title: 30a

value: Patient 13

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

tag: side

tag: lobe location

tag: p53 mutation

tag: egfr

value: Not Hypermethylated/ Unmethylated

tag: number of fractions

tag: cycles completed


title: tumor-infiltrating type 1 conventional dendritic cells, Wild type, Day13, rep1

status: Public on Apr 10 2026

type: SRA

city: Xiamen

first: Hongjiao

last: Wang

address: xiangannanlu

country: China

institute: xiamen university

description:
Library name: Sample 4
WT_DC1_1

library_source: transcriptomic

data_processing:
Data quality control: Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstreamanalyses were basedon the clean data with high quality.                                                                                Reads mapping to the reference genome: Reference genome and gene model annotation files were downloadedfrom genome website. Use HISAT2 (2.2.1) to build the index of thereference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotationfiletocreate splice-aware alignments, providing better alignment accuracycompared to other non-splice alignment tools.                     Quantification of gene expression level: featureCounts (2.0.6) was used to count the reads numbers mappedtoeach gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequenceper Millions base pairs sequenced, considers the effect of sequencingdepthand gene length for the reads count at the same time, and is currentlythe most commonly used method for estimating gene expressionlevels.                         Differential expression analysis: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control theerror discovery rate. The threshold of significant differential expression：padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm10
Supplementary files format and content: CSV file includes raw counts for each sample.

molecule: total RNA

organism: Mus musculus

source_name: B16-F10 subcutaneous tumor

extract_protocol:
Total RNA were extracted using Life-Trizol. A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations.
Messenger RNA (mRNA) was enriched from total RNA using oligo(dT) magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Subsequently, the cDNA fragments underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification to generate the final sequencing library.

tag: tissue

value: B16-F10 subcutaneous tumor

tag: cell type


title: 23a

type: RNA

city: Miami

first: Glaucia Maria

middle: de

last: Mendonça Fernandes

state: FL

address: 4060 SW 97th PL

department: HWCOM Cellular and Molecular Medicine

country: USA

institute: Florida International University

description: Arraystar Human m6A Single Nucleotide resolution in microarray hybridization were performed based on the Arraystar’s standard protocols. total RNA was divided into two fractions. treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human m6A Single Nucleotide Arrays (8x15K, Arraystar) at 60°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Raw data was extracted using Agilent Feature Extraction software, retaining probe signals with "P" or "M" quality flags in at least 15 samples. Intensities from MazF-Digested (Cy5-labeled) and MazF-Undigested (Cy3-labeled) samples were normalized using RNA spike-in controls. The normalized MazF-Digested intensities represent the "m6A site abundance" for comparison across samples.
The m6A site abundance was calculated using the normalized intensity of MazF-Digested (Cy5-labeled) RNA, adjusted with spike-in controls. The percentage of m6A methylation (%Modified) was determined by comparing the normalized intensities of MazF-Digested (Cy5) and MazF-Undigested (Cy3) samples, incorporating a correction factor based on sample amounts.

label: MazF-Digested (Cy5-labelled), MazF-Undigested (Cy3-labelled)

organism: Homo sapiens

source_name: Progression Disease

label_protocol: "MazF-Digested" and "MazF-Undigested" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Tissue specimens for molecular analysis were selected based on clinical history as PD or psPD, determined by an interdisciplinary tumor board.

extract_protocol: The purity and amount of total RNA samples were determined with NanoDrop ND-1000. RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. Results were provided in Sample QC report.

treatment_protocol: All samples were collected from the original second surgery and stored as archival formalin-fixed paraffin-embedded (FFPE) tissue.

tag: subject

value: Patient 6

tag: batch

value: First

value: Glioblastoma

value: Deceased

value: Female

value: Right

value: Frontal

value: Positive

value: No

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered


title: 33a

source_name: pseudo Progression Disease

value: Patient 19

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

tag: lobe location

value: Temporal


title: 22a

value: Patient 5

tag: tissue

value: Parietal

tag: p53 mutation

tag: egfr

tag: number of fractions

tag: cycles completed


title: 17a

tag: subject

value: Patient 3

tag: batch

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin


title: 14a

value: Patient 2

value: First

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered


title: 13a

value: Patient 1

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

tag: side

value: Left


title: GM12878 RNA-seq library, IL2 , 6h , replicate 1

city: Atlanta

first: Alexander

middle: O. D.

last: Gulka

state: Georgia

address: 1510 Clifton Rd NE

institute: Emory University

description: Library name: GM12878_RNA_IL2_6h_rep1

data_processing:
Data were processed using the ENCODE RNA-seq pipeline (v1.2.4, https://github.com/ENCODE-DCC/rna-seq-pipeline), executed using Singularity containers. Reads were mapped to the hg38 reference genome using STAR and gene-level expression quantifications were produced using RSEM.
Assembly: hg38
Supplementary files format and content: RSEM gene-level expression quantifications for each biological replicate, provided as tab-separated value (TSV) files.

molecule: polyA RNA

growth_protocol: GM12878 cells were cultured in suspension using RPMI-1640 medium (Thermo Scientific, A1049101) supplemented with 2 mM L-glutamine (Thermo Scientific, 25030081), 15% fetal bovine serum (FBS; Fisher Scientific, 10-082-147), and 100U/mL penicillin/streptomycin (Fisher Scientific, 15-140-122). HepG2 cells were cultured in Eagle’s Minimal Essential Medium (ATCC, 30-2003) supplemented with 10% FBS and 100U/mL penicillin/streptomycin.  HepG2 cells were passaged using Trypsin-EDTA (Fisher Scientific, 25-200-072). All cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were harvested by centrifugation at 500 x g for 5 min, and after removing supernatant cell pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Cells were disrupted using QIAshredder columns (Qiagen, 79656) and total RNA was prepared using RNeasy Mini kits (Qiagen, 74104) as per manufacturer protocol. RNA quality was assessed using High Sensitivity RNA ScreenTapes (Agilent, 5067-5580) run on an Agilent 4200 TapeStation system.
PolyA-enriched, stranded RNA-seq libraries were generated from 500ng total RNA for each sample using the Illumina Stranded mRNA prep kit (Illumina, 20040534) following manufacturer protocol. Completed libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) with dsDNA High Sensitivity Assay reagents (Thermo Fisher Scientific, Q32854), and library size distributions was evaluated using High Sensitivity D1000 ScreenTapes on an Agilent 4200 TapeStation system.  Libraries were sequenced (150bp paired-end) on an Illumina NovaSeq platform.

treatment_protocol: BRM014 (MedChemExpress, HY-119374) was prepared as a 10mM stock in dimethyl sulfoxide (DMSO) and used at a final concentration of 10µM unless otherwise indicated. Vehicle controls were treated with an equivalent concentration of DMSO. For initial stimulus panel, cells were treated with lipopolysaccharide (Sigma L9641, 10ng/mL), tumor necrosis factor alpha (Genscript Z01001, 25ng/mL), interferon gamma (Genscript, Z02986, 100ng/mL), interleukin 2 (Sigma, 11011456001, 50U/mL), dexamethasone (MedChemExpress, HY-14648, 500nM), or doxorubicin (Selleck Chem, E2516, 500nM) for 6h. For BAFinh pretreatment experiments, 10µM BRM014 (or DMSO vehicle) was added to cells 30min prior to the addition of either 100ng/mL IFN-γ or 500nM Dex for 1h or 6h.

