title: p53null SOFT mammary tumors Sample 2

description:
Library name: Sample_2
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

data_processing:
Raw reads were mapped to the mouse reference genome (GRCm38) and counts and transcripts per million (TPMs) were estimated using Kallisto quant (version 0.46.1). Genes with fewer than combined 10 raw counts were excluded from further analyses. Differential expression analysis between soft (n = 22) and stiff (n = 21) mammary tumors was performed using the edgeR package (version 4.6.2) (63), within the statistical computing language R (version 4.3.1).
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: kallisto output .tsv files exported from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

extract_protocol:
Tumor tissues were mechanically digested in DNA lysis buffer (4 M guanidine thiocynate, 100 mM Tris/HCl pH 7.4, 30 mM EDTA pH 8.0, 1% Triton X-100, 100 mM b-mercaptoethanol). Lysates were incubated with acid-washed diatomaceous earth to enhance nucleic acid binding, followed by silica column-based purification (Promega). Column-bound DNA was purified through sequential washes with guanidine- and ethanol-based DNA wash buffers. RNA was isolated from the DNA flowthrough by sodium acetate-phenol:chloroform extraction. The aqueous phase was incubated with acid-washed diatomaceous earth and ethanol to promote RNA binding to the column, followed by purification through guanidine- and ethanol-based RNA wash buffers. DNA was used in WES, and RNA was used in RNA-Seq and RT-qPCR analyses.
RNA-Seq libraries were prepared as previously described (60), with the following modifications. Briefly, 1 mg total RNA was enriched for poly(A) transcripts using oligo(dT)-conjugated magnetic beads (KAPA mRNA HyperPrep Kit, Roche, Cat # 08098123702), followed by fragmentation, template-switch reverse transcription, and dual-index barcode PCR amplification (Roche, Cat #KK8725). To minimize ribosomal RNA contamination, two consecutive rounds of bead binding using 25 mL were performed, and intact poly(A) RNA was eluted in 5 mL nuclease-free water at 65 °C for 2 mins. Custom-magnetic immobilizers—3 mm × 1 mm neodymium disc magnets (K&J Magnetics) embedded at a 45 o angle in polydimethylsiloxane (PDMS) at the base of 0.2 mL PCR tubes—were used to localize magnetic beads during washes and minimize carryover. Enriched RNA was chemically fragmented and reverse-transcribed using a modified SMART-Seq3 protocol (61). Briefly, RNA was fragmented by heating a 1:1 mixture of RNA and 2X fragmentation buffer (50 mM Tris-HCl pH 8.3, 60 mM NaCl, 6 mM MgCl₂, 13.3% PEG-8000, 0.27% Triton X-100, and 2.7 µM oligo(dT)₃₀) at 94 °C for 2 min, to generate a target library size of 300–400 bp (corresponding to ~120–220 bp inserts). Samples were cooled on ice and combined with 3 µL of 4X reverse transcription master mix (25 mM Tris-HCl pH 8.3, 30 mM NaCl, 3 mM MgCl₂, 4 mM neutralized GTP, 32 mM DTT, 2 mM each dNTP, 4 µM template-switching oligo), 1 U/µL Ribolock RNase inhibitor (Thermo, Cat #EO0381), and 2 U/µL Maxima H Minus Reverse Transcriptase (Thermo, Cat #EP0751). First-strand synthesis was performed at 42 °C for 90 mins, followed by 10 cycles of 2 mins each at 50 °C and 42 °C, with enzyme inactivation at 85 °C for 5 mins. cDNA fragments were size-selected on a 2% agarose gel (200-650 bp), excised, dissolved in solubilization buffer, incubated with acid-washed diatomaceous earth, followed by column-based purification (Promega) and eluted with pre-heated elution buffer. Libraries were amplified using KAPA HiFi master mix and dual-index barcodes, for 16–18 cycles of 98 °C 15 sec, 60 °C 30 sec, 72 °C 1 min, with amplification monitored from cycle 14 by gel electrophoresis. Final libraries were ethanol-precipitated with linear acrylamide and sodium acetate and stored at –80 °C. Single-end, 150-bp sequencing was performed on a HiSeq 4000 (The University of California, San Francisco, Center for Advanced Technology).

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150lo, scRNAseq

status: Public on Mar 24 2026

type: SRA

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

country: China

institute: Sichuan University

description:
10x Genomics
CL2

library_source: transcriptomic

data_processing:
Sequencing data from 10x Genomics were mapped against the mm10 genome and quantified using the CellRanger software with default settings to generate raw gene expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
C57BL/6J mice were sacrificed by cervical dislocation, and bone marrow cells were isolated from the tibia, femur and pelvis. Then, RBC lysis buffer (Biosharp) was used to remove erythrocytes. For progenitor analysis, Lin− bone marrow progenitors were enriched by magnetic beads using biotinylated rat anti-mouse antibodies against CD3, CD11b, Gr-1, CD45R/B220, and Ter119, followed by negative selection with anti-rat microbeads (Miltenyi Biotec). Enriched Lin− cells were then stained with antibodies against CD34, CD135, CD127, Sca1, CD117, CD48, and CD150 to label hematopoietic progenitors and streptavidin-PE-Cy7 to label Lin+ cells.
For 10x scRNA-seq, CD150hi SCA1hi, CD150hi SCA1lo, and CD150lo LT-HSC from mice of different ages were sorted by using FACS AriaTM III sorter. After centrifugation, cells were resuspended in DPBS + 0.04% BSA for library preparation using the Chromium™ Single Cell 3’ reagents. And scRNA-seq datasets were produced following the manufacturer’s instructions. Suspended cells were loaded on a Chromium Controller (10X Genomics) to generate Gel beads in EMulsion (GEMs). Immediately following GEMs generation, the Gel Bead is dissolved, primers are released, and any co-partitioned cell is lysed. Mixed the cell lysate with a Master Mix containing reverse transcription reagents and incubated the GEMs to produce barcoded full-length cDNA from polyadenylated mRNA. Then cDNA was amplified to generate sufficient mass for library construction, and sequencing was performed on an Illumina Hi-Seq X Ten with pair end 150bp (PE150).
For CITE-seq, the cells consistent with the above were stained with the surface proteins TotalSeq-B antibodies CD201, CD9, and CD63 (Biolegend), to enable protein detection in addition to Single Cell 3’ v3 and Single Cell V(D)J Feature Barcoding technology from 10x Genomics. Single-cell RNA-seq libraries were prepared following the manufacture’s introduction as described briefly above, and sequencing was performed on an Illumina with pair end 150bp (PE150).

tag: tissue

value: Bone marrow

tag: cell type

value: LT-HSC

tag: sorted cells

tag: age

value: 2 months-old

tag: library type

value: GEX


title: MSC2 [A1-2]

city: guangzhou

first: Wu

middle: Meng

last: ye

state: Guangdong

address: Guangzhou Yuexiu

department: The Biotherapy Center,

institute: the Third Affiliated Hospital, Sun Yat-Sen University

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  and 2 ng/mL basic fibroblast growth factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmentedninto short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: mesenchymal cells were treated with wogonin for 24h

value: umbilical cord

value: mesenchymal stem cells

tag: treatment

value: no treatment


title: MSC3-wogonin [C-3]

value: 25uM wogonin 24h


title: 8 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1lo, scRNAseq

description:
10x Genomics
SL8

value: 8 months-old


title: MecomWT:R751W, bio rep 2

city: Tokyo

first: Mayuko

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The University of Tokyo

description:
Library name: Sample 5
hKI2

data_processing:
The fastq file was imported into R (https://www.r-project.org) for analysis and mapped to the mouse reference genome (mm10). Reads were then counted using Feature Count, and the resulting data were normalized by the TPM method. Differentially expressed genes were identified using DESeq2 in R.
Assembly: mm10
Supplementary files format and content: csv file include TPM for each Sample

source_name: mouse bone marrow

extract_protocol:
the SLAM-LSK (CD150+, CD48-, lineage-, Sca1+, cKit+) population was sorted directly into TRIZOL-LS using FACS Aria III (BD Biosciences, San Jose, CA, USA).
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420)Low-input: For RNA less than 50ng, rRNA-depletion and library synthesis by Takara SMARTer kit (usually input RNA amount is not defined due to low RNA concentration)

value: mouse bone marrow

tag: cell line

tag: genotype


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150lo, CITE-seq, rep1

description:
10x Genomics
Ab-CL

library_source: other

molecule: protein

value: ADT


title: MSC3 [A1-3]


title: WT#5(TCRseq)

