title: Cortical neurons, shOpa1, shAtf4, Day 11, Rep5

first: Alexandre

last: Blais

institute: University of Ottawa

description: SP flowcell PE50

data_processing:
fastq files were verified with multiQC.
Sequencing adaptors were trimmed and duplicates were removed.
ATAC peaks were called using MACS2.
Bigwig files were generated using bamCoverage for data visualization.
Assembly: mm10
Supplementary files format and content: Consensus peaks from all ATAC-seq samples, in BED format on the mm10 genome assembly. Peaks called with MACS2 and consensus peaks called with rmspc

extract_protocol:
Cells were treated with DnaseI to eliminate DNA contamination. Tn5 transposomes were applied to lysed chromatin. Transposed chromatin was purified using Zymo DNA Clean & Concentrator-5 columns.
Transposed DNA libraries were prepared using NEBNext Ultra II Q5 Master Mix and Illumina-compatible unique 5′-i5 and 3′-i7 barcode sequences.

value: brain

value: primary cell

value: cortical neurons

value: neuron differentiation


title: PEO1_DAC_R2

status: Public on Jun 22 2026

type: SRA

city: Bloomington

first: Heather

last: O'Hagan

state: Indiana

country: USA

institute: Indiana University

description:
Library name: Sample 8
Column name in PEO1_RNA_seq_raw_count.txt: DAC_2

library_source: transcriptomic

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
Reads were aligned to the hg38 genome followed by calculation of raw read counts using STAR (version 2.7.11a)
Assembly: hg38
Supplementary files format and content: Tab-deliminated file includes raw counts for each sample from STAR

molecule: total RNA

organism: Homo sapiens

growth_protocol: PEO1 cells were cultured in RPMI media with 10% fetal bovine serum (FBS) and 2μM sodium pyruvate in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNAs were collected using RNeasy Mini Kit (QIAgen, 74106)
RNA libraries for RNA-seq were preparing using Plasmidsaurus in-house RNA-Seq pipeline

treatment_protocol: PEO1 cells were mock-treated or treated with cisplatin (13μM, 16h) and/or DAC (100nM, 72h)

tag: cell line

tag: cell type

value: Primary ovarian cancer cells

tag: treatment

value: DAC

tag: time

value: 72 hour


title: Muscle, Individual 2, Summer (N2)

city: Santiago

first: Rorigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

description: Library name: sm_2_N2

library_source: other

data_processing:
Processed data files were generated from raw small RNA sequencing reads following standard quality control and preprocessing steps. Raw FASTQ files provided at the lane level were concatenated per sample, and only read 1 (R1) files were retained, as small RNA inserts are fully contained within R1 reads.
Assembly: https://doi.org/10.6084/m9.figshare.28726535.v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

molecule: other

organism: Orestias ascotanensis

source_name: Muscle

growth_protocol: Specimens were collected from the Ascotan Salt Pan (21°29'46.5"S 68°15'26.3"W) at an elevation of 3,740 meters above sea level in July 2019 (n=7) and January 2020 (n=7) using a fishing net. Euthanasia was performed by administering an overdose of tricaine methanesulphonate (MS-222, 500 mg L−1; Sigma-Aldrich). Tissue samples from gills, skin, and muscle were harvested on-site. Each tissue sample was individually preserved in RNAlater (Invitrogen) immediately after dissection to stabilize and protect RNA. The samples were transported on ice to the laboratory and subsequently stored at -80°C until RNA extraction.

extract_protocol:
For small RNA sequencing, total RNA samples were enriched for short RNA species by size selection using denaturing polyacrylamide gel electrophoresis on Novex™ TBE–Urea gels (Invitrogen) run in TBE Running Buffer (LC6675). Gel fragments corresponding to the expected size range of small RNAs, including mature microRNAs, were excised and purified.
Small RNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina, 15016911) according to the manufacturer’s instructions. Libraries were sequenced by Quick Biology (Pasadena, CA, USA) on an Illumina NextSeq 500 platform using paired-end 75 bp reads. Although paired-end sequencing was performed, only read 1 (R1), which fully covers the mature small RNA insert, was used for downstream analyses.

tag: tissue

value: Muscle

value: summer

tag: batch


title: Grp8, mCherry quartile sort, lower middle quartile

city: Cleveland

first: Kenneth

last: Matreyek

state: Ohio

address: 2103 Cornell Rd, Room 5104

department: Pathology

institute: Case Western Reserve University

description: Library name: Grp8, eeBxb1, mCherry bin 2

library_source: genomic

data_processing:
DNA was sequenced using a NextSeq 550 Mid output (130 million reads) 150 cycle kit (Illumina) at the Case Western Reserve University Genomics Core Facility
Reads were converted to fastq format and demultiplexed by the Case Western Reserve University Genomics Core Facility.  Paired-end reads were combined using PEAR (PMC3933873) using default statistical settings.
Each paired end read was tested for exact matches from the expected library and included as a read for the appropriate library member if applicable.  Read count relative to total number of reads in the sample was used to calculate read frequency for each expected library member.
Read frequencies for quartiles from the same fluorophore sort and the same group were used to calculate a weighted average Sort-Seq score for each fluorophore for expected library member.  Scores were averaged across groups to provide a final Sort-Seq score for each expected library member.  The Sort-Seq scores were used for further analysis in the manuscript.
Assembly: Synthetic Sequences
Supplementary files format and content: "processed_data_counts_frequencies.csv" is a comma separated values data table containing read counts and read frequencies for all observed DNA sequences (library_sequence, column 1).  Each row represents a DNA sequence of interest, and each column represents either a read count ("_counted") or a read frequency ("_freq") for each sample ("IXXXX", corresponding with IXXXX from file names as described in SAMPLES section).

molecule: genomic DNA

organism: synthetic construct

growth_protocol: DMEM with 10% FBS, 1 % Penicillin / Streptomycin, and 2 ug/mL doxycycline.

extract_protocol:
Genomic DNA was extracted using a Dneasy Blood and Tissue Kit (Qiagen, 69506) and DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265)
Extracted genomic DNA was used as a template to produce a 1564 nucleotide amplicon spanning the genomic integration junction.  Samples were run with gel electrophoresis, the appropriate band was extracted using a Bio-Rad Freeze 'N Squeeze DNA Gel Extraction Spin Column (Bio-Rad, 7326165) and cleaned using a Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4004).  The resulting DNA was used as the template for to produce a 299 nudleotide amplicon surrounding the DNA sequence of interest using distinct indices for each quartile to be run on the same Illumina NextSeq 550 kit run.  Samples were again run with gel electrophoresis, extracted, and cleaned.  DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265).  DNA amplicons were pooled to a final concentration of 10-20ng/uL in 21uL of nuclease free water using 15-20ng of DNA from each quartile prior to running the Illumina NextSeq 550 kit.

value: Cultured Cells

tag: genotype

value: Recombination into


title: PEO1_DAC_R1

description:
Library name: Sample 7
Column name in PEO1_RNA_seq_raw_count.txt: DAC_1


title: PEO1_Cis_R3

description:
Library name: Sample 6
Column name in PEO1_RNA_seq_raw_count.txt: Pt_3

value: Cisplatin


title: Grp8, mCherry quartile sort, lower quartile

description: Library name: Grp8, eeBxb1, mCherry bin 1


title: Skin, Individual 5, Summer (N1)

description: Library name: ss_5_N1

source_name: Skin

value: Skin

value: winter


title: PEO1_Cis_R2

description:
Library name: Sample 5
Column name in PEO1_RNA_seq_raw_count.txt: Pt_2


title: Muscle, Individual 1, Summer (N2)

description: Library name: sm_1_N2


title: Vehicle-treated hiPSC-CMs, biological replicate 2

city: Chicago

first: Jacob

middle: D

last: Cunningham

state: IL

address: 1500 W Monroe St. Unit 221

department: Cell & Molecular Physiology

institute: Loyola University Chicago

description:
Library name: HS7VFC_2_control_rep2
hiPSC-CMs treated with vehicle

data_processing:
FASTQ files were generated and demultiplexed using BCL Convert v4.3.6 and fqtk v0.3.1.
Reads were filtered using fastp v0.24.0 with poly-X tail trimming, 3-prime quality-based tail trimming, a minimum Phred quality score of 15, and a minimum retained read length of 50 bp.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text matrix containing UMI-deduplicated, strand-specific gene-level counts for all 12 samples. Rows represent genes identified by gene_id, with gene annotation fields where available, and columns represent the GEO library names. Counts were generated using featureCounts from UMI-deduplicated aligned reads.

source_name: WTC-mEGFP-ACTN2-cl85 (AICS-0075-085)

growth_protocol: Human iPSCs were maintained on Matrigel-coated culture plates in mTeSR Plus medium. At approximately 70%–80% confluence, cardiac differentiation was initiated with RPMI 1640 containing B-27 supplement without insulin and 7.5 µM CHIR99021. On differentiation day 2, medium was replaced with RPMI 1640 containing B-27 supplement without insulin and 5 µM IWP-2. On day 4, cells were maintained in RPMI 1640 containing B-27 supplement without insulin. From days 6–14, cells were maintained in RPMI 1640 containing complete B-27 supplement, with medium changed every other day. Cardiomyocytes were metabolically enriched using glucose-free RPMI 1640 containing B-27 supplement without insulin and 10 mM sodium L-lactate. After selection, cardiomyocytes were dissociated with TrypLE, replated on Matrigel-coated plates at 3 × 10^6 cells/mL, and maintained in RPMI 1640 containing complete B-27 supplement.

extract_protocol:
Total RNA was extracted by Plasmidsaurus from cells preserved in Zymo DNA/RNA Shield
Poly(A) mRNA was captured from total RNA using a poly(dT)VN primer containing a sample barcode, a unique molecular identifier (UMI), and the Read 1 sequence. Reverse transcription and second-strand cDNA synthesis were followed by tagmentation. Libraries were indexed and amplified to add unique dual indexes and Illumina P5/P7 adapter sequences. Libraries were prepared as stranded, single-end, approximately 90-bp 3-prime-end-counting RNA-sequencing libraries.

treatment_protocol: Human iPSC-derived cardiomyocytes were assigned to four experimental conditions: vehicle control, sacubitrilat alone, endothelin-1 alone, or endothelin-1 plus sacubitrilat. Cells were treated with 10 nM endothelin-1 and/or 16 uM sacubitrilat for 48 hours simultaneously with endothelin-1. Control cells received the corresponding vehicle treatment.

