title: A375, si-FOSL1, #2

description: Library name: S11_A375-siFOSL1-5

data_processing:
RNAseq: Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1). Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a). Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30. Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Cut&Run:  Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1) (34). Processed raw reads were then aligned to human genome GRCh38 using BOWTIE2 (v2.4.1). Peak Calling was performed to identify regions of open chromatin using MACS2 (v 2.1.1.20160309). Only peaks significantly enriched over background with q <0.01 were considered confident and subjected to downstream analysis. Peaks were annotated by ChIPseeker (v1.32.1) with gene model TxDb.Hsapiens.UCSC.hg38.knownGene (v 3.15.0). Consensus peak identifiers were obtained by GenomicRanges (v1.48.0). Peaks were then normalized and differential enrichment between experimental groups evaluated using DEseq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: text file, raw reads count data

value: siRNAs targeting human FRA1


title: Fasted Male Control-3

status: Public on Jul 30 2025

type: SRA

city: Lexington

first: Robert

middle: N

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

country: USA

institute: University of Kentucky

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogenes methods
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Assembly: mm39
Supplementary files format and content: xls files include RPKM and total counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated from livers using the Qiagen Rneasy Mini kit. Novogene isolated mRNA from the total RNA provided by the investigators using poly-T oligo-attached magnetic beads.
mRNA libraries were constructed by Novogene using random hexamers and dUTP. The library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, following Novogenes methods.

tag: tissue

value: Liver

tag: Sex

value: Male

tag: genotype

value: Control

tag: treatment

value: HFD-fed for 12-weeks; Fasted at necropsy


title: IR64, leaf, severe drought, Day 6, rep 1

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

description:
Library name: IRLS6D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6D1

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

molecule: polyA RNA

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were surface sterilized with 375 ppm of pefurazoate at 15°C for 24 h. Then the seeds were soaked in water to germinate in a dark place at 30°C for two days. The calcined clay (Profile Greens Grade, PROFILE Products LLC, http://www.profileevs.com) was used as the soil. The soil was washed with water before use, then dried, filled in the pots (24.5 cm upper outer diameter, 20 cm lower outer diameter, 30 cm height; SP2530P, Tecs Inc., http://www.tecs.ne.jp) up to a depth of 25cm, and irrigated with modified Kimura B (Yoshida et al., 1976) culture solution (273.2 µM K2SO4, 546.9 µM MgSO4.7H2O, 182.0 µM NaH2PO4.2H2O, 182.3 µM CaCl2.2H2O, 182.4 µM CaSO4.2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg L-1 FeC6H5O7.nH2O [pH 5.5]). The germinated seeds were individually planted in separate pots, and they were cultivated in a growth chamber (Nippon Medical & Chemical Instruments Co., http://www.nihonika.co.jp) under a 14 h light/ 10 h dark photoperiod, with 50% relative humidity (R.H.) at daytime and 60% R.H. at nighttime. The temperature in the growth chamber was maintained at 25°C at nighttime and varied from 25°C to 30°C at daytime.  We used iPOTs (Numajiri et al. 2021), which is a pot that incorporates auto-irrigation system to mimic soil condition similar to the drought stress in the field. The water level in the supply pot, connected in parallel with the pots through a hose, was maintained at a height of 10 cm to ensure that the upper layers of the pots were moistened during the irrigation period.

extract_protocol:
The leaf samples were frozen in liquid nitrogen immediately after sampling, ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: In the moderate drought treatment, water supply from the supply pot was stopped on the 14 days after sowing, allowing water to drain from the inside of the pots through the hose. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf

tag: cultivar

value: severe drought

tag: days after_treatment

tag: replicate


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day15

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

library_source: genomic

data_processing:
NextFlow methylseq pipeline (https://nf-co.re/methylseq/), version 2.6.0 with default settings
Assembly: hg38 plus lambda phage and pUC19 spike-in controls
Supplementary files format and content: Methylation coverage (bismark output)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. Cells were harvested at each day from day 0 (hiPSC) to day 15.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Micro kit from hiPSCs and cells from the meiosis induction at various time points. For some of the samples, DDX4+ and DDX4- cells were sorted prior to extraction (see sample information). Libraries were prepared from 200 ng DNA using the NEB Enzymatic Methyl-Seq kit (NEB #E7120) following the manufacturer’s instructions. Briefly, control DNA (methylated pUC19 and unmethylated λ phage) was spiked into each sample. Next, samples were sheared to ~300 bp using a Covaris S2 sonicator. Enzymatic methyl conversion was performed, and libraries were amplified using unique dual index primers. For the pilot experiment, 2 x 150 bp paired end sequencing was performed on an Illumina MiSeq. For the follow-up experiment, 2 x 150 bp paired end sequencing was performed on an Illumina NovaSeq.
Methyl-seq (NEB enzymatic kit)

treatment_protocol: Samples in the pilot experiment were fixed cells, and samples in the follow-up experiment were unfixed cells.

tag: cell line

tag: cell type

value: Unsorted


title: A375, si-FOSL1, #1

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: S10_A375-siFOSL1-4

extract_protocol:
RNAseq: RNA extracted from A375 and 1205Lu cells was quantified with a Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA). Cut&Run: Cut&Run was performed with A375 and 1205Lu cells using CUTANA ChIC/CUT&RUN Kit version 4.0 (EpiCypher, Cat. # SKU: 14–1048). Briefly, 500,000 cells were collected and re-suspended in Wash Buffer and mixed with 10 μl activated ConA beads. 0.5 μg FRA1 antibody (Abcam, Cat. # ab252421) or 1 μl IgG antibody were added and incubated overnight at 4°C. Beads were washed twice in 200 μl Cell Permeabilization Buffer (CPB) prior to the addition of 2.5 μl CUTANA pAG-MNase in 50 μl of CPB per reaction. Beads were again washed twice in 200 μl CPB and suspended in 50 μl CPB. For chromatin digestion, 1 μl of 100 mM CaCl2 was added to activate the MNase. 33 μl of Stop Master Mix was added to terminate the MNase activity after 2h incubation at 4°C. To isolate DNA from the supernatant, 119 μl SPRlselect were added and incubated for 5 minutes at room temperature. SPRIselect beads were washed twice with 85% Ethanol and air-dried. To elute DNA, 17 μl of 0.1X TE Buffer were added.
RNAseq: The samples were then processed for RNA sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA). Briefly, 100 ng of RNA were used to generate cDNA and a strand-specific library following the manufacturer’s protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were normalized, denatured, and sequenced on the Illumina NovaSeq 6000 sequencer with the S1–200 reagent kit to generate approximately 60 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). Cut&Run:  Eluted DNA was quantified with the Qubit fluorometer, and 0.6 to 5 nanograms of enriched DNA was used for library preparation using the Kapa HyperPrep Kit (Roche, Cat. # 07962347001) following EpiCypher’s parameters for indexing PCR and library amplification as described in the CUT&RUN Library Prep Manual. The final libraries were Qubit quantitated and screened on the Agilent TapeStation D1000 ScreenTape (Agilent Technologies) to assess the fragment size distribution. Following final quantification using the Kapa Library Quantification Kit (Roche, Cat. # 07960140001), the libraries were sequenced on the NextSeq 500 using a Mid-output 150-cycle Kit in 2×50 configuration to generate 6–8 million read-pairs per sample (Illumina).

value: human melanoma cell


title: IR64, leaf, severe drought, Day 5, rep 2

description:
Library name: IRLS5D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5D2


title: IR64, leaf, severe drought, Day 6, rep 3

description:
Library name: IRLS6D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6D3


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day13


title: Duodenum tissue，CED3

city: Nanjing

first: Xiaohan

last: Jiang

state: Jiangsu

address: No. 300 guangzhou road, nanjing city, China

country: China

institute: Department of digestive endoscopy

description: All.DEG.Expression

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp  software.
Reference genome and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built using  Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference  genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to  each gene. And then FPKM of each gene was calculated based on the length  of the gene and reads count mapped to this gene.
(For DESeq2 with biological replicates) Differential expression analysis of  two conditions/groups (two biological replicates per condition) was performed  using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: Csv files with FPKM data.

source_name: duodenum tissue

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. 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. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

value: duodenum tissue

value: Celiac disease delayed-type hypersensitivity (DTH) mouse model with enhanced gluten stimulation


title: A375, si-NT, #3

description: Library name: S09_A375-siNT-6

value: non-targeting siRNAs


title: Duodenum tissue，CED2

description: All.DEG.Expression


title: IR64, leaf, severe drought, Day 5, rep 1

description:
Library name: IRLS5D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5D1