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 19a

tag: subject

value: Patient 4

tag: batch

tag: tissue

tag: lobe location

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

tag: wbc

tag: number of fractions

tag: cycles completed


title: tumor-infiltrating type 1 conventional dendritic cells, Dyrk1a knock out, Day13, rep2

description:
Library name: Sample 2
cKO_DC1_2

value: B16-F10 subcutaneous tumor


title: tumor-infiltrating type 1 conventional dendritic cells, Dyrk1a knock out, Day13, rep1

description:
Library name: Sample 1
cKO_DC1_1


title: tumor-infiltrating type 1 conventional dendritic cells, Dyrk1a knock out, Day13, rep3

description:
Library name: Sample 3
cKO_DC1_3


title: GM12878 RNA-seq library, LPS , 6h , replicate 2

description: Library name: GM12878_RNA_LPS_6h_rep2

value: LPS


title: brain cortex in BTBR mice with bacterial treatment, replication 6

city: hong kong

first: Yuqi

last: Wu

state: hong kong (SAR)

address: the chinese university of hong kong

country: Hong Kong

institute: the chinese university of hong kong

description: Library name: c3_9

data_processing:
Raw sequencing data were first processed with fastp (v0.23.2) to remove adapter sequences and low-quality reads under default parameters.
The resulting high-quality reads were aligned to the mouse reference genome (GRCm39) using HISAT2 (v2.2.1).
Transcript assembly and quantification were performed to generate gene-mapped read counts and Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) values.
Assembly: mm10, hg38(GRCh38)
Supplementary files format and content: tab-delimited text file included raw counts for each cell sample
Supplementary files format and content: tab-delimited text file included raw counts for each mouse sample

source_name: brain

extract_protocol:
Total RNA was isolated from cells or tissue samples using the Vazyme RNA Isolation Kit V2 (Nanjing, China) in strict accordance with the manufacturer’s instructions.
mRNA enrichment, library construction, and high-throughput sequencing were performed by Novogene Co., Ltd. (Beijing, China). The final libraries were sequenced on an Illumina NovaSeq 6000X platform, generating 150-bp paired-end reads.

value: brain

tag: genotype

value: BTBR

value: bacterial oral gavage


title: brain cortex in BTBR mice with bacterial treatment, replication 5

description: Library name: c3_8


title: GM12878 RNA-seq library, IL2 , 6h , replicate 2

description: Library name: GM12878_RNA_IL2_6h_rep2


title: GM12878 RNA-seq library, TNF , 6h , replicate 2

description: Library name: GM12878_RNA_TNF_6h_rep2

value: TNF


title: GM12878 RNA-seq library, TNF , 6h , replicate 1

description: Library name: GM12878_RNA_TNF_6h_rep1


title: GM12878 RNA-seq library, IFNg , 6h , replicate 1

description: Library name: GM12878_RNA_IFNg_6h_rep1

value: IFNg


title: GM12878 RNA-seq library, LPS , 6h , replicate 1

description: Library name: GM12878_RNA_LPS_6h_rep1


title: P3-S10_11

city: Acton

first: Manuel

middle: Xavier

last: Duval

state: MA

address: 12 Abel Jones Pl

institute: double-strand

hyb_protocol: RNA-probe hybridizations were performed at 65°C for 17 hours, followed by digital counting on an nCounter Digital Analyzer (NanoString, Seattle, WA, USA)

scan_protocol: standard protocol

data_processing: NanoString Cancer Immune Panel Std_12 transcripts raw counts were loaded into R with the R NanoStringNCTools package. RNA quantity values were normalized with the R RUVSeq package RUV method

label: not provided

source_name: Peripheral Blood Mononuclear Cell

label_protocol: For gene expression analysis, 150 ng of RNA per sample was used using a 770-gene NanoString pan cancer immune profiling panel

extract_protocol: At each timepoint, 5 × 105 PBMCs were processed for RNA extraction using the Purelink mRNA mini kit (Thermo Fisher catalogue #12183018A)

treatment_protocol: Baseline and longitudinally collected cryopreserved peripheral blood mononuclear cells (PBMCs) were thawed quickly by swirling in a 37°C waterbath and transferred to 15-mL falcon centrifuge tubes containing RPMI + 10% fetal bovine serum (FBS), 100 μg/mL RNase free DNase I.  Cell suspensions were and incubated at room temperature for 20 min and collected at 300 × g for 7 minutes. Cell pellets 53were washed once by suspending in RPMI + 2% FBS, centrifuged at 300 × g for 7 minutes and resuspended in phosphate-buffered saline (PBS) with 2% FBS and counted. 5 × 105cells were processed for nanoString analysis