value: WTC-mEGFP-ACTN2-cl85 (AICS-0075-085)

value: induced pluripotent stem cell-derived cardiomyocyte

value: heterozygous endogenous C-terminal ACTN2-mEGFP tag

value: 16 uM DMSO, 48 hours

value: Biological replicate 2


title: Muscle, Individual 5, Summer (N1)

description: Library name: sm_5_N1


title: PEO1_Cis_R1

description:
Library name: Sample 4
Column name in PEO1_RNA_seq_raw_count.txt: Pt_1


title: Grp7, miRFP670 quartile sort, upper quartile

description: Library name: Grp7, eeBxb1, miRFP670 bin 4


title: PEO1_Untreated_R3

description:
Library name: Sample 3
Column name in PEO1_RNA_seq_raw_count.txt: UT_3

value: Untreated


title: Gills, Individual 4, Summer (N1)

description: Library name: sg_4_N1

source_name: Gills

value: Gills


title: PEO1_Untreated_R2

description:
Library name: Sample 2
Column name in PEO1_RNA_seq_raw_count.txt: UT_2

value: Primary ovarian cancer cells


title: Grp7, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp7, eeBxb1, miRFP670 bin 3


title: Skin, Individual 4, Summer (N1)

description: Library name: ss_4_N1


title: 61243_12_TALL5955-T-ALL_GEX

city: Monrovia

first: Srividya

last: Swaminathan

state: CA

address: 1218 S Fifth Ave, BRC2064

institute: Beckman Research Institute of City of Hope

description:
Library name: COHP_61243
Run #2: T-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

library_source: transcriptomic single cell

data_processing:
BCL Convert (formerly known as bcl2fastq) was usedto convert base call (BCL) files generated during sequencing into FASTQ files. Raw FASTQ file reads were aligned to the GRCh38  assembly using Cell Ranger v7.2.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz files are tsv files generated from CellRanger Counts pipeline containing valid cell barcodes.
Supplementary files format and content: features.tsv.gz files are generated from CellRanger Counts pipeline containing list of feautres/genes.
Supplementary files format and content: matrix.mtx.gz files are generated from CellRanger Counts pipeline containing counts to form the gene-barcode matrix

source_name: Blood

extract_protocol:
Following the manual removal of pathogenic B cells from B-ALL samples and pathogenic T cells from T-ALL samples through magnetic microbead separation, we employed scRNA-seq for the remainnig immune compartments.
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v4.2.7 to convert base call (BCL) files into FASTQ files.

value: Blood

value: PBMC

value: CD3 positive T cell depletion

tag: age

tag: Sex

value: male

tag: disease

value: T-ALL

tag: child/adult

value: Adult


title: Grp7, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp7, eeBxb1, miRFP670 bin 2

value: Cultured Cells

value: Recombination into


title: PEO1_Untreated_R1

description:
Library name: Sample 1
Column name in PEO1_RNA_seq_raw_count.txt: UT_1

value: 72 hour


title: hiSCs, lenti-MNDA, rep1

city: Beijing

first: Haihan

last: Xiao

address: Building N5, Jinyu Intelligent Manufacturing Factory, Haidian District, Beijing, China

country: China

institute: Everlife Biomed Co. Ltd. China

description: Library name: MNDA-rep1

data_processing:
Raw reads were processed with quality control to remove low-quality reads with a Phred quality score below 20, adapter sequences, and reads containing more than 5% ambiguous bases (N), thereby producing high-quality clean reads. The clean reads were aligned to the human reference genome Homo_sapiens.GRCh38.p13 (Gencode) using the HISAT2 software with default parameters, and the number of reads mapped to each gene was counted using FeatureCounts to obtain the raw gene expression counts.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: human induced pluripotent stem cell-derived Sertoli-like cells

growth_protocol:
The protein-coding sequences of NR5A1 and GATA4 were cloned into the transactivator vector of the Tet-On 3G Tetracycline Inducible Gene Expression System (Clonetech). Subsequently, the modified transactivator vector and response vector were co-introduced into commercially available human iPSCs via electroporation. Doxycycline (DOX)-induced expression cassette of NR5A1 and GATA4 was integrated into the cellular genome through homologous recombination. Genetically engineered founder cells were obtained after puromycin selection.
The founder cells were cultured on plates coated with iMatrix-511 SILK extracellular matrix in StemFit Basic03 medium (Ajinomoto) supplemented with human basic fibroblast growth factor (bFGF). Differentiation was initiated by switching the culture medium to DOX-conditioned medium, consisting of MEM Alpha medium supplemented with 10% KnockOut Serum Replacement, 1 × GlutaMAX, 1 × non-essential amino acids, and 5 μg/mL DOX. After 3 days of differentiation induction, cells were dissociated with TrypLE Express solution and re-plated onto LN521-precoated culture plates. DOX-conditioned medium was refreshed every other day, and differentiation was maintained for another 6 days to obtain mature hiSCs.

extract_protocol:
Total cellular RNA was extracted using Trizol reagent. Messenger RNA (mRNA) was specifically enriched from the total RNA using oligo(dT) capture beads.
RNA-seq libraries were constructed using the RNA-seq Library Prep Kit for Illumina (Cat. No. NR605, Vazyme, China), following the kit’s recommended procedures, including RNA fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adapter ligation, and PCR amplification.

treatment_protocol: hiSCs were transduced with MNDA-overexpressing lentivirus or empty control lentivirus at an MOI of 100 for 48 h. The culture medium was subsequently exchanged for G418 selection medium (final concentration 300 μg/mL), and cells were cultured for another 48 h. MNDA-overexpressing hiSCs and control cells were harvested after drug selection.

value: MNDA overexpression


title: 61242_11_TALL5955-T-ALL_GEX

description:
Library name: COHP_61242
Run #1: T-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Muscle, Individual 4, Summer (N1)

description: Library name: sm_4_N1

value: Muscle

value: winter


title: 61241_10_BALL1424-B-ALL_GEX

description:
Library name: COHP_61241
Run #2: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: CD19 positive B cell depletion

value: B-ALL


title: Input

description: Library name: Input

data_processing:
Raw reads were processed with quality control to remove low-quality reads with a Phred quality score below 20, adapter sequences, and reads containing more than 5% ambiguous bases (N), thereby producing high-quality clean reads. The clean reads were aligned to the human reference genome Homo_sapiens.GRCh38.p14 (GENCODE) via the Bowtie2 software package with the mismatch parameter set as `-N 1`. The resulting aligned BAM files were subsequently converted into BigWig files using the bamCoverage function from deepTools.
Assembly: Homo_sapiens.GRCh38.p14
Supplementary files format and content: BigWig files of ChIP-seq signal tracks for Input, IgG control IP and MNDA IP samples

growth_protocol:
The protein-coding sequences of NR5A1 and GATA4 were cloned into the transactivator vector of the Tet-On 3G Tetracycline Inducible Gene Expression System (Clonetech). Subsequently, the modified transactivator vector and response vector were co-introduced into commercially available human iPSCs via electroporation. Doxycycline (DOX)-induced expression cassette of NR5A1 and GATA4 was integrated into the cellular genome through homologous recombination. Genetically engineered founder cells were obtained after puromycin selection.
The founder cells were cultured on plates coated with iMatrix-511 SILK extracellular matrix in StemFit Basic03 medium (Ajinomoto) supplemented with human basic fibroblast growth factor (bFGF). Differentiation was initiated once cells reached approximately 70% confluence by switching the culture medium to DOX-conditioned medium, consisting of MEM Alpha medium supplemented with 10% KnockOut Serum Replacement, 1 × GlutaMAX, 1 × non-essential amino acids, and 5 μg/mL DOX. After 3 days of differentiation induction, cells were dissociated with TrypLE Express solution and re-plated onto LN521-precoated culture plates. DOX-conditioned medium was refreshed every other day, and differentiation was maintained for another 6 days to obtain mature hiSCs.

extract_protocol:
Cells were dissociated using TrypLE, harvested by centrifugation, and subsequently fixed and crosslinked in 1% formaldehyde at room temperature for 10 min. ChIP samples were prepared using a commercial Enzymatic ChIP Assay Kit. Chromatin fragmentation was achieved via MNase digestion at 37 °C for 20 min, followed by sonication to generate input chromatin. For MNDA immunoprecipitation, 15 μg input chromatin was incubated with 2 μg anti-MNDA antibody (Cat. No. 13576-1-AP, Proteintech, China) for target enrichment, while normal rabbit IgG was processed in parallel as the negative control. DNA from input, IgG control IP, and MNDA IP samples was finally purified with a DNA Clean & Concentrator kit.
Sequencing libraries were constructed from the three purified DNA samples with a DNA Library Prep Kit for Illumina. After size separation via 2% agarose gel electrophoresis, target DNA fragments were recovered by gel extraction to generate final ChIP-seq libraries.

treatment_protocol: hiSCs were stimulated with human IFNα at a final concentration of 100 ng/mL for 48 h to induce MNDA expression.