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day13


title: A375, FRA1 (CutRun), #1

description: Library name: S01_A375-FRA1-1

data_processing:
RNAseq: Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1). Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a). Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30. Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Cut&Run:  Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1) (34). Processed raw reads were then aligned to human genome GRCh38 using BOWTIE2 (v2.4.1). Peak Calling was performed to identify regions of open chromatin using MACS2 (v 2.1.1.20160309). Only peaks significantly enriched over background with q <0.01 were considered confident and subjected to downstream analysis. Peaks were annotated by ChIPseeker (v1.32.1) with gene model TxDb.Hsapiens.UCSC.hg38.knownGene (v 3.15.0). Consensus peak identifiers were obtained by GenomicRanges (v1.48.0). Peaks were then normalized and differential enrichment between experimental groups evaluated using DEseq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: text file, raw reads count data
Library strategy: CUT&Run


title: A375, si-NT, #2

description: Library name: S08_A375-siNT-5


title: Duodenum tissue，CED1

description: All.DEG.Expression


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day13


title: A375, si-NT, #1

description: Library name: S07_A375-siNT-4


title: A375, si-FOSL1, #3

description: Library name: S12_A375-siFOSL1-6


title: Duodenum tissue，CTR3

description: All.DEG.Expression

value: WT with non-enhanced gluten stimulation


title: 1205Lu, si-FOSL1, #3

description: Library name: S06_1205-siFOSL1-3


title: IR64, leaf, severe drought, Day 4, rep 3

description:
Library name: IRLS4D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4D3


title: Duodenum tissue，CTR2

description: All.DEG.Expression


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day11


title: 1205Lu, si-FOSL1, #2

description: Library name: S05_1205-siFOSL1-2


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day11


title: Duodenum tissue，CTR1

description: All.DEG.Expression


title: 1205Lu, si-FOSL1, #1

description: Library name: S04_1205-siFOSL1-1


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day11


title: CR_Input

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

description: CUT&RUN IGG Input

data_processing:
RNA Seq: QC by FASTQC, UMI extraction using UMI_Tools (discarding 6bp spacer per Takara's manual. Alignment to CAST/C57  N-Masked GRCm38 genomes using STAR "“--twopassMode Basic, --alignEndsType EndToEnd, --outSAMattributes NH HI NM MD". UMI Deduplication using UMI_Tools “—method=unique, --unpaired-reads=discard, --paired”. BAM files were then split into genomes using SNPSplit v0.3.4. BAM files were sorted using BAMtools v2.5.1, and read couts were quantified HTSeq-count v0.9.1 “—additional-attr=genename, -r pos, -t exon, -I gene_id, --stranded=reverse" and GRCm38.102.gtf.
CUT&RUN: Reads were analyzed using FASTQC and trimmed via Trimmomatic. Trimmed reads were aligned to the N-masked C57/CAST genome (mm10) using Bowtiw2 with "--local. -N 1" and paired-end unout. Aligned reads were converted to BAM, sorted and deduplicated using SAMtools v1.11.  SNPsplit was used to isolate paternal and maternal reads with the “—paired” flag.  Peaks were called on split bam files using MACS2 with “-g mm -f BAMPE –nomodel –shift -160 –extsize 150  --broad” settings for H3K9me3, with IgG as an input control. Samples were run with their phased input control. Files were lifted-over to mm39 for visualization and analysis.
Assembly: mm10 for alignment. Mm39 liftover for CUT&RUN.
Supplementary files format and content: BED File containing peaks for CUT&RUN data. HTSeq files containing read counts per transcript per genotype.

extract_protocol:
RNA: RNeasy micro kit (Qiagen, 74004) standard cell culture RNA protocol with DNase digestion. CUT&RUN: Per EpiCypher CUTANA CUT&RUN kit (14-1048, v3.1)
RNA: the Takara SMARTer® Stranded Total RNA-seq Kit v3- Pico Input Mammalian, Takara Biosciences, 634485. CUT&RUN: EpiCypher CUTANA CUT&RUN kit (14-1048, v3.1)

tag: strain

value: CAST/Eij x C47BL/6J

value: Trophoblast Stem Cells

value: WT

tag: antibody

value: CUTANA Kit Rabbit IgG Negative Control Antibody, 13-0042


title: IR64, leaf, severe drought, Day 3, rep 3

description:
Library name: IRLS3D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3D3


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day9


title: 1205Lu, si-NT, #3

description: Library name: S03_1205-siNT-3


title: CR_2

description: CUT&RUN


title: IR64, leaf, severe drought, Day 2, rep 3

description:
Library name: IRLS2D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2D3


title: IR64, leaf, severe drought, Day 3, rep 1

description:
Library name: IRLS3D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3D1


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day9


title: 1205Lu, si-NT, #2

description: Library name: S02_1205-siNT-2


title: IR64, leaf, severe drought, Day 4, rep 2

description:
Library name: IRLS4D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4D2


title: 1205Lu, si-NT, #1

description: Library name: S01_1205-siNT-1


title: CR_1

description: CUT&RUN


title: RNA_3


title: IR64, leaf, severe drought, Day 2, rep 2

description:
Library name: IRLS2D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2D2


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day9


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day7


title: 126-3211E_1

city: CHAPEL HILL

first: Xuejun

last: Sun

state: NC

address: Booker Creek Apts, 2525 Booker Creek Rd Apt 15F

department: Biostatistics

institute: University of North Carolina Chapel Hill

description: Library name: sample 23

data_processing:
Data were processed into FASTQ files and analyzed using the EdgeSeq parser software (HTG Molecular Diagnostics, Inc.)
Assembly: hg38
Supplementary files format and content: processed data in csv format, each row represents one gene and each column represents one sample

source_name: Endometrial tissue

extract_protocol: miRNAs were isolated using HTG EdgeSeq reagents and libraries synthesized in the HTSF at the University of North Carolina. Barcodes samples were pooled, and sequencing was performed on an Illumina NextSeq 500 platform (75 cycles, High Output v2 kit).

value: Endometrial tissue

tag: batch

tag: infection group

value: Endo- Uninfected


title: RNA_2


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day7


title: IR64, leaf, severe drought, Day 2, rep 1

description:
Library name: IRLS2D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2D1


title: 126-3160E_1

description: Library name: sample22


title: IR64, leaf, severe drought, Day 1, rep 3

description:
Library name: IRLS1D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1D3


title: IR64, leaf, severe drought, Day 3, rep 2

description:
Library name: IRLS3D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3D2


title: 126-3158E_1

description: Library name: sample21


title: RNA_1


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day7


title: IR64, leaf, severe drought, Day 1, rep 2

description:
Library name: IRLS1D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1D2


title: H2axfl/flCre+ (neuronKO) + Saline, rep2

city: Toulouse Cedex 3

first: Nicolas

last: Blanchard

address: CHU Purpan BP3028

department: Inserm UMR1291

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (Infinity)

data_processing:
Raw sequencing reads were processed using the nf-core RNAseq pipeline v.3.9
Read are trimmed using Trimgalore v.0.6.7.
rRNAs are filtered out using SortMeRNA v.4.3.4.
Reads are aligned to the Mus musculus GRCm39 genome assembly and the annotation from Ensembl7 release 107 using STAR v.2.7.10a.
Assembly: GRCm39 v107
Supplementary files format and content: raw.counts.tsv : tab delimited raw counts
Supplementary files format and content: tpm.counts.tsv : tab-delimited trancript-per-million counts

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
After sorting, neuronal nuclei were centrifuged at 1000 g for 7 min at 4°C and pellet was resuspended in RLT buffer (Qiagen) supplemented with 1% (vol/vol) β-mercaptoethanol (final concentration 143mM, Sigma). Samples were homogenized through QiaShredder columns (Qiagen) and stored at -80°C until processing. Bulk nuclear RNA extraction was performed using RNeasy Micro Kit (Qiagen) following manufacturer’s instructions.
RNA concentration was quantified using Qubit RNA HS Assay Kit on a Qubit Fluorometer (Invitrogen). The quality was evaluated on an Agilent 4150 TapeStation with the High Sensibility RNA ScreenTape kit (Agilent). Libraries were then produced using the llumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina), according to the manufacturer’s instructions, including a few modifications. Ribosomal RNA (rRNA) and mitochondrial ribosomal RNA were depleted using DNA probes that bind to rRNA targets, both of which are enzymatically digested. The remaining RNAs were fragmented for 4 min and reverse transcribed into cDNA, retaining the strand orientation information. The fragments were indexed and amplified by PCR. The libraries were quantified using the Qubit 1X dsDNA HS kit on the Qubit Fluorometer (Invitrogen), and evaluated on an Agilent 4150 TapeStation with the High Sensitivity D5000 Kit (Agilent).

treatment_protocol: Osmotic minipump implantation.  Mouse recombinant IL-1 (Immunotools GmbH, Germany) was dissolved in sterile saline solution (0.9% NaCl) containing 0.1% Bovine serum albumin as a carrier. Mice were implanted subcutaneously (s.c) in the interscapular region with osmotic minipumps (model AZT2004, Alzet, Charles River). Minipumps were filled with saline (saline + carrier) or IL-1 solution per the manufacturer's instructions. Model 2004 minipumps delivered fluid at a rate of 0.25 L/h for up to 35 days. Concentration of IL-1 in each minipump was calculated to infuse 5 g. kg-1. day-1 7. After 24h of priming in saline solution at 37°C, minipumps were surgically implanted in mice anesthetized with Avertin (tribromoethanol, 250 mg. kg-1, AlphaAesar, Merck). S.c. injections of 0.05 mg. kg-1 of Buprenorphine (AnimalCare) were used perioperatively to prevent pain during the recovery of the mice. Two (2) weeks post-implantation, to prevent minipump expulsion, mice were lightly anesthetized with 4% Isoflurane, potential skin adherences at the tip of the pumps were disconnected and a surgical clip (Reflex clip 9 mm, WPI) was placed instead.

value: hippocampus

value: neuronal nuclei

value: fl/flCre+

value: saline


title: 126-3150E_1

description: Library name: sample20


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day6


title: H2axfl/flCre- + Saline, rep1

value: fl/flCre-


title: IR64, leaf, severe drought, Day 1, rep 1

description:
Library name: IRLS1D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1D1

value: leaf

value: severe drought


title: 126-3149E_1

description: Library name: sample19


title: H2axfl/flCre- + IL-1β, rep1


title: 126-3142E_1

description: Library name: sample18


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day6

value: Unsorted


title: H2axfl/flCre+ (neuronKO) + IL-1β, rep4


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day5


title: H2axfl/flCre- + IL-1β, rep3


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day5


title: IR64, leaf, control (severe drought), Day 12, rep 3

description:
Library name: IRLS12C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12C3

value: control (severe drought)


title: 126-3109E_1

description: Library name: sample16


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day5


title: IR64, leaf, severe drought, Day 0, rep 2

description:
Library name: IRLS0D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0D2