value: Peripheral Blood Mononuclear Cell

value: Internal Control

tag: dose

value: Single

tag: subject id


title: P8-S48_10

tag: cell type


title: P3-S17_06


title: P2-S15_05


title: P6-S38_08

value: Double


title: P13-S72_03


title: P7-S39_09


title: P4-S26_07


title: brain cortex in BTBR mice with bacterial treatment, replication 4

description: Library name: c3_7

tag: treatment


title: GM12878 RNA-seq library, PBS , 6h , replicate 2

description: Library name: GM12878_RNA_PBS_6h_rep2

tag: cell line

value: PBS

tag: timepoint


title: GM12878 RNA-seq library, DMSO , 6h , replicate 2

description: Library name: GM12878_RNA_DMSO_6h_rep2

value: DMSO

tag: inhibitor/protac concentration


title: brain cortex in BTBR mice with vehicle treatment, replication 3

description: Library name: c1_7

value: vehicle treatment

tag: batch


title: brain cortex in BTBR mice with bacterial treatment, replication 2

description: Library name: c3_4

tag: tissue


title: HepG2 RNA-seq library, BRM014 (10uM) , 24h , replicate 2

description: Library name: HepG2_RNA_BRM014_10uM_24h_rep2

value: Hepatocellular carcinoma


title: P12-S64_02


title: brain cortex in BTBR mice with bacterial treatment, replication 1

description: Library name: c3_2


title: GM12878 RNA-seq library, PBS , 6h , replicate 1

description: Library name: GM12878_RNA_PBS_6h_rep1

value: Lymphoblastoid cell line


title: brain cortex in BTBR mice with bacterial treatment, replication 3

description: Library name: c3_6


title: P3-S16_08


title: P7-S37_11


title: P9-S53_01


title: P6-S36_10


title: P4-S23_09


title: HepG2 RNA-seq library, BRM014 (10uM) , 24h , replicate 1

description: Library name: HepG2_RNA_BRM014_10uM_24h_rep1


title: brain cortex in BTBR mice with vehicle treatment, replication 1

description: Library name: c1_3


title: P11-S63_01


title: GM12878 RNA-seq library, DMSO , 6h , replicate 1

description: Library name: GM12878_RNA_DMSO_6h_rep1


title: 267

tag: subject

value: Patient 61

value: Second

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Right

tag: lobe location

value: Temporal

value: Positive

value: Yes

value: Hypermethylated/ Methylated

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered


title: P3-S10_12_3

tag: cell type

value: Peripheral Blood Mononuclear Cell

value: Internal Control

tag: dose

value: Single

tag: subject id


title: P2-S11_07


title: HepG2 RNA-seq library, DMSO , 24h , replicate 2

description: Library name: HepG2_RNA_DMSO_24h_rep2

tag: cell line

tag: treatment

value: DMSO

tag: timepoint

tag: inhibitor/protac concentration


title: P13-S74_05

value: Double


title: P12-S70_04


title: P1-S8_04


title: P11-S67_03


title: P10-S62_02


title: brain cortex in BTBR mice with vehicle treatment, replication 2

description: Library name: c1_5

tag: tissue

value: brain

tag: genotype

value: BTBR

value: vehicle treatment

tag: batch


title: colon in BTBR mice with bacterial treatment, replication 9

description: Library name: R3_9

source_name: colon

value: colon

value: bacterial oral gavage


title: HepG2 ATAC-seq library, BRM014 (10uM) , 24h , replicate 2

description: Library name: HepG2_ATAC_BRM014_10uM_24h_rep2

library_source: genomic

data_processing:
Data were processed using the Encyclopedia Of DNA Elements (ENCODE) ATAC-seq Pipeline, (v2.2.0, https://github.com/ENCODE-DCC/atac-seq-pipeline), executed using Singularity containers. Briefly, adapter trimming was performed using cutadaptwith parameters -e 0.1 -m 5 and reads were aligned to the hg38 reference genome using Bowtie2 [106]. Reads were filtered using SAMtools, PCR duplicates were flagged and removed using Picard, and peaks and signal tracks were generated using MACS2.
Assembly: hg38
Supplementary files format and content: Processed data files  consist of pooled ATAC-seq signal tracks (fold-change over background) generated by combining all biological replicates for each experimental condition, in bigwig format.

molecule: genomic DNA

extract_protocol:
Cells were harvested by centrifugation at 500 x g for 5 min, resuspended in cold base media (GM12878: RPMI-1640; HepG2: EMEM) supplemented with 10% DMSO, and immediately flash-frozen in liquid nitrogen to minimize recovery of chromatin accessibility following inhibitor removal. Frozen samples were rapidly thawed in a 37°C water bath and cells were pelleted by centrifugation. After washing with cold 1x PBS, cells were resuspended in cold nuclear permeabilization buffer (1x PBS, 5% w/v bovine serum albumin, 0.2% w/v IGEPAL CA-630, 1mM dithiothreitol, 1x cOmplete EDTA-free Protease Inhibitor Cocktail) and nuclei were extracted by incubation with rocking for 5 minutes at 4°C. Nuclei were pelleted and resuspended in tagmentation buffer (33mM Tris-acetate pH 7.8, 66mM potassium acetate, 11mM magnesium acetate, 16% v/v dimethylformamide).
50,000 nuclei were tagmented for 1h at 37°C with Tn5 (Illumina, 20034197). Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen, 28004) and amplified by 7-8 cycles of PCR using NEBNext High-Fidelity Q5 polymerase (New England Biolabs, M0541). Amplified libraries were size-selected using SPRIselect beads (Beckman Coulter, B23318), quantified using a Qubit fluorometer (Thermo Fisher Scientific) with dsDNA High Sensitivity Assay reagents (Thermo Fisher Scientific, Q32854), and library size distributions was evaluated using High Sensitivity D1000 ScreenTapes on an Agilent 4200 TapeStation system.  Libraries were sequenced (150bp paired-end) on an Illumina NovaSeq platform.

treatment_protocol: BRM014 (MedChemExpress, HY-119374) was prepared as a 10mM stock in dimethyl sulfoxide (DMSO) and used at a final concentration of 10µM unless otherwise indicated. Vehicle controls were treated with an equivalent concentration of DMSO. ACBI1 (opnMe, ACBI1) was similarly prepared as a 10mM stock in DMSO and used at a final concentration of 1µM. For stimulus experiments, cells were treated with  interferon gamma (Genscript, Z02986, 100ng/mL) or dexamethasone (MedChemExpress, HY-14648, 500nM) for 1 or 6h. For BAFinh pretreatment, 10µM BRM014 was added to cells 30min prior to the addition of either 100ng/mL IFN-γ or 500nM Dex for 1h or 6h.

value: Hepatocellular carcinoma


title: colon in BTBR mice with bacterial treatment, replication 10

description: Library name: R3_10


title: brain cortex in C57 mice healthy control, replication 2

description: Library name: c6

value: WT

value: NC


title: brain cortex in C57 mice healthy control, replication 1

description: Library name: c5


title: HepG2 RNA-seq library, DMSO , 24h , replicate 1

description: Library name: HepG2_RNA_DMSO_24h_rep1


title: HepG2 ATAC-seq library, DMSO , 24h , replicate 2

description: Library name: HepG2_ATAC_DMSO_24h_rep2


title: P9-S45_02


title: HepG2 ATAC-seq library, BRM014 (10uM) , 24h , replicate 1

description: Library name: HepG2_ATAC_BRM014_10uM_24h_rep1


title: P1-S5_06


title: P9-S47_08


title: P8-S43_10


title: P7-S35_11


title: P8-S40_01


title: brain cortex in C57 mice healthy control, replication 3

description: Library name: c7


title: HepG2 ATAC-seq library, DMSO , 24h , replicate 1

description: Library name: HepG2_ATAC_DMSO_24h_rep1


title: P8-S41_04


title: P8-S42_07


title: P9-S46_05


title: colon in BTBR mice with bacterial treatment, replication 7

description: Library name: R3_7


title: colon in BTBR mice with bacterial treatment, replication 8

description: Library name: R3_8


title: GM12878 ATAC-seq library, BRM014 (10uM) +Dex , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_Dex_10uM_6h_rep1