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

country: USA

institute: Frederick National Labroatory for Cancer Research

description: Library name: WT5_S17

data_processing:
Reads were aligned to mouse TRA and TRB reference from imgt.202214-2.sv8 using miXCR v4.7.0 with default settings. Clone assembly and extraction were also done using miXCR v4.7.0 with default settings
Assembly: Mouse mm10
Supplementary files format and content: Text delimited text files containing the TRA and TRB clones
Library strategy: TCR-Seq

source_name: lymph nodes

extract_protocol:
10⁶ CD8⁺ T cells were sorted from lymph nodes and spleens of WT, β5i-KO, β5t-KO and BIT mice (9–12 weeks old, male, n = 4–5 individual mice per group, >98% purity.Total RNA was prepared from sorted cells with the RNeasy Kit (Qiagen). The quality of RNA was assessed by Bioanalyzer (Agilent).
The library was made by using the SMARTer® Mouse TCR a/b Profiling Kit (Takara)

value: lymph nodes

value: TCRbeta highCD4-CD8+ T cells


title: MSC1 [A1-1]


title: WTG2

status: Public on Mar 23 2026

city: Qingdao

first: Panpan

last: Zhang

address: No. 72, Coastal Road, Aoshanwei Sub-district, Jimo District, Qingdao City, Shandong Province

institute: ShanDong University

description: Library name: sample17

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 24h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

value: 114-2(wild type)

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: WTG3

description: Library name: sample18


title: B6.Sst1S BMDMs Biological reolicate 3

city: Baltimore

first: Somnath

last: Shee

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

description: Library name: SSR5-1

data_processing:
Image analysis and base calling were conducted by HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v0.36, and the filtered reads were aligned to the Mus musculus GRCm38 reference genome (ENSEMBL) using the splice-aware STAR aligner v2.5.2b, generating BAM files.
Gene hit counts were quantified using featureCounts from the Subread package v1.5.2, counting only uniquely mapped reads overlapping annotated exon regions, with strand specificity applied where appropriate.
Differential expression analysis was performed using the  DESeq2 package86. Genes with an adjusted p-value <0.05 and a log₂ fold change > 1 or <-1 were deemed differentially expressed between groups.
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM counts (transcript per million) for each sample

source_name: bone marrow derived macrophages

growth_protocol: BMDMs were isolated from the tibias and femurs of mice and were differentiated into macrophages in RPMI-Glutamax (Thermo Fisher Scientific; 61870127) containing 10% heat-inactivated FBS (Millipore Sigma, Catalog no.- F4135), 1X antibiotic antimycotic Solution (Sigma Aldrich; A5955) and 10% (v/v) L929 fibroblast-conditioned medium (as a source of M-CSF) for 5 days. L929 fibroblast cell lines were cultured in DMEM-Glutamax (Thermo Fisher Scientific; 10566016) containing 10% heat-inactivated FBS, 10 mM HEPES, and 1X antibiotic antimycotic Solution. L929 cells were mycoplasma-negative (Venorgem Mycoplasma detection kit; Millipore Sigma- MP0025). BMDMs were washed, scrapped out, counted, and replated overnight prior to the experiments. All experiments were done with confluency of BMDMs 60-75%.

extract_protocol:
BMDMs were lysed in TRIzol (Thermo Fisher Scientific; 15596026), and RNA was extracted using Qiagen RNeasy Mini Kit (74104) and RNase-free DNase Set (Qiagen; 79254), following the manufacturer’s protocol. RNA purity and concentration was quantified using Nanodrop One (Thermo Fisher Scientific) and stored at -80 ºC.
Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were generated with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94°C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end-repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flow cell. After clustering, the flow cell was loaded on the Illumina HiSeq 4000 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

treatment_protocol: BMDMs were either left untreated or treated with 10 ng/ml of murine-TNFα (Peprotech; 315-01A) in  RPMI-Glutamax containing 10% heat-inactivated FBS and 10% (v/v) L929 fibroblast-conditioned medium, for 18 hours (overnight) at 37°C in 5% CO2. This followed by infection with Mtb H37Rv for 4 hours at MOI=10. After 4 hours, extracellular Mtb were removed by extensive washing with warm RPMI media and RPMI+ TNFα was added to the cells. RNA was isolated after 24 hours.

value: bone marrow derived macrophages

value: 10 ng/ml TNFα pretreatment (18 hours), followed by Mtb H37Rv (MOI=10; 24 hours) infection in the continued presence of TNFα


title: WTCW3

description: Library name: sample15

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: Dnag3N2

description: Library name: sample8

value: nag3 deletion strain

value: Modified Mendal’s medium with 2% N-GlcNAc as carbon resource


title: WT, bio rep 2

description:
Library name: Sample 2
WT2

value: WT


title: 8 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150lo, scRNAseq

description:
10x Genomics
CL8

value: Bone marrow

value: LT-HSC

value: GEX


title: biol rep 2, B2h, MDCKII cells, 7 d old cells reseeded for 2 h

city: Tampere

first: Elina

last: Mantyla

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University Foundation

description: Library name: EKRN190001847-1A

data_processing:
Quantified libraries were pooled and sequenced on the Illumina platform using paired-end 150 bp reads (Illumina Sequencing PE150 Illumina), generating approximately 6 Gb of raw data per sample. Base calling was done using Illumina software (CASAVA base calling), generating raw FASTQ files.
Sequencing reads were mapped to CanFam_3.1 (domestic dog, canis lupus familiaris). Gene-level counts were generated using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome.
For bioinformatics analysis, raw data were processed through Novogene’s in-house Perl scripts, and the data were quality checked with FastQC. Relative expression levels were normalized based on gene length and sequencing depth (fragments per kilobase of transcript per million mapped reads, FPKM).
Assembly: GCF_000002285.3 (CanFam3.1)
Supplementary files format and content: csv file "genes_readcount_Mantyla.csv" includes raw counts for each sample
Supplementary files format and content: csv file "genes_FPKM_Mantyla.csv" includes FPKM values for each sample

organism: Canis lupus familiaris

source_name: cell line

growth_protocol: Madine Darby canine kidney type II epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 5 % penicillin-streptomycin  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy midi kit (Qiagen).
The mRNA quantity and integrity were assessed using the 5200 Fragment Analyzer. The libraries  were produced and sequencing with bioinformatics analysis was done by Novogene. RNA libraries for RNA-seq were prepared from mRNA enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies). Insert size was checked on an Agilent 2100 and quantified using quantitative PCR. Oligonucleotide sequences of adapters from TruSeqTM RNA Sample Prep Kit.

treatment_protocol: Cells were grown until full maturity (7 d), or grown for 7 d, detached and reseeded for 2 h

value: cell line

value: MDCKII

value: epithelial

value: Grown for 7 d, detached, and reseeded for 2 h


title: Dnag3CW3

description: Library name: sample3


title: Dnag3G2

description: Library name: sample5


title: Dnag3G1

description: Library name: sample4


title: WTCW2

description: Library name: sample14


title: biol rep 2, B7d, MDCKII cells, 7 d old cells

description: Library name: EKRN190001849-1A

value: Grown for 7 d


title: WTCW1

description: Library name: sample13

value: strain


title: WTN1

description: Library name: sample10

value: 114-2(wild type)


title: B6 BMDMs Biological replicate 1

description: Library name: SSR4-1

value: WT C57BL/6J


title: Dnag3N3

description: Library name: sample9


title: B6 BMDMs Biological replicate 2

description: Library name: SSR4-2

value: bone marrow derived macrophages


title: S2, 7minEdU 15minBrdU, control, rep1

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

description:
Library name: MinION_1_Control
ONT MinION sequencing performed on S2 cells treated with EdU and BrdU pulses

library_source: genomic

data_processing:
Raw Oxford Nanopore sequencing data in POD5 format were processed using a custom DNAscent analysis pipeline. First, POD5 files were converted to FAST5 using the Oxford Nanopore pod5 utility. Basecalling was performed with Guppy v6.4.2 (dna_r10.4.1_e8.2_400bps_5khz_hac DNAscent indexing was used to generate searchable indices from the FAST5 files and sequencing summary data. Replication detection was performed with DNAscent (GPU-accelerated) using a minimum read length threshold of 15 kb. ForkSense analysis was conducted with all detection modes enabled, including forks, origins, terminations, analogues, and stress signatures, using EdU and BrdU as replication markers. Bedgraph files were generated using DNAscent utility scripts to visualize replication features across the genome.configuration, GPU-enabled). Reads were aligned to the Drosophila melanogaster dm6 reference genome using Minimap2 v2.24 with the map-ont preset, followed by conversion and indexing using Samtools v1.10.
Assembly: Drosophila dm6
Supplementary files format and content: BED files of EdU and BrdU labeled tracks identified as left forks, right forks, origins, or terminations

