) values for each genotype and treatment.

source_name: whole cells

growth_protocol: Exponential growing yeast cells in YEP media supplemented with 2% raffinose (final) were treated with 80 μg/ml (final) benomyl for 3 hours. The 'G2' samples were collected when cells were arrested in G2/M phase.

extract_protocol:
Cell walls were removed by zymolyase. The total RNA extracts were prepared with the PureLink RNA Mini Kit (Invitrogen), purified with the DNA-free Kit (Invitrogen).
The cDNA libraries were constructed by Novogene, based on Illumina standard protocol. Quality controls for the RNA samples and during the RNA-sequencing procedures were included.

treatment_protocol: Galactose (final 2%) was then added to induce DSBs (PGAL-HO) for 1-hour, to collect the '1G' samples.

value: W303 derivatives

value: Pol{eta}-deficient cells

value: G2/M arrest + 1-hr DSB


title: SC_S149_Control2


title: deltaDbp7_EV_3

description: Whole cell RNA from yeast

source_name: deltaDbp7_EV_whole cell RNA


title: deltaDbp7_EV_2

description: Whole cell RNA from yeast


title: WT_EV_2

description: Whole cell RNA from yeast


title: deltaDbp7_EV_1

description: Whole cell RNA from yeast


title: SC_S139_Control2


title: SC_S142_Control2


title: WT 1G rep 3

description:
WT_1G_3
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx

value: Wild type


title: WT 1G rep 2

description:
WT_1G_2
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: BK1S4


title: BK1S1


title: 91/RTH_D


title: rad30Δ 1G rep 3

description:
r30_1G_3
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: rad30Δ 1G rep 1

description:
r30_1G_1
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: rad30Δ G2 rep 3

description:
r30_G2_3
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx

value: G2/M arrest


title: WT 1G rep 1

description:
WT_1G_1
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: SC_S13_Control1


title: WT G2 rep 3

description:
WT_G2_3
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: rad30Δ G2 rep 2

description:
r30_G2_2
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: BA1S3


title: WT G2 rep 1

description:
WT_G2_1
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: SC_S136_Control2


title: SC_S137_Control2


title: GC-Po-KdNc4

city: Wuhan

first: Ying

last: Huang

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdNc4_FRAS190012316-1a_1

data_processing:
Reads were filtered by removing adapters, low quality reads and unknown bases.
Clean reads were mapped to Gallus_gallus-5.0 of Ensembl using HISAT2 v2.1.0.
Genes expression levels were quantified by a software package: stringtie v1.3.4d.
Differentially expressed genes were calculated by Deseq2 v1.26.0.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited gtf files include "cov", "FPKM", "TPM" values for each Sample, which generated by stringtie.

organism: Gallus gallus

source_name: ovary

growth_protocol: The primary granulosa cells were pre-cultured with Medium 199 (Gibco, USA) and 5% FBS (Gibco, USA) overnight (16h).

extract_protocol:
Total RNA was extracted from primary granulosa cells using TRIzol reagent (Invitrogen, USA) following the manufacturer’s protocol.
The sequencing library was generated under the instruction manual with NEB Next UltraTM RNA Library Prep Kit for Illumina (NEB, USA). Obtained cDNA libraries were sequenced on an Illumina Nova platform and generated paired-end reads.

treatment_protocol: The primary granulosa cells transfected with AR-specific siRNA (AR-siRNA) or NC nonsense siRNA (NC-siRNA) using Lipofectamine 3000 (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, respectively.

tag: breed

value: White Leghorn

tag: cell type

value: primary granulosa cells

tag: sirna

value: NC-siRNA


title: SC_S138_Control2

value: control


title: 91/RTH_A

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.


title: SC_S141_Control2


title: SC_S135_Control2


title: rad30Δ G2 rep 1

description:
r30_G2_1
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx

tag: genotype


title: 91/RTH_C


title: GC-Po-KdNc3

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdNc3_FRAS190012315-1a_1


title: WT G2 rep 2

description:
WT_G2_2
raw_counts.xlsx
diff_exp_r30_vs_WT.xlsx


title: 88/RTH_D


title: SC_S133_Control2


title: 88/RTH_C


title: GC-Po-KdAr4

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdAr4_FRAS190012313-1a_1

value: AR-siRNA


title: Subcutaneous tissue treatment3percent-3

city: Shanghai

first: Tianji

last: Ji

state: Shanghai

address: 1678 Dongfang Road

department: Department of Pediatric Cardiology

institute: Shanghai Children's Medical Center

data_processing:
Alignment was performed using STAR (version 2.5.2b) to mouse genome (Gencode, GRCm38) and mouse transcripts gtf file (Gencode vM10). The following STAR parameter was used: "STAR --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c --outSAMunmapped Within KeepPairs"
Read counts for individual samples were compiled by genes.
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw read count of each gene

source_name: Subcutaneous tissues surrounding engineered cartilage

growth_protocol: Bone marrow mesenchymal stem cells (BMSCs) isolated from New Zealand white rabbits were seeded into poly (lactic-co-glycolic acid) (PLGA) scaffolds (6 mm diameter and 2 mm depth, 3.9 x 106 cells/scaffold) and then cultured in the chondrogenic medium (DMEM with high glucose, 10 ng/mL TGFβ1, 100 ng/mL IGF1, ITS (1X), 25 µg/mL ascorbic acid, 40 ng/mL dexamethasone) for 4 weeks to prepare engineered cartilage. PCL/collagen nanofibrous membranes were fabricated by electrospinning.