value: human induced pluripotent stem cell-derived Sertoli-like cells

tag: chip antibody


title: Grp7, miRFP670 quartile sort, lower quartile

description: Library name: Grp7, eeBxb1, miRFP670 bin 1


title: 61240_9_BALL1424-B-ALL_GEX

description:
Library name: COHP_61240
Run #1: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Gills, Individual 3, Summer (N1)

description: Library name: sg_3_N1

value: Gills


title: Grp7, mKG quartile sort, upper quartile

description: Library name: Grp7, eeBxb1, mKG bin 4


title: 61238_7_BALL029-B-ALL_GEX

description:
Library name: COHP_61238
Run #1: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: female


title: 61239_8_BALL029-B-ALL_GEX

description:
Library name: COHP_61239
Run #2: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Blood


title: Skin, Individual 3, Summer (N1)

description: Library name: ss_3_N1

value: Skin


title: ChIP-IgG

description: Library name: IgG_control

value: IgG


title: 61237_6_HD563_GEX

description:
Library name: COHP_61237
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: PBMC

value: Healthy


title: Grp7, mKG quartile sort, upper middle quartile

description: Library name: Grp7, eeBxb1, mKG bin 3


title: 61236_5_HD563_GEX

description:
Library name: COHP_61236
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Adult


title: 61235_4_HD560_GEX

description:
Library name: COHP_61235
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: CD3 positive T cell depletion

value: male


title: 61234_3_HD560_GEX

description:
Library name: COHP_61234
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Gills, Individual 2, Summer (N1)

description: Library name: sg_2_N1


title: 61233_2_HD555_GEX

description:
Library name: COHP_61233
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Grp7, mKG quartile sort, lower quartile

description: Library name: Grp7, eeBxb1, mKG bin 1

value: Cultured Cells

value: Recombination into


title: ChIP-MNDA

description: Library name: MNDA

value: MNDA


title: 61232_1_HD555_GEX

description:
Library name: COHP_61232
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Skin, Individual 2, Summer (N1)

description: Library name: ss_2_N1

value: winter


title: 57980_BALL937_2_GEX

description:
Library name: COHP_57980
Run #2: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: CD19 positive B cell depletion


title: Grp7, mCherry quartile sort, upper quartile

description: Library name: Grp7, eeBxb1, mCherry bin 4


title: 57979_BALL937_1_GEX

description:
Library name: COHP_57979
Run #1: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: B-ALL


title: Muscle, Individual 2, Summer (N1)

description: Library name: sm_2_N1

value: Muscle


title: 57978_HD574_2_GEX

description:
Library name: COHP_57978
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Grp7, mCherry quartile sort, upper middle quartile

description: Library name: Grp7, eeBxb1, mCherry bin 3


title: 57977_HD574_1_GEX

description:
Library name: COHP_57977
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Gills, Individual 1, Summer (N1)

description: Library name: sg_1_N1

value: Gills


title: 58326_4H_T-ALL6070_GEX

description:
Library name: COHP_58326
Run #2: T-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: T-ALL


title: 58325_4G_T-ALL6070_GEX

description:
Library name: COHP_58325
Run #1: T-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Blood


title: Grp7, mCherry quartile sort, lower middle quartile

description: Library name: Grp7, eeBxb1, mCherry bin 2


title: Skin, Individual 1, Summer (N1)

description: Library name: ss_1_N1

value: Skin


title: 58324_3F_B-ALL1192_GEX

description:
Library name: COHP_58324
Run #2: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: female


title: Grp7, mCherry quartile sort, lower quartile

description: Library name: Grp7, eeBxb1, mCherry bin 1


title: 58323_3E_B-ALL1192_GEX

description:
Library name: COHP_58323
Run #1: B-ALL
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: PBMC


title: Muscle, Individual 1, Summer (N1)

description: Library name: sm_1_N1


title: 58322_2D_HD553_GEX

description:
Library name: COHP_58322
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Healthy


title: Grp6, miRFP670 quartile sort, upper quartile

description: Library name: Grp6, eeBxb1, miRFP670 bin 4


title: 58321_2C_HD553_GEX

description:
Library name: COHP_58321
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Adult


title: HedTi

city: Qingdao

first: Runhua

last: Liu

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: Shandong University

description:
Library name: HedTi
HepG2 cells after 48 hours of treatment with DMSO

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: cell culture


title: Grp6, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp6, eeBxb1, miRFP670 bin 3


title: 58320_1B_HD562_GEX

description:
Library name: COHP_58320
Run #2: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: HedSi

description:
Library name: HedSi
HepG2 cells after 48 hours of treatment with DMSO


title: Grp6, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp6, eeBxb1, miRFP670 bin 2


title: J30OE3

city: Zhengzhou

first: Yangyang

last: Ji

state: Henan

address: No. 1, Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Sample6

data_processing:
The raw paired-end reads were trimmed and quality controlled by fastp (Version 0.23.4) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (Version 2.2.1) software.
The mapped reads of each sample were assembled by StringTie (Version 2.2.1) in a reference-based approach.
RSEM (Version 1.3.3) was used to quantify gene abundances.
Differential expression analysis was performed using the DESeq2 (Version 1.42.0).
Assembly: GRCh38
Supplementary files format and content: count and tpm

extract_protocol:
Total RNA was extracted from the cells using TRIzol reagent according the manufacturer’s instructions.
The RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000(NanoDrop Technologies). Only high-quality RNA sample(OD 260/280 =1.8~2.2, OD 260/230 ≥ 2.0, RQN ≥ 6.5, 28S:18S ≥1.0,>1μg) was used to construct sequencing library.

value: ESCC cell

value: HOXC9 overexpression


title: 58319_1A_HD562_GEX

description:
Library name: COHP_58319
Run #1: Healthy
Sequencing run was performed on the NovaSeq X Series platform with 25B reagent kit (300 Cycle). NovaSeq Control Software 1.2.2.48004 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: J30OE2

description: Library name: Sample5


title: HedEi

description:
Library name: HedEi
HepG2 cells after 48 hours of treatment with DMSO


title: J30OE1

description: Library name: Sample4


title: Grp6, miRFP670 quartile sort, lower quartile

description: Library name: Grp6, eeBxb1, miRFP670 bin 1

value: Cultured Cells

value: Recombination into


title: J30nc2

description: Library name: Sample2

value: WT


title: J30nc3

description: Library name: Sample3


title: Grp6, mKG quartile sort, upper quartile

description: Library name: Grp6, eeBxb1, mKG bin 4


title: Heb2Tiii

description:
Library name: Heb2Tiii
HepG2 cells after 48 hours of treatment with 2.5 μM FBX-DMEP


title: Heb2Tii

description:
Library name: Heb2Tii
HepG2 cells after 48 hours of treatment with 2.5 μM FBX-DMEP


title: Grp6, mKG quartile sort, upper middle quartile

description: Library name: Grp6, eeBxb1, mKG bin 3


title: zmccd8 Water stress Rep3

city: Legnaro

first: Leonardo

last: Buzzicotti

state: Italy PD

address: Vle dell'Università, 16

country: Italy

institute: Università di Padova

description:
Library name: MT_DR_3
RNA sequencing of zmccd8 Water stress Rep3

data_processing:
Clean paired-end reads were aligned to the Zea mays reference genome (Zm-B73-REFERENCE-NAM-5.0) using Hisat2 v2.0.5.
Raw reads were filtered to remove adaptor sequences, ambiguous reads ('N' > 10%), and low-quality reads (Qscore <= 5) using fastp/Trimmomatic.
Clean reads were aligned to the Zea Mays reference genome (Genome assembly: Zm-B73-REFERENCE-NAM-5.0) using HISAT2 software with default parameters.
Gene expression quantification was performed using featureCounts (Subread package). FPKM values were calculated to estimate gene expression levels.
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: gene_fpkm.xls: FPKM normalized gene expression counts

organism: Zea mays

source_name: Root

growth_protocol: Seeds from the maize (Zea mays L.) inbred line B73  and from a zmccd8::Ds insertional mutant line in the B73 genetic background  were washed in demineralized water and germinated on wet filter paper in the dark at 25 °C. Seedlings with the greatest phenotypic uniformity were selected and were individually transplanted into pots (7x7x18 cm) filled with 100% vermiculite as substrate. All plants were grown for four weeks under the following controlled conditions: 16/8 h light/dark photoperiod, 40/50%  relative humidity, air temperature of 23/20 °C, and a light intensity of 280 μmol m⁻² s⁻¹.

extract_protocol:
Total RNA was extracted from approximately 90 mg of frozen root tissue using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich), following the manufacturer's instructions. RNA concentration was determined using a NanoDrop™ OneC spectrophotometer, and RNA integrity was verified by 1% agarose gel electrophoresis and assessed using an Agilent Bioanalyzer 2100 system
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations at elevated temperature. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dUTP was used instead of dTTP to generate a strand-specific library. 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. The library fragments were purified with AMPure XP system and PCR amplified.

treatment_protocol: The control (CT) plants were supplied three times per week with a complete Hoagland nutrient solution. The nitrogen-deficient (0N) plants received the same formulation as the control, except that 1 mM KNO₃ was replaced with an equimolar concentration of KCl . Plants submitted to water stress (WS) received the complete nutrient solution only on the day of transplanting, with no further irrigation thereafter.

value: Root

value: zmccd8::Ds insertional mutant

value: Water stress


title: zmccd8 Water stress Rep2

description:
Library name: MT_DR_2
RNA sequencing of zmccd8 Water stress Rep2


title: Heb2Ti

description:
Library name: Heb2Ti
HepG2 cells after 48 hours of treatment with 2.5 μM FBX-DMEP


title: J30nc1

description: Library name: Sample1


title: Grp6, mKG quartile sort, lower middle quartile

description: Library name: Grp6, eeBxb1, mKG bin 2


title: zmccd8 Water stress Rep1

description:
Library name: MT_DR_1
RNA sequencing of zmccd8 Water stress Rep1


title: zmccd8 Nitrogen deficiency Rep3

description:
Library name: MT_N_3
RNA sequencing of zmccd8 Nitrogen deficiency Rep3

value: Nitrogen deficiency


title: LS8817, day14, Palbo, rep1, techrep3, ATAC

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description: Library name: day14_Palbo_Biorep1.3

data_processing:
Adapters were trimmed using cutadapt
Reads were aligned with bowtie2 2.3.4.3 to the hg38 genome. Following this, duplicate reads and reads mapping to the mitochondrial genome were removed.
Bam files were converted to bedpe files, which were then converted to tagAlign files for MACS2 to call peaks on, areas of the genome enriched for aligned sequencing reads, indicating hyperaccessibility. MACS2 parameters were -g 2.7e9 -p 0.2 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits.
Reproducible peaks across technical replicates per condition were kept using Irreproducible Discovery Rate (Li et al. 2011)
A master nonredundant peak set was generated using a custom iterative peak filtering script which selects the peak with the lowest q-value generated by MACS2 from a set of overlapping peaks
Peaks were fixed to 500bp in length, with 250bp extending from the summit identified by MACS2
Fragment counts under peaks were counted using chromVAR’s getCounts function(Schep et al. 2017)
Assembly: hg38
Supplementary files format and content: Files ending in "scaleFactornorm.bw" are coverage bigwig tracks normalized by sequencing depth. Files ending in "scaleFactornorm_cutsCoverage.bw" are normalized coverage of Tn5 insertion sites (fragment ends). If the file contained the string "merged" it means that bams across biological and technical replicates for that condition were merged prior to generating the bigwig file.
Supplementary files format and content: .narrowPeak files are peaks called for each technical replicate by MACS2.
Supplementary files format and content: summits.bed files are the summits of peaks identified by MACS2

source_name: soft tissue sarcoma

growth_protocol: Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.