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: S2 cell stocks were maintained in T225 Flasks with room temperature Schneider S2 Media supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin, and 100 µg/mL Streptomycin. Cells were passaged 1:5 dilution (1-part old media: 5-part final volume) when flasks reached 90-100% confluency (fully confluent). New stocks were thawed and maintained after 30 passages.

extract_protocol:
uHMW gDNA extraction and library preparation was conducted as a variation on New England Biolab’s adaption for their T3050L Kit for Oxford Nanopore Sequencing. EB+ was prepared by supplementing 1mL of Monarch Elution Buffer 2 with 2µL of 10% Triton X-100. 100 million previously labeled and frozen cells were resuspended to a concentration of 50 million cells per 100uL 1x PBS and divided into two 1.5mL Eppendorf for parallel extraction. The cells were lysed using 100µL Nuclei Prep Buffer and 50µL of 10mg/mL RNase A and mixed at room temperature for two minutes. Nuclei Lysis Solution was prepared using 200µL Nuclei Lysis Buffer and 80µL 1mg/mL Proteinase K. The nuclei were then lysed using 150µL Nuclei Lysis Solution. The sample was inverted to mix, incubated at 56oC and 300rpm for 10 minutes, then incubated at room temperature for 20 minutes. The sample was precipitated using 150µL of Precipitation Enhancer, two DNA Capture Beads, and 700µL of isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were then washed twice with 500µL each of Wash Buffer before incubating in 200µL 1mg/mL Proteinase K for 16 hours at room temperature. The following morning, the precipitation step was repeated with 75µL Precipitation Enhancer and 350µL isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were washed twice more with 500µL each Wash Buffer, the beads with naked DNA were transferred to a spin column and quickly tapped on an absorbent pad to remove excess buffer, then transferred to 385µL of EB+ buffer. The DNA was allowed to solubilize at room temperature for 16 hours. The sample was poured into a bead retainer seated in a 1.5mL LoBind Eppendorf tube and spun at 16,000xg for one minute. The sample was examined and if DNA strands were visible between the flow through and the beads, the sample was spun again. The sample was mixed gently with a wide-bore pipette until maximally solubilized, pipetted roughly 10-20 times, then stored in the fridge.
Sample libraries were prepared using Oxford Nanopore’s Ultra-Long Sequencing Kit (Cat# SQK-ULK114, Batch #ULK114.20.0003). Dilute fragmentation mix was prepared using 6µL Fragmentation Mix (FRA) and 244µL Fragmentation dilution buffer (FDB) before the dilute fragmentation mix was mixed with the sample via gently pipetting with a wide-bore pipette for two minutes at room temperature. The sample was then incubated for eight more minutes at room temperature followed by 10 minutes at 75oC, five minutes on ice, and finally five minutes at room temperature. 5µL of Rapid Adaptor (RA) was added and mixed thoroughly via wide-bore pipetting and the sample was incubated at room temperature for 30 minutes. Precipitation and sample clean-up was carried out by adding a precipitation star sample followed by 500µL Precipitation Buffer (PTB). The sample was precipitated on a vertical rotating mixer for 20 minutes at 6 rpm. The sample was then spun briefly, and the supernatant was removed. The sample was eluted in 300µL Elution Buffer (EB) overnight at room temperature before being stored at 4oC.

treatment_protocol: 24-hours prior to labeling, a fully confluent flask was passaged 1:2 or 1:3 to achieve 60-80% confluency at the time of labeling to ensure cells were actively replicating. The two flasks of cells resulting from this split were labeled at the same time and combined during a later step. The day of labeling, old media was removed and immediately replaced with 25 mL of new media supplemented with 10µM EdU. Cells were returned to the 25oC incubator for 3 or 7 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently washed three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). Cells were then incubated with 25mL of new media supplemented with 10µM BrdU. For HU treatment, 1mM was added to the BrdU media. Cells were returned to the 25 oC incubator for 6 or 15 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently wash three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). The cells were then incubated with 25mL of new media supplemented with 50µM thymidine. Cells were returned to the 25 oC incubator for 20 minutes before harvesting. Cells from pairs of flasks labeled at the same time were combined into a single 50mL conical and 200µL of cells were set aside on ice for later counting and labeling validation. The remaining cells were pelleted at 600xg for 5 minutes and the old media was removed. The cells were then washed via resuspending in 10mL 1x PBS and subsequent pelleting at 600xg for 5 minutes. This wash step was repeated once. After washing, the cells were resuspended into 1mL 1x PBS, transferred to a 1.5mL Eppendorf tube, and pelleted at 600xg for 5 minutes.

value: Embryonic Cells

value: 7 minutes EdU followed by 15 minutes BrdU

tag: batch


title: WTG1

description: Library name: sample16

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: Dnag3G3

description: Library name: sample6

value: nag3 deletion strain


title: WT, bio rep 1

description:
Library name: Sample 1
WT1

value: mouse bone marrow

value: WT


title: scRNA-seq,Y-TNF,ADT

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: Y-TNF_ADT

data_processing:
Raw sequencing data were processed using the Cell Ranger multi pipeline (v9.0.1). Reads were aligned to the mm10-2020-A mouse reference genome for gene expression and to vdj_GRCm38_alts_ensembl-7.0.0 for V(D)J data. Sample demultiplexing was performed using antibody-derived hashtag oligos (HTOs). Filtered feature-barcode matrices were imported into Seurat44 (v5.1.0) for downstream analysis.
Assembly: mm10-2020-A, vdj_GRCm38_alts_ensembl-7.0.0
Supplementary files format and content: CellRanger output filtered_bc(GEX) files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: CellRanger output filtered_bc(TCR) files: filtered_contig_annotations.csv

source_name: spleen

extract_protocol:
Splenic CD8⁺ T cells were enriched using the EasySep™ Mouse CD8⁺ T Cell Isolation Kit (STEMCELL Technologies, cat. #19853) according to the manufacturer’s instructions. Enriched cells were stained with Live/Dead Fixable Aqua Dead Cell Stain (Invitrogen, cat. #L34966; 1:1000 dilution in PBS) for 5 minutes at room temperature. A surface antibody cocktail (1:300 final dilution) was prepared in 1% BSA/PBS and supplemented with TruStain FcX™ PLUS (anti-mouse CD16/32, BioLegend, cat. #156604; 5 μL per sample). 25 μL of this cocktail were added to each sample, followed by a 10-minute incubation at 4°C. Subsequently, 25 μL of a TotalSeq™-C antibody cocktail (1:50 final dilution), along with a TotalSeq™-C Hashtag antibody (0.2 μg per sample), were added and samples were incubated for 30 minutes at 4°C. Details of the antibodies used are provided in Table 1. To minimize aggregate formation, all antibody cocktails were centrifuged at 14,000 × g for 10 minutes at 4°C prior to use. After staining, cells were washed once in 1% BSA/PBS and live CD3e⁺CD8a⁺ T cells were sorted using the Aurora Cell Sorter. Post-sort, cells were counted and assessed for viability. The final suspension was adjusted to 1,300 cells per μL, and equal numbers of cells from up to four samples were pooled prior to library preparation
45k cell per pooled sample were subjected to droplet-based massively parallel single-cell RNA sequencing. cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  V(D)J target enrichment (TCR) was performed on the full-length cDNA.  Gene Expression, Enriched TCR and Feature libraries were prepared as recommended by the 10x Genomics Chromium GEM-X Single Cell 5' Reagent Kits User Guide (v3 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Immune Receptor Mapping user guide, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium GEM-X Single Cell 5’ Kit v3, 16 rxns (PN-1000699), Chromium GEM-X Single Cell 5’ Chip Kit (PN-1000698), Chromium Single Cell Mouse TCR Amplification Kits (PN-1000254), Dual Index Kit TT Set A, 96 rxns (PN-1000215), Chromium GEM-X Single Cell 5' Feature Barcode Kit v3, 16 rxns (PN-1000703) and Dual Index Kit TN Set A, 96 rxns (PN-1000250) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeqX plus S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library and 5000 reads/cell for each V(D)J and Feature library.