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day6


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day4


title: H2axfl/flCre+ (neuronKO) + Saline, rep1


title: 126-3035E_1

description: Library name: sample15


title: H2axfl/flCre+ (neuronKO) + IL-1β, rep3


title: IR64, leaf, control (severe drought), Day 12, rep 1

description:
Library name: IRLS12C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12C1


title: IR64, leaf, severe drought, Day 0, rep 3

description:
Library name: IRLS0D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0D3


title: 126-3103E_1

description: Library name: sample13

value: Endo- Cervix


title: IR64, leaf, severe drought, Day 0, rep 1

description:
Library name: IRLS0D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0D1


title: H2axfl/flCre+ (neuronKO) + Saline, rep3


title: H2axfl/flCre+ (neuronKO) + IL-1β, rep1


title: IR64, leaf, control (severe drought), Day 11, rep 3

description:
Library name: IRLS11C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11C3


title: 126-3094E_1

description: Library name: sample12


title: IR64, leaf, control (severe drought), Day 11, rep 2

description:
Library name: IRLS11C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11C2


title: H2axfl/flCre- + Saline, rep2


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day4


title: 126-3067E_1

description: Library name: sample11


title: H2axfl/flCre- + IL-1β, rep2


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day3


title: IR64, leaf, control (severe drought), Day 11, rep 1

description:
Library name: IRLS11C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11C1


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day3


title: H2axfl/flCre+ (neuronKO) + IL-1β, rep2


title: 126-3050E_1

description: Library name: sample10


title: IR64, leaf, control (severe drought), Day 10, rep 3

description:
Library name: IRLS10C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10C3


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day3


title: IR64, leaf, control (severe drought), Day 12, rep 2

description:
Library name: IRLS12C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12C2


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day2


title: 126-3181E_1

description: Library name: sample8

value: Endo+


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day4


title: IR64, leaf, control (severe drought), Day 10, rep 2

description:
Library name: IRLS10C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10C2


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day2


title: hippocampus, encephalitis rep 2

data_processing:
For differentially expressed gene analyses, raw sequencing reads were processed using nf-core/rnaseq pipeline (v3.2) 12,13. Briefly, quality of raw sequencing files was checked using fastqc (v.0.11.9) [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/], reads were trimmed using trimgalore (v.0.6.6) [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] to remove Illumina universal adapter sequences. Quality of trimmed reads was assessed using fastqc (v.0.11.9) and indicated complete removal of adapter sequences. Trimmed reads were aligned to GRCm39 mouse genome reference assembly and genome annotation from Ensembl (mm39, release 103) using STAR (v.2.6.1d) 14 and read quantification was performed using salmon (v.1.4.0) 15. Exploration and differential expression analysis of RNAseq data was performed using R [https://www.R-project.org/] (v.4.1.3) / RStudio (v.202202.0, build 443) and DESeq2 R package (v1.34.0) 16 using a custom script. Salmon transcript-abundance estimates were imported using the tximport R package (v 1.22.0) 17 and summarized at the gene level using the ‘salmon_tx2gene’ file generated by nfcore/rnaseq pipeline. Raw count matrix was filtered to remove lowly expressed genes. Genes having a minimum of 10 normalized reads in 3 of the 4 replicates in any of the Uninfected, Latency or Encephalitis samples were kept. Principal component analyses and hierarchical clustering using variance-stabilized normalized counts indicated that samples clustered together according to their group. Differential expression analyses were performed using DESq2::DESeq() function and extracted using DESq2::results() function with a ‘lfcThreshold’ parameter of 1 and an ‘alpha’ parameter of 0.05 (i.e. adjusted p-value ≤ 0.05). Functional enrichment analyses were performed using clusterProfiler (v 4.2.2) 18 R packages.
Assembly: GRCm39 mouse genome reference assembly and genome annotation from Ensembl (mm39, release 103)
Supplementary files format and content: filetype .xlsx: unfiltered normalized and raw count matrices, and variance-stabilized normalized count matrix
Supplementary files format and content: filetype .xlsx: variance-stabilized normalized count matrix

extract_protocol:
Microdissected hippocampi were disrupted with ultra-turrax® in ice-cold QIAzol Lysis Reagent (Qiagen). Total RNA was purified with RNeasy Lipid Tissue Mini Kit (Qiagen).
Libraries were generated with the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and the IDT ILMN RNA UDI B Lig 96 Idx 96 Spl index kit (Illumina) following the manufacturer’s instructions. Briefly, RNA quantity was normalized, ribosomal RNA was depleted then RNA was fragmented and denatured. After cDNA synthesis, anchors were ligated and libraries were amplified.

treatment_protocol: Intraperitoneal (i.p.) injection with 200 Pru-derived tachyzoites (Pru.SAG1-OVA leading to encephalitis, or Pru.GRA6-OVA leading to latency) in 200 µL of PBS, or with 200 µL of PBS only for the uninfected group.

value: infection Pru.SAG1-OVA


title: hippocampus, encephalitis rep 3


title: IR64, leaf, control (severe drought), Day 9, rep 3

description:
Library name: IRLS9C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9C3


title: hippocampus, encephalitis rep 4


title: 126-3105E_1

description: Library name: sample7


title: hippocampus, encephalitis rep 1


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day2


title: IR64, leaf, control (severe drought), Day 9, rep 2

description:
Library name: IRLS9C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9C2


title: 126-3077E_1

description: Library name: sample5


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day1


title: IR64, leaf, control (severe drought), Day 9, rep 1

description:
Library name: IRLS9C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9C1


title: hippocampus, latency rep 4

value: infection Pru.GRA6-OVA


title: 126-3190E_1

description: Library name: sample9


title: IR64, leaf, control (severe drought), Day 8, rep 3

description:
Library name: IRLS8C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8C3


title: 126-1149E_1

description: Library name: sample4


title: hippocampus, latency rep 3


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day1


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day1


title: 126-1114E_1

description: Library name: sample3


title: IR64, leaf, control (severe drought), Day 10, rep 1

description:
Library name: IRLS10C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10C1


title: 126-3095E_1

description: Library name: sample6


title: hippocampus, latency rep 2


title: 126-1109E_1

description: Library name: sample2


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,hiPSC

value: hiPSC


title: IR64, leaf, control (severe drought), Day 8, rep 2

description:
Library name: IRLS8C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8C2


title: IR64, leaf, control (severe drought), Day 8, rep 1

description:
Library name: IRLS8C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8C1


title: hippocampus, uninfected rep 4

value: PBS


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,hiPSC


title: IR64, leaf, control (severe drought), Day 7, rep 3

description:
Library name: IRLS7C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7C3


title: hippocampus, latency rep 1


title: 126-1101E_1

description: Library name: sample1

value: Endometrial tissue


title: CAR37_AZD5991_Mouse1_Mixed_Plate2

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

description: Library name: AZD5991_CAR37_EP1_Plate2

library_source: transcriptomic single cell

data_processing:
Reads were demultiplexed (bcl2fastq v2.20), trimmed (trimmomatic v0.36), and aligned to the hg19 reference human genome using STAR aligner (2.5.2b). HTSeq (0.9.1) read counts were used as input to generate a Seurat object in R. Cells with more than 30% mitochondrial DNA (mtDNA) and less than 200 genes expressed (nFeature) were excluded from the analysis. Reads were normalized (NormalizeData) and scaled (ScaleData) using Seurat in R. Number of genes expressed, number of read counts, and mtDNA percentage were regressed out.
Assembly: hg19
Supplementary files format and content: HTSeq Matrix: All.DESeq2_RawCount_matrix.txt

source_name: Spleen - PDX

extract_protocol:
Single cells were sorted into a 96-well plate with each well containing 1% 2-mercaptoethanol and 10 µL of TCL buffer (Qiagen). RNA purification was performed using RNA-SPRI beads (Beckman) prior to cDNA synthesis.
Full-length single cell RNA-Seq libraries were prepared using the Smart-Seq2 protocol. Single cells were sorted into a 96-well plate with each well containing 1% 2-mercaptoethanol and 10 µL of TCL buffer (Qiagen). RNA purification was performed using RNA-SPRI beads (Beckman) prior to cDNA synthesis. RNA was reverse-transcribed using Maxima RNAse H-minus (ThermoFisher) in the presence of biotinylated oligo-dT30VN (/5BiosG/ AAGCAGTGGTATCAACGCAGAGTACT(30)VN), biotinylated template-switching oligonucleotides (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACATrGrG+G), and betaine. cDNA amplification was performed using 2x KAPA HiFi Hotstart Ready Mix (Roche) and biotinylated ISPCR primers (/5BiosG/ AAGCAGTGGTATCAACGCAGAGT). Tagmentation was performed on 0.15 ng of amplified cDNA using the Nextera XT kit (Illumina) and amplified with Nextera indexes. Smart-Seq2 libraries were sequenced paired-end on an Illumina NextSeq500 sequencer.

treatment_protocol: Splenic cells were harvested from DFTL-69579 engrafted mice on treatment day 14 from the vehicle and CAR-37 cohorts and on treatment day 15 from the AZD5991 and CAR-37+AZD5991 cohorts within 1 hour of receiving the final AZD5991 dose. Cells were stained with antibodies against human CD45, EGFR, and CD5. Cells were stained with DAPI to gate on viability. Tumor cells were gated as CD45+, CD5+, EGFR-. CART T cells were gated as CD45+, CD5+, EGFR+. Mixed plats/cells were gated as CD45+ and CD5+ and were later differentiated as tumor or CAR T cells during analysis. Single cells were sorted into 96-well plates using a Sony SH800, immediately centrifuged, and stored at -80°C until library preparation.