extract_protocol:
Samples were harvested with the murine tissues entangled were removed, flash frozen on dry ice. Total RNA was harvested using Trizol reagent and evaluated by agarose gel electrophoresis and Agilent 2100 Bioanalyzer. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: About 1 h before electrospinning, axitinib was added to the solution at mass ratios of 0% or 3% ((weight of axitinib )/( total weight of PCL and collagen)). Rabbit's engineered cartilage was encapsulated in the PCL/collagen nanofibrous membrane and subcutaneously implanted into nude mice.

value: BALB/c nude

value: Subcutaneous tissues

value: 12 weeks post-implantaion

value: 3% Axitinib treatment


title: GC-Po-KdAr3

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdAr3_FRAS190012312-1a_1


title: Subcutaneous tissue treatment3percent-2


title: GC-Po-KdNc2

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdNc2_FRAS190012314-1a_1


title: 88/RTH_A

value: Validation

value: Prior to RT


title: GC-Po-KdAr2

description:
follicle
preovulatory
35-40 weeks
s20190308-GC-Po-KdAr2_FRAS190012311-1a_1


title: BA1S1

value: No


title: Subcutaneous tissue treatment3percent-1


title: Subcutaneous tissue ctrl-3

value: untreated


title: Subcutaneous tissue ctrl-2


title: SC_S131_Control2


title: SC_S132_Control2


title: SC_S130_Control2


title: SC_S134_Control2


title: 87/RTH_A

value: Yes


title: SC_S12_Control1


title: Subcutaneous tissue ctrl-1


title: 87/RTH_C

value: After 20 Gy


title: CON2-colon

city: Hangzhou

first: Luoyi

last: Zhu

state: Zhejiang

address: 866 Yuhang Tang Road

institute: Zhejiang University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
RNA extracted from mouse liver and colon tissues using Trizol reagent. Total amount and integrity of RNA were accurately detected with an Agilent RNA 6000 Nano Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: post natal day 42

value: colon


title: CON3-colon


title: 87/RTH_D

value: After treatment completion


title: 86/RTH_D


title: 86/RTH_A


title: liver_J8

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

description: Gene expression in liver of NN offspring

hyb_protocol: 600ng of Cy3-cRNA was then fragmented with a specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridization was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analyzed using the package limma from R.

organism: Oncorhynchus mykiss

source_name: Liver, condition NN, fish J8

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

extract_protocol: Total RNA was extracted from liver from 6 fish per treatment, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations.T he concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

treatment_protocol: Offspring from 4 different conditions : NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the high carbohydrate/low protein (HC/LP) diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet) were fed during 36 weeks with a commercial diet. Liver were sampled at the end of the trial.

tag: FISH identification

value: liver

tag: condition

value: NN

tag: Sex

value: F


title: liver_J7

source_name: Liver, condition NN, fish J7


title: SC_S128_Control2

source_name: Mouse small intestine stem cells

value: control


title: liver_J5

source_name: Liver, condition NN, fish J5


title: CON4-colon

tag: strain


title: liver_J6

source_name: Liver, condition NN, fish J6

value: M


title: 84/RTH_D

tag: cohort

tag: xerostomia

tag: time point


title: 84/RTH_C


title: SC_S126_Control2


title: DSS1-colon

value: DSS


title: SC_S127_Control2


title: SC_S129_Control2


title: CON3-liver

source_name: liver


title: DSS3-colon


title: liver_J4

source_name: Liver, condition NN, fish J4


title: 86/RTH_C

source_name: serum


title: SC_S124_Control2


title: DSS2-colon


title: CON1-liver


title: liver_J17

description: Gene expression in liver of NH offspring

source_name: Liver, condition NH, fish J17

value: NH


title: 82/RTH_D


title: SC_S123_Control2


title: liver_J16

source_name: Liver, condition NH, fish J16


title: DSS4-liver


title: SC_S125_Control2


title: 84/RTH_A


title: SC_S122_Control2


title: 82/RTH_C


title: SC_S121_Control2


title: CON4-liver


title: DSS1-liver


title: liver_J10

source_name: Liver, condition NH, fish J10


title: SC_S11_Control1


title: 81/RTH_C


title: liver_J18

source_name: Liver, condition NH, fish J18


title: liver_J14

source_name: Liver, condition NH, fish J14


title: DSS3-liver


title: IgG 15000 cell [CUT&RUN]

source_name: E10.5 yolk sac erythro-myeloid progenitors

tag: developmental stage

value: Ezh2fl/fl; Tie2-Cre+/+  Wild type

value: yolk sac


title: liver_J35

description: Gene expression in liver of HH offspring

source_name: Liver, condition HH, fish J35

value: HH


title: H3K27me3 15000 cell [CUT&RUN]


title: SC_S119_Control2

tag: diet


title: liver_J15

source_name: Liver, condition NH, fish J15


title: SC_S118_Control2


title: liver_J34

source_name: Liver, condition HH, fish J34


title: 81/RTH_A

value: Validation

value: No

value: Prior to RT


title: 80/RTH_C

value: After 20 Gy


title: 81/RTH_D


title: Testes_KO_TAM16_FP4_S40

city: LA JOLLA

first: Sahar

last: Taheri

state: California

address: 9500 GILMAN DR.