value: spleen

value: CD8 T cells


title: Dnag3CW1

description: Library name: sample1

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: WTN2

description: Library name: sample11

value: Modified Mendal’s medium with 2% N-GlcNAc as carbon resource


title: biol rep 1, A2h, MDCKII cells, 7 d old cells reseeded for 2 h

description: Library name: EKRN190001848-1A

value: cell line

value: MDCKII

value: epithelial


title: scRNA-seq,O-WT,ADT

description: Library name: O-WT_ADT


title: scRNA-seq,Y-WT,GEX

description: Library name: Y-WT_GEX

library_source: transcriptomic single cell

molecule: polyA RNA


title: Dnag3N1

description: Library name: sample7

value: strain


title: scRNA-seq,O-WT,TCR

description: Library name: O-WT_TCR

data_processing:
Raw sequencing data were processed using the Cell Ranger multi pipeline (v9.0.1). Reads were aligned to the mm10-2020-A mouse reference genome for gene expression and to vdj_GRCm38_alts_ensembl-7.0.0 for V(D)J data. Sample demultiplexing was performed using antibody-derived hashtag oligos (HTOs). Filtered feature-barcode matrices were imported into Seurat44 (v5.1.0) for downstream analysis.
Assembly: mm10-2020-A, vdj_GRCm38_alts_ensembl-7.0.0
Supplementary files format and content: CellRanger output filtered_bc(GEX) files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: CellRanger output filtered_bc(TCR) files: filtered_contig_annotations.csv
Library strategy: TCR-Seq


title: Dnag3CW2

description: Library name: sample2


title: GAA-CH, BSA-Palmitate, rep3

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

description:
Library name: GAA_bsaPalm_3
clean reads

data_processing:
Adapter sequences and low-quality reads were filtered with SOAPnuke. Clean reads were obtained with an output read quality of Phred+33.
Clean reads were aligned to the hg38 genome with STAR-2.7.10b and counts generated uing featurecounts. Variance stabilized transformation was used to generate vst normalized count table. Deseq2 and limma were used for differential expression analysis. Direct comparisons were made between treatment conditions. DOSE Gene Set Enrichment Analysis was performed with the DOSE package, in R.
Assembly: hg38
Supplementary files format and content: raw counts
Supplementary files format and content: csv file

source_name: skin fibroblasts

growth_protocol: Skin fibroblasts of Pompe disease patients were grown in DMEM + 10% FBS and PenStrep.

extract_protocol:
Total RNA was extracted with RNAseasy lipid tissue kit.
mRNA was enriched with oligo dT beads that target the poly A tail. mRNA molecules were fragmented and synthesized into first strand cDNA using random primers. The second strand was synthesized with dUTP instead of dTTP and cDNA was subject to end-repair and 3' adenylation. Adaptors were then ligated to the 3' adenylated cDNA fragments after which were PCR amplified. Libraries were then circularized and amplified to make a DNA nanball and sequenced on the DNBSEQ-G400.

treatment_protocol: Cells were treated for 24h with fatty acid-free BSA as a control, or BSA palmitate (200uM), and then flash frozen in liquid nitrogen prior to RNA extraction.

value: skin fibroblasts

value: fibroblast

value: GAA-CH, Pompe disease

value: BSA-Palmitate


title: scRNA-seq,M-WT,ADT

description: Library name: M-WT_ADT


title: scRNA-seq,M-WT,TCR

description: Library name: M-WT_TCR


title: scRNA-seq,O-WT,GEX

description: Library name: O-WT_GEX


title: scRNA-seq,M-WT,GEX

description: Library name: M-WT_GEX


title: GAA-CH, BSA-Palmitate, rep1

description:
Library name: GAA_bsaPalm_1
clean reads


title: scRNA-seq,Y-WT,TCR

description: Library name: Y-WT_TCR


title: GAA-CH, BSA, rep1

description:
Library name: GAA_bsa_1
clean reads

value: BSA


title: scRNA-seq,Y-WT,ADT

description: Library name: Y-WT_ADT


title: CrWT rep 2

city: Beijing

first: Yan

last: Li

address: Haidian

institute: Capital Normal University

description: Library name: CrWT_2

data_processing:
Reads were mapped to the Chlamydomonas reinhardtii genome using bowtie2. Only the uniquely mapped reads were saved.
Assembly: Chlamydomonas reinhardtii CC-4532 v6.1
Supplementary files format and content: bed files were the output result from HOMER callpeak progress, containing the location information of peaks.

organism: Chlamydomonas reinhardtii

source_name: single cells

extract_protocol:
Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii.  To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology.  Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression.  To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach.  RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex.  This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.
The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5' Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a "T" base overhang. Adaptor ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

value: single cells


title: scRNA-seq,M-TNF,GEX

description: Library name: M-TNF_GEX


title: EX008_9

city: Los Angeles

first: Brandon

last: Tsai

state: California

address: 405 Hilgard Ave

institute: University of California, Los Angeles

description:
Library name: EX008_9
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.

data_processing:
FASTQs demultiplexed followed by primer and adapter removal, read filtering and trimming
ASV inference using DADA2 pipeline
Taxonomy assignment against RefSeq database using DECIPHER v2.26.0 and phylogenetic tree construction using phangorn v2.11.1
Filtering using phyloseq v1.42.0 — removed samples with fewer than 5000 reads and features not present in at least 5% of samples (3 or more)
Data agglomerated at species level — 684 ASVs identified, mean 150 ± 65 per sample retained across 39 samples
Assembly: NCBI RefSeq 16S rRNA database
Supplementary files format and content: 684 taxa x 39 samples, raw ASV counts after filtering and agglomeration to species level

organism: human gut metagenome

source_name: stool

extract_protocol:
DNA extracted from frozen stool aliquots using phenol-chloroform extraction with mechanical disruption. Samples suspended in extraction buffer (200 mM Tris pH 8.0, 200 mM NaCl, 20 mM EDTA), 20% SDS, phenol/chloroform/isoamyl alcohol (25:24:1), and 0.1mm zirconia/silica beads (BioSpec Products). Microbial cells lysed by bead-beating for 2 minutes followed by 2 rounds of phenol/chloroform/isoamyl alcohol extraction. DNA precipitated in ethanol, resuspended in TE buffer with 100 mg/mL RNase, and purified using QIAamp mini spin columns (Qiagen).
V4-V5 region of 16S rRNA gene amplified using primers 563F (AYTGGGYDTAAAGNG) and 926R (CCGTCAATTYHTTTRAGT) with unique 12-base Golay barcodes and additional offset nucleotides. Amplicons purified with Qiaquick PCR Purification Kit (Qiagen), quantified using Agilent TapeStation 2200, and pooled at equimolar amounts. Libraries prepared using TruSeq DNA Library Preparation Kit (Illumina) per manufacturer instructions and sequenced paired-end 250x250 bp on Illumina MiSeq.

treatment_protocol: Patients enrolled in PRESTO neoadjuvant exercise intervention trials. Stool samples collected weekly via pre-paid courier service over the course of structured exercise intervention.