value: Lymphoblastoid cell line

value: BRM014 + Dex


title: colon in BTBR mice with bacterial treatment, replication 6

description: Library name: R3_6


title: P3-S10_12_2


title: colon in BTBR mice with bacterial treatment, replication 5

description: Library name: R3_5


title: GM12878 ATAC-seq library, BRM014 (10uM) +Dex , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_Dex_10uM_6h_rep2


title: P10-S54_09


title: P10-S52_06


title: P10-S51_03


title: P3-S10_12_1


title: colon in BTBR mice with bacterial treatment, replication 4

description: Library name: R3_4


title: GM12878 ATAC-seq library, BRM014 (10uM) +Dex , 1h , replicate 2

description: Library name: GM12878_ATAC_BRM014_Dex_10uM_1h_rep2


title: P13-S68_03


title: GM12878 ATAC-seq library, BRM014 (10uM) +IFNg , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_IFNg_10uM_6h_rep2

value: BRM014 + IFNg


title: GM12878 ATAC-seq library, BRM014 (10uM) +Dex , 1h , replicate 1

description: Library name: GM12878_ATAC_BRM014_Dex_10uM_1h_rep1


title: colon in BTBR mice with bacterial treatment, replication 3

description: Library name: R3_3


title: P13-S69_06


title: P9-S49_10


title: P13-S71_09


title: GM12878 ATAC-seq library, BRM014 (10uM) +IFNg , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_IFNg_10uM_6h_rep1


title: colon in BTBR mice with bacterial treatment, replication 2

description: Library name: R3_2


title: P12-S58_02


title: P12-S59_05


title: P11-S60_07


title: GM12878 ATAC-seq library, BRM014 (10uM) +IFNg , 1h , replicate 1

description: Library name: GM12878_ATAC_BRM014_IFNg_10uM_1h_rep1


title: P11-S57_04


title: colon in BTBR mice with vehicle treatment, replication 8

description: Library name: R1_8


title: P12-S61_08


title: GM12878 ATAC-seq library, BRM014 (10uM) +Veh , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_Veh_10uM_6h_rep2

value: BRM014 + Veh


title: colon in BTBR mice with vehicle treatment, replication 7

description: Library name: R1_7


title: colon in BTBR mice with vehicle treatment, replication 9

description: Library name: R1_9


title: colon in BTBR mice with vehicle treatment, replication 6

description: Library name: R1_6


title: colon in BTBR mice with bacterial treatment, replication 1

description: Library name: R3_1


title: GM12878 ATAC-seq library, BRM014 (10uM) +Veh , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_Veh_10uM_6h_rep1


title: GM12878 ATAC-seq library, BRM014 (10uM) +Veh , 1h , replicate 1

description: Library name: GM12878_ATAC_BRM014_Veh_10uM_1h_rep1


title: P7-S31_06

value: Peripheral Blood Mononuclear Cell


title: P11-S56_01


title: GM12878 ATAC-seq library, BRM014 (10uM) +IFNg , 1h , replicate 2

description: Library name: GM12878_ATAC_BRM014_IFNg_10uM_1h_rep2


title: P7-S34_09


title: colon in BTBR mice with vehicle treatment, replication 5

description: Library name: R1_5


title: GM12878 ATAC-seq library, BRM014 (10uM) +Veh , 1h , replicate 2

description: Library name: GM12878_ATAC_BRM014_Veh_10uM_1h_rep2


title: P6-S33_11


title: P6-S30_05


title: P10-S55_11


title: P4-S21_10


title: P7-S29_03


title: P6-S32_08


title: GM12878 ATAC-seq library, DMSO+Dex , 6h , replicate 2

description: Library name: GM12878_ATAC_DMSO_Dex_6h_rep2

value: DMSO + Dex


title: P4-S19_04


title: P6-S28_02


title: colon in BTBR mice with vehicle treatment, replication 4

description: Library name: R1_4


title: colon in BTBR mice with vehicle treatment, replication 2

description: Library name: R1_2


title: GM12878 ATAC-seq library, DMSO+Dex , 1h , replicate 2

description: Library name: GM12878_ATAC_DMSO_Dex_1h_rep2


title: colon in BTBR mice with vehicle treatment, replication 1

description: Library name: R1_1


title: GM12878 ATAC-seq library, DMSO+Dex , 1h , replicate 1

description: Library name: GM12878_ATAC_DMSO_Dex_1h_rep1


title: colon in BTBR mice with vehicle treatment, replication 3

description: Library name: R1_3


title: P4-S20_07


title: P4-S18_01


title: GM12878 ATAC-seq library, DMSO+IFNg , 6h , replicate 2

description: Library name: GM12878_ATAC_DMSO_IFNg_6h_rep2

value: DMSO + IFNg


title: GM12878 ATAC-seq library, DMSO+Dex , 6h , replicate 1

description: Library name: GM12878_ATAC_DMSO_Dex_6h_rep1


title: P3-S14_11

value: Single


title: P3-S13_09


title: P3-S10_12

value: Internal Control


title: P2-S7_05


title: colon in C57 mice healthy control, replication 5

description: Library name: Rc57_5


title: colon in C57 mice healthy control, replication 4

description: Library name: Rc57_8


title: P1-S4_10


title: GM12878 ATAC-seq library, DMSO+IFNg , 6h , replicate 1

description: Library name: GM12878_ATAC_DMSO_IFNg_6h_rep1


title: P2-S6_02


title: P3-S10_03


title: GM12878 ATAC-seq library, DMSO+IFNg , 1h , replicate 2

description: Library name: GM12878_ATAC_DMSO_IFNg_1h_rep2


title: P2-S9_08


title: P1-S2_04


title: colon in C57 mice healthy control, replication 3

description: Library name: Rc57_3


title: P3-S12_06


title: P1-S3_07


title: LD11-2170 Broad-leaf TP4 replicate 3

city: Urbana

first: Bishal

last: Tamang

state: IL

address: 1201 W Gregory Dr

institute: University of Illinois

description:
Library name: LD11_T4_R3
Broad-leaf genotype leaf emergence stage biological replicate 3

data_processing:
Raw reads were quality-checked using FastQC v0.11.9 and MultiQC v1.12
Reads were quantified using Salmon v1.9.0 with the Glycine max Wm82.a6.v1 reference transcriptome
Transcript-level abundances were summarized to gene-level counts using tximport v1.22.0
Differential expression analysis was performed using DESeq2 v1.34.0 with time-series design
Assembly: Glycine max Wm82.a6.v1 (Phytozome)
Supplementary files format and content: raw_counts_matrix.txt: Tab-delimited gene-level raw counts matrix with gene IDs as rows and sample names as columns. TPM_values.txt: Tab-delimited TPM-normalized expression values with gene IDs as rows and sample names as columns.