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Genome_build: Mus musculus genome build GRCm38
Supplementary_files_format_and_content: pg-2021-testes-expr.txt: Tab-delimited text file includes log2(TPM+1).

source_name: Testes

extract_protocol:
Total RNA from mouse testicles was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA) following manufacturer’s instructions. RNA concentration was measured using the NanoDrop™ OneC (Thermo Scientific, Waltham, Massachusetts). The RNA Integrity Number (RIN) was assessed using the 4200 TapeStation system and the TapeStation RNA ScreenTape & Reagents (Agilent Technologies, Santa Clara, CA).
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demultiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

value: GIV-KO (Girdin fl/fl-UBC-Cre-ERT2)

value: Testes


title: 80/RTH_D

value: After treatment completion


title: 82/RTH_A


title: 79/RTH_C

value: Yes


title: 79/RTH_D


title: Testes_WT_TAM19_FP6_S42

value: WT (Girdin fl/fl)


title: SC_S120_Control2


title: Testes_KO_TAM15_FP3_S39


title: Testes_WT_TAM21_FP8_S43


title: SC_S114_Control2


title: Testes_WT_TAM18_FP5_S41


title: SC_S113_Control2


title: SC_S112_Control2


title: CR Liver [34CR-L]

city: Madison

first: Heidi

middle: Hayang

last: Pak

state: WI

address: 2500 Overlook Terrace

department: Medicine

institute: University of Wisconsin-Madison

description:
34CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL

data_processing:
Illumina bcl2fastq v2.20.
Fastq data from lanes 1 and 2 merged.
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: .csv files with expression estimation with RSEM.

source_name: Liver

extract_protocol:
Mice were euthanized by cervical dislocation and tissues were harvested and flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were placed on the following diets for 16 weeks: AL, CR, and TR.al.

value: Liver

value: CR


title: SC_S115_Control2

data_processing:
Samples were aligned to the transcriptome using Bowtie2 and gene expression was quantified using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Txt files including the gene expression matrix

source_name: Mouse small intestine stem cells

value: control


title: liver_J33

source_name: Liver, condition HH, fish J33

value: liver

value: F


title: SC_S111_Control2


title: Testes_KO_TAM14_FP2_S38


title: 80/RTH


title: liver_J26

description: Gene expression in liver of HN offspring

source_name: Liver, condition HN, fish J26

value: HN


title: liver_J27

source_name: Liver, condition HN, fish J27

value: M


title: SC_S117_Control2


title: 77/RTH_D


title: SC_S116_Control2


title: Control Liver [30NA-L]

description:
30NA-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv

value: ad libitum


title: liver_J32

source_name: Liver, condition HH, fish J32

value: HH


title: Testes_KO_TAM13_FP1_S37


title: liver_J31

source_name: Liver, condition HH, fish J31


title: liver_J21

source_name: Liver, condition HN, fish J21


title: 77/RTH_A

source_name: serum

value: Validation


title: 78/RTH_A

value: Prior to RT


title: 78/RTH_D


title: SC_S109_Control2


title: SC_S110_Control2


title: CR iWAT [34CR-iWAT]

description:
34CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT

source_name: iWAT

value: iWAT


title: TR.al iWAT [29TR-iWAT]

description:
29TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: 79/RTH


title: liver_J29

source_name: Liver, condition HH, fish J29


title: liver_J25

source_name: Liver, condition HN, fish J25


title: 78/RTH_C

value: After 20 Gy


title: liver_J23

source_name: Liver, condition HN, fish J23


title: SC_S108_Control2


title: 75/RTH_D


title: SC_S106_Control2


title: Control iWAT [30NA-iWAT]

description:
30NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv


title: CR iWAT [26CR-iWAT]

description:
26CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: SC_S10_Control1


title: 77/RTH_C

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.


title: liver_J22

source_name: Liver, condition HN, fish J22


title: 76/RTH_D

value: No


title: Control Liver [28NA-liver]

description:
28NA-liver
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv


title: muscle_J9

description: Gene expression in muscle of NN offspring

source_name: Muscle, condition NN, fish J9

extract_protocol: Total RNA was extracted from 6 muscle of 6 fish per treatment, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations.T he concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

treatment_protocol: Offspring from 4 different conditions : NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the high carbohydrate/low protein (HC/LP) diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet) were fed during 36 weeks with a commercial diet. Muscle were sampled at the end of the trial.

value: muscle

value: NN


title: CR Liver [25CR-L]

description:
25CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: 76/RTH_A


title: CR Liver [26CR-L]

description:
26CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: SC_S104_Control2

extract_protocol:
Lgr5+ cells were extracted from mice either fed a control diet or high fat diet using FACS
Smart-seq2 (Picelli et al., 2014)


title: muscle_J4

source_name: Muscle, condition NN, fish J4


title: 75/RTH_C

value: Yes


title: muscle_J7

source_name: Muscle, condition NN, fish J7


title: CR iWAT [25CR-iWAT]

description:
25CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: 75/RTH


title: 76/RTH_C


title: SC_S102_Control2


title: SC_S107_Control2


title: CR Liver [24CR-L]

description:
24CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL

source_name: Liver

value: Liver


title: muscle_J6

source_name: Muscle, condition NN, fish J6


title: CR iWAT [24CR-iWAT]