value: stool

tag: patient

tag: week


title: GAA-CH, BSA, rep2

description:
Library name: GAA_bsa_2
clean reads


title: WTN3

description: Library name: sample12

value: 114-2(wild type)


title: EX008_7

description:
Library name: EX008_7
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: scRNA-seq,M-TNF,TCR

description: Library name: M-TNF_TCR


title: EX008_6

description:
Library name: EX008_6
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX019 Timepoint 7

type: protein

description: SOMAscan aptamer hybridization

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Median signal normalization is performed using Adaptive Normalization by Maximum Likelihood (ANML) for specimen types and studies shown to be consistent with predefined population references or, alternatively, using median normalization to a study specific reference.

source_name: plasma

label_protocol: not applicable

extract_protocol: Remote (in-home) blood collection was coordinated using Workpath, Inc. Workpath – a HIPAA compliant platform – organizes, verifies, and dispatches mobile medical services. Using the Workpath dashboard and partnering with Phlebotek, Inc. a third-party mobile phlebotomy vendor, appointments were scheduled for a trained phlebotomist to visit patients’ residence to collect fasted blood samples. The dashboard also permits real-time monitoring enabling blood collection and delivery to be tracked remotely by the Exercise Oncology study team. Participants were instructed to adhere to Exercise-Oncology blood collection procedures prior to every blood collection. Blood collection was scheduled between 0700 and 1000 h, after an 8-hr water-only fast. Two separate 7  mL EDTA, one 10 mL Serum, and one 10 mL STRECK tube blood samples were obtained. Samples were transported to a designated MSK facility for processing and stored at −80 °C. Blood collection was performed weekly.

treatment_protocol: All patients received 150 minutes per week: ≈30 minutes per treatment five times weekly. After a one week ‘ramp-up’ period in which duration and/or intensity were progressively increased, all subsequent sessions starting in week two were conducted at ≈70% of the pre-exercise submaximal exercise capacity for ≈30 minutes per session. The intensity of each session was individually prescribed to each patient based on workload (the speed and incline) and heart rate response measured during the pre-exercise CFT.

tag: cancer

value: Prostate


title: GAA-CH, BSA-Palmitate, rep2

description:
Library name: GAA_bsaPalm_2
clean reads


title: EX005_6

description:
Library name: EX005_6
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: ScRNA-seq,Y-TNF,GEX

description: Library name: Y-TNF_GEX

value: spleen


title: scRNA-seq,Y-TNF,TCR

description: Library name: Y-TNF_TCR

value: CD8 T cells


title: scRNA-seq,M-TNF,ADT

description: Library name: M-TNF_ADT


title: CrWT rep 3

description: Library name: CrWT_3

value: WT


title: EX008_3

description:
Library name: EX008_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX008_8

description:
Library name: EX008_8
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: CrWT rep 1

description: Library name: CrWT_1


title: EX005_2

description:
Library name: EX005_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX008_10

description:
Library name: EX008_10
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX019 Timepoint 5

description: SOMAscan aptamer hybridization


title: EX008_5

description:
Library name: EX008_5
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX005_5

description:
Library name: EX005_5
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX008_12

description:
Library name: EX008_12
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Crpaf1 rep 3

description: Library name: Crpaf1_3


title: EX018_4

description:
Library name: EX018_4
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Crskip rep 3

description: Library name: Crskip_3

value: skip


title: Patient EX019 Timepoint 3

description: SOMAscan aptamer hybridization


title: Patient EX018 Timepoint 3

description: SOMAscan aptamer hybridization


title: Patient EX019 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX017_4

description:
Library name: EX017_4
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX017 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX019 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX019 Timepoint 6

description: SOMAscan aptamer hybridization


title: Patient EX018 Timepoint 5

description: SOMAscan aptamer hybridization


title: EX008_1

description:
Library name: EX008_1
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX017 Timepoint 3

description: SOMAscan aptamer hybridization


title: EX018_5

description:
Library name: EX018_5
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX005_1

description:
Library name: EX005_1
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX017_1

description:
Library name: EX017_1
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX019 Timepoint 4

description: SOMAscan aptamer hybridization


title: EX015_5

description:
Library name: EX015_5
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX005_4

description:
Library name: EX005_4
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX015_4

description:
Library name: EX015_4
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX018 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX018 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX016 Timepoint 4

description: SOMAscan aptamer hybridization


title: EX018_2

description:
Library name: EX018_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX018 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX017_2

description:
Library name: EX017_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX012_8

description:
Library name: EX012_8
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX017_3

description:
Library name: EX017_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX016 Timepoint 3

description: SOMAscan aptamer hybridization


title: Patient EX015 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX015 Timepoint 3

description: SOMAscan aptamer hybridization


title: EX012_5

description:
Library name: EX012_5
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX012_6

description:
Library name: EX012_6
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX012_7

description:
Library name: EX012_7
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX017 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX015_2

description:
Library name: EX015_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX017 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX016 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX012_2

description:
Library name: EX012_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX012_4

description:
Library name: EX012_4
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX014 Timepoint 3

description: SOMAscan aptamer hybridization

value: Breast


title: EX015_3

description:
Library name: EX015_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX015 Timepoint 5

description: SOMAscan aptamer hybridization


title: Patient EX016 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 10

description: SOMAscan aptamer hybridization


title: EX012_9

description:
Library name: EX012_9
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX010_3

description:
Library name: EX010_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX012 Timepoint 9

description: SOMAscan aptamer hybridization


title: Patient EX014 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX015 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX014 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX012_3

description:
Library name: EX012_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX006_1

description:
Library name: EX006_1
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: EX010_2

description:
Library name: EX010_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX012 Timepoint 7

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 8

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 6

description: SOMAscan aptamer hybridization


title: EX010_1

description:
Library name: EX010_1
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX014 Timepoint 2

description: SOMAscan aptamer hybridization


title: EX006_3

description:
Library name: EX006_3
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: Patient EX012 Timepoint 3

description: SOMAscan aptamer hybridization


title: P01gDNA

type: genomic

city: Shanghai

first: Xiaotong

last: Ma

address: No. 12, middle Urumqi Road

department: Department of Laboratory Medicine

institute: Huashan hospital

description: Methylome in Blood gDNA Samples from MPN Patient 1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human lnfinium MethylationEPlc Beadchip (llumina) using standard lumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended llumina scanner setting

data_processing:
The data were mainly analyzed using ChAMP[1]package in R. And we used β value to represent DNA methylation level / the proportion of methylated each CpG site . First , we filtered probes with detection p-value <0.01 , probes with <3 beads in at least 5% of samples , non-CpG probes , multi-hit probes , probes located in chromosome X and Y and (SNP-related probes)  in turn, the final probes for subsequent analysis were 820,000 . Then β value matrix were normalized using BMIQ[2] for adjusting type I and type II probe bias . Next, we used SVA[3](Singular Value Decomposition Analysis) to analysis the batch effect caused by BeadChip Slide and Array , then applied Combat[4] to correct this batch effect. We annotated all CpG sites using EPICanno.ilm10b4.hg19[5]. Differential Methylated CpGs Position(probes) were calculated by champ.DMP() function , the adj.p values were computed using the Benjamini-Hochberg method[6]. CpGs having |Δβ|≥0.20 / 0.10 / 0.06 and adjusted p-value≤0.05 / p-value≤0.01 were considered as DMPs. Differential Methylated Region were calculated using ProbeLasso[7] , all CpGs were for DMR calling and minSigProbesLasso、lassoRadius、boundary were the default value . In order to evaluate the DMP and DMR biologic processes ,cellular components ,molecular and pathway , we conducted Gene Ontology(GO)[8] and KEGG[9] enrichment analysis respectively using R package. Finally, we use Functional Epigenetic Modules to infer differential methylated gene modules in protein to protein interaction network(PPI) using FEM[10] package. Additionally , we use Conumee[11] package to analysis copy number variation.
[processed value definition] Average Beta

label: Cy3 and Cy5

source_name: blood

label_protocol: Standard lllumina Protocol

extract_protocol: cell-free DNA and gDNA was extracted from plasma samples using Qiagen DNeasy Blood & Tissue Kit (50)#69504 according to standard instructions

value: blood

tag: disease state

value: Myeloproliferative Neoplasms

tag: individual

value: Patient 1

tag: group

value: gDNA


title: Patient EX015 Timepoint 1

description: SOMAscan aptamer hybridization


title: EX006_2

description:
Library name: EX006_2
Weekly stool sample collected via pre-paid courier from cancer patient enrolled in PRESTO neoadjuvant exercise intervention trial. 16S rRNA V4-V5 amplicon sequencing of gut microbiome. DNA extracted by phenol-chloroform bead-beating with QIAamp purification. Amplified with primers 563F/926R with Golay barcodes. Sequenced paired-end 250x250 bp using TruSeq DNA Library Preparation Kit.