extract_protocol:
Cells were treated in culture medium with DNase (Worthington cat# LS002007) at a final concentration of 200 U/mL at 37 °C for 30 mins, then washed twice with PBS at 500g, RT. Approximately ~50,000-60,000 cells were used for each transposition reaction. Following permeabilization, 2.5 µL of Illumina TDE1 enzyme was used for transposition at 37°C for 30 minutes.
Libraries were PCR amplified for 8-13 cycles with Illumina i5 or i7 barcoded primers and were cleaned up pre- and post-amplification following the manufacturer’s instructions using Zymo DNA Clean and Concentrator-5 Kit. Fragment length distribution and DNA amount was quantified via Tapestation and Qubit to assess for quality prior to sequencing.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with either 1 µM palbociclib or 100 nM doxorubicin, with media changes every 2–3 days until harvest.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day14 palbociclib (1uM)


title: LS8817, day14, Palbo, rep1, techrep2, ATAC

description: Library name: day14_Palbo_Biorep1.2


title: zmccd8 Nitrogen deficiency Rep2

description:
Library name: MT_N_2
RNA sequencing of zmccd8 Nitrogen deficiency Rep2


title: Grp6, mKG quartile sort, lower quartile

description: Library name: Grp6, eeBxb1, mKG bin 1


title: zmccd8 Control Rep3

description:
Library name: MT_CT_3
RNA sequencing of zmccd8 Control Rep3

value: Control


title: zmccd8 Nitrogen deficiency Rep1

description:
Library name: MT_N_1
RNA sequencing of zmccd8 Nitrogen deficiency Rep1


title: Grp6, mCherry quartile sort, upper quartile

description: Library name: Grp6, eeBxb1, mCherry bin 4


title: zmccd8 Control Rep2

description:
Library name: MT_CT_2
RNA sequencing of zmccd8 Control Rep2


title: zmccd8 Control Rep1

description:
Library name: MT_CT_1
RNA sequencing of zmccd8 Control Rep1


title: LS8817, day14, Palbo, rep1, techrep1, ATAC

description: Library name: day14_Palbo_Biorep1.1


title: Grp6, mCherry quartile sort, upper middle quartile

description: Library name: Grp6, eeBxb1, mCherry bin 3


title: Wild-type Water stress Rep3

description:
Library name: WT_DR_3
RNA sequencing of Wild-type Water stress Rep3

value: Wild-type B73


title: LS8817, day14, Doxo, rep1, techrep3, ATAC

description: Library name: day14_Doxo_Biorep1.3

value: day14 doxorubicin (100nM)


title: Wild-type Water stress Rep2

description:
Library name: WT_DR_2
RNA sequencing of Wild-type Water stress Rep2


title: Grp6, mCherry quartile sort, lower middle quartile

description: Library name: Grp6, eeBxb1, mCherry bin 2


title: Wild-type Water stress Rep1

description:
Library name: WT_DR_1
RNA sequencing of Wild-type Water stress Rep1


title: LS8817, day14, Doxo, rep1, techrep2, ATAC

description: Library name: day14_Doxo_Biorep1.2


title: Grp6, mCherry quartile sort, lower quartile

description: Library name: Grp6, eeBxb1, mCherry bin 1


title: Wild-type Nitrogen deficiency Rep2

description:
Library name: WT_N_2
RNA sequencing of Wild-type Nitrogen deficiency Rep2


title: Wild-type Nitrogen deficiency Rep3

description:
Library name: WT_N_3
RNA sequencing of Wild-type Nitrogen deficiency Rep3


title: LS8817, day14, Doxo, rep1, techrep1, ATAC

description: Library name: day14_Doxo_Biorep1.1


title: Wild-type Nitrogen deficiency Rep1

description:
Library name: WT_N_1
RNA sequencing of Wild-type Nitrogen deficiency Rep1


title: Grp5, miRFP670 quartile sort, upper quartile

description: Library name: Grp5, eeBxb1, miRFP670 bin 4


title: LS8817, day10, Palbo, rep1, techrep3, ATAC

description: Library name: day10_Palbo_Biorep1.3

value: day10 palbociclib (1uM)


title: Wild-type Control Rep2

description:
Library name: WT_CT_2
RNA sequencing of Wild-type Control Rep2


title: Wild-type Control Rep3

description:
Library name: WT_CT_3
RNA sequencing of Wild-type Control Rep3


title: Grp5, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp5, eeBxb1, miRFP670 bin 3


title: Wild-type Control Rep1

description:
Library name: WT_CT_1
RNA sequencing of Wild-type Control Rep1


title: OVCAR3_p65_IgG_CT_C&R_R2

description: Library name: Sample 20

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.12.1)
Reads were aligned to the hg38 genome followed by calculation of raw read counts using Bowtie2 (version 2.5.1)
Peaks were called using MACS (version 3.0.3)
Consistent peaks across the two biological replicates were identified using Irreproducible Discovery Rate (IDR) method as per the ENCODE ChIP-seq analysis pipeline with IDR cutoff of 0.05 for STAT3 and 0.01 for p65
Assembly: hg38
Supplementary files format and content: NarrowPeak (called peaks) after IDR analysis
Supplementary files format and content: bigWig represent the computed average of bigWig files from two biological replicates
Library strategy: CUT&RUN

growth_protocol: OVCAR3 cells were cultured in DMEM media with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN was performed according to CUTANA CUT&RUN protocol using CUTANA Concanavalin A (ConA) magnetic beads (EpiCypher, 21-1401) and pAG-MNase (EpiCypher, 15-1016)
CUT&RUN libraries were preparing using NEBNext Ultra DNA Library kit (New England Biolab, E76450) as per the manufacturer’s instructions

treatment_protocol: OVCAR3 cells were mock-treated or treated with cisplatin (15uM, 16h) and/or DAC (100nM, 72h)

value: Primary ovarian cancer cells

value: Mix of cells from all treatments

tag: antibody

value: IgG (MilliporeSigma, 12-0370)

value: 72 hour


title: Grp5, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp5, eeBxb1, miRFP670 bin 2

value: Cultured Cells

value: Recombination into


title: LS8817, day10, Palbo, rep1, techrep2, ATAC

description: Library name: day10_Palbo_Biorep1.2


title: OVCAR3_p65_IgG_CT_C&R_R1

description: Library name: Sample 19


title: OVCAR3_p65_C&R_Cis_DAC_R2

description: Library name: Sample 18

value: Cisplatin + DAC


title: Grp5, miRFP670 quartile sort, lower quartile

description: Library name: Grp5, eeBxb1, miRFP670 bin 1


title: OVCAR3_p65_C&R_Cis_DAC_R1

description: Library name: Sample 17


title: DRT3_MUT_Ara_rep2

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description:
Library name: HCL11_04
A3508

data_processing:
Raw reads were processed with BBDuk (v39.83) to filter for Himar transposon-end-containing reads, trim adapter sequences and low-quality bases, and trim transposon sequence to leave only the 16–17 bp of genomic sequence mappable to the E. coli MG1655 reference genome (NC_000913.3). Processed reads were aligned with Bowtie2 (v1.3.1) with no allowance for mismatches. Alignments were sorted and indexed using SAMtools (v1.17). Strand-specific coverage tracks were generated with bamCoverage (v3.5.6) with no normalization, using parameters that identified the TA dinucleotide within the read as the insertion site (bin size = 1, offset = –1). Mapped reads were assigned to annotated genes with featureCounts (v2.0.2) using the --read2pos 5 flag. The resulting count matrices were passed to PyDESeq2 (v0.5.3) for differential insertion analysis with default parameters. Five independent biological replicates were included for every comparison. Genome build: E. coli MG1655 (NC_000913.3).
Assembly: ASM584v2
Supplementary files format and content: .txt file with gene-level raw read count matrix generated by featureCounts. Rows correspond to annotated genes (Geneid from the GFF annotation) and columns correspond to individual samples. Values are unnormalized integer read counts representing the number of reads uniquely assigned to each gene.

organism: Escherichia coli

extract_protocol:
Mutant library plates were grown at 37 °C for 18 hours, after which all colonies were scraped from the plates. Genomic DNA was extracted from these cells using the Wizard Genomic DNA Purification kit (Promega).
Extracted gDNA was digested with MmeI (2 U MmeI per 1 µg gDNA) at 37 °C for 1 hour, followed by enzyme inactivation at 65 °C for 20 min. Digested DNA was purified using QIAquick PCR Purification columns (Qiagen). Sequencing adaptors were ligated onto digested mini-transposons with T4 DNA ligase at 16 °C for 14 hours, followed by another QIAquick PCR purification cleanup. PCR amplification and Illumina barcoding were performed for 25 cycles with Q5 Hot Start HF DNA polymerase (NEB), using an annealing temperature of 65 °C and an extension time of 20 sec. The 173 bp product was gel-extracted using the QIAquick Gel Extraction kit (Qiagen) and sequenced on the Element AVITI system in single-end mode, 150 reads per end.