description:
24CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT

value: CR


title: SC_S105_Control2

source_name: Mouse small intestine stem cells

value: control


title: muscle_J8

source_name: Muscle, condition NN, fish J8


title: AD_TG_4

city: Ulsan city

first: Chiyeol

last: Choi

state: 울산

address: Republic of Korea

country: South Korea

institute: UNIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Meninge

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Meninge

value: 20 weeks


title: AD_TG_3


title: 57/RTH_D

value: After treatment completion


title: 57/RTH_C


title: TR.al Liver [18TR-L]

description:
18TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: muscle_J18

description: Gene expression in muscle of NH offspring

source_name: Muscle, condition NH, fish J18

value: NH

value: M


title: muscle_J35

description: Gene expression in muscle of HH offspring

source_name: Muscle, condition HH, fish J35

value: HH

value: F


title: TR.al Liver [24TR-L]

description:
24TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: 72/RTH_D

value: Validation


title: SE1S3

value: Discovery


title: AD_TG_1


title: muscle_J16

source_name: Muscle, condition NH, fish J16


title: 72/RTH_C

source_name: serum

value: After 20 Gy


title: SJ1S3


title: SC_S103_Control2


title: TR.al Liver [23TR-L]

description:
23TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: muscle_J5

source_name: Muscle, condition NN, fish J5


title: muscle_J17

source_name: Muscle, condition NH, fish J17


title: SC_S100_Control2


title: AD_B6_3


title: muscle_J32

source_name: Muscle, condition HH, fish J32


title: 57/RTH

value: Prior to RT


title: AD_B6_2


title: TR.al Liver [15TR-L]

description:
15TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: CR iWAT [16CR-iWAT]

description:
16CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT

source_name: iWAT

value: iWAT


title: TR.al iWAT [18TR-iWAT]

description:
18TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: GJ1S3

value: No


title: Control iWAT [21NA-iWAT]

description:
21NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv

value: ad libitum


title: SC_S101_Control2


title: 72/RTH

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.

value: Yes


title: TR.al iWAT [15TR-iWAT]

description:
15TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: AD_B6_4


title: AD_TG_2


title: TR.al iWAT [23TR-iWAT]

description:
23TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: WJ1S3


title: muscle_J34

source_name: Muscle, condition HH, fish J34

value: muscle


title: muscle_J15

source_name: Muscle, condition NH, fish J15


title: muscle_J10

source_name: Muscle, condition NH, fish J10


title: KE1S3


title: muscle_J25

description: Gene expression in muscle of HN offspring

source_name: Muscle, condition HN, fish J25

value: HN


title: SJL_B6_2

value: Meninge


title: SJL_B6_1

value: 20 weeks


title: CR Liver [16CR-L]

description:
16CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL

source_name: Liver

value: Liver

value: CR


title: Control Liver [8NA-L]

description:
8NA-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv


title: muscle_J33

source_name: Muscle, condition HH, fish J33


title: BM2S3

value: After treatment completion


title: muscle_J31

source_name: Muscle, condition HH, fish J31

value: HH


title: muscle_J29

source_name: Muscle, condition HH, fish J29

value: M


title: muscle_J21

source_name: Muscle, condition HN, fish J21

value: F


title: SJL_B6_4

source_name: Meninge


title: AD_B6_1


title: LG1S3

value: Discovery


title: WT1_Treg

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCm38 of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCm38 as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 4.0 including CPM values for each sample
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw Paired-End Fastq Files

source_name: Spleen

extract_protocol:
Cells were sorted directly into SmartSeq low-input RNA kit lysis buffer
DNA libraries were prepared using Nextera XT Kit and RNAseq were prepared using SMART-Seq HT Kit.

treatment_protocol: WT and Transgenic Mouse were administered Tamoxifin for 5 consecutive days, followed by isolation of spleen, staining and flow sorting

tag: mouse genotype

tag: organ

value: Flow sorted eGFP+ Treg

value: TIM-3-FLAG-GFP+FoxP3+CD4 cells


title: TR.al Liver [11TR-L]

description:
11TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL

tag: tissue


title: Control iWAT [8NA-iWAT]

description:
8NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv

value: iWAT


title: PC1S3

value: No


title: Control iWAT [9NA-iWAT]

description:
9NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv

value: ad libitum


title: SJL_B6_3


title: muscle_J23

source_name: Muscle, condition HN, fish J23


title: _Transgenic_GFPhi_M3_Treg

value: Foxp3-eGFP-Cre-ERT2 x FSF-TIM-3

value: Flow sorted eGFP+Tim3+ Treg

value: TIM-3+FLAG+GFP+FoxP3+CD4 cells


title: muscle_J22

source_name: Muscle, condition HN, fish J22

value: muscle

value: HN


title: DW1S3

source_name: serum


title: PJ2S3


title: PJ1S3

value: Yes


title: BW1S3


title: Control Liver [9NA-L]

description:
9NA-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv

value: Liver


title: muscle_J27

source_name: Muscle, condition HN, fish J27


title: WT_2Treg


title: TR.al iWAT [11TR-iWAT]

description:
11TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: GA1S3

value: After treatment completion


title: Transgenic_GFPhi_M2_Treg


title: DOHH2 cultivated with TSC 3D, rep 4

city: Rennes

first: Julien

last: Saint-Vanne

address: 2 avenue du professeur Léon Bernard - CS 34317

data_processing:
Illumina software used for basecalling.
FastQC control quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using STAR with parameters :                     --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread
Differential gene expression analysis was performed for all populations (DOHH2 and HLY1) cells using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