title: P02cfDNA

type: other

description: Methylome in Blood cfDNA Samples from MPN Patient 2

molecule: other

value: Patient 2

value: cell-free DNA


title: Patient EX012 Timepoint 1

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX012 Timepoint 5

description: SOMAscan aptamer hybridization


title: P03gDNA

description: Methylome in Blood gDNA Samples from MPN Patient 3

value: Patient 3


title: P02gDNA

description: Methylome in Blood gDNA Samples from MPN Patient 2


title: Patient EX010 Timepoint 3

description: SOMAscan aptamer hybridization


title: time point 10, replicate 5 (treated)

city: Cleveland

first: Kristi

last: Lin-Rahardja

state: OH

address: 10900 Euclid Ave

department: Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
Library name: EC5_5
column names match library name

data_processing:
concatenate lanes for each sample/replicate (e.g. for WT1 R1, cat L001 and L002; repeat for WT1 R2)
align using STAR alignReads
count using srun featureCounts, saving each result as a .tsv
in R, compile all the separated .tsvs into one matrix
average the sequencing replicates (R1 and R2 per sample), then quantile normalize the counts by group (treated or control) using qsmooth package. Convert ENSEMBL IDs to gene symbols from org.Hs.eg.db
Assembly: using STAR aligner and Homo_sapiens_GRCh38.113
Supplementary files format and content: first column shows gene symbols (translated from ENSEMBL ID to SYMBOL via org.Hs.eg.db), remaining columns represent each sample.
Supplementary files format and content: Each value in the matrix represents the quantile-normalized count for that gene+sample

source_name: bone

growth_protocol: allow growth to 80-90% confluency before treatment period (G1) and after treatment period (G2). Cells will be sampled for RNA extraction and drug screening after G2 is complete.

extract_protocol:
Qiagen Allprep kit used for all extraction
STAR aligner was used to align and count reads

treatment_protocol: Expose R1-7 to EC70 of VDC or EC for 5 days. Initial date of exposure counts as day 1. At day 5, drugged medium will be removed, cells will be washed with PBS, and drug-free medium will be replaced for G2.

value: bone

value: Ewings sarcoma

value: VDC-EC

tag: time


title: time point 10, replicate 10 (control)

description:
Library name: EC5_10
column names match library name

value: DMSO


title: Patient EX010 Timepoint 2

description: SOMAscan aptamer hybridization

value: Prostate


title: time point 10, replicate 8 (control)

description:
Library name: EC5_8
column names match library name


title: time point 10, replicate 6 (treated)

description:
Library name: EC5_6
column names match library name


title: time point 10, replicate 2 (treated)

description:
Library name: EC5_2
column names match library name


title: Patient EX008 Timepoint 9

description: SOMAscan aptamer hybridization


title: time point 9, replicate 10 (control)

description:
Library name: VDC5_10
column names match library name


title: Patient EX008 Timepoint 10

description: SOMAscan aptamer hybridization


title: time point 9, replicate 8 (control)

description:
Library name: VDC5_8
column names match library name


title: time point 9, replicate 9 (control)

description:
Library name: VDC5_9
column names match library name


title: Patient EX008 Timepoint 7

description: SOMAscan aptamer hybridization


title: Patient EX010 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX008 Timepoint 5

description: SOMAscan aptamer hybridization


title: time point 9, replicate 5 (treated)

description:
Library name: VDC5_5
column names match library name


title: time point 9, replicate 1 (treated)

description:
Library name: VDC5_1
column names match library name


title: Patient EX008 Timepoint 8

description: SOMAscan aptamer hybridization


title: Patient EX008 Timepoint 4

description: SOMAscan aptamer hybridization


title: Patient EX008 Timepoint 3

description: SOMAscan aptamer hybridization


title: Patient EX008 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX010 Timepoint 1

description: SOMAscan aptamer hybridization


title: time point 8, replicate 10 (control)

description:
Library name: EC4_10
column names match library name


title: Patient EX008 Timepoint 6

description: SOMAscan aptamer hybridization


title: Patient EX008 Timepoint 1

description: SOMAscan aptamer hybridization


title: time point 9, replicate 4 (treated)

description:
Library name: VDC5_4
column names match library name


title: Patient EX006 Timepoint 3

description: SOMAscan aptamer hybridization

value: Endometrial


title: time point 8, replicate 9 (control)

description:
Library name: EC4_9
column names match library name


title: time point 8, replicate 4 (treated)

description:
Library name: EC4_4
column names match library name


title: time point 8, replicate 6 (treated)

description:
Library name: EC4_6
column names match library name


title: P01cfDNA

description: Methylome in Blood cfDNA Samples from MPN Patient 1


title: time point 8, replicate 3 (treated)

description:
Library name: EC4_3
column names match library name


title: time point 8, replicate 8 (control)

description:
Library name: EC4_8
column names match library name


title: time point 8, replicate 7 (treated)

description:
Library name: EC4_7
column names match library name


title: Patient EX006 Timepoint 1

description: SOMAscan aptamer hybridization


title: Patient EX006 Timepoint 2

description: SOMAscan aptamer hybridization


title: P03cfDNA

description: Methylome in Blood cfDNA Samples from MPN Patient 3


title: time point 8, replicate 2 (treated)

description:
Library name: EC4_2
column names match library name


title: time point 8, replicate 5 (treated)

description:
Library name: EC4_5
column names match library name


title: Patient EX005 Timepoint 6

description: SOMAscan aptamer hybridization


title: time point 7, replicate 7 (treated)

description:
Library name: VDC4_7
column names match library name


title: Patient EX005 Timepoint 5

description: SOMAscan aptamer hybridization


title: Patient EX004 Timepoint 2

description: SOMAscan aptamer hybridization


title: Patient EX005 Timepoint 7

description: SOMAscan aptamer hybridization


title: time point 7, replicate 1 (treated)

description:
Library name: VDC4_1
column names match library name


title: Patient EX005 Timepoint 1

description: SOMAscan aptamer hybridization


title: Patient EX005 Timepoint 2

description: SOMAscan aptamer hybridization


title: time point 6, replicate 10 (control)

description:
Library name: EC3_10
column names match library name


title: time point 6, replicate 8 (control)

description:
Library name: EC3_8
column names match library name


title: Patient EX005 Timepoint 4

description: SOMAscan aptamer hybridization


title: NeoBC069

type: RNA

city: Sevilla

first: María

middle: Ángeles

last: Domínguez

state: Seleccione

address: Avenida Manuel Siurot s/n

country: Spain

institute: Instituto de Biomedicna de Sevilla

description: Gene expression data from FFPE tissue sample from a patient with HER2-positive, hormone receptor–negative breast cancer treated with neoadjuvant chemotherapy plus anti-HER2 agents

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemented Transcriptome Analysis Console (TAC) 4.0 software.

label: biotin

source_name: Breast cancar patient treated with neoadjuvant therapy

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

extract_protocol: RNA extraction was performed from 8–10 10 µm sections of formalin-fixed paraffin-embedded (FFPE) samples obtained from diagnostic biopsies using a RecoverAll™ Total Nucleic Acid Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's recommendations with modifications in the protease digestion stage, where prolonged incubation at 50 °C for three hours was used to optimize the recovery of nucleic acids.