title: LS8817, day10, Palbo, rep1, techrep1, ATAC

description: Library name: day10_Palbo_Biorep1.1


title: LS8817, day10, Doxo, rep1, techrep3, ATAC

description: Library name: day10_Doxo_Biorep1.3

value: day10 doxorubicin (100nM)


title: OVCAR3_p65_C&R_DAC_R2

description: Library name: Sample 16

value: DAC


title: Grp5, mKG quartile sort, upper quartile

description: Library name: Grp5, eeBxb1, mKG bin 4


title: Control_IgG_negative_control

first: Norihiro

last: Goto

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: Control_IgG
Control_IgG

data_processing:
Paired-end sequencing reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were sorted and merged using Samtools.
Peaks were called using SEACR
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: H3K27ac_peak_counts.txt.gz is a tab delimited text of counts for filtered peaks
Library strategy: CUT&Run

organism: Mus musculus

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated using TrypLE Express for 10 min at 37 °C, filtered through a 40 μm cell strainer, and 500,000 cells were collected, centrifuged, and washed twice with PBS. H3K27ac CUT&RUN libraries were prepared using the CUTANA CUT&RUN kit (EpiCypher, 14-1048) according to the manufacturer’s instructions.
CUT&RUN libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. Paired-end sequencing was performed on an Illumina NextSeq 2000.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: LS8817, day10, Doxo, rep1, techrep2, ATAC

description: Library name: day10_Doxo_Biorep1.2

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2


title: OVCAR3_p65_C&R_Cis_R2

description: Library name: Sample 14

value: Cisplatin


title: OVCAR3_p65_C&R_DAC_R1

description: Library name: Sample 15


title: MATAC_3

city: Hangzhou

first: Yi

last: Wang

state: Zhejiang

address: Shangtang Road

institute: Zhejiang Provincial People's Hospital

description: Library name: Sample6

data_processing:
Raw sequencing data were processed using SeekSoul tools (SeekGene, v1.2.1) to generate gene expression matrices, followed by downstream analysis using the Seurat R package (version 4.4). Potential doublets were identified and removed via DoubletFinder, and low-quality cells were excluded and low-quality cells were filtered out if the number of genes was <300 or the ratio of mitochondrial reads was >10%. After normalization and clustering, cell identities were annotated using the SingleR package in conjunction with classical marker genes. Specifically, macrophages were subdivided into unpolarized (M0), activated (activated_M), lipid-associated (LAM), and alternatively activated (M2a and M2c) subtypes. The canonical markers used were Lyz2 and Adgre1 for M0; Nos2, Mki67 for activated_M; Trem2, and Gpnmb for LAM; Arg1 and Chil3 for M2a; Mertk for M2c. Subpopulation proportions were then compared between the control and MATAC-treated groups to assess shifts in macrophage polarization. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed on the marker genes of the M2c cluster using clusterProfiler to elucidate its key functional pathways.
Assembly: Mouse mm10
Supplementary files format and content: 26020165_M0_1_barcodes.tsv.gz, 26020165_M0_2_barcodes.tsv.gz, 26020165_M0_3_barcodes.tsv.gz, 26020165_PPS_1_barcodes.tsv.gz, 26020165_PPS_2_barcodes.tsv.gz, 26020165_PPS_3_barcodes.tsv.gz
Supplementary files format and content: 26020165_M0_1_features.tsv.gz, 26020165_M0_2_features.tsv.gz, 26020165_M0_3_features.tsv.gz, 26020165_PPS_1_features.tsv.gz, 26020165_PPS_2_features.tsv.gz, 26020165_PPS_3_features.tsv.gz
Supplementary files format and content: 26020165_M0_1_matrix.mtx.gz, 26020165_M0_2_matrix.mtx.gz, 26020165_M0_3_matrix.mtx.gz, 26020165_PPS_1_matrix.mtx.gz, 26020165_PPS_2_matrix.mtx.gz, 26020165_PPS_3_matrix.mtx.gz

source_name: bone marrow

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and dissociated using Collagenase IV (Sigma C5138-500MG), Papain (Solarbio G8430) and Hyaluronidase (Solarbio H8030). DNase I (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using SeekMate Tinitan Fluorescence Cell Counter (SeekGene M002C) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then resuspended at 1x10^6 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C).
Single-cell RNA-Seq libraries were prepared using SeekOne DD Single Cell 3' library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42C for 90 minutes and inactivated at 85C for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3' polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on the GeneMind SURFSeq 5000 with PE150 read length.

value: bone marrow

value: BMDM

value: treatment with MATAC for 48 h


title: LS8817, day10, Doxo, rep1, techrep1, ATAC

description: Library name: day10_Doxo_Biorep1.1


title: Grp5, mKG quartile sort, upper middle quartile

description: Library name: Grp5, eeBxb1, mKG bin 3


title: OVCAR3_p65_C&R_Cis_R1

description: Library name: Sample 13

value: Primary ovarian cancer cells


title: Grp5, mKG quartile sort, lower middle quartile

description: Library name: Grp5, eeBxb1, mKG bin 2


title: MATAC_2

description: Library name: Sample5


title: LS8817, Cycling, rep2, techrep3, ATAC

description: Library name: Cycling_Biorep2.3


title: OVCAR3_p65_C&R_Untreated_R2

description: Library name: Sample 12

value: Untreated


title: LS8817, Cycling, rep2, techrep2, ATAC

description: Library name: Cycling_Biorep2.2


title: Grp5, mKG quartile sort, lower quartile

description: Library name: Grp5, eeBxb1, mKG bin 1


title: MATAC_1

description: Library name: Sample4


title: Grp5, mCherry quartile sort, upper quartile

description: Library name: Grp5, eeBxb1, mCherry bin 4


title: OVCAR3_p65_C&R_Untreated_R1

description: Library name: Sample 11

value: 72 hour


title: M0_3

description: Library name: Sample3

value: treatment with PBS for 48 h


title: LS8817, Cycling, rep2, techrep1, ATAC

description: Library name: Cycling_Biorep2.1


title: Grp5, mCherry quartile sort, upper middle quartile

description: Library name: Grp5, eeBxb1, mCherry bin 3

value: Cultured Cells

value: Recombination into


title: OVCAR3_STAT3_IgG_CT_C&R_R2

description: Library name: Sample 10

value: Mix of cells from all treatments


title: LS8817, Cycling, rep1, techrep2, ATAC

description: Library name: Cycling_Biorep1.2


title: OVCAR3_STAT3_IgG_CT_C&R_R1

description: Library name: Sample 9


title: M0_2

description: Library name: Sample2


title: M0_1

description: Library name: Sample1


title: Grp5, mCherry quartile sort, lower middle quartile

description: Library name: Grp5, eeBxb1, mCherry bin 2


title: OVCAR3_STAT3_C&R_Cis_DAC_R2

description: Library name: Sample 8

value: Cisplatin + DAC


title: Grp5, mCherry quartile sort, lower quartile

description: Library name: Grp5, eeBxb1, mCherry bin 1


title: Mouse extraorbital lacrimal gland ZT21 biological replicate 3

city: weifang

first: Hongyu

last: Li

state: shandong Province

address: 7166 Baotong West Street, Weicheng District, Weifang City, Shandong Province

institute: Shandong Second Medical University

description:
Library name: LG_C21_3
ZT21; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

data_processing:
Raw sequencing reads were evaluated using FastQC for read-level quality control.
Adapter trimming and quality filtering were performed using Trimmomatic v0.39 and fastp v0.23.2.
Pre- and post-processing summaries were reviewed for base quality, adapter content, sequence length distribution, and read retention.
Clean reads were aligned to the Mus musculus reference genome mm10/GRCm38 using HISAT2 v2.2.1.
Gene-level raw read counts were generated using featureCounts v2.0.0 with the corresponding reference gene annotation.
Transcript abundance values were estimated as TPM using RSEM v1.3.3.
Assembly: Mus musculus mm10 / GRCm38
Supplementary files format and content: LG_time_series_gene_read_counts.txt.gz: Tab-delimited text file containing a gene-level raw read count matrix for all 24 samples. Rows represent genes and columns represent individual samples.
Supplementary files format and content: LG_time_series_gene_TPM.txt.gz: Tab-delimited text file containing a gene-level TPM expression matrix for all 24 samples. Rows represent genes and columns represent individual samples.

source_name: extraorbital lacrimal gland

growth_protocol: Male C57BL/6J mice were purchased at 8 weeks of age and acclimated to the animal facility for 2 weeks before sample collection. Mice were housed under controlled conditions with a 12-h light/12-h dark cycle. Lights were on at 7:00 AM and off at 7:00 PM. The illumination during the light phase was approximately 150 lux, ambient temperature was maintained at 22 ± 2 °C, and relative humidity was maintained at 50 ± 10%. Mice were provided ad libitum access to water and a standard rodent maintenance diet.

extract_protocol:
Extraorbital lacrimal gland tissues were dissected using sterile instruments, immediately flash-frozen in liquid nitrogen, and stored at -80 °C until RNA extraction. Total RNA was extracted using TRIzol reagent following a standard phenol-chloroform workflow. Briefly, frozen tissues were pulverized under liquid nitrogen, homogenized in 1 mL pre-chilled TRIzol, incubated at room temperature for complete lysis, and clarified by centrifugation. The supernatant was mixed with chloroform for phase separation, and the aqueous phase was transferred to a fresh tube. RNA was precipitated with isopropanol, washed once with 75% ethanol, briefly air-dried, and dissolved in RNase-free DEPC-treated water. RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Only RNA samples meeting library-construction criteria were used for sequencing library preparation.
For each sample, approximately 1 μg of total RNA was used for library preparation. Polyadenylated RNA was enriched using oligo-dT beads and fragmented, followed by first- and second-strand cDNA synthesis. Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit according to the manufacturer’s protocol, including end repair, adapter ligation, size selection of approximately 300–400 bp fragments, and PCR enrichment. Final libraries were quantified using Qubit 4.0, checked for fragment size distribution and yield, and sequenced on the BGIseq-500 platform to generate 150-bp paired-end reads. All 24 libraries were processed in the same sequencing batch.

treatment_protocol: No experimental treatment was applied. Mice were maintained under a standard 12:12 light-dark cycle. Extraorbital lacrimal glands were collected at eight Zeitgeber time points across a 24-h cycle: ZT0, ZT3, ZT6, ZT9, ZT12, ZT15, ZT18, and ZT21. Three biological replicates were collected at each time point.

value: extraorbital lacrimal gland

tag: strain

tag: zeitgeber time

value: wild type

value: same sequencing batch


title: LS8817, Cycling, rep1, techrep1, ATAC

description: Library name: Cycling_Biorep1.1

value: soft tissue sarcoma

value: liposarcoma


title: orgCorti_Casz1-KO_rep4

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: Library name: KO4

data_processing:
Paired fastq files were processed to filter out low quality reads using Trimmomatic (sliding window trimming); filtered reads were mapped using STAR aligner, and mapped reads were quantified using featureCounts; genes were filtered out if expression was not higher than 1 count per million in at least 3 samples; feature counts were analyzed for differential gene expression between genotype groups using edgeR.
Assembly: mm10; GRCm38.M23
Supplementary files format and content:
FeatureCounts.txt: columns = read counts for each sample; rows = entrezgene_ids
edgeR_Casz1cKOvsWT.txt:  entrezgene_ids, logFC, logCPM, Pvalues, FDR

extract_protocol:
RNA was isolated from organ of Corti samples using the RNeasy Micro Kit (Qiagen).
Total RNA was reverse-transcribed with Maxima H- RT with oligo-dT and template switching oligo primers. Full length cDNA was tagmented with Illumina Nextera XT Library Prep kits, and sequenced on a NextSeq2000 DNA sequencer (Illumina).