source_name: Lymphoma B cell line/ primary tonsil stromal cells

extract_protocol:
2D and 3D co-cultures were performed over 3 and 10 days, respectively. Then, cells were stained for 20 min on ice with mouse anti-human CD20 APC-H7 and mouse anti-human CD73 PE and sorted by the FACSAria II (BD Biosciences).RNA extraction from DOHH2 was done using Nucleospin RNA XS Micro kit (PN 740990) from Macherey Nagel (Hoerdt, France).
RNA libraries were prepared (with 10ng of total RNA)  for sequencing using standard Illumina protocols

treatment_protocol: not applicable

tag: cell line

tag: culture dimension

tag: culture condition

value: stroma


title: muscle_J26

source_name: Muscle, condition HN, fish J26


title: liver_J9

description: Gene expression in liver of NN offspring

source_name: Liver, condition NN, fish J9

value: liver

value: NN

value: M


title: Control iWAT [7NA-iWAT]

description:
7NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv

source_name: iWAT


title: Transgenic_GFPLow_M2_Treg

value: Flow sorted eGFP-Tim3+ Treg

tag: cell type

value: TIM-3+FLAG+GFP-FoxP3-CD4 cells


title: PW1S3

value: Discovery


title: CR iWAT [2CR-iWAT]

description:
2CR-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT

value: iWAT

value: CR


title: Transgenic_GFPLow_M3_Treg

value: Foxp3-eGFP-Cre-ERT2 x FSF-TIM-3


title: PZ1S3


title: Control Liver [7NA-L]

description:
7NA-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv

value: ad libitum


title: TR.al Liver [6TR-L]

description:
6TR-L
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL


title: Transgenic_GFPhi_M1_Treg

value: Flow sorted eGFP+Tim3+ Treg

value: TIM-3+FLAG+GFP+FoxP3+CD4 cells


title: Vav-Ezh2-KO28

description: Sample 34

data_processing:
We used TopHat (v2.0.13) to align short reads to the mouse (GRCm38/mm10) reference genome.
The mapping parameter “−g 1” was used to allow one alignment to the reference for a given read.
‘featureCounts’ software was used to count reads based on the RefSeq gene model.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab delimited format with RPKM

source_name: E10.5 yolk sac erythro-myeloid progenitors

extract_protocol:
500 erythro-myeloid progentors were prepared for RNA-seq using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech). cDNA libraries were pre-amplified using 16 cycles of PCR.
cDNA libraries were prepared using Nextera XT (Illumina). Samples were sequenced using the Illumina NextSeq 500/550 platform, generating 75 bp single-end reads.

tag: developmental stages

value: yolk sac

tag: genotype

value: Ezh2fl/fl; Vav-CreTg/+  Ezh2 KO mediated by Vav-Cre


title: DOHH2 cultivated with TSC 2D, rep 2

growth_protocol: 2D and 3D co-cultures were performed over 3 and 10 days, respectively.


title: DOHH2 cultivated with TSC 3D, rep 5


title: Control iWAT [1NA-iWAT]

description:
1NA-iWAT
edgeRglm_ISOFORM_CRiWAT-NAiWAT.csv
edgeRglm_GENE_CRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv


title: CR Liver [2CR-L]

description:
2CR-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_CRL-TRL
edgeRglm_GENE_CRL-TRL

value: Liver


title: DOHH2 cultivated with TSC 3D, rep 2


title: DOHH2 cultivated with TSC 3D, rep 3


title: Control Liver [1NA-L]

description:
1NA-L
edgeRglm_ISOFORM_CRL-NAL.csv
edgeRglm_GENE_CRL-NAL.csv
edgeRglm_ISOFORM_TRL-NAL.csv
edgeRglm_GENE_TRL-NAL.csv


title: DOHH2 cultivated with TSC 2D, rep 3


title: TR.al iWAT [6TR-iWAT]

description:
6TR-iWAT
edgeRglm_ISOFORM_TRiWAT-NAiWAT.csv
edgeRglm_GENE_TRiWAT-NAiWAT.csv
edgeRglm_ISOFORM_CRiWAT-TRiWAT
edgeRglm_GENE_CRiWAT-TRiWAT


title: ZR1S3

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.

extract_protocol: total RNA was isolated from 200 μL serum samples using miRCURY RNA Isolation kit (QIAGEN, Hilden, Germany)

value: Yes

value: After treatment completion


title: DOHH2 cultivated with TSC 3D, rep 1

value: stroma


title: DOHH2 cultivated with TSC 2D, rep 1


title: MG1S3


title: Vav-Ezh2-KO10

description: Sample 30


title: KM1S3


title: Vav-Ezh2-KO26

description: Sample 32


title: Transgenic_GFPLow_M1_Treg


title: P21_volume_3

first: Sijuan

last: Sun

address: No.1678, Dongfang Road

institute: Shanghai Children’s Medical Center (SCMC) affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected.We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were  filtered with GATK standard filter method and other parameters (cluster:3;  WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to  annotation for the Variablesite.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of   genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS  event.
PPI analysis of differentially expressed genes was based on the STRING  database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: FPKM

source_name: RV free wall myocardium

extract_protocol:
Myocardium of RV free wall was rapidly removed from executed mice and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: myocardium

tag: treatment method

value: volume overload(AVF)