organism: Glycine max

source_name: mature leaf

growth_protocol: Soybean plants were grown in growth chambers under controlled conditions (25C day/20C night, 16h photoperiod, 60% relative humidity). Seeds were germinated in soil and plants were maintained until shoot apical meristem collection at specified developmental timepoints.

extract_protocol:
Total RNA was extracted from shoot apical meristem tissue using TRIzol reagent followed by purification with RNeasy Mini Kit (Qiagen). RNA quality was assessed using Agilent 2100 Bioanalyzer (RIN > 8.0 required). RNA concentration was determined using Qubit fluorometer.
Strand-specific RNA-seq libraries were prepared from polyA-selected mRNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Libraries were quantified using Qubit and quality-checked using Agilent 2100 Bioanalyzer before pooling for sequencing.

treatment_protocol: No treatment applied. This study compares genotypes with functional GmJAG1 (broad-leaf) versus D9H mutation in GmJAG1 (narrow-leaf) to identify genes regulated by GmJAG1 during leaf development.

value: mature leaf

value: LD11-2170; Functional GmJAG1


title: GM12878 ATAC-seq library, DMSO+Veh , 6h , replicate 2

description: Library name: GM12878_ATAC_DMSO_Veh_6h_rep2

value: DMSO + Veh


title: colon in C57 mice healthy control, replication 1

description: Library name: Rc57_1

value: colon


title: GM12878 ATAC-seq library, DMSO+IFNg , 1h , replicate 1

description: Library name: GM12878_ATAC_DMSO_IFNg_1h_rep1


title: LD11-2170 Broad-leaf TP4 replicate 1

description:
Library name: LD11_T4_R1
Broad-leaf genotype leaf emergence stage biological replicate 1


title: LD11-2170 Broad-leaf TP3 replicate 3

description:
Library name: LD11_T3_R3
Broad-leaf genotype late development stage biological replicate 3

source_name: young leaf

value: young leaf


title: LD11-2170 Broad-leaf TP3 replicate 2

description:
Library name: LD11_T3_R2
Broad-leaf genotype late development stage biological replicate 2


title: LD11-2170 Broad-leaf TP2 replicate 2

description:
Library name: LD11_T2_R2
Broad-leaf genotype mid development stage biological replicate 2

source_name: developing leaf

value: developing leaf


title: colon in C57 mice healthy control, replication 2

description: Library name: Rc57_2

value: WT


title: LD11-2170 Broad-leaf TP3 replicate 1

description:
Library name: LD11_T3_R1
Broad-leaf genotype late development stage biological replicate 1


title: GM12878 ATAC-seq library, DMSO+Veh , 1h , replicate 1

description: Library name: GM12878_ATAC_DMSO_Veh_1h_rep1


title: LD11-2170 Broad-leaf TP4 replicate 2

description:
Library name: LD11_T4_R2
Broad-leaf genotype leaf emergence stage biological replicate 2


title: GM12878 ATAC-seq library, DMSO+Veh , 1h , replicate 2

description: Library name: GM12878_ATAC_DMSO_Veh_1h_rep2


title: LD11-2170 Broad-leaf TP2 replicate 3

description:
Library name: LD11_T2_R3
Broad-leaf genotype mid development stage biological replicate 3


title: B2KO.UTI.5

city: Richardson

first: Xintong

last: Dong

state: TX

address: 800 W Campbell Rd

department: Biological Sciences

institute: University of Texas at Dallas

description:
Library name: B2KO.UTI.5
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.UTI.5

data_processing:
Fastq reads were aligned to the Mus musculus reference genome (ENSEMBL GRCm39.113) using STAR (version 2.7.11b) with default parameters to generate BAM files.
Assembly: BAM files were analyzed using featureCounts (version 2.0.8) to generate gene count file with ENSEMBL IDs
Supplementary files format and content: "counts_with_gene_name.csv" contains raw gene counts
Supplementary files format and content: "tpm_with_gene_name.txt" contains TPM values for each sample

source_name: Bladder

extract_protocol:
Bladders were homogenized in 500 µL TRIzol reagent (Thermo Fisher Scientific; #15596026) using a handheld homogenizer. Lysates were centrifuged at 17,000 x g for 5 min at 4 °C. RNA was purified from 450 µL lysate using the Zymo Direct-zol RNA Miniprep Kit (Zymo Research; R2050) according to the manufacturer’s protocol. RNA concentration and purity were assessed by ThermoScientific Nanodrop One (cat# 13-400-525).
Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.

value: Bladder

value: Mrgprb2 KO


title: P1-S1_01


title: LD11-2170 Broad-leaf TP2 replicate 1

description:
Library name: LD11_T2_R1
Broad-leaf genotype mid development stage biological replicate 1


title: B2KO.UTI.3

description:
Library name: B2KO.UTI.3
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.UTI.3


title: B2KO.UTI.4

description:
Library name: B2KO.UTI.4
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.UTI.4


title: LD11-2170 Broad-leaf TP1 replicate 2

description:
Library name: LD11_T1_R2
Broad-leaf genotype early development stage biological replicate 2

source_name: leaf primordium

value: leaf primordium


title: GM12878 ATAC-seq library, ACBI1 (1uM) , 24h , replicate 2

description: Library name: GM12878_ATAC_ACBI1_1uM_24h_rep2

value: Lymphoblastoid cell line


title: B2KO.UTI.2

description:
Library name: B2KO.UTI.2
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.UTI.2


title: GM12878 ATAC-seq library, DMSO+Veh , 6h , replicate 1

description: Library name: GM12878_ATAC_DMSO_Veh_6h_rep1


title: LD11-2170 Broad-leaf TP0 replicate 3

description:
Library name: LD11_T0_R3
Broad-leaf genotype vegetative meristem stage biological replicate 3

source_name: shoot apical meristem

value: shoot apical meristem


title: LD11-2170 Broad-leaf TP1 replicate 1

description:
Library name: LD11_T1_R1
Broad-leaf genotype early development stage biological replicate 1


title: LD11-2170 Broad-leaf TP1 replicate 3

description:
Library name: LD11_T1_R3
Broad-leaf genotype early development stage biological replicate 3


title: LD11-2170 Broad-leaf TP0 replicate 2

description:
Library name: LD11_T0_R2
Broad-leaf genotype vegetative meristem stage biological replicate 2


title: B2KO.UTI.1

description:
Library name: B2KO.UTI.1
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.UTI.1


title: GM12878 ATAC-seq library, ACBI1 (1uM) , 24h , replicate 1

description: Library name: GM12878_ATAC_ACBI1_1uM_24h_rep1


title: GM12878 ATAC-seq library, BRM014 (10uM) , 24h , replicate 4

description: Library name: GM12878_ATAC_BRM014_10uM_24h_rep4


title: B2KO.PBS.5

description:
Library name: B2KO.PBS.5
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.PBS.5