value: Spleen - PDX

value: Cell

value: Mixed


title: Fasted Male LKO-1

value: Liver

value: Male

value: CPT1a LKO

value: HFD-fed for 12-weeks; Fasted at necropsy


title: IR64, leaf, control (severe drought), Day 7, rep 2

description:
Library name: IRLS7C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7C2

value: leaf


title: pilot_ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,hiPSC

value: Unsorted


title: Microbiota of Breast from subject Patient_9 [DM71]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Breast
DM71

data_processing:
demultiplexing from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
ASV generation qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 225 --p-trunc-len-r 215 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
host read decontamination bowtie2 -x GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV.fasta -S bowtie2_SAM_output.txt -f -p 4 2> percentuals_aligned_bowtie2.txt
taxonomic assignment qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads decontaminated_rep-seqs.qza --o-classification taxonomy.qza
further analyses R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: SILVA 138 (16S database)
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence (already decontaminated through Bowtie2)
Supplementary files format and content: feature_abundance_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: paired-end (2x300) amplicon sequencing

source_name: Breast

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Breast

tag: patient id

tag: condition

value: Healthy

tag: city

value: Rural

tag: cancer grade

value: II

tag: chemotherapy

value: yes


title: IR64, leaf, control (severe drought), Day 7, rep 1

description:
Library name: IRLS7C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7C1

tag: tissue

value: control (severe drought)


title: hippocampus, uninfected rep 2

value: hippocampus

value: PBS


title: hippocampus, uninfected rep 3


title: CAR37_AZD5991_Mouse0_Mixed_Plate2

description: Library name: AZD5991_CAR37_EP0_Plate2

value: Spleen - PDX


title: CAR37_Mouse1_Tumor_Plate2

description: Library name: CAR37_EP1_Spleen_Tumor_Sort_Plate2

value: Cell

value: Tumor


title: hippocampus, uninfected rep 1


title: Microbiota of Breast from subject Patient_8 [DM70]

description:
16s rRNA v3-v4 sequencing of human Breast
DM70

value: III

value: no


title: IR64, leaf, control (severe drought), Day 6, rep 3

description:
Library name: IRLS6C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6C3


title: CAR37_AZD5991_Mouse3_Mixed_Plate2

description: Library name: AZD5991_CAR37_EP3_Plate2

value: Mixed


title: HDM, airway epithelium, adult

city: La Jolla

first: Xin

state: CA

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California, San Diego

description: scRNA-seq

data_processing:
For scRNA-seq, Cell Ranger (version 3.0.2) was used to initially align the raw reads onto the mouse reference genome (mm10) and generate the feature-barcode matrix. Next, R package Seurat (version 4.0) (Hao et al., 2021) was used to perform data quality control, normalization, scaling, principal components analysis (PCA) and the canonical correlation analysis (CCA) based data integration. Briefly, to filter out low-quality cells or doublets, cells with fewer than 200 or more than 4,000 unique features, or more than 15% mitochondrial contents were removed from further analysis. Then "LogNormalize" was used to normalize the feature expression. A total of 2,000 top variable features were identified by function FindVariableFeatures and kept for PCA. Top 20 significant components were chosen to conduct dimensional reduction by uniform manifold approximation and projection (UMAP) with default parameters. The expression features of marker genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: mouse mm10
Supplementary files format and content: For scRNA-seq, h5 files from cellranger.

growth_protocol: All mice were in B6 background or have been back crossed to B6 background for at least 3 generations. Littermates were used as controls in all experiments. All mice were housed in facilities accredited by American Association for Accreditation of Laboratory Animal Care (AAALAC) at University of California San Diego. All animal husbandry and experiments were approved by Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Following perfusion, lung were inflated with dissociation buffer (Collagenase/Dispase/DNAseI) and incubated at 37C for 30min in a shaking incubator. After washes, red blood cells were removed through RBC lysis buffer. Epithelial cells were isolated by magnetic bead sorting through removing CD45+ and CD31+ cells. Remaining cells were stained with Epcam (APC) antibody and DAPI was used to sort for live cells. tdTomato+, Epcam+ cells were sorted to enrich for PNEC population.
For scRNA, single cell libraries were generated from sorted epithelial cells by using Chromium Single Cell 3’ v3 kit (10X Genomics).

treatment_protocol: Tamoxifen dissolved in corn oil was administrated intraperitoneally at the dose of 50 mg/kg twice at post-natal stages. Saline or HDM was administered intranasally 4 times over the regimented course of 4 weeks. Mouse lungs were collected 24 hours the last dose.

tag: age

value: Adult, 12 weeks old

tag: genotype

value: Tamoxifen injection at P10, P12

tag: challenge

value: HDM


title: IR64, leaf, control (severe drought), Day 6, rep 2

description:
Library name: IRLS6C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6C2

value: leaf

tag: cultivar

tag: treatment

tag: days after_treatment


title: Microbiota of Breast from subject Patient_8 [DM52]

description:
16s rRNA v3-v4 sequencing of human Breast
DM52

value: Breast

value: Cancer


title: CAR37_AZD5991_Mouse1_CART_Plate3

description: Library name: AZD5991_CAR37_EP1_Plate3

tag: cell line

tag: cell type

value: CART


title: control saline, airway epithelium, adult

description: scRNA-seq

tag: strain

value: saline


title: IR64, leaf, control (severe drought), Day 6, rep 1

description:
Library name: IRLS6C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6C1

value: control (severe drought)

tag: replicate


title: Microbiota of Breast from subject Patient_7 [DM69]

description:
16s rRNA v3-v4 sequencing of human Breast
DM69

value: Healthy

value: Rural

value: II

value: yes


title: IR64, leaf, control (severe drought), Day 5, rep 3

description:
Library name: IRLS5C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5C3


title: CAR37_AZD5991_Mouse1_Mixed_Plate1

description: Library name: AZD5991_CAR37_EP1_Plate1

value: Spleen - PDX

value: Cell

tag: batch


title: Microbiota of Breast from subject Patient_6 [DM68]

description:
16s rRNA v3-v4 sequencing of human Breast
DM68

tag: patient id


title: CAR37_AZD5991_Mouse3_CART_Plate3

description: Library name: AZD5991_CAR37_EP3_Plate3


title: D10KOHC2

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end--very-sensitive--local--no-mixed--no-discordant--no-unal--phred33-I10-X700. Then, Sambamba was used to remove duplicate reads and samtools was used to sort the data. Peaks were called using MACS2 (v.2.2.7.1) with the following parameters: --SPMR--nomodel--extsize 200--keep-dup all--q 0.001. Reads that mapped to mitochondrial DNA or unassigned sequences were discarded. For paired-end sequencing data, only transformed into read coverage files (bigwig format) using deepTools with RPKM normalization. For the sample without repeats, differential binding region was analysis by manorm (v.1.3.0) with P-value <= 0.05.
Assembly: mm10
Supplementary files format and content: Fastq
Library strategy: CUT&Tag

source_name: OSKM D10

extract_protocol:
Around 100000 living cells were collected for each sample CUT&Tag library construction.
For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein, N259-YH01) was used. Around 1×105 living cells were collected for each sample, and the CUT&Tag library was sequenced on a illumina nova6000, carried out by CNGB.

value: OSKM D10

value: Tsc1 KO


title: Microbiota of Breast from subject Patient_6 [DM50]

description:
16s rRNA v3-v4 sequencing of human Breast
DM50

tag: condition


title: Microbiota of Breast from subject Patient_9 [DM53]

description:
16s rRNA v3-v4 sequencing of human Breast
DM53

tag: city


title: CAR37_AZD5991_Mouse3_Mixed_Plate1

description: Library name: AZD5991_CAR37_EP3_Plate1

value: Mixed


title: D10WTHC2

value: Tsc1 WT


title: IR64, leaf, control (severe drought), Day 5, rep 1

description:
Library name: IRLS5C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5C1


title: IR64, leaf, control (severe drought), Day 5, rep 2

description:
Library name: IRLS5C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5C2


title: Microbiota of Breast from subject Patient_5 [DM67]

description:
16s rRNA v3-v4 sequencing of human Breast
DM67

tag: cancer grade


title: CAR37_Mouse1_Tumor_Plate1

description: Library name: CAR37_EP1_Tumor_Plate1

value: Tumor


title: Microbiota of Breast from subject Patient_5 [DM49]

description:
16s rRNA v3-v4 sequencing of human Breast
DM49

tag: chemotherapy


title: D10WTT3


title: D5KOT3

source_name: OSKM D5

value: OSKM D5


title: IR64, leaf, control (severe drought), Day 4, rep 2

description:
Library name: IRLS4C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4C2

tag: tissue

value: leaf


title: CAR37_AZD5991_Mouse0_CART

description: Library name: AZD5991_CAR37_EP0_CART


title: Microbiota of Breast from subject Patient_4 [DM66]

description:
16s rRNA v3-v4 sequencing of human Breast
DM66

value: Breast


title: IR64, leaf, severe drought, Day 4, rep 1

description:
Library name: IRLS4D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4D1

value: severe drought


title: CAR37_AZD5991_Mouse0_Mixed_Plate1

description: Library name: A37_EP0_Plate1


title: IR64, leaf, control (severe drought), Day 4, rep 1

description:
Library name: IRLS4C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4C1


title: Microbiota of Breast from subject Patient_4 [DM48]

description:
16s rRNA v3-v4 sequencing of human Breast
DM48

value: Cancer


title: D5WTT3


title: IR64, leaf, control (severe drought), Day 3, rep 3

description:
Library name: IRLS3C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3C3

value: control (severe drought)


title: CAR37_Mouse1_CART_Plate3

description: Library name: CAR37_EP1_Plate3

value: CART


title: Microbiota of Breast from subject Patient_3 [DM65]

description:
16s rRNA v3-v4 sequencing of human Breast
DM65

value: Healthy

value: Urban

value: I


title: D10KOT3


title: AZD5991_Mouse1_Tumor_Plate1

description: Library name: AZD5991_EP1_Plate1

value: Spleen - PDX


title: IR64, leaf, control (severe drought), Day 3, rep 2

description:
Library name: IRLS3C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3C2


title: 3DMyc_rep2

city: Daejeon

first: RAMIN

last: SEO

country: South Korea

institute: Korean Advanced Institute of Science and Technology

description:
myc2
rescue_gene_count_matrix

data_processing:
HISAT2 aligned the trimmed reads to reference mouse genome
StringTie measured the gene expression in FPKM and TPM
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each sample

source_name: Pancreas

extract_protocol:
RNA was harvested using Tri Reagent (Invitrogen)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) following manufacturer's protocols

value: Pancreas

value: Pancreatic cancer cells

value: Myc overexpression/Cxcl5 knockout

value: culture media


title: IR64, leaf, control (severe drought), Day 4, rep 3

description:
Library name: IRLS4C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS4C3