tag: treatment  age

value: postnatal day 7

tag: test age

value: postnatal day 21


title: BM1S3

data_processing: The reference miRNA for normalization was selected using the NormiRazor. Based on the assumption that no single miRNA is suitable as a reference in serum miRNA qPCR profiling experiments30, we found that the most stable reference was the average expression level of two miRNAs (miR-142-5p and miR-23b-3p). Differentially expressed miRNAs were shortlisted on the basis of univariate, Benjamini-Hochberg adjusted, p values. Then, the expression levels of selected miRNAs were validated using the miRCURY LNA miRNA Custom PCR Panels (QIAGEN, Hilden, Germany). Selection of miRNAs for this part of the study was based on three criteria: expression in at least two thirds of samples, fold change greater than 1.5 or smaller than 0.67 and Benjamini-Hochberg adjusted p values <0.25. The normalization was performed using the formula ∆Ct = Ct(reference) - Ct(miRNA of interest), which provides a higher value for higher miRNA expression, facilitating its use and interpretation as a biomarker. Quantitative Real-Time PCR (qPCR) was performed in duplicates using the miRCURY LNA SYBR Green system (QIAGEN, Hilden, Germany) in a 96-well format. Undetectable expression (negative result) was reported if expression was not detected >37 PCR cycles. UniSp2, UniSp4, and UniSp5 were used as RNA isolation spike-in controls and UniSp6 was used as cDNA synthesis spike-in control.

tag: cohort

value: Discovery

value: No


title: DOHH2 2D, rep 4

source_name: Lymphoma B cell line

value: no stroma


title: P21_volume_2

tag: strain


title: Vav-Ezh2-KO1

description: Sample 26


title: RW1S3

tag: xerostomia

tag: time point


title: P21_volume_1


title: WJ1S2

value: After 20 Gy


title: DOHH2 2D, rep 3


title: DOHH2 2D, rep 2


title: ZR1S2


title: Vav-Ezh2-KO9

description: Sample 28


title: SJ1S2


title: Tie2-Ezh2-KO13

description: Sample 21

value: Ezh2fl/fl; Tie2-CreTg/+  Ezh2 KO mediated by Tie2-Cre


title: Tie2-Ezh2-KO11

description: Sample 19


title: HLY1 cultivated with TSC 3D, rep 2


title: P21_sham_3

value: operated-sham


title: P21_sham_2


title: Tie2-Ezh2-KO9

description: Sample 9


title: P21_sham_1


title: Tie2-Ezh2-KO17

description: Sample 23


title: P14_volume_3

value: postnatal day 14


title: HLY1 cultivated with TSC 3D, rep 1


title: P14_volume_2


title: HLY1 cultivated with TSC 3D, rep 3


title: P14_volume_1


title: Tie2-Ezh2-KO7

description: Sample 7

value: yolk sac


title: SE1S2


title: RW1S2


title: HLY1 3D, rep 1


title: PC1S2


title: Vav-Ezh2-WT6

description: Sample 38

value: Ezh2fl/fl; Vav-Cre+/+  Wild type without Vav-Cre


title: PZ1S2


title: Tie2-Ezh2-WT10

description: Sample 5

value: Ezh2fl/fl; Tie2-Cre+/+  Wild type without Tie2-Cre


title: HLY1 cultivated with TSC 2D, rep 3


title: Vav-Ezh2-WT4

description: Sample 36


title: Tie2-Ezh2-WT4

description: Sample 3


title: DOHH2 2D, rep 1


title: PJ1S2

value: Yes


title: HLY1 3D, rep 2


title: HLY1 cultivated with TSC 2D, rep 2


title: PW1S2


title: P14_sham_2


title: HLY1 3D, rep 3


title: PJ2S2


title: Tie2-Ezh2-WT12

description: Sample 13


title: P14_sham_3


title: KM1S2


title: P14_sham_1


title: Mdivi1_Ly6G

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.0)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

source_name: BM Ly6G+ myeloid cells

extract_protocol:
Bone marrow cells were harvested from individual mice. HSCPs were purified using EasySep Mice CD117 positive selection kit and mutant clone was FACS sorted. Ly6G+ mutant myeloid BM cells were FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BM

value: Ly6G+ myeloid cells

tag: treatment

value: Mdivi


title: HLY1 2D, rep 3


title: IMQ + rYopM_LRR1-3, rep2

city: Münster

first: Karin

last: Loser

address: Von-Esmarch-Str. 58

department: Experimental Dermatology

country: Germany

institute: University of Münster

data_processing:
Trimming: Trimmomatic 0.36 (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
Alignment: hisat 2.1.0 (Parameter: default)
Sorting: samtools sort names (Version: Version: 1.2-25-gf995b71-dirty using htslib 1.2.1-39-g5ffc4a2-dirty)
Counting: htseq-count 0.9.1 (Parameter: --minaqual 0, --stranded reverse)
Differential Expression Analysis inside R: R version 3.4.4 (2018-03-15) plus Bioconductor BiocInstaller_1.28.0 using Platform: x86_64-w64-mingw32/x64 (64-bit) and Running under: Windows 10 x64 (build 9200), used R-packages: DESeq2_1.18.1
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_180613.sortn.cnt: The count files (Output of htseq-count) are tab-separated plain-text files: 1. column gene name, 2. column read count.

source_name: total skin

growth_protocol: Mice were housed under SPF conditions. Food and water were provided ad libitum.