value: Breast cancer

tag: Sex

value: Female


title: time point 7, replicate 6 (treated)

description:
Library name: VDC4_6
column names match library name

tag: tissue


title: Patient EX005 Timepoint 3

description: SOMAscan aptamer hybridization


title: NeoBC068


title: Patient EX004 Timepoint 3

description: SOMAscan aptamer hybridization


title: NeoBC071


title: time point 7, replicate 8 (control)

description:
Library name: VDC4_8
column names match library name

tag: cell type


title: time point 7, replicate 5 (treated)

description:
Library name: VDC4_5
column names match library name


title: time point 7, replicate 2 (treated)

description:
Library name: VDC4_2
column names match library name


title: time point 6, replicate 9 (control)

description:
Library name: EC3_9
column names match library name


title: time point 6, replicate 6 (treated)

description:
Library name: EC3_6
column names match library name


title: time point 6, replicate 5 (treated)

description:
Library name: EC3_5
column names match library name


title: Patient EX004 Timepoint 1

description: SOMAscan aptamer hybridization


title: time point 6, replicate 7 (treated)

description:
Library name: EC3_7
column names match library name


title: NeoBC065


title: time point 6, replicate 4 (treated)

description:
Library name: EC3_4
column names match library name


title: NeoBC078


title: NeoBC062


title: NeoBC067


title: time point 6, replicate 3 (treated)

description:
Library name: EC3_3
column names match library name


title: NeoBC020


title: time point 5, replicate 9 (control)

description:
Library name: VDC3_9
column names match library name


title: NeoBC019


title: time point 6, replicate 1 (treated)

description:
Library name: EC3_1
column names match library name


title: time point 5, replicate 10 (control)

description:
Library name: VDC3_10
column names match library name


title: 24h_timepoint

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description:
Library name: 24h_timepoint
BD Rhapsody

data_processing:
Read alignment + counting; STAR (BD Analysis pipeline v1.11)
Assembly: Cylindrotheca closterium (GCA_933822405.4)
Supplementary files format and content: zip file of raw count matrix in csv format
Supplementary files format and content: zip file of filtered count matrix in csv format
Supplementary files format and content: Merged Seurat file in .rds format

organism: Cylindrotheca closterium

source_name: sexual culture

growth_protocol: Two sexually compatible strains of C. closterium were obtained from the BCCM/DCG culture collection (https://bccm.belspo.be/about-us/bccm-dcg): CA1-15 as the MT- strain (DCG 0923) and ZW2-20 as its MT+ partner (DCG 0922). Cultures were grown in natural seawater supplemented with Guillard’s F/2 Marine Water enrichment solution (Sigma-Aldrich) and antibiotics to avoid bacterial growth: 0.7 g/L ampicillin, 0.5 g/L penicillin, 0.2 g/L streptomycin en 0.1 g/L gentamicin.

extract_protocol:
Surface-attached benthic C. closterium cells were suspended using a cell scraper and flasks were gently vortexed to separate cells. Next, 575µL of culture was loaded on the BD Rhapsody cartridge.
Cells were processed using BD Rhapsody (single cartridge, cartridge reagent kit, cDNA and WTA amplification kit), following the manufacturers’ protocols for reverse transcription, cDNA amplification, and library construction.

treatment_protocol: At the start of the experiment, cultures from both mating types were inoculated at a density of 2000 cells/mL and were grown in a 12:12 day:night rhythm for three days, after which medium was refreshed. On the fourth day, cells were suspended by gentle scraping and 15mL of medium was transferred to small culture flasks (25 cm², VWR®), which were put in complete darkness for two days to synchronize the entry into sexual reproduction 7. Still in the dark, cells were resuspended by scraping and cultures of the compatible mating types were pooled at the same density, as determined using Burker Chamber counts under a Axiovert 40C inverted microscope. We then transferred 15 mL of suspended crossed cells to new culture flasks, which were moved into continuous light and a temperature of 21°C. Crossed cultures were allowed to develop for a specific duration of time before single-cell RNA sequencing: 12h, 19h or 24h.

value: sexual culture

tag: strain

value: Mix of ZW2.20 and CA1.15

tag: timepoint


title: NeoBC017

tag: age


title: NeoBC018


title: Treatment-6

first: Bi-Sen

last: Ding

state: Sichuan

address: Wuhou District, Renmin three paragraphs

department: The West China Second UniversityHospital of Sichuan University

description:
Library name: Treatment-6
Singleron GEXSCOPE®

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the CeleScope software v1.15.0
Assembly: Sscrofa11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Liver

extract_protocol:
Liver samples were obtained through surgical biopsy, preserved in SCelLiVe® Tissue Storage Solution, and minced into small pieces. The tissue was digested at 37°C for 40 minutes using a digestion solution containing 1 mg/ml Collagenase I, 1 mg/ml Collagenase II, 1 mg/ml Dispase II, and 10 U/ml DNase I. After obtaining the cell suspension, red blood cells were removed, and the sample was centrifuged at 50 g for 2 minutes to isolate non-parenchymal cells (NPCs).
Library was performed according to the manufacter's instruction(GEXSCOPE® Single Cell RNA Library Kit)

treatment_protocol: For the analysis of minipig non-parenchymal cells, a MASH model was successfully established over a 3-month period using a high-fat, high-sugar diet combined with intraperitoneal injection of carbon tetrachloride . Pre-treatment samples were obtained via surgical biopsy. Subsequently, a 9-month treatment regimen with a ROCK2 inhibitor was administered. Post-treatment samples were then collected via surgical biopsy, followed by single-cell library construction and sequencing.

value: Liver

value: NPCs


title: 12h_timepoint

description:
Library name: 12h_timepoint
BD Rhapsody


title: time point 5, replicate 8 (control)

description:
Library name: VDC3_8
column names match library name

tag: treatment


title: Treatment-4

description:
Library name: Treatment-4
Singleron GEXSCOPE®


title: 19h_timepoint

description:
Library name: 19h_timepoint
BD Rhapsody


title: Treatment-5

description:
Library name: Treatment-5
Singleron GEXSCOPE®


title: Treatment-3

description:
Library name: Treatment-3
Singleron GEXSCOPE®


title: NeoBC021

description: Gene expression data from FFPE tissue sample from a patient with HER2-positive, hormone receptor–negative breast cancer treated with neoadjuvant chemotherapy plus anti-HER2 agents


title: time point 5, replicate 7 (treated)

description:
Library name: VDC3_7
column names match library name

tag: cell line


title: NeoBC063


title: Treatment-2

description:
Library name: Treatment-2
Singleron GEXSCOPE®


title: time point 5, replicate 6 (treated)

description:
Library name: VDC3_6
column names match library name

tag: genotype


title: colon, CDs_3

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

description:
Library name: sample9
CDs_3:fpkm

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Ensembl
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare forhybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: colon

value: WT

value: DSS+lotus node charcoal carbon dots


title: colon, CDs_2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample8
CDs_2:fpkm


title: colon, CDs_1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample7
CDs_1:fpkm


title: Treatment-1

city: Chengdu

institute: Sichuan University

description:
Library name: Treatment-1
Singleron GEXSCOPE®


title: time point 5, replicate 5 (treated)

description:
Library name: VDC3_5
column names match library name


title: MASH-5

description:
Library name: MASH-5
Singleron GEXSCOPE®


title: colon, Model_3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample6
Model_3:fpkm

value: DSS


title: MASH-6

description:
Library name: MASH-6
Singleron GEXSCOPE®


title: colon, Model_2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample5
Model_2:fpkm


title: MASH-2

description:
Library name: MASH-2
Singleron GEXSCOPE®


title: MASH-3

description:
Library name: MASH-3
Singleron GEXSCOPE®


title: colon, Model_1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample4
Model_1:fpkm


title: MASH-1

description:
Library name: MASH-1
Singleron GEXSCOPE®


title: time point 5, replicate 4 (treated)

description:
Library name: VDC3_4
column names match library name


title: time point 5, replicate 1 (treated)

description:
Library name: VDC3_1
column names match library name


title: colon, Blank_3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample3
Blank_3:fpkm


title: colon, Blank_2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample2
Blank_2:fpkm


title: time point 4, replicate 8 (control)

description:
Library name: EC2_8
column names match library name


title: time point 4, replicate 9 (control)

description:
Library name: EC2_9
column names match library name


title: DHT+Ab

city: Incheon

first: Jong-Hyuk

last: Sung

address: 32 Songdogwahak-ro

country: South Korea

institute: Epi Biotech Co., Ltd.