title: LPS +3A2 -3

city: Houston

first: Long

middle: Jiang

last: Shao

state: Texas

address: 1825 Pressler St, SRB 401L

department: Institute of Molecular Medicine

institute: The University of Texas Health

description:
Library name: Sun9_ LPS-3A2
Pluto RNA-seq pipeline

data_processing:
Differential gene expression analysis was performed using standard RNA-seq analysis pipelines.
FASTQ files were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2
Transcript assembly was conducted with the Pluto RNA-seq pipeline
Raw count data were normalized and expressed as counts per million (CPM).
Differential expression analyses and data visualization were performed using R packages including edgeR, pheatmap, ggplot2, and RColorBrewer.
Assembly: FASTQ files were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: txt files include gene_symbol and FPKM for each sample

growth_protocol: Raw264.7 cells (#TIB-71, ATCC) were cultured in 35 mm dishes in DMEM supplemented with 10% FBS overnight to 80% confluence.

extract_protocol:
After treatments, total RNAs were isolated from cells using TRIzol Reagent (Invitrogen), followed by purification with the PureLink RNA Mini Kit (Invitrogen). RNA samples with concentrations of 150 ng/µL and RIN values >8 were used for RNA sequence study performed by the Cancer Genomics Center at The University of Texas Health Science Center at Houston for RNA-seq analysis.
RNA samples were subjected to rRNA depletion, strand-specific library preparation, and paired-end 150-bp sequencing on the Illumina NovaSeq X platform. Library quality was assessed using an Agilent Bioanalyzer prior to sequencing.

treatment_protocol: RAW264.7 cells were treated with LPS (100 ng/mL; Sigma, Cat# L4391-1MG) or LPS (100 ng/mL) plus 3A2 (MMP14-neutralizing antibody, 50 µg/mL) for 24 hours. All treatments were performed in biological triplicates.

value: Macrophage

value: plain

value: Raw264.7 treated with LPS (100 ng/mL) and 3A2 (50 μg)

value: 24 hrs


title: Grp4, miRFP670 quartile sort, upper quartile

description: Library name: Grp4, eeBxb1, miRFP670 bin 4


title: OVCAR3_STAT3_C&R_Cis_DAC_R1

description: Library name: Sample 7

value: Primary ovarian cancer cells


title: Muscle, Individual 3, Summer (N1)

description: Library name: sm_3_N1

data_processing:
Processed data files were generated from raw small RNA sequencing reads following standard quality control and preprocessing steps. Raw FASTQ files provided at the lane level were concatenated per sample, and only read 1 (R1) files were retained, as small RNA inserts are fully contained within R1 reads.
Assembly: https://doi.org/10.6084/m9.figshare.28726535.v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

extract_protocol:
For small RNA sequencing, total RNA samples were enriched for short RNA species by size selection using denaturing polyacrylamide gel electrophoresis on Novex™ TBE–Urea gels (Invitrogen) run in TBE Running Buffer (LC6675). Gel fragments corresponding to the expected size range of small RNAs, including mature microRNAs, were excised and purified.
Small RNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina, 15016911) according to the manufacturer’s instructions. Libraries were sequenced by Quick Biology (Pasadena, CA, USA) on an Illumina NextSeq 500 platform using paired-end 75 bp reads. Although paired-end sequencing was performed, only read 1 (R1), which fully covers the mature small RNA insert, was used for downstream analyses.

value: Muscle

value: winter


title: Mouse extraorbital lacrimal gland ZT21 biological replicate 2

description:
Library name: LG_C21_2
ZT21; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: OVCAR3_STAT3_C&R_DAC_R2

description: Library name: Sample 6

value: DAC

value: 72 hour


title: LPS +3A2 -1

description:
Library name: Sun7_LPS-3A2
Pluto RNA-seq pipeline


title: LPS +3A2 -2

description:
Library name: Sun8 LPS-3A2
Pluto RNA-seq pipeline


title: Grp4, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp4, eeBxb1, miRFP670 bin 3

data_processing:
DNA was sequenced using a NextSeq 550 Mid output (130 million reads) 150 cycle kit (Illumina) at the Case Western Reserve University Genomics Core Facility
Reads were converted to fastq format and demultiplexed by the Case Western Reserve University Genomics Core Facility.  Paired-end reads were combined using PEAR (PMC3933873) using default statistical settings.
Each paired end read was tested for exact matches from the expected library and included as a read for the appropriate library member if applicable.  Read count relative to total number of reads in the sample was used to calculate read frequency for each expected library member.
Read frequencies for quartiles from the same fluorophore sort and the same group were used to calculate a weighted average Sort-Seq score for each fluorophore for expected library member.  Scores were averaged across groups to provide a final Sort-Seq score for each expected library member.  The Sort-Seq scores were used for further analysis in the manuscript.
Assembly: Synthetic Sequences
Supplementary files format and content: "processed_data_counts_frequencies.csv" is a comma separated values data table containing read counts and read frequencies for all observed DNA sequences (library_sequence, column 1).  Each row represents a DNA sequence of interest, and each column represents either a read count ("_counted") or a read frequency ("_freq") for each sample ("IXXXX", corresponding with IXXXX from file names as described in SAMPLES section).

extract_protocol:
Genomic DNA was extracted using a Dneasy Blood and Tissue Kit (Qiagen, 69506) and DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265)
Extracted genomic DNA was used as a template to produce a 1564 nucleotide amplicon spanning the genomic integration junction.  Samples were run with gel electrophoresis, the appropriate band was extracted using a Bio-Rad Freeze 'N Squeeze DNA Gel Extraction Spin Column (Bio-Rad, 7326165) and cleaned using a Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4004).  The resulting DNA was used as the template for to produce a 299 nudleotide amplicon surrounding the DNA sequence of interest using distinct indices for each quartile to be run on the same Illumina NextSeq 550 kit run.  Samples were again run with gel electrophoresis, extracted, and cleaned.  DNA concentration was calculated using a Qubit 4 fluorometer (Thermo Fisher, Q33238) using a Qubit Broad Range dsDNA assay kit (Thermo Fisher, Q33265).  DNA amplicons were pooled to a final concentration of 10-20ng/uL in 21uL of nuclease free water using 15-20ng of DNA from each quartile prior to running the Illumina NextSeq 550 kit.

value: Cultured Cells

value: Recombination into


title: Mouse extraorbital lacrimal gland ZT21 biological replicate 1

description:
Library name: LG_C21_1
ZT21; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: OVCAR3_STAT3_C&R_DAC_R1

description: Library name: Sample 5


title: Grp4, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp4, eeBxb1, miRFP670 bin 2


title: LPS -3

description:
Library name: Sun6 _LPS
Pluto RNA-seq pipeline

value: Raw264.7 treated with LPS (100 ng/mL)


title: Mouse extraorbital lacrimal gland ZT18 biological replicate 3

description:
Library name: LG_C18_3
ZT18; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

value: extraorbital lacrimal gland


title: LPS- 2

description:
Library name: Sun5 _LPS
Pluto RNA-seq pipeline


title: Grp4, miRFP670 quartile sort, lower quartile

description: Library name: Grp4, eeBxb1, miRFP670 bin 1


title: OVCAR3_STAT3_C&R_Cis_R2

description: Library name: Sample 4

value: Cisplatin


title: Mouse extraorbital lacrimal gland ZT18 biological replicate 2

description:
Library name: LG_C18_2
ZT18; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

value: wild type

value: same sequencing batch


title: OVCAR3_STAT3_C&R_Cis_R1

description: Library name: Sample 3


title: Grp4, mKG quartile sort, upper quartile

description: Library name: Grp4, eeBxb1, mKG bin 4


title: Mouse extraorbital lacrimal gland ZT18 biological replicate 1

description:
Library name: LG_C18_1
ZT18; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: OVCAR3_STAT3_C&R_Untreated_R2

description: Library name: Sample 2

value: Untreated


title: Grp4, mKG quartile sort, upper middle quartile

description: Library name: Grp4, eeBxb1, mKG bin 3


title: LPS-1

description:
Library name: Sun4 _LPS
Pluto RNA-seq pipeline

value: Macrophage


title: LIME-seq, fecal samples, TVA diet#5

city: Pasadena

first: Cheng-Wei

last: Ju

address: 1200 E California Blvd

institute: California Institute of Technology

description: Library name: YPO-10

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.6)
PCR duplicates were removed with the BBMap tool (https://sourceforge.net/projects/bbmap/).
Random barcodes at reads end were trimmed, and low-quality reads were removed using the cutadapt tool again
Then the remaining reads were aligned to the mouse genome (GRCm38) using  bowtie2 (version 2.5.1) allowing a maximum of three mismatches.
Cleaned reads that failed to align to the human genome were applied using Kraken2 with its standard database, which contains bacterial, archaeal, viral, and human sequences. Based on the aligned results from Kraken2, we normalized the data by calculating the reads per million. Then we performed student t-test (two tailed) to calculate the p value for the differential expression.
Assembly: GRCm38
Assembly: Kraken 2 standard database
Supplementary files format and content: tsv file containing the reads of various microbial abundance from fecal RNAs.
Supplementary files format and content: csv file containing the p value, fold change, and mutation ratio at modified sites in fecal RNAs (aligned on microbiome)

source_name: Fecal

extract_protocol:
Total RNA was isolated from stool samples using TRIzol following standard protocols.
Briefly, RNA was fragmented before end-repaired, and ligated to 3′ adapters, followed by reverse transcription using a robust HIV reverse transcriptase to enable efficient readthrough at methylated nucleotides. cDNA products were subsequently ligated to adapters, PCR-amplified, and sequenced on an Illumina NovaSeq platform (PE150). Only R1 reads have been applied for the downstream analysis.

value: Fecal

value: TVA diet


title: OVCAR3_STAT3_C&R_Untreated_R1

first: Heather

last: O'Hagan

institute: Indiana University

description: Library name: Sample 1


title: Grp4, mKG quartile sort, lower middle quartile

description: Library name: Grp4, eeBxb1, mKG bin 2


title: Mouse extraorbital lacrimal gland ZT15 biological replicate 3

description:
Library name: LG_C15_3
ZT15; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: Mouse extraorbital lacrimal gland ZT15 biological replicate 2

description:
Library name: LG_C15_2
ZT15; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: LIME-seq, fecal samples, TVA diet#4

description: Library name: YPO-09


title: Grp4, mKG quartile sort, lower quartile

description: Library name: Grp4, eeBxb1, mKG bin 1


title: LIME-seq, fecal samples, TVA diet#3

description: Library name: YPO-08


title: LNCaP CE Acetalax 10uM 4h, replicate 3

first: Yves

last: Pommier

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
Library name: LNCaP_CE_Acetalax4h_rep3
LNCaP chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
24_LNCaP_CE_Acetalax_3_S24_001

data_processing:
Raw FASTQ files were processed using the RENEE RNA-seq analysis pipeline. Quality control was performed using FastQC. Reads were aligned to the human reference genome (hg38) using STAR (v2.7). Gene-level quantification was performed using RSEM.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Processed data files include gene-level expression matrices in FPKM and/or raw counts format for all samples. Files contain one row per gene and one column per sample, with gene symbols and expression values.