value: PBS


title: B2KO.PBS.4

description:
Library name: B2KO.PBS.4
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.PBS.4


title: B2KO.PBS.2

description:
Library name: B2KO.PBS.2
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.PBS.2


title: LD11-7311 Narrow-leaf TP4 replicate 1

description:
Library name: 745_T4_R1
Narrow-leaf genotype leaf emergence stage biological replicate 1

value: LD11-7311; D9H mutation in GmJAG1


title: LD11-7311 Narrow-leaf TP3 replicate 2

description:
Library name: 745_T3_R2
Narrow-leaf genotype late development stage biological replicate 2


title: LD11-7311 Narrow-leaf TP3 replicate 1

description:
Library name: 745_T3_R1
Narrow-leaf genotype late development stage biological replicate 1


title: GM12878 ATAC-seq library, BRM014 (10uM) , 24h , replicate 3

description: Library name: GM12878_ATAC_BRM014_10uM_24h_rep3


title: GM12878 ATAC-seq library, DMSO , 24h , replicate 4

description: Library name: GM12878_ATAC_DMSO_24h_rep4

value: DMSO


title: LD11-7311 Narrow-leaf TP2 replicate 3

description:
Library name: 745_T2_R3
Narrow-leaf genotype mid development stage biological replicate 3


title: LD11-7311 Narrow-leaf TP2 replicate 2

description:
Library name: 745_T2_R2
Narrow-leaf genotype mid development stage biological replicate 2


title: B2KO.PBS.3

description:
Library name: B2KO.PBS.3
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.PBS.3


title: LD11-7311 Narrow-leaf TP4 replicate 3

description:
Library name: 745_T4_R3
Narrow-leaf genotype leaf emergence stage biological replicate 3


title: GM12878 ATAC-seq library, DMSO , 24h , replicate 3

description: Library name: GM12878_ATAC_DMSO_24h_rep3


title: LD11-2170 Broad-leaf TP0 replicate 1

description:
Library name: LD11_T0_R1
Broad-leaf genotype vegetative meristem stage biological replicate 1


title: GM12878 ATAC-seq library, BRM014 (10uM) , 24h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10uM_24h_rep2


title: B2KO.PBS.1

description:
Library name: B2KO.PBS.1
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as B2KO.PBS.1


title: LD11-7311 Narrow-leaf TP3 replicate 3

description:
Library name: 745_T3_R3
Narrow-leaf genotype late development stage biological replicate 3


title: LD11-7311 Narrow-leaf TP2 replicate 1

description:
Library name: 745_T2_R1
Narrow-leaf genotype mid development stage biological replicate 1


title: LD11-7311 Narrow-leaf TP1 replicate 3

description:
Library name: 745_T1_R3
Narrow-leaf genotype early development stage biological replicate 3


title: GM12878 ATAC-seq library, DMSO , 24h , replicate 2

description: Library name: GM12878_ATAC_DMSO_24h_rep2


title: LD11-7311 Narrow-leaf TP1 replicate 2

description:
Library name: 745_T1_R2
Narrow-leaf genotype early development stage biological replicate 2


title: LD11-7311 Narrow-leaf TP4 replicate 2

description:
Library name: 745_T4_R2
Narrow-leaf genotype leaf emergence stage biological replicate 2


title: WT.UTI.5

description:
Library name: WT.UTI.5
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.UTI.5


title: LD11-7311 Narrow-leaf TP1 replicate 1

description:
Library name: 745_T1_R1
Narrow-leaf genotype early development stage biological replicate 1


title: LD11-7311 Narrow-leaf TP0 replicate 3

description:
Library name: 745_T0_R3
Narrow-leaf genotype vegetative meristem stage biological replicate 3


title: WT.UTI.4

description:
Library name: WT.UTI.4
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.UTI.4


title: LD11-7311 Narrow-leaf TP0 replicate 2

description:
Library name: 745_T0_R2
Narrow-leaf genotype vegetative meristem stage biological replicate 2


title: GM12878 ATAC-seq library, BRM014 (10uM) , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_10uM_6h_rep1


title: WT.UTI.2

description:
Library name: WT.UTI.2
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.UTI.2


title: PI 612713B Narrow-leaf TP4 replicate 3

description:
Library name: 713B_T4_R3
Narrow-leaf genotype leaf emergence stage biological replicate 3

value: PI 612713B; D9H mutation in GmJAG1


title: GM12878 ATAC-seq library, BRM014 (1uM) , 6h , replicate 3

description: Library name: GM12878_ATAC_BRM014_1uM_6h_rep3


title: GM12878 ATAC-seq library, BRM014 (1uM) , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_1uM_6h_rep2


title: WT.PBS.4

description:
Library name: WT.PBS.4
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.PBS.4


title: PI 612713B Narrow-leaf TP2 replicate 2

description:
Library name: 713B_T2_R2
Narrow-leaf genotype mid development stage biological replicate 2


title: WT.PBS.5

description:
Library name: WT.PBS.5
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.PBS.5


title: GM12878 ATAC-seq library, BRM014 (10uM) , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10uM_6h_rep2


title: PI 612713B Narrow-leaf TP3 replicate 3

description:
Library name: 713B_T3_R3
Narrow-leaf genotype late development stage biological replicate 3


title: PI 612713B Narrow-leaf TP3 replicate 1

description:
Library name: 713B_T3_R1
Narrow-leaf genotype late development stage biological replicate 1


title: PI 612713B Narrow-leaf TP4 replicate 1

description:
Library name: 713B_T4_R1
Narrow-leaf genotype leaf emergence stage biological replicate 1


title: WT.UTI.3

description:
Library name: WT.UTI.3
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.UTI.3


title: LD11-7311 Narrow-leaf TP0 replicate 1

description:
Library name: 745_T0_R1
Narrow-leaf genotype vegetative meristem stage biological replicate 1


title: WT.UTI.1

description:
Library name: WT.UTI.1
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.UTI.1


title: GM12878 ATAC-seq library, BRM014 (100nM) , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_100nM_6h_rep2


title: PI 612713B Narrow-leaf TP3 replicate 2

description:
Library name: 713B_T3_R2
Narrow-leaf genotype late development stage biological replicate 2


title: PI 612713B Narrow-leaf TP2 replicate 1

description:
Library name: 713B_T2_R1
Narrow-leaf genotype mid development stage biological replicate 1


title: GM12878 ATAC-seq library, BRM014 (1uM) , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_1uM_6h_rep1