title: 3DMyc_rep1

description:
myc1
rescue_gene_count_matrix


title: AZD5991_Mouse0_Tumor_Plate2

description: Library name: AZD5991_EP0_Plate2

value: Cell


title: 3DHif1a_rep3

description:
hif1a3
rescue_gene_count_matrix

value: mutant Hif1a overexpression/Cxcl5 knockout


title: CAR37_Mouse1_Mixed_Plate2

description: Library name: CAR37_EP1_Plate2

value: Mixed


title: Microbiota of Breast from subject Patient_17 [DM79]

description:
16s rRNA v3-v4 sequencing of human Breast
DM79

value: II

value: yes


title: AZD5991_Mouse0_Tumor_Plate1

description: Library name: AZD5991_EP0_Plate1

value: Tumor


title: Microbiota of Breast from subject Patient_2 [DM46]

description:
16s rRNA v3-v4 sequencing of human Breast
DM46

value: Breast

value: Cancer

value: Rural

value: III


title: IR64, leaf, control (severe drought), Day 2, rep 3

description:
Library name: IRLS2C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2C3

value: leaf

value: control (severe drought)


title: 3DHif1a_rep2

description:
hif1a2
rescue_gene_count_matrix


title: Microbiota of Breast from subject Patient_17 [DM61]

description:
16s rRNA v3-v4 sequencing of human Breast
DM61

value: Urban


title: IR64, leaf, control (severe drought), Day 2, rep 2

description:
Library name: IRLS2C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2C2


title: 3DHif1a_rep1

description:
hif1a1
rescue_gene_count_matrix

value: Pancreas


title: Microbiota of Breast from subject Patient_16 [DM78]

description:
16s rRNA v3-v4 sequencing of human Breast
DM78

value: Healthy


title: Vehicle_Mouse0_Tumor_Plate1

description: Library name: V0_PD_Plate1

value: Spleen - PDX

value: Vehicle


title: 3DMyc_rep3

description:
myc3
rescue_gene_count_matrix

value: Pancreatic cancer cells

value: Myc overexpression/Cxcl5 knockout

value: culture media


title: 2-3DKO_rep2

description:
3dko2
rescue_gene_count_matrix

value: Cxcl5 knockout


title: IR64, leaf, control (severe drought), Day 2, rep 1

description:
Library name: IRLS2C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS2C1


title: pAV-MAF_3

first: Shunya

last: Sadaki

address: 1-1-1 Tennodai

department: Anatomy and embryology

institute: University of Tsukuba

description: Library name: c3

data_processing:
CLC Genomics Workbench (Version 10.1.1; Qiagen, Hilden, Netherlands)
Assembly: hg19
Supplementary files format and content: Excel files include expression values normalized by quantile

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from human myotubes on day 4 of infection using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA).
The RNA-seq library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) after ribosomal RNA (rRNA) depletion (NEBNext rRNA Depletion Kit; New England Biolabs).

value: skeletal muscle

value: iPS cell-derived myotubes


title: Microbiota of Breast from subject Patient_2 [DM64]

description:
16s rRNA v3-v4 sequencing of human Breast
DM64

value: Breast

value: yes


title: IR64, leaf, control (severe drought), Day 3, rep 1

description:
Library name: IRLS3C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS3C1


title: Microbiota of Breast from subject Patient_15 [DM77]

description:
16s rRNA v3-v4 sequencing of human Breast
DM77

value: II


title: pAV-MAF_1

description: Library name: c1


title: 2-3DKO_rep1

description:
3dko1
rescue_gene_count_matrix


title: IR64, leaf, control (severe drought), Day 1, rep 2

description:
Library name: IRLS1C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1C2


title: pAV-MAF_2

description: Library name: c2


title: pAV-MAFB_3

description: Library name: b3


title: Microbiota of Breast from subject Patient_15 [DM59]

description:
16s rRNA v3-v4 sequencing of human Breast
DM59

value: Cancer


title: IR64, leaf, control (severe drought), Day 0, rep 3

description:
Library name: IRLS0C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0C3

value: leaf


title: IR64, leaf, control (severe drought), Day 1, rep 1

description:
Library name: IRLS1C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1C1

value: control (severe drought)


title: Microbiota of Breast from subject Patient_16 [DM60]

description:
16s rRNA v3-v4 sequencing of human Breast
DM60

value: Urban

value: III


title: Microbiota of Breast from subject Patient_14 [DM76]

description:
16s rRNA v3-v4 sequencing of human Breast
DM76

value: Healthy


title: pAV-MAFB_2

description: Library name: b2


title: 2-3DWT_rep2

description:
3dwt2
rescue_gene_count_matrix

value: Pancreas

value: WT


title: IR64, leaf, control (severe drought), Day 0, rep 2

description:
Library name: IRLS0C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0C2


title: Microbiota of Breast from subject Patient_14 [DM58]

description:
16s rRNA v3-v4 sequencing of human Breast
DM58


title: pAV-MAFB_1

description: Library name: b1


title: 3D KO_rep2

description:
d3_cxcl5_2
2D3D_Cxcl5_gene_count_matrix

value: Pancreatic cancer cells


title: 126-3117E_1

description: Library name: sample17

value: Endometrial tissue

tag: infection group

value: Endo- Uninfected


title: Microbiota of Breast from subject Patient_13 [DM75]

description:
16s rRNA v3-v4 sequencing of human Breast
DM75

value: Rural


title: IR64, leaf, control (severe drought), Day 1, rep 3

description:
Library name: IRLS1C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS1C3


title: 3D KO_rep1

description:
d3_cxcl5_1
2D3D_Cxcl5_gene_count_matrix

tag: genotype

value: Cxcl5 knockout

value: culture media


title: pAV-MAFA_3

description: Library name: a3

value: skeletal muscle

value: iPS cell-derived myotubes


title: IR64, leaf, moderate drought, Day 12, rep 3

description:
Library name: IRLM12D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12D3

value: moderate drought


title: Microbiota of Breast from subject Patient_13 [DM57]

description:
16s rRNA v3-v4 sequencing of human Breast
DM57

value: Breast

value: Cancer

value: II

value: yes


title: 3D WT_rep3

description:
d3_ctrl_3
2D3D_Cxcl5_gene_count_matrix


title: IR64, leaf, moderate drought, Day 12, rep 2

description:
Library name: IRLM12D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12D2

value: leaf


title: Microbiota of Breast from subject Patient_12 [DM74]

description:
16s rRNA v3-v4 sequencing of human Breast
DM74

value: Healthy

value: no


title: 3D WT_rep2

description:
d3_ctrl_2
2D3D_Cxcl5_gene_count_matrix

value: Pancreas

value: WT


title: 2-3DWT_rep1

description:
3dwt1
rescue_gene_count_matrix

value: Pancreatic cancer cells


title: pAV-MAFA_1

description: Library name: a1


title: Microbiota of Breast from subject Patient_12 [DM56]

description:
16s rRNA v3-v4 sequencing of human Breast
DM56


title: pAV-MAFA_2

description: Library name: a2


title: 3D KO_rep3

description:
d3_cxcl5_3
2D3D_Cxcl5_gene_count_matrix


title: IR64, leaf, moderate drought, Day 12, rep 1

description:
Library name: IRLM12D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12D1


title: IR64, leaf, moderate drought, Day 11, rep 3

description:
Library name: IRLM11D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11D3


title: pAV-mCherry_3

description: Library name: m3


title: 3D WT_rep1

description:
d3_ctrl_1
2D3D_Cxcl5_gene_count_matrix


title: pAV-mCherry_2

description: Library name: m2


title: 2D KO_rep3

description:
d2_cxcl5_3
2D3D_Cxcl5_gene_count_matrix


title: IR64, leaf, control (severe drought), Day 0, rep 1

description:
Library name: IRLS0C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS0C1

value: control (severe drought)


title: sample3-after, scRNAseq

first: yang

last: sun

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human with GRCh38 and mouse with mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagents were added
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: colon

value: Intestinal tissue single cell suspension

value: Epithelial cells, Stromal cells, Immune cells

value: after using SBJD


title: IR64, leaf, moderate drought, Day 11, rep 2

description:
Library name: IRLM11D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11D2


title: 2D KO_rep2

description:
d2_cxcl5_2
2D3D_Cxcl5_gene_count_matrix

value: Cxcl5 knockout

value: culture media


title: Microbiota of Breast from subject Patient_10 [DM72]

description:
16s rRNA v3-v4 sequencing of human Breast
DM72

value: Breast

value: Urban

value: III


title: IR64, leaf, moderate drought, Day 11, rep 1

description:
Library name: IRLM11D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11D1

value: moderate drought


title: IR64, leaf, moderate drought, Day 10, rep 3

description:
Library name: IRLM10D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10D3

value: leaf


title: 2D KO_rep1

description:
d2_cxcl5_1
2D3D_Cxcl5_gene_count_matrix


title: sample3-before, scRNAseq

description: 10x Genomics

value: before using SBJD


title: Microbiota of Breast from subject Patient_10 [DM54]

description:
16s rRNA v3-v4 sequencing of human Breast
DM54

value: Cancer

value: yes


title: 2D WT_rep3

description:
d2_ctrl_3
2D3D_Cxcl5_gene_count_matrix

value: Pancreas

value: WT


title: Microbiota of Breast from subject Patient_11 [DM55]

description:
16s rRNA v3-v4 sequencing of human Breast
DM55

value: I


title: 2D WT_rep2

description:
d2_ctrl_2
2D3D_Cxcl5_gene_count_matrix

value: Pancreatic cancer cells


title: sample1-after, scRNAseq

description: 10x Genomics

value: colon

value: Intestinal tissue single cell suspension


title: sample2-after, scRNAseq

description: 10x Genomics

value: Epithelial cells, Stromal cells, Immune cells

value: after using SBJD


title: IR64, leaf, moderate drought, Day 10, rep 2

description:
Library name: IRLM10D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10D2


title: Microbiota of Breast from subject Patient_1 [DM45]

description:
16s rRNA v3-v4 sequencing of human Breast
DM45

value: II


title: Microbiota of Breast from subject Patient_11 [DM73]