source_name: prostate cancer (cell line)

growth_protocol: PC3 and LNCaP cells were cultured under standard conditions. PC3 cells were maintained in F-12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin. LNCaP cells were cultured in RPMI-1640 medium containing 10% FBS and 1% penicillin–streptomycin. Cells were grown at 37 °C in a humidified 5% CO₂ incubator and routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed using the Agilent TapeStation system. 800 ng of high-quality RNA (poly(A)+) from each sample was used for library preparation.
Poly(A) mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490). Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7765) with sample purification beads and NEBNext Unique Dual Index primers (E6440S). Libraries were sequenced on an Illumina NextSeq 2000 instrument using paired-end 100 bp reads.

treatment_protocol: For short-term drug exposure, cells were treated with Acetalax at 10 µM for 4 hours. Control samples received no treatment. Chronic exposure (CE) derivatives were generated by culturing parental cells under gradually increasing Acetalax concentrations over multiple passages until stable resistance was established. CE cells were cultured in drug-free medium for two weeks prior to RNA extraction.

value: prostate cancer (cell line)

value: LNCaP CE

value: epithelial cancer cell line

value: Acetalax 10 µM, 4 h


title: Mouse extraorbital lacrimal gland ZT15 biological replicate 1

description:
Library name: LG_C15_1
ZT15; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: LNCaP CE Acetalax 10uM 4h, replicate 2

description:
Library name: LNCaP_CE_Acetalax4h_rep2
LNCaP chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
23_LNCaP_CE_Acetalax_2_S23_001


title: Grp4, mCherry quartile sort, upper quartile

first: Kenneth

last: Matreyek

institute: Case Western Reserve University

description: Library name: Grp4, eeBxb1, mCherry bin 4


title: LIME-seq, fecal samples, TVA diet#2

description: Library name: YPO-07


title: Mouse extraorbital lacrimal gland ZT12 biological replicate 3

description:
Library name: LG_C12_3
ZT12; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: Grp4, mCherry quartile sort, upper middle quartile

description: Library name: Grp4, eeBxb1, mCherry bin 3


title: LNCaP CE Acetalax 10uM 4h, replicate 1

description:
Library name: LNCaP_CE_Acetalax4h_rep1
LNCaP chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
22_LNCaP_CE_Acetalax_1_S22_001


title: LIME-seq, fecal samples, TVA diet#1

description: Library name: YPO-06


title: Mouse extraorbital lacrimal gland ZT12 biological replicate 2

description:
Library name: LG_C12_2
ZT12; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: LNCaP CE control, replicate 3

description:
Library name: LNCaP_CE_control_rep3
LNCaP chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
21_LNCaP_CE_control_3_S21_001


title: Mouse extraorbital lacrimal gland ZT12 biological replicate 1

description:
Library name: LG_C12_1
ZT12; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: LNCaP CE control, replicate 2

description:
Library name: LNCaP_CE_control_rep2
LNCaP chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
20_LNCaP_CE_control_2_S20_001


title: LIME-seq, fecal samples, control diet#5

description: Library name: YPO-05

value: Control diet


title: Grp4, mCherry quartile sort, lower quartile

description: Library name: Grp4, eeBxb1, mCherry bin 1


title: Grp4, mCherry quartile sort, lower middle quartile

description: Library name: Grp4, eeBxb1, mCherry bin 2


title: LIME-seq, fecal samples, control diet#4

description: Library name: YPO-04


title: LNCaP CE control, replicate 1

description:
Library name: LNCaP_CE_control_rep1
LNCaP chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
19_LNCaP_CE_control_1_S19_001


title: Grp3, miRFP670 quartile sort, upper quartile

description: Library name: Grp3, eeBxb1, miRFP670 bin 4


title: LIME-seq, fecal samples, control diet#3

description: Library name: YPO-03


title: Mouse extraorbital lacrimal gland ZT9 biological replicate 2

description:
Library name: LG_C9_2
ZT9; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: PC3 CE Acetalax 10uM 4h, replicate 3

description:
Library name: PC3_CE_Acetalax4h_rep3
PC3 chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
18_PC3-CE_Acetalax_3_S18_001

value: PC3 CE


title: Mouse extraorbital lacrimal gland ZT9 biological replicate 3

description:
Library name: LG_C9_3
ZT9; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: Grp3, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp3, eeBxb1, miRFP670 bin 3

value: Cultured Cells


title: Mouse extraorbital lacrimal gland ZT9 biological replicate 1

description:
Library name: LG_C9_1
ZT9; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: PC3 CE Acetalax 10uM 4h, replicate 2

description:
Library name: PC3_CE_Acetalax4h_rep2
PC3 chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
17_PC3-CE_Acetalax_2_S17_001


title: Grp3, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp3, eeBxb1, miRFP670 bin 2

value: Recombination into


title: LIME-seq, fecal samples, control diet#2

description: Library name: YPO-02


title: LIME-seq, fecal samples, control diet#1

description: Library name: YPO-01


title: Mouse extraorbital lacrimal gland ZT6 biological replicate 3

description:
Library name: LG_C6_3
ZT6; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: PC3 CE Acetalax 10uM 4h, replicate 1

description:
Library name: PC3_CE_Acetalax4h_rep1
PC3 chronic-exposure (Acetalax-resistant) cells treated with Acetalax (10 µM) for 4 hours prior to RNA extraction.
16_PC3-CE_Acetalax_1_S16_001


title: PC3 CE control, replicate 3

description:
Library name: PC3_CE_control_rep3
PC3 chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
15_PC3-CE_control_3_S15_001


title: Grp3, miRFP670 quartile sort, lower quartile

description: Library name: Grp3, eeBxb1, miRFP670 bin 1


title: Mouse extraorbital lacrimal gland ZT6 biological replicate 2

description:
Library name: LG_C6_2
ZT6; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: Grp3, mKG quartile sort, upper quartile

description: Library name: Grp3, eeBxb1, mKG bin 4


title: Mouse extraorbital lacrimal gland ZT6 biological replicate 1

description:
Library name: LG_C6_1
ZT6; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: F3_WT5moPFC

first: Sarah

last: Scheinman

state: Illinois

address: Northwestern Univ 303 E., Ave IL

department: Psychiatry and Behavioral Sciences

institute: Northwestern University

description: Library name: F3_WT5moPFC

data_processing:
Isolated DNA from prefrontal cortical nuclear extracts were prepared for CUT&RUN (Cleavage Under Target and Release Using Nuclease) sequencing according to the manufacturer’s protocol (14-1048, EpiCypher). Cortical nuclei were washed with CUT&RUN wash buffer (200mM HEPES, 150mM NaCl, 0.5mM spermidine), bound to activated ConA beads, permeabilized in wash buffer (wash buffer + 0.002% digitonin), incubated with 1ug/sample H3K27ac antibodies (ab4729), washed in wash buffer, incubated with calcium-activated pAG-MNase. CUT&RUN enriched DNA was then purified using a column clean up kit optimized for small fragments. Library preparation was carried out using the NEBNext Ultra II DNA Library Prep Kit (NEB #E7103). Briefly, purified DNA was repaired, ligated to sequencing adapters, and PCR-amplified to generate Next Generation Sequencing (NGS) libraries for each sample. Genome-wide sequencing with 150-bp paired-end reads was carried out by NovoGene Corporation (Sacramento, CA) using the NovaSeq PE150.
The basic analysis workflow for paired-end CUT&RUN sequencing data was carried out using SciDAP: NGS Bioinformatics Platform (Kartashov & Barski, 2015). In brief, TrimGalore was used to trim the raw fastq riles and remove adaptors, the trimmed fastq files were then mapped to the mouse (mm10) genome using Bowtie2 (Langmead et al., 2009), formatted to account for fragments based on paired-end BAM, broad and narrow peaks called using the MACS2 tool (Zhang et al., 2008) with default parameters, and differential peak analysis was performed using DiffBind (Ross-Innes et al., 2012) with a multiple-testing adjusted false discovery threshold >0.1. The workflow was loosley based on the CUT-RUNTools-2.0 pipeline (https://github.com/fl-yu/CUT-RUNTools-2.0).
Assembly: Mus musculus (mm10) Genome Reference Consortium Mouse Build 38 (mm10). Strain: C57BL/6J.
Supplementary files format and content: Fast Q Files
Library strategy: CUT&Run

source_name: Brain

extract_protocol:
Nuclei extraction from mouse brain tissue
NEBNExt Ultra II DNA Library Prep Kit

value: Brain


title: M3_WT5moPFC

description: Library name: M3_WT5moPFC


title: PC3 CE control, replicate 2

description:
Library name: PC3_CE_control_rep2
PC3 chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
14_PC3-CE_control_2_S14_001


title: Grp3, mKG quartile sort, upper middle quartile

address: 2103 Cornell Rd, Room 5104

description: Library name: Grp3, eeBxb1, mKG bin 3


title: Mouse extraorbital lacrimal gland ZT3 biological replicate 3

description:
Library name: LG_C3_3
ZT3; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

value: extraorbital lacrimal gland


title: M2_WT5moPFC

description: Library name: M2_WT5moPFC


title: F2_WT5moPFC

description: Library name: F2_WT5moPFC


title: PC3 CE control, replicate 1

description:
Library name: PC3_CE_control_rep1
PC3 chronic-exposure (Acetalax-resistant) cells cultured under standard conditions; no drug treatment prior to RNA extraction.
13_PC3-CE_control_1_S13_001


title: Grp3, mKG quartile sort, lower middle quartile

description: Library name: Grp3, eeBxb1, mKG bin 2


title: LNCaP parental Acetalax 10uM 4h, replicate 3

description:
Library name: LNCaP_parental_Acetalax4h_rep3
LNCaP parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
12_LNCaP_Actetalax_3_S12_001