extract_protocol:
Skin was removed and frozen in RNAlater. Total RNA was extracted with the Extractme Total RNA Kit from DNA Gdansk.
Quality checked (Bioanalyzer RIN value) total RNA was enriched for Poly(A) RNA (NEBNext Poly(A) Isolation Module, NEB) and used for directional RNA library preparation (NEBNext Ultra RNA II directional, NEB) according to manufacturer's instructions.

treatment_protocol: Mice were shaved on the lower back and 62.5 mg IMQ or a vehicle cream was applied daily for 7 consecutive days. From occurrence of first macroscopic disease symptoms on, like erythema and swelling, (day 4) 50 µg rYopM or the truncated rYopM_LRR1-3 was injected subcutaneously to mice of the respective groups. IMQ was applied in the morning, rYopM and the truncated protein were injected in the evening. The morning after the last injection mice were euthanized and skin biopsies were taken for RNA extraction.

tag: strain/background

value: Balb/c

tag: genotype/variation

value: wild type

value: skin

tag: days after first imq application

tag: days of treatment

value: 4 days

value: IMQ + rYopM_LRR1-3


title: HLY1 cultivated with TSC 2D, rep 1

tag: cell line

tag: culture dimension

value: stroma


title: MG1S2

value: Discovery

value: After 20 Gy


title: Mdivi2_Ly6G

tag: tissue

tag: cell type


title: HLY1 2D, rep 2

tag: culture condition

value: no stroma


title: Vehicle1_Ly6G

value: Vehicle


title: LG1S2

value: No


title: IMQ + rYopM, rep2

value: IMQ + rYopM


title: Mdivi_KIT

source_name: BM HSCPs

value: HSCPs


title: IMQ + rYopM, rep1


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep6

city: St. Louis

first: Jeffrey

last: Szymanski

email: jeszyman@gmail.com, szymanski@wustl.edu

state: Missouri

address: 4511 Forest Park

institute: Washington University in Saint Louis

description: Adult male and female littermate CD-1 mice were maintianed on a mixed genetic background. Male and female mice aged 8 weeks or greater were used in all groups with gender and littermate-matched controls.

data_processing:
Basecalls performed using CASAVA version 1.8
Transcript abundance was quantified in Salmon (v. 1.0)
Transcript-level TPM values were summarized to gene-level counts and abundance using tximport (v. 3.10)
Genome_build: GRCm38.76
Supplementary_files_format_and_content: Tab-separated values of gene-level counts and abundance modified from tximport output

source_name: Cardiac intraventricular septum

extract_protocol:
RNA was isolated from intraventricular septum using TRIzol (Invitrogen) and DNAse-treated with TURBO DNA-free kit (Ambion)
Sequencing libraries were constructed by GTAC at Washington University School of Medicine. Briefly, sequencing libraries were prepared using the Roche KAPA RNA HyperPrep kit per manufacturer's recommendations. Libraries were sequenced with the Illumina NovaSeq S4 (2 x 150 bp) to a median depth of 42.7 million +/- 3.8 million reads.

treatment_protocol: 2wk and 6wk groups were treated with a single dose of 25-Gy ionizing radiation while under isoflourane anesthesia. ctrl group recevied anesthesia but no irradiation.

value: single dose 25 Gy gamma irradiation

tag: post treatment recovery (weeks)


title: GA1S2

first: Konrad

last: Stawiski

value: Yes


title: DW1S2


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep5


title: Vehicle2_Ly6G

value: BM

value: Ly6G+ myeloid cells


title: KE1S2


title: IMQ + PBS, rep1

value: Balb/c

value: IMQ + PBS


title: GJ1S2


title: IMQ + rYopM_LRR1-3, rep1

value: wild type

value: skin


title: BM2S2


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep4


title: A549-shPGCIa3

city: Chungju-si

first: Ji Hong

last: Lim

address: 268, Chungwon-daero

institute: Konkuk University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line from lung adenocarcinoma

growth_protocol: Control and PPARGC1A knocked-down A549 cells were cultured in DMEM containing 10% fetal bovine serum.

extract_protocol:
RNA was isolated from control or PPARGC1A knocked-down A549 cells by use of TRIzol (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 lung adenocarcinoma cells were infected with lentivirus expressing shRNA targeting control or PPARGC1A and selected by puromycin for 5 days.

tag: genotype


title: IMQ + rYopM, rep3

value: 4 days


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep3


title: IMQ + PBS, rep2


title: HLY1 2D, rep 1


title: WJ1S1

city: Lodz

address: Mazowiecka 15

institute: Medical University of Lodz

value: Prior to RT


title: BW1S2

value: Discovery


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep1


title: A549-shControl3

value: shRNA-control


title: BM1S2

value: After 20 Gy


title: vehicle cream, rep2

value: vehicle cream


title: mid_siTRPS1_2_RepliSeq

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
Library strategy: Repli-seq
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

source_name: MCF-7 cells

extract_protocol:
For ChIP-seq, the crosslinked protein-DNA complex was extracted from the sonicated nuclei and isolated with antibody. For Repli-seq, EdU incorporated nascent DNA was sonicated and enriched with streptavidin magnetic beads. For extrachromosomal DNA sequencing, extrachromosomal DNA was purified from the nuclei treated with ATP-dependent exonuclease to remove linear genomic DNA.
Enriched DNA for ChIP-seq, Repli-seq or extrachromosomal DNA sequencing was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Sequencing adaptors were ligated to the DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by Qubit 2.0 and subjected to HiSeq X Ten or HiSeq 2500 sequencing according to the manufacturer’s instructions.