description:
16s rRNA v3-v4 sequencing of human Breast
DM73

value: Breast

value: Healthy


title: 2D WT_rep1

description:
d2_ctrl_1
2D3D_Cxcl5_gene_count_matrix

value: culture media


title: Microbiota of Breast from subject Patient_1 [DM63]

description:
16s rRNA v3-v4 sequencing of human Breast
DM63

value: Urban


title: sample2-before, scRNAseq

description: 10x Genomics


title: sample1-before, scRNAseq

description: 10x Genomics


title: HD30.c01w1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
Library name: HD30.c01w1
healthy donor HD30

data_processing:
Raw RNA-seq reads were aligned to the GRCh37 reference human genome using TopHat (v2.0.3). For paired-end data, only the first read was aligned. Mapped reads were then assembled to transcripts using Cufflinks. Assemblies were merged across all sequenced samples using Cuffmerge and FPKM values were used for downstream analyses
Assembly: GRCh37
Supplementary files format and content: FPKM values for genes across sample

source_name: PBMC

extract_protocol:
Peripheral blood samples (PBMC) were collected into CPT tubes (BD) at baseline and before each romidepsin intravenous infusion. RNA purification was carried out using TRI Reagent® (Molecular Research Center), as recommended, and controlled for quality using the Bioanalyzer (Agilent)
RNA-Seq was carried out on tru-seq and script libraries

value: PBMC

tag: subject status

value: healthy donor

tag: treatment cycle

tag: cycle week

value: control

tag: subject id


title: Panc02 spheroid, M1_rep3

description:
P-M1_3.gtf
M1_gene_count_matrix

tag: cell line

tag: treatment


title: IR64, leaf, moderate drought, Day 10, rep 1

description:
Library name: IRLM10D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10D1

value: leaf

tag: cultivar

value: moderate drought

tag: days after_treatment


title: HD31.c01w1

description:
Library name: HD31.c01w1
healthy donor HD31

value: romidepsin


title: IR64, leaf, moderate drought, Day 9, rep 1

description:
Library name: IRLM9D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9D1

tag: replicate


title: Panc02 spheroid, M1_rep2

description:
P-M1_2.gtf
M1_gene_count_matrix

value: Pancreas

tag: cell type

value: WT


title: Csnk2bTreg-/- mouse 5

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor B16.F10

extract_protocol:
-
RNA quality was assessed on a Bioanalyzer 2100 using a RNA 6000 Pico chip (both from Agilent, Santa Clara, CA). 2 ng of total RNA (integrity > 8) was used to generate full-length cDNA amplified  using SmartSeq V4 (Takarabio). Barcoded libraries have been generated using Nextera XT kit (Illumina). Library was quantified using the Qubit HS assay kit (Thermo Fisher) and the library size distribution was determined using the Bioanalyzer HS DNA assay (Agilent).

treatment_protocol: untreated

value: tumor B16.F10

value: CD4+Foxp3- T cells

value: KO

value: untreated


title: p4510.c03w1

description:
Library name: p4510.c03w1
CTCL patient p4510, treatment cycle 3, week 1

value: CTCL patient


title: pAV-mCherry_1

description: Library name: m1

value: skeletal muscle

value: iPS cell-derived myotubes


title: IR64, leaf, moderate drought, Day 8, rep 3

description:
Library name: IRLM8D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8D3

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

extract_protocol:
The leaf samples were frozen in liquid nitrogen immediately after sampling, ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.


title: 126-3201E_1

description: Library name: sample14

value: Endometrial tissue

tag: batch

value: Endo- Cervix


title: IR64, leaf, moderate drought, Day 8, rep 2

description:
Library name: IRLM8D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8D2


title: Panc02 spheroid, M0_rep3

description:
P-M0_3.gtf
M1_gene_count_matrix

value: Pancreatic cancer cells


title: p4510.c01w1

description:
Library name: p4510.c01w1
CTCL patient p4510, treatment cycle 1, week 1

value: PBMC


title: IR64, leaf, moderate drought, Day 9, rep 2

description:
Library name: IRLM9D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9D2


title: Csnk2bTreg-/- mouse 4


title: IR64, leaf, moderate drought, Day 9, rep 3

description:
Library name: IRLM9D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9D3


title: IR64, leaf, moderate drought, Day 8, rep 1

description:
Library name: IRLM8D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8D1


title: Panc02 spheroid, M0_rep2

description:
P-M0_2.gtf
M1_gene_count_matrix


title: IR64, leaf, moderate drought, Day 7, rep 3

description:
Library name: IRLM7D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7D3


title: p4510.c02w1

description:
Library name: p4510.c02w1
CTCL patient p4510, treatment cycle 2, week 1


title: Panc02 spheroid, M0_rep1

description:
P-M0_1.gtf
M1_gene_count_matrix


title: Panc02 spheroid, M1_rep1

description:
P-M1_1.gtf
M1_gene_count_matrix


title: Cebpa Fl/Fl, Spc-CreER, iSuReCre, Perinatal_2a (RNA-seq)

city: Rochester

first: Douglas

middle: Glenn

last: Brownfield

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
Library name: Cebpa_Floxed_sample2a
10x Genomics

data_processing:
Fastq files were generated using Cellranger v 7.2. The sequenced files were mapped to the GRCm38/mm10, supplemented with tdTomato, PhiMut, and WPRE transcripts as per the iSuRe-Cre construct
Assembly: GRCm38/mm10
Supplementary files format and content: tab-seperated values files and matrix files

source_name: perinatal mouse lung

extract_protocol:
Cells from PN25 SftpcCreER;iSuReCre;Cebpawt/fl and SftpcCreER;iSuReCre;Cebpafl/fl mice (2 weeks after TMX) were isolated and enriched (EpCAM+) as per protocol described below.
Single cell RNA sequencing was performed using the Chromium Single Cell 3’ system (10x Genomics) at the single cell sequencing core at Mayo Clinic according to manufacturer’s instruction (10x Genomics). Sequencing depth is an average of 75k reads per cell to detect lowly expressed genes.

treatment_protocol: Tamoxifen induce Cebpa deletion and lineage labeling

value: perinatal mouse lung

value: Alveolar type 2

value: Cebpa Fl/Fl, Spc-CreER, mTmG

tag: group

value: Experimental


title: IR64, leaf, moderate drought, Day 7, rep 2

first: Taiji

institute: National Agriculture and Food Research Organization

description:
Library name: IRLM7D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7D2

value: leaf

value: moderate drought


title: Csnk2bTreg-/- mouse 3

value: tumor B16.F10


title: Csnk2bfl/fl mouse 5

value: CD4+Foxp3- T cells

value: WT


title: IR64, leaf, moderate drought, Day 7, rep 1

description:
Library name: IRLM7D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7D1


title: Csnk2bTreg-/- mouse 2

value: KO

value: untreated


title: Csnk2bTreg-/- mouse 1


title: Cebpa WT/Fl, Spc-CreER, iSuReCre, Perinatal_1a (RNA-seq)

description:
Library name: Control_sample1a
10x Genomics

value: Cebpa WT/Fl, Spc-CreER, mTmG

value: Control


title: Csnk2bfl/fl mouse 4


title: Panc02 spheroid, ctrl_rep2

description:
P-C_2.gtf
M1_gene_count_matrix

value: Pancreas

value: control


title: Panc02 spheroid, ctrl_rep1

description:
P-C_1.gtf
M1_gene_count_matrix

value: Pancreatic cancer cells


title: IR64, leaf, moderate drought, Day 6, rep 3

description:
Library name: IRLM6D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6D3


title: Media control for PEA_MC8

type: RNA

city: Portland

first: Xiao

last: Shi

state: Oregon

address: 3181 SW Sam Jackson PK Rd

department: dept. of psychiatry

institute: Oregon Health and Science University

description: Media control

data_processing:
The data analysis were performed according to the manufacturers instructions using Expression Suit software:
For the normalization it uses the mean expression value of all expressed and qualified miRNAs (Calculated on the mean expression value sheet). The ΔCq value for a miRNA was calculated as: ΔCq = Cq value of the miRNA – mean normalizer Cq value in the same group.
Target miRNA signals normalized to vehicle control;ΔΔCq = ΔCq for treated samples – ΔCq for vehicle control samples.The fold change (relative quantification value) for each miRNA was calculated as: 2^ - ΔΔCq.
DeltadeltaCt based fold-change calculations from the raw threshold cycle data by using Excel
Matrix normalized worksheet reports normalized signal (against mean expression value). Media control was used to exclude miRNAs from serum sources and not used for normalization.
In fold Change worksheet, relative quantification value for each miRNA was calculated as: 2 ^- ΔΔCq.  ΔΔCq = ΔCq for treated samples – ΔCq for vehicle control samples.For statistics, we used unbiased robust procedures including matched-pairs estimators of the effect sizes and rank-based testing of associations in the interest of minimizing confounding of associations by technical causes, and then to further interrogate those results with extensive sensitivity analyses designed to probe the volatility of the conclusions depending on our choice of analytical methods.

label: FAM

source_name: Extracellular vesicle for culture media

label_protocol: PCR assays were performed using the TaqMan Low Density Arrays (4444913, ThermoFisher Scientific) following the Manufacturer’s instructions. RNA (with 8-10ng of miRNA measured by Qubit miRNA assay kit) was reverse transcribed using Megaplex RT primer human pool set V3.0 (4444750, ThermoFisher Scientific) and MultiScribe Reverse Transcriptase (4311235, ThermoFisher Scientific) according to the user guide. To increase the sensitivity of qPCR analysis for miRNA targets, cDNA was pre-amplified (14 cycles) with Megaplex PreAmp primers human pool set V3.0(4444748, ThermoFisher Scientific) before qPCR.

extract_protocol: Total RNA was extracted with MagMax mirVana total RNA isolation kit.