value: LNCaP


title: Mouse extraorbital lacrimal gland ZT3 biological replicate 2

description:
Library name: LG_C3_2
ZT3; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

value: wild type


title: Grp3, mKG quartile sort, lower quartile

description: Library name: Grp3, eeBxb1, mKG bin 1


title: Mouse extraorbital lacrimal gland ZT3 biological replicate 1

description:
Library name: LG_C3_1
ZT3; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle

value: same sequencing batch


title: LNCaP parental Acetalax 10uM 4h, replicate 2

description:
Library name: LNCaP_parental_Acetalax4h_rep2
LNCaP parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
11_LNCaP_Actetalax_2_S11_001


title: Grp3, mCherry quartile sort, upper quartile

description: Library name: Grp3, eeBxb1, mCherry bin 4


title: Mouse extraorbital lacrimal gland ZT0 biological replicate 3

description:
Library name: LG_C0_3
ZT0; biological replicate 3; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: F1_WT5moPFC

description: Library name: F1_WT5moPFC


title: LNCaP parental Acetalax 10uM 4h, replicate 1

description:
Library name: LNCaP_parental_Acetalax4h_rep1
LNCaP parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
10_LNCaP_Actetalax_1_S10_001


title: M1_WT5moPFC

description: Library name: M1_WT5moPFC


title: Grp3, mCherry quartile sort, upper middle quartile

description: Library name: Grp3, eeBxb1, mCherry bin 3


title: Mouse extraorbital lacrimal gland ZT0 biological replicate 2

description:
Library name: LG_C0_2
ZT0; biological replicate 2; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: F2_WT18moPFC

description: Library name: F2_WT18moPFC


title: LNCaP parental control, replicate 3

description:
Library name: LNCaP_parental_control_rep3
LNCaP parental cells cultured under standard conditions; no drug treatment; RNA extracted for transcriptomic profiling
09_LNCaP_control_3_S9_001


title: M3_WT18moPFC

description: Library name: M3_WT18moPFC


title: Grp3, mCherry quartile sort, lower middle quartile

description: Library name: Grp3, eeBxb1, mCherry bin 2


title: Mouse extraorbital lacrimal gland ZT0 biological replicate 1

description:
Library name: LG_C0_1
ZT0; biological replicate 1; male C57BL/6J mouse extraorbital lacrimal gland; 12:12 light-dark cycle


title: Grp3, mCherry quartile sort, lower quartile

description: Library name: Grp3, eeBxb1, mCherry bin 1


title: M2_WT18moPFC

description: Library name: M2_WT18moPFC


title: LNCaP parental control, replicate 2

description:
Library name: LNCaP_parental_control_rep2
LNCaP parental cells cultured under standard conditions; no drug treatment; RNA extracted for transcriptomic profiling
08_LNCaP_control_2_S8_001


title: WT_3_inf

first: Benson

last: Otarigho

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 24.0.rc1  that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Sequences were mapped to W274 C elegans genome
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Assembly: Genome_build: Caenorhabditis elegans genome WS274
Supplementary files format and content: tabular files include htseq-count/values for each Sample

organism: Caenorhabditis elegans

source_name: C elegans whole animal

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC. These animals were infected with S. aureus for 4 hours at 25C

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Purification of Total RNA was done using the TURBO DNase.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: C elegans whole animal

value: Wild type (N2)

value: Animals were infected with S. aureus for 4 hours wash with M9 buffer, and frozen (-80 C), total RNA extacted


title: LNCaP parental control, replicate 1

description:
Library name: LNCaP_parental_control_rep1
LNCaP parental cells cultured under standard conditions; no drug treatment; RNA extracted for transcriptomic profiling
07_LNCaP_control_1_S7_001


title: Grp2, miRFP670 quartile sort, upper quartile

description: Library name: Grp2, wtBxb1, miRFP670 bin 4


title: WT_2_inf


title: F3_WT18moPFC

description: Library name: F3_WT18moPFC


title: PC3 parental Acetalax 10uM 4h, replicate 3

description:
Library name: PC3_parental_Acetalax4h_rep3
PC3 parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
06_PC3_Acetalax_3_S6_001


title: Grp2, miRFP670 quartile sort, upper middle quartile

description: Library name: Grp2, wtBxb1, miRFP670 bin 3


title: M1_WT18moPFC

description: Library name: M1_WT18moPFC


title: WT_1_inf


title: Grp2, miRFP670 quartile sort, lower middle quartile

description: Library name: Grp2, wtBxb1, miRFP670 bin 2


title: F1_WT18moPFC

description: Library name: F1_WT18moPFC


title: PC3 parental Acetalax 10uM 4h, replicate 2

description:
Library name: PC3_parental_Acetalax4h_rep2
PC3 parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
05_PC3_Acetalax_2_S5_001


title: nmr2_3_inf


title: Grp2, miRFP670 quartile sort, lower quartile

description: Library name: Grp2, wtBxb1, miRFP670 bin 1


title: Rice leaf, moderate salinity, rep 2

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

description:
Library name: Moderate.Salinity.Rep2
10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1 (Dual Index)

data_processing:
Raw reads were pseudoaligned to the IRGSP1.0 transcriptome (Kawahara et al., 2013) and quantified with scKB (Hsu et al., 2022).
High-quality nuclei were selected with COPILOT (Hsu et al., 2022; minimum 600 UMIs per nucleus) and doublets were removed with DoubletFinder (McGinnis et al., 2019).
Nuclear transcriptomes were loaded into separate Seurat objects with Seurat v5.1.0 (Hao et al., 2024) and counts were normalized and scaled (5000 most variable features).
Nuclei with >10% chloroplast reads were removed. All rRNA, all organellar genes, and nuclear genes with fewer than 100 counts across all nuclei were removed for downstream analyses.
To integrate the samples, integration anchors across all libraries were identified and projected with RPCA (reciprocal principal component analysis) with Seurat's IntegrateLayers().
Nuclei were clustered and manually annotated with tissue systems and cell types (metadata columns TissueSystem and CellAnnotation).
Assembly: IRGSP1.0
Supplementary files format and content: OsLeafStressIntegrated.rds: Fully processed, integrated, and annotated dataset (Seurat v5 R object).
Supplementary files format and content: Gene counts output from COPILOT (Hsu et al., 2022); contains filtered, high-quality cells with doublets removed. Sparse matrices in Market Exchange (MEX) format, consisting of gzipped tsv files of barcodes and genes, and gzipped matrix files.

organism: Oryza sativa

source_name: Developing third leaf, ~6cm

growth_protocol: Oryza sativa cv. Nipponbare rice seeds were germinated in moist, dark conditions at 30°C for 96 h prior to planting. Rice seedlings were grown in a Conviron growth chamber with a 12 h day/night cycle, 30°C/25°C day/night temperatures, 700 μmol/m2/s light intensity, and 80% relative humidity. Pots were weighed daily and were re-watered to their original weight with tap water to maintain their set SWC until the third leaves had emerged ~1 cm beyond the sheath collar, for a full length of ~6-7cm.

extract_protocol:
Nuclei were isolated as described in Guillotin et al., (Guillotin et al., 2023) with modifications. Briefly, for each condition, one developing leaf from the shoot apical meristem to the green leaf tip (6-7 cm), was dissected at ZT 2 (Zeitgeber Time) and placed in 300 µL of ice cold lysis buffer [0.3 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 15 mM Tris-HCl, 20 mM MES, 10 mM MgCl₂, 60 mM KCl, 15 mM NaCl, 0.5 mM spermine and spermidine, 0.05% Triton X-100, 5 mM DTT, 1 mM PMSF, 1% Protease Inhibitor Cocktail, 0.4 u/µl Protector RNase Inhibitor, 0.4% BSA, 1% DEPC] and chopped with a razor blade for four minutes. The macerated tissue was gently ground with a micropestle, then filtered through a 20µm microcentrifuge-top filter and centrifuged at 500 x g for 10 minutes. The pellet of nuclei was resuspended in 300 µL of wash buffer [0.3 M sucrose, 15 mM Tris-HCl, 15 mM MES, 60 mM KCl, 15 mM NaCl, 2 mM EDTA, 0.5 mM spermine and spermidine, 0.05% Triton X-100, 5 mM DTT, 1 mM PMSF, 1% Protease Inhibitor Cocktail, 0.2 u/µl Protector RNase Inhibitor, 0.4% BSA] and centrifuged at 500 x g for 5 minutes. The pellet of nuclei was resuspended in 80 µL of final buffer [0.3 M sucrose, 15 mM Tris-HCl, 15 mM MES, 60 mM KCl, 15 mM NaCl, 0.5 mM spermine and spermidine, 5 mM DTT, 1% Protease Inhibitor Cocktail, 0.2 u/µl Protector RNase Inhibitor, 1% BSA] and filtered through a 10µm microcentrifuge-top filter.
Approximately 16,000 nuclei per sample were prepared for sequencing using the 10X Genomics Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 (Dual Index) protocol without modification on the 10X Genomics Chromium X instrument. Libraries were sequenced at Génome Québec (Montréal, QC, Canada) for sequencing of 100 bp paired-end reads on a NovaSeq 6000 (Illumina, San Diego, CA, USA).

treatment_protocol: Stable gravimetric soil water content (SWC) was achieved by mixing oven-dried soil with tap water or NaCl made with tap water, as follows: 3 g water/g soil for the well-watered control; 1.5 g water/g soil for mild drought; 1 g water/g soil for moderate drought; 3 g of 100 mM NaCl/g soil for the mild salinity; 3 g of 200 mM NaCl/g soil for the moderate salinity. Mild salinity had a consistent electrical conductivity (EC) of 1.25 mS/cm throughout the experiment, while moderate salinity had an EC of 2.5 mS/cm; well-watered control had an EC of 0.5 mS/cm.

value: Developing third leaf, ~6cm

tag: cultivar

value: Nipponbare

value: Moderate salinity; 3 g 200 mM NaCl / g soil


title: PC3 parental Acetalax 10uM 4h, replicate 1

description:
Library name: PC3_parental_Acetalax4h_rep1
PC3 parental cells treated with Acetalax (10 µM) for 4 hours before RNA extraction
04_PC3_Acetalax_1_S4_001

value: prostate cancer (cell line)

tag: cell line

value: epithelial cancer cell line