description:
Library name: Sample 3
10x Genomics

data_processing:
Raw base call files were converted to FASTQ files using BCL Convert v4.3.6. FASTQ files were processed with Cell Ranger v9.0.1 using the count pipeline for alignment, barcode filtering, and UMI counting. Reads were aligned to the mouse reference genome GRCm39-2024-A, and gene-by-cell count matrices were generated for each sample
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole dorsal skin

extract_protocol:
Dorsal skin was collected from male C3H/HeN mice after treatment in the vehicle, DHT, or DHT plus anti-DKK3 antibody groups. Hair was removed prior to skin harvest, and excised skin was trimmed to remove excess fat and connective tissue, minced, and dissociated into single cells. Tissue fragments were digested in HBSS containing calcium with Liberase TL (0.5 mg/mL), hyaluronidase (0.1 mg/mL), and DNase I (0.1 mg/mL) for 1.5 h at 37°C with shaking, followed by sequential filtration through 70 μm and 40 μm strainers. Red blood cells were removed using ACK lysis buffer, and debris was depleted by Percoll density-gradient centrifugation. The resulting live single-cell suspension was used for library preparation.
Single-cell suspensions were processed using the Chromium GEM-X Single Cell 3' RNA library v4 kit (10x Genomics) according to the manufacturer's instructions. Single cells were partitioned into GEMs with barcoded gel beads, and polyadenylated RNA was captured with barcoded oligonucleotides for reverse transcription and cDNA synthesis. Amplified cDNA was used to generate 3' gene expression libraries, which were sequenced on an Illumina platform.

value: whole dorsal skin

value: 9 weeks old

value: male

value: DHT + anti-DKK3 antibody


title: time point 5, replicate 3 (treated)

description:
Library name: VDC3_3
column names match library name

value: bone

value: Ewings sarcoma

value: VDC-EC


title: M393-1,bhlh151-KO#40-1

first: Han tian

last: Wei

address: Chinese Academy of Forestry

institute: Chinese Academy of Forestry

description: Library name: Sample 13

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2. Genes with an adjusted P-value < 0.01 found by DESeq2 were assigned as differentially expressed.
Assembly: Genome Sequence Archive in National Genomics Data Center (https://ngdc.cncb.ac.cn/gwh) under the accession number GWHBJXC00000000 (Bio-Project ID: PRJCA010836)
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

organism: Populus alba x Populus glandulosa

source_name: root tissue

extract_protocol:
For total RNA extraction, we followed the protocol as described in the RNAprep Pure Plant Kit (TIANGEN, Beijing, China).
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: root tissue

value: 84k poplar

value: root cells


title: W92-3,bHLH58-OE#20-3

description: Library name: Sample 12


title: M393-3,bhlh151-KO#40-3

description: Library name: Sample 15


title: colon, Blank_1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample1
Blank_1:fpkm


title: W92-2,bHLH58-OE#20-2

description: Library name: Sample 11


title: W393-1,bHLH151-OE#17-1

description: Library name: Sample 16


title: W393-2,bHLH151-OE#17-2

description: Library name: Sample 17


title: W393-3,bHLH151-OE#17-3

description: Library name: Sample 18


title: M393-2,bhlh151-KO#40-2

description: Library name: Sample 14


title: time point 5, replicate 2 (treated)

description:
Library name: VDC3_2
column names match library name


title: W92-1,bHLH58-OE#20-1

description: Library name: Sample 10


title: MASH-4

description:
Library name: MASH-4
Singleron GEXSCOPE®


title: M92-3,bhlh58-KO#6-3

description: Library name: Sample 9


title: DHT

description:
Library name: Sample 2
10x Genomics

value: DHT


title: time point 4, replicate 6 (treated)

description:
Library name: EC2_6
column names match library name


title: Control

description:
Library name: Sample 1
10x Genomics

value: Vehicle (corn oil)


title: time point 4, replicate 7 (treated)

description:
Library name: EC2_7
column names match library name


title: M92-1,bhlh58-KO#6-1

description: Library name: Sample 7


title: time point 4, replicate 5 (treated)

description:
Library name: EC2_5
column names match library name


title: DM-3,bhlh58/151-KO#32-3

description: Library name: Sample 6


title: DM-2,bhlh58/151-KO#32-2

description: Library name: Sample 5


title: time point 4, replicate 4 (treated)

description:
Library name: EC2_4
column names match library name


title: CirculatingExTRM_rep2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description: Library name: RNA_CirculatingExTRM_rep2

data_processing:
Raw ATAC-seq and RNA-seq reads were trimmed using Trim Galore (v0.6.7) to remove adapters and low-quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (NCBI build 38, mm10) using HISAT2 (v2.2.1).
Aligned reads were sorted and indexed with SAMtools (v1.15).
For ATAC-seq, peaks were called using MACS2 (v2.2.7.1) with FDR = 0.01, window size = 300, and gapsize = 300.
HOMER (v4.11) was used to generate tag directories and annotate peaks to the nearest promoter (annotatePeaks.pl).
HOMER (v4.11) was used to generate tag directories and annotate peaks to the nearest promoter (annotatePeaks.pl).
For RNA-seq, gene-level quantification was performed using StringTie (v3.0.1) with TPM and FPKM normalization.
Assembly: Mus musculus genome, NCBI build 38 (mm10).
Supplementary files format and content: Processed ATAC-seq data include normalized BigWig coverage tracks and peak BED files. Processed RNA-seq data include FPKM expression tables generated by StringTie. Raw sequencing data for both assays are provided as compressed FASTQ files (paired-end reads).

source_name: Lung

growth_protocol: Mice were maintained under specific pathogen-free conditions with a 12-hour light/dark cycle and were provided with food and water ad libitum.

extract_protocol:
At designated time points (day 49 or day 71 after transfer), circulating ex-TRM cells were isolated from peripheral blood, and tissue TRM and TCIRC cells were sorted from lungs using flow cytometry based on CD45.1/CD45.2, Ly5.1/Ly5.2, and CD69 expression. Sorted cells (3,000–50,000 per population) were pelleted and processed for nuclei isolation using lysis buffer prior to transposition (ATAC-seq) or RNA extraction (RNA-seq).
For ATAC-seq, nuclei were subjected to transposition using the Illumina Tn5 transposase (15027865, 15027866) in a 40 µL reaction for 30 min at 37 °C with shaking. Fragmented DNA was purified with a QIAGEN MinElute kit and PCR-amplified for 11–12 cycles. For RNA-seq, total RNA was extracted from sorted cells and converted into cDNA libraries using a strand-specific RNA-seq kit following the manufacturer’s instructions. All libraries were sequenced on an Illumina NextSeq 500/550 platform with 50-cycle paired-end reads.

treatment_protocol: Recipient C57BL/6 (Ly5.2) or BALB/c-nu/nu mice were sensitized intranasally with OVA to induce allergic airway inflammation. Effector Th2 cells derived from OT-II creER^T2 or DO11.10 TCR transgenic mice were transferred intravenously. Tamoxifen was administered intraperitoneally to induce Cre-mediated recombination, and OVA rechallenge was performed as indicated.

value: Lung

value: CD4+ Tcell

value: 6-10 weeks old

value: female

tag: host strain

value: Balb/c


title: DM-1,bhlh58/151-KO#32-1

description: Library name: Sample 4


title: time point 4, replicate 3 (treated)

description:
Library name: EC2_3
column names match library name


title: WT-3,Wild type (84K)-3

description: Library name: Sample 3

value: Wild type (84K)


title: WT-1,Wild type (84K)-1

description: Library name: Sample 1


title: time point 4, replicate 1 (treated)

description:
Library name: EC2_1
column names match library name


title: CirculatingExTRM_rep1

description: Library name: RNA_CirculatingExTRM_rep1


title: time point 4, replicate 2 (treated)

description:
Library name: EC2_2
column names match library name


title: WT-2,Wild type (84K)-2

description: Library name: Sample 2


title: CirculatingExTcirc_rep2

description: Library name: RNA_CirculatingExTcirc_rep2


title: TissueExTRM_rep1

description: Library name: RNA_TissueExTRM_rep1