value: U2OS cell

tag: activation agent

value: media only

tag: time

value: 3 hour


title: Csnk2bfl/fl mouse 3

tag: tissue


title: Retina, PBS, scRNA-seq

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

institute: UNIST

description: 10x Genomics

data_processing:
Fastq files were mapped to the mouse reference (mm10). The initial quality control and the combined gene expression matrix were performed using Cell Ranger pipeline (version 7.0.1; 10X Genomics Chromium).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
The retinal cells were gently resuspended after being washed twice at 4°C for 5 minutes at 300g in cold Ca2+ and Mg2+ free 0.04 percent BSA/PBS. The samples were then counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) with acridine orange (AO) and propidium iodide (PI) staining (Logos Biosystems, cat no. F23001).
The 10x Chromium controller and Next Gem Single cell 3' Reagent v3.1 kits (10x genomics, PN-1000123) were used to prepare Single Cell RNA-seq libraries according to the 10x Chromium Single Cell 3' v3.1 protocol (10x Genomics, document no. CG000315). To generate single-cell Gel Bead-in-emulsion (GEM), the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip (10x genomics, PN-1000120). Poly-adenylated mRNA from single cells was uniquely barcoded and reverse-transcribed within GEM. After barcoded full-length cDNA was generated from mRNA through GEM-RT incubation, the barcoded cDNA molecules were amplified with PCR. For 3’ Gene Expression Library construction, the enriched cDNA was sequentially subjected to the enzymatic fragmentation, end-repair, A-tailing, adaptor ligation and index PCR.

value: Retina

tag: strain

tag: genetic modification

value: P23H Rho mutation

tag: age

value: 1-4 months old

value: intravitreal injection of PBS


title: IR64, leaf, moderate drought, Day 6, rep 2

city: Tsukuba

last: Kawakatsu

address: 3-1-3 Kan-nondai

description:
Library name: IRLM6D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6D2

value: leaf

value: moderate drought


title: Media control for PEA_MC7

description: Media control

value: 2 hour


title: Cebpa Fl/Fl, Spc-CreER, iSuReCre, Perinatal_2b (RNA-seq)

description:
Library name: Cebpa_Floxed_sample2b
10x Genomics

value: perinatal mouse lung

value: Alveolar type 2

tag: genotype

value: Cebpa Fl/Fl, Spc-CreER, mTmG

value: Experimental


title: Csnk2bfl/fl mouse 2

value: tumor B16.F10

value: CD4+Foxp3- T cells

value: WT

value: untreated


title: IR64, leaf, moderate drought, Day 6, rep 1

description:
Library name: IRLM6D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6D1


title: Media control for PEA_MC6

description: Media control

value: U2OS cell

value: media only

value: 1 hour


title: Retina, si-NRL, scRNA-seq

description: 10x Genomics

value: Retina

value: P23H Rho mutation

value: intravitreal injection of cp-asiNRL


title: Panc02 spheroid, ctrl_rep3

description:
P-C_3.gtf
M1_gene_count_matrix

value: Pancreas

value: Pancreatic cancer cells

value: control


title: Cebpa WT/Fl, Spc-CreER, iSuReCre, Perinatal_1b (RNA-seq)

description:
Library name: Control_sample1b
10x Genomics

value: perinatal mouse lung

value: Cebpa WT/Fl, Spc-CreER, mTmG

value: Control


title: Media control for PEA_MC4

description: Media control

value: 0 hour


title: Media control for PEA_MC5

description: Media control


title: sublibrary 16, batch 2, scRNAseq

city: Chapel Hill

first: Mark

last: Zylka

state: North Carolina

address: 116 Manning Drive, CB 7250, Unive7008B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

description: SPLiT-seq

data_processing:
Demultiplexing was done based on the index sequences (4th barcode in the SPLiT-seq library prep that marks each sublibrary) using bcl2fastq (Illumina).
Raw reads were filtered based on their quality using fastp and processed via Alevin-fry, which utilizes Salmon for parsing basic barcode and UMI and mapping of the reads to the constructed reference index. Barcode sequences (24 bp = three 8 bp barcode sequences) were extracted from R2 reads and R1 reads with unique molecular identifiers (UMIs) were pseudoaligned with structural constraints (“--sketch” option) to corresponding intronic or exonic reads in the splici (for spliced + intron) index assembled using a GENCODE M25 (GRCm38.p6) mouse reference genome. To filter cellular barcodes (CBs; 24 bp), the list of expected barcode sequences was given to Alevin-fry and only the barcodes that were within the hamming distance of 1 of the expected barcode sequences were retained.
The nucleus by gene matrix from Alevin-fry was imported to Seurat (v3.1.1) in R. To filter out low-quality nuclei, nuclei expressing fewer than 1000 UMIs or 500 genes were removed. Nuclei expressing greater than 10% mitochondrial transcripts were also removed. Genes were removed if they were not expressed in at least 30 nuclei. The filtered Seurat object was divided by each animal after assigning each nucleus to the corresponding animal based on the first 8 bp barcode sequences, and normalized using SCTransform 32. After normalization, all samples were merged and clustering and visualization of the merged dataset were performed using Uniform Manifold Approximation and Projection (UMAP), with the first 100 principal components (PCs) at a resolution of 2. The Seurat FindMarkers function was employed to discover genetic markers linked to distinct cellular subtypes. The classification of each cluster into specific cell types was achieved by utilizing the expression levels of well-established marker genes and by correlating our clusters to annotated cell clusters in other published datasets.
Assembly: GRCm38.p6
Supplementary files format and content: seuat object (.rds file)

source_name: Right cortical hemisphere

extract_protocol:
To isolate nuclei from brain tissue, the right cortical hemisphere was dissected and homogenized. Prior to tissue homogenization, the following buffers were made: NIM1, homogenization, and resuspension buffers. NIM1 buffer was made by mixing 1190 μl of distilled water, 250 μl of 1.5M sucrose, 37.5 μl of 1M KCL, 7.5 μl of 1M MgCl2, 15 μl of 1M Tris Buffer, pH 8.0. Homogenization buffer was made by mixing 960 μl of NIM1 buffer, 1 μl of 1M DTT (Thermo Fisher Scientific), 10 μl of 40 U/μl RNase inhibitor (Enzymatics), 10 μl of 20 U/μl SUPERase-in RNase inhibitor (Thermo Fisher Scientific), 10 μl of 20 mg/ml BSA and 10 μl of 10% Triton X-100. Resuspension buffer was made by mixing 990 μl of PBS, 1.25 μl of 40 U/μl RNase inhibitor (Enzymatics), 2.5 μl of 20 U/μl SUPERase-in RNase inhibitor (Thermo Fisher Scientific), 10 μl of 20 mg/ml BSA and 5 μl of 10% Tween. Tenbroeck tissue homogenizer (Bellco Glass) was cleaned with distilled water, 100% ethanol and then distilled water and submerged in homogenization buffer. The tissue was homogenized using Tenbroeck tissue homogenizer and further homogenized by pipetting up and down 10-15 times using wide-bore pipette tips. Lysate (1.0 mL) was transferred into a DNA LoBind 1.5 mL tube (Eppendorf) and mixed. Homogenates was passively filtered with a 40 μm strainer (Falcon) into a 15 mL tube and then centrifuged at 500 x g for 5 minutes at 4 °C. The supernatant was carefully aspirated and the nuclei were resuspended gently with wide-bore tip in 1.0 mL cold resuspension buffer. After centrifugation and aspiration of the supernatant, the nuclei suspension was passively filtered again with a 40 μm strainer into a 15 ml tube. The nuclei suspension was fixed on ice for 10 minutes by slowly adding 3.0 ml of 1.33% formaldehyde. After 10 minutes, 20 μl of 10% Tween was added to the suspension and centrifuged at 500 x g for 5 minutes at 4 °C. The supernatant was carefully aspirated and the nuclei were resuspended in 1.8 mL cold resuspension buffer. After counting the nuclei, 200 μl of DMSO was added to the suspension and the isolated nuclei suspension was stored in -80°C until the library preparation step.
Libraries from nuclei were prepared using the Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) method which utilizes a combinatorial barcoding technique to identify the cellular origin of RNA during snRNAseq analysis. 7,000 nuclei from each sample were used for library preparation. Cortical samples from a total of 92 CC mice were successfully processed. All libraries were pooled and sequenced on an Illumina NovaSeq 6000-S4.

value: Right cortical hemisphere

value: 13-14 weeks old

value: Brain cells

value: all 14 CC strains included


title: sublibrary 14, batch 2, scRNAseq

description: SPLiT-seq


title: sublibrary 15, batch 2, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 5, rep 2

description:
Library name: IRLM5D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5D2

source_name: leaf

value: leaf

value: moderate drought


title: vector only,MCF10A, 500ng/mL doxycycline,rep_2

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

institute: University at Albany - SUNY

description: Library name: deltaNp63_control_dox_2

data_processing:
For RNAseq, Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Assembly: ENSEMBL homo sapies v104 transcriptome release
Supplementary files format and content: tab-separated value files containing standardized ENSMBL gene name, gene length, estimated tag counts, and transcripts per million (TPM) values; output from Kallisto that was imported into DEseq2 via tximport.

source_name: mammary gland

growth_protocol: Human mammary epithelial cell line MCF10A was cultured in 1:1 Dulbecco’s Modified Eagle’s Medium: Ham’s F-12 (Gibco, #11330-032), supplemented with 5% Horse Serum, (Gibco, #16050-122), 20 ng/mL epidermal growth factor (Peprotech, #AF-100-15), 0.5 µg/mL hydrocortisone (Sigma, #H-0888), 100 ng/mL cholera toxin (Sigma, #C-8052), 10 µg/mL insulin (Sigma, #I-1882), and 1% penicillin-streptomycin (Gibco, #15240-062).

extract_protocol:
For RNAseq, Total RNA was extracted using Zymo Quick RNA miniprep. PolyA+ mRNA was extracted using oligo-d(T) beads before library construction.
RNAseq libraries were constructed from polyA+ RNA by Azenta/GeneWiz.