title: GM12878 ATAC-seq library, BRM014 (10uM) , 6h , replicate 3

description: Library name: GM12878_ATAC_BRM014_10uM_6h_rep3


title: PI 612713B Narrow-leaf TP1 replicate 3

description:
Library name: 713B_T1_R3
Narrow-leaf genotype early development stage biological replicate 3


title: WT.PBS.3

description:
Library name: WT.PBS.3
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.PBS.3


title: PI 612713B Narrow-leaf TP1 replicate 2

description:
Library name: 713B_T1_R2
Narrow-leaf genotype early development stage biological replicate 2


title: WT.PBS.2

description:
Library name: WT.PBS.2
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.PBS.2


title: PI 612713B Narrow-leaf TP1 replicate 1

description:
Library name: 713B_T1_R1
Narrow-leaf genotype early development stage biological replicate 1


title: PI 612713B Narrow-leaf TP0 replicate 1

description:
Library name: 713B_T0_R1
Narrow-leaf genotype vegetative meristem stage biological replicate 1


title: GM12878 ATAC-seq library, BRM014 (100nM) , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_100nM_6h_rep1


title: GM12878 ATAC-seq library, BRM014 (10nM) , 6h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10nM_6h_rep2


title: GM12878 ATAC-seq library, BRM014 (10nM) , 6h , replicate 1

description: Library name: GM12878_ATAC_BRM014_10nM_6h_rep1


title: PI 532462A Broad-leaf TP4 replicate 3

description:
Library name: 462A_T4_R3
Broad-leaf genotype leaf emergence stage biological replicate 3

value: PI 532462A; Functional GmJAG1


title: PI 532462A Broad-leaf TP3 replicate 2

description:
Library name: 462A_T3_R2
Broad-leaf genotype late development stage biological replicate 2


title: B12

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

description:
Library name: B12
10X Genomics

library_source: transcriptomic single cell

data_processing:
Barcode separation and alignment was performed with cellranger multi (v7.1.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files of cell barcodes
Supplementary files format and content: Tab-separated values files of genes (features)
Supplementary files format and content: Space-separated matrix file of expression data

source_name: Bone marrow

growth_protocol: Mice were lethally irradiated and reconsituted with a competitive transplant of 50:50 CD45.1+ Tet2+/+ and CD45.2+ Tet2+/- bone marrow cells.

extract_protocol:
Three viably frozen bone marrow samples from separate mice were pooled per treatment group were flow cytometry sorted for live (DAPI-) CD45.2+ cells. Samples were also sorted by cKit marker expression. After sorting, cells were pooled 50:50 cKit+:cKit- per treatment group.
Library preparation was performed using 10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit (v3.1) according to manufacturer's instructions.

treatment_protocol: After 1mo engraftment period, mice were treated 7mo with Butyrate+/-B12. Mice were given twice-weekly IP injections of 0.29μg B12 or PBS (control). For butyrate supplementation, mice were given drinking water with 100mM NaButyrate or 100mM NaCl (control). At the end of the treatment period, mice were euthanized and cells extracted from organs and viably frozen.

value: Bone marrow

value: B12 + NaCl


title: WT.PBS.1

description:
Library name: WT.PBS.1
Column name in "counts_with_gene_name.csv" and "tpm_with_gene_name.txt" as WT.PBS.1


title: GM12878 ATAC-seq library, DMSO , 6h , replicate 3

description: Library name: GM12878_ATAC_DMSO_6h_rep3


title: PI 532462A Broad-leaf TP3 replicate 3

description:
Library name: 462A_T3_R3
Broad-leaf genotype late development stage biological replicate 3


title: B12+Butyrate

description:
Library name: B12+Butyrate
10X Genomics

value: B12 + Butyrate


title: PI 612713B Narrow-leaf TP0 replicate 2

description:
Library name: 713B_T0_R2
Narrow-leaf genotype vegetative meristem stage biological replicate 2


title: PI 532462A Broad-leaf TP4 replicate 1

description:
Library name: 462A_T4_R1
Broad-leaf genotype leaf emergence stage biological replicate 1

value: mature leaf


title: GM12878 ATAC-seq library, DMSO , 6h , replicate 1

description: Library name: GM12878_ATAC_DMSO_6h_rep1


title: PI 612713B Narrow-leaf TP0 replicate 3

description:
Library name: 713B_T0_R3
Narrow-leaf genotype vegetative meristem stage biological replicate 3


title: GM12878 ATAC-seq library, DMSO , 6h , replicate 2

description: Library name: GM12878_ATAC_DMSO_6h_rep2


title: Control

description:
Library name: Control
10X Genomics

value: PBS + NaCl


title: PI 532462A Broad-leaf TP4 replicate 2

description:
Library name: 462A_T4_R2
Broad-leaf genotype leaf emergence stage biological replicate 2


title: PI 612713B Narrow-leaf TP2 replicate 3

description:
Library name: 713B_T2_R3
Narrow-leaf genotype mid development stage biological replicate 3

value: developing leaf


title: PI 532462A Broad-leaf TP2 replicate 3

description:
Library name: 462A_T2_R3
Broad-leaf genotype mid development stage biological replicate 3


title: PI 612713B Narrow-leaf TP4 replicate 2

description:
Library name: 713B_T4_R2
Narrow-leaf genotype leaf emergence stage biological replicate 2


title: PI 532462A Broad-leaf TP2 replicate 2

description:
Library name: 462A_T2_R2
Broad-leaf genotype mid development stage biological replicate 2


title: Butyrate

description:
Library name: Butyrate
10X Genomics

value: PBS + Butyrate


title: PI 532462A Broad-leaf TP3 replicate 1

description:
Library name: 462A_T3_R1
Broad-leaf genotype late development stage biological replicate 1

value: young leaf


title: GM12878 ATAC-seq library, BRM014 (10uM) , 2h , replicate 1

description: Library name: GM12878_ATAC_BRM014_10uM_2h_rep1


title: GM12878 ATAC-seq library, BRM014 (10uM) , 2h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10uM_2h_rep2


title: PI 532462A Broad-leaf TP0 replicate 1

description:
Library name: 462A_T0_R1
Broad-leaf genotype vegetative meristem stage biological replicate 1


title: PI 532462A Broad-leaf TP1 replicate 1

description:
Library name: 462A_T1_R1
Broad-leaf genotype early development stage biological replicate 1


title: PI 532462A Broad-leaf TP0 replicate 3

description:
Library name: 462A_T0_R3
Broad-leaf genotype vegetative meristem stage biological replicate 3


title: Multiome_Spen+/-;Rosa26-Icn2_GEX_repl1

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description: Library name: SpenNotch2_8_RNA

data_processing:
Multiome data was processed as previously described (Barisic et al, Cancer Cell). Briefly, Multiome fastq files were aligned and processed with CellRanger Arc version 2.0.2 (10x Genomics). CellRanger outputs were then processed individually using Signac version 1.5.0. MACS2 was used to call peaks using the default settings.
Assembly: mm10
Supplementary files format and content: ATAC fragments
Supplementary files format and content: Gene count matrices