value: Breast cancer cells

tag: antibodies

value: Streptavidin-biotin (Invitrogen, 65002)


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep6


title: mid_siTRPS1_1_RepliSeq


title: A549-shPGCIa2


title: vehicle cream, rep1


title: Cardiac intraventricular septal tissue, 6 weeks post irradiation, rep2


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep5


title: mid_siNS_RepliSeq

value: siNS


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep4

value: single dose 25 Gy gamma irradiation


title: RW1S1

tag: cohort

value: Yes


title: A549-shPGCIa1


title: MO0003b -RACIN

city: Epalinges

first: Raphael

last: Genolet

address: Biopole 3, Chemin des Boveresses 155

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

description: beta TCR repertoire

data_processing:
Deep sequencing of the TCR alpha and beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Genome_build: IMGT data base was used to identifiy TCR
Supplementary_files_format_and_content: txt files containing the list of TCR and their frequencies

source_name: peripheral blood mononuclear cell (PBMC)

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction
Libraries were prepare using targeted TCR amplification (Bobisse et al, Nat Commun. 2018 Mar 15;9(1):1092.
TCRseq

value: PBMC

tag: Sex

value: male

tag: tumor type

value: prostate

tag: radiotherapy

value: before treatment


title: PZ1S1

tag: xerostomia

tag: time point


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep3

tag: strain

tag: treatment


title: A549-shControl1


title: SJ1S1


title: MO0003a -RACIN

description: alpha TCR repertoire


title: Vehicle_KIT

value: BM

value: HSCPs

value: Vehicle


title: ZR1S1

value: Prior to RT


title: SE1S1

value: Discovery

value: No


title: late_siTRPS1_2_RepliSeq

tag: genotype/variation


title: A549-shControl2

tag: cell line

value: shRNA-control


title: IMQ + PBS, rep3

tag: strain/background

value: Balb/c

value: wild type

value: skin

tag: days after first imq application

tag: days of treatment

value: 4 days

value: IMQ + PBS


title: Cardiac intraventricular septal tissue, control, rep6

value: untreated


title: late_siTRPS1_1_RepliSeq

tag: cell type

value: Breast cancer cells

value: Streptavidin-biotin (Invitrogen, 65002)


title: MO0001b -RACIN

description: beta TCR repertoire

value: PBMC

value: female

value: ovary


title: Cardiac intraventricular septal tissue, control, rep5

tag: post treatment recovery (weeks)


title: PC1S1


title: Cardiac intraventricular septal tissue, control, rep4


title: MO0001a -RACIN

description: alpha TCR repertoire

value: before treatment


title: PJ1S1

value: Yes


title: PW1S1

value: Prior to RT


title: early_siTRPS1_2_RepliSeq


title: MO0002a +RACIN

description: alpha TCR repertoire


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep1

value: single dose 25 Gy gamma irradiation


title: Cardiac intraventricular septal tissue, 2 weeks post irradiation, rep2


title: early_siTRPS1_1_RepliSeq


title: early_siNS_RepliSeq

value: siNS


title: Cardiac intraventricular septal tissue, control, rep3


title: MG1S1

value: Discovery


title: AGR_S4

city: Caen

first: Francois

last: Gravey

state: Normandy

address: Esplanade de la paix

department: Microbiology

institute: Normandy Université

data_processing:
fastqc
STAR alingment
Htseq
EdgeR package
Genome_build: S. lugdunensis reference genome: N920143 NC_017353.1
Supplementary_files_format_and_content: Count tables

organism: Staphylococcus lugdunensis

source_name: Bacteria

growth_protocol: 37°C - Aerobic - Brain Heart Infusion agar

extract_protocol: Direct-zol RNA miniprep kit

treatment_protocol: Wild type strain versus complete deltion of agrA gene in S. lugdunensis

value: complete agrA deletion


title: late_siNS_RepliSeq


title: KM1S1

source_name: serum


title: AGR_S2


title: eccDNA_trps1

description: extrachromosomal DNA

data_processing:
Library strategy: extrachromosomal DNA-seq
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

source_name: MCF-10A cells

value: TRPS1 overexpression

value: Normal breast epithelial cells


title: eccDNA_ctrl

description: extrachromosomal DNA

value: control


title: Cardiac intraventricular septal tissue, control, rep1


title: GJ1S1

value: No


title: AGR_S1


title: MO0002b +RACIN

description: beta TCR repertoire


title: PJ2S1


title: KE1S1


title: Cardiac intraventricular septal tissue, control, rep2

value: untreated


title: siTRPS1_2_CDC16_ChIPSeq

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

value: Breast cancer cells


title: GA1S1


title: AGR_S3


title: DW1S1


title: siTRPS1_2_APC1_ChIPSeq

value: APC1 (ProteinTech, 21748-1-AP)


title: WT_S3

value: Wild Type


title: BW1S1


title: WT_S2


title: CBL-RUNX1mut2Ly6G

tag: strain background

value: CBL/RUNX1 mutant

value: BM Ly6G+ myeloid cells


title: WT1Ly6G

value: wild type


title: siNS_APC1_ChIPSeq

tag: antibodies


title: siTRPS1_1_CDC16_ChIPSeq


title: BM2S1

tag: cohort


title: WT_S4