treatment_protocol: 500ng/mL doxycycline for 24hrs

value: mammary gland

value: WT

value: 500ng/mL doxycycline for 24hrs


title: vector only,MCF10A, 500ng/mL doxycycline,rep_3

description: Library name: deltaNp63_control_dox_3


title: Media control for PEA_MC3

description: Media control

value: U2OS cell

value: media only


title: sublibrary 13, batch 2, scRNAseq

description: SPLiT-seq


title: vector only,MCF10A, 500ng/mL doxycycline,rep_1

description: Library name: deltaNp63_control_dox_1


title: IR64, leaf, moderate drought, Day 4, rep 3

description:
Library name: IRLM4D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4D3


title: IR64, leaf, moderate drought, Day 5, rep 3

description:
Library name: IRLM5D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5D3


title: IR64, leaf, moderate drought, Day 5, rep 1

description:
Library name: IRLM5D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5D1


title: Media control for PEA_MC2

description: Media control


title: deltaNp63beta,MCF10A, 500ng/mL doxycycline,rep_3

description: Library name: deltaNp63_beta_dox_3


title: sublibrary 12, batch 2, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 4, rep 2

description:
Library name: IRLM4D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4D2


title: sublibrary 11, batch 2, scRNAseq

description: SPLiT-seq


title: deltaNp63beta,MCF10A, 500ng/mL doxycycline,rep_2

description: Library name: deltaNp63_beta_dox_2


title: IR64, leaf, moderate drought, Day 4, rep 1

description:
Library name: IRLM4D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4D1


title: Vehicle control for PEA_VC6

description: Vehicle control

value: water

value: 24 hours


title: deltaNp63beta,MCF10A, 500ng/mL doxycycline,rep_1

description: Library name: deltaNp63_beta_dox_1


title: sublibrary 10, batch 2, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 3, rep 3

description:
Library name: IRLM3D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3D3


title: sublibrary 9, batch 2, scRNAseq

description: SPLiT-seq


title: Csnk2bfl/fl mouse 1

value: tumor B16.F10

value: CD4+Foxp3- T cells

value: untreated


title: deltaNp63alpha,MCF10A, 500ng/mL doxycycline,rep_3

description: Library name: deltaNp63_alpha_dox_3


title: deltaNp63alpha,MCF10A, 500ng/mL doxycycline,rep_2

description: Library name: deltaNp63_alpha_dox_2


title: Vehicle control for PEA_VC2

description: Vehicle control


title: Vehicle control for PEA_VC4

description: Vehicle control


title: sublibrary 7, batch 1, scRNAseq

description: SPLiT-seq


title: Vehicle control for PEA_VC3

description: Vehicle control


title: IR64, leaf, moderate drought, Day 3, rep 2

description:
Library name: IRLM3D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3D2


title: sublibrary 8, batch 1, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 3, rep 1

description:
Library name: IRLM3D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3D1


title: Methyl Capture, EA4, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

city: Irvine

first: Farah

last: Rahmatpanah

address: Med  scie 1 RM C220

department: Pathology

institute: UCI

description: EA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv

data_processing:
Sequencing reads were aligned to reference genome using hg38 using Bowtie2 and deduplicated to remove PCR artifacts with Strand NGS 3.1
Peaks were identified with MACS2 version callpeak function using a band width of 300 bp and a false discovery rate of q < 0.05. No control sample was used for input. A consensus peakset was derived from the aligned reads of AA and EA prostate cancer stroma samples and AA and EA CAF samples that were sequenced. For stroma samples, a minimum threshold of five of thirty-two methylated samples were used for considering a region as methylated. For AA and EA CAFs before treatment, a minimum of one of seven samples were used. For all AA CAFs and EA CAFs before, during, and after treatment, a minimum of one of nine AA CAFs and one of twelve EA CAFs were used.
Assembly: GRCh38/hg38
Supplementary files format and content: Methyl capture consesus peaksets of each AA and EA TAS sample with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of AA CAF samples treated with 5AzaC at all time points with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of AA&EA CAF samples before treatment with 5AzaC with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of EA CAFs treated with 5AzaC at all time points with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Library strategy: methyl- captured DNA-Seq

source_name: Prostate

growth_protocol: Fresh prostatectomy tissue was examined to confirm the location of tumor and a 2-5 mm cube of tumor-adjacent stroma was removed. The tissues were placed in transport medium consisting of tissue culture medium without growth factors, placed on ice. Tissue specimens were cut into 2 mm pieces for digestion in a Sterilgard hood using sterile techniques. To ensure that tissue strips have been selected as tumor-adjacent stroma, largely free of other components, one face of the strip was removed with a scalpel and used for frozen section preparation. If further trimming was necessary, the tumor-stroma boundary was marked on the back of the frozen section slide under a microscope using a Pilot Ultrafine permanent fine point pen. The top of the slide was sterilized with an alcohol swab, dried, and the tissue strip was overlaid on the corresponding frozen section for manual trimming in the hood. Trimmed tissue was digested by collagenase Type I and Hyaluronidase Type II at 37ºC in the cell culture incubator. Cell suspensions were cultured in stroma cell selection media consisting of RPMI medium supplemented with 5% FCS, 1 nM testosterone and 10 ng/mL fibroblast growth factor, which selected for fibroblasts over succeeding passages. Frozen stocks of passages 1 to 5 primary cultures were prepared.

extract_protocol:
Tissue blocks were evaluated by a pathologist to identify the tumor adjacent stroma area from which gDNA could be extracted. The FFPE RNA/DNA Purification Plus Kit (Cat # 54300, Norgen Biotek Corp) was used to isolate total gDNA from patient specimens.
Genomic DNA is fragmented, quantified and assessed for quantity and quality using an Agilent 2100 Bioanalyzer and a Qubit fluorimeter, respectively. Fragmented gDNA is used to capture methylated DNAs (MethylCollectorTM Ultra, Active Motif, Cat # 55005). Methylated fractions are used to construct standard fragment libraries with Bio Scientific’s NEXTFLEX Rapid DNA-Seq Kit 2.0. For NGS, all methyl- captured DNA is sequenced at the University of California, Irvine genomic Core facility.
Bio Scientific’s NEXTFLEX Rapid DNA-Seq

treatment_protocol: At passage 5, a portion of the cells were placed in serum-free medium and incubating for 24 h. CAFs (n=7), all after passage 5, were cultured in the presence of PBS or low-dose (0.3µM). CAFs were treated with 5AzaC for 24 hours, followed by culture for 10 days in drug-free medium.

value: Prostate

tag: race

value: EA

tag: tumor stage

tag: primary gleason

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)

value: Post-5AzaC (10 day)

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%

tag: duplicated reads

value: Cancer Associated Fibroblast


title: Media control for PEA_MC1

description: Media control

tag: cell type

tag: activation agent

value: 0 hour


title: IR64, leaf, moderate drought, Day 2, rep 3

description:
Library name: IRLM2D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2D3

tag: tissue

value: leaf

tag: cultivar

tag: treatment

tag: days after_treatment

tag: replicate


title: sublibrary 5, batch 1, scRNAseq

description: SPLiT-seq

value: Right cortical hemisphere

tag: age

value: 13-14 weeks old

value: Brain cells

tag: genotype

value: all 14 CC strains included


title: Methyl Captue, EA4, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: race

tag: tumor stage

tag: primary gleason


title: IR64, leaf, moderate drought, Day 2, rep 2

description:
Library name: IRLM2D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2D2

value: moderate drought


title: PEA6

description: Test

value: U2OS cell

value: selective HRH1 agonist PEA (200uM)

tag: time


title: deltaNp63alpha,MCF10A, 500ng/mL doxycycline,rep_1

description: Library name: deltaNp63_alpha_dox_1

value: mammary gland

tag: cell line

value: WT

value: 500ng/mL doxycycline for 24hrs


title: sublibrary 4, batch 1, scRNAseq

description: SPLiT-seq


title: sublibrary 6, batch 1, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 1, rep 3

description:
Library name: IRLM1D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1D3


title: IR64, leaf, moderate drought, Day 2, rep 1

description:
Library name: IRLM2D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2D1


title: Methyl Capture, EA4, Cancer Associated Fibroblast, no 5AzaC treatment

description:
EA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv
CAF_-5AzaC_Cutoff_1_Consensus_Peakset_2024.tsv

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads


title: PEA5

description: Test

tag: cell type

tag: activation agent

value: 24 hours


title: Methyl Capture, EA3, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

tag: tissue

value: Prostate

tag: aligned reads/%

tag: duplicated reads


title: sublibrary3, batch 1, scRNAseq

description: SPLiT-seq

tag: age


title: IR64, leaf, moderate drought, Day 1, rep 2

description:
Library name: IRLM1D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1D2

tag: cultivar

tag: treatment

tag: days after_treatment

tag: replicate


title: PEA4

description: Test

tag: time


title: Methyl Captue, EA3, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: race

value: EA

tag: tumor stage

tag: primary gleason


title: Vehicle control for PEA_VC5

description: Vehicle control

value: water


title: Vehicle control for PEA_VC1

description: Vehicle control


title: sublibrary2, batch 1, scRNAseq

description: SPLiT-seq

tag: genotype


title: PEA3

description: Test


title: PEA1

description: Test


title: sublibrary1, batch 1, scRNAseq

description: SPLiT-seq


title: IR64, leaf, moderate drought, Day 0, rep 3

description:
Library name: IRLM0D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0D3


title: Methyl Capture, EA2, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)

value: Post-5AzaC (10 day)

tag: time to_relapse_since_last_f/u_(months)

value: Cancer Associated Fibroblast


title: Methyl Captue, EA2, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: tissue

tag: total #_of_reads

tag: cell type


title: IR64, leaf, moderate drought, Day 0, rep 1

description:
Library name: IRLM0D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0D1

value: leaf


title: Methyl Capture, EA3, Cancer Associated Fibroblast, no 5AzaC treatment

tag: age

tag: aligned reads/%

tag: duplicated reads


title: Media control for Wnt3a_MC5

description: Media Control

tag: activation agent

value: media only

value: 0 hour


title: Media control for Wnt3a_MC6

description: Media Control