source_name: spleen

extract_protocol:
RNA and DNA were extracted following the manufacturers protocol (multiome, 10x geomics)
libraries were constructed following the manufacturers protocol (multiome, 10x geomics)

value: spleen

value: unimmunized MZB/FOB/AiBCs


title: Multiome_Spen+/-;Rosa26-Icn2_GEX_repl2

description: Library name: SpenNotch2_12_RNA


title: Multiome_Spen+/-;Rosa26-Icn2_ATAC_repl1

description: Library name: SpenNotch2_8_ATAC

library_source: genomic single cell


title: Multiome_Rosa26-Icn2_ATAC_repl2

description: Library name: Notch2GOF_10_ATAC


title: Dex TM71 postcapture, rep 1

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
Library name: Dex TM71 postcapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons

data_processing:
Hi-C reads were filtered and mapped via HiCUP v0.9.286 using the in silico digested hg38 genome provided by Arima. Read alignment and loop calling (for post-capture libraries) were performed using the Arima CHiC pipeline. Compartments were called from pre-capture libraries with HOMER v4.11.19 using 100 kb sliding windows with a step of 50 kb (via the superRes and res options, respectively).
Assembly: v
Supplementary files format and content: bedGraph of compartment calls from Homer
Supplementary files format and content: Bedpe showing loops called in at least two samples for each experiment (called by CHiCAGO via the Arima CHiC pipeline).

source_name: Trabecular mehswork cells

growth_protocol: Trabecular meshwork primary cells were cultured from human TM tissue derived from healthy donor corneal rings (ages 62-83 years), leftover from corneal transplantation surgeries performed at the Duke Ophthalmology Clinical Service. TM cells isolation, characterization and culture was performed as per consensus recommendations for TM cells culture. Primary TM cells were cultured in Dulbecco’s Modified Eagle complete growth medium (DMEM) containing low glucose with 10% heat inactivated FBS (fetal bovine serum), 1X Penicillin-Streptomycin and GlutaMAX supplement at 37°C in an aseptic incubator at 5% CO2. All the experiments on primary TM cells were performed between passage 2-6.

extract_protocol:
For each experiment, approximately five million cells from three TM cell lines were used for capture Hi-C. Cells were crosslinked with 2% formaldehyde in PBS for 10 min, quenched  with 125mM glycine for 5 min at room temperature, lysed and processed using Arima-HiC+ kit and Arima Hi-C promoter panel.
Libraries were prepared using the Arima Library Prep Module (Arima Genomics, CA, USA) according to the manufacturer’s protocols. Each library was sequenced twice, once before and once after target capture, on the NextSeq 2000 platform (Illumina, CA, USA) at a read length of 150 base pairs.

value: Trabecular mehswork cells

value: Dexamethasone


title: PI 532462A Broad-leaf TP2 replicate 1

description:
Library name: 462A_T2_R1
Broad-leaf genotype mid development stage biological replicate 1


title: PI 532462A Broad-leaf TP0 replicate 2

description:
Library name: 462A_T0_R2
Broad-leaf genotype vegetative meristem stage biological replicate 2

value: shoot apical meristem


title: PI 532462A Broad-leaf TP1 replicate 3

description:
Library name: 462A_T1_R3
Broad-leaf genotype early development stage biological replicate 3

value: leaf primordium


title: GM12878 ATAC-seq library, BRM014 (10uM) , 0.5h , replicate 1

description: Library name: GM12878_ATAC_BRM014_10uM_0p5h_rep1

value: Lymphoblastoid cell line


title: GM12878 ATAC-seq library, BRM014 (10uM) , 1h , replicate 1

description: Library name: GM12878_ATAC_BRM014_10uM_1h_rep1


title: Dex TM70 postcapture, rep 3

description:
Library name: Dex TM70 postcapture, rep 3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: PI 532462A Broad-leaf TP1 replicate 2

description:
Library name: 462A_T1_R2
Broad-leaf genotype early development stage biological replicate 2


title: GM12878 ATAC-seq library, BRM014 (10uM) , 1h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10uM_1h_rep2


title: Dex TM71 postcapture, rep 2

description:
Library name: Dex TM71 postcapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex TM71 postcapture, rep 3

description:
Library name: Dex TM71 postcapture, rep 3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Multiome_Rosa26-Icn2_GEX_repl2

description: Library name: Notch2GOF_10_RNA


title: Dex TM70 postcapture, rep 2

description:
Library name: Dex TM70 postcapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Multiome_Spen+/-;Rosa26-Icn2_ATAC_repl2

description: Library name: SpenNotch2_12_ATAC


title: GM12878 ATAC-seq library, BRM014 (10uM) , 0.5h , replicate 2

description: Library name: GM12878_ATAC_BRM014_10uM_0p5h_rep2


title: GM12878 ATAC-seq library, DMSO , 2h , replicate 2

description: Library name: GM12878_ATAC_DMSO_2h_rep2

value: DMSO


title: Dex TM70 postcapture, rep 1

description:
Library name: Dex TM70 postcapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Multiome_Rosa26-Icn2_ATAC_repl1

description: Library name: Notch2GOF_2_ATAC


title: GM12878 ATAC-seq library, DMSO , 2h , replicate 1

description: Library name: GM12878_ATAC_DMSO_2h_rep1


title: Control TM71 postcapture, rep 3

description:
Library name: Control TM71 postcapture, rep 3
Ethanol vehicle control sample used for control vs dexamethasone comparisons

value: Control


title: Multiome_Rosa26-Icn2_GEX_repl1

description: Library name: Notch2GOF_2_RNA


title: Control TM71 postcapture, rep 1

description:
Library name: Control TM71 postcapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: GM12878 ATAC-seq library, DMSO , 0.5h , replicate 2

description: Library name: GM12878_ATAC_DMSO_0p5h_rep2


title: GM12878 ATAC-seq library, DMSO , 1h , replicate 1

description: Library name: GM12878_ATAC_DMSO_1h_rep1


title: Multiome_Spen+/-_GEX_repl2

description: Library name: SpenLOF_15_RNA


title: Control TM70 postcapture, rep 2

description:
Library name: Control TM70 postcapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: GM12878 ATAC-seq library, DMSO , 1h , replicate 2

description: Library name: GM12878_ATAC_DMSO_1h_rep2


title: Control TM70 postcapture, rep 3

description:
Library name: Control TM70 postcapture, rep 3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control TM71 postcapture, rep 2

description:
Library name: Control TM71 postcapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control TM62 postcapture, rep 3

description:
Library name: Control TM62 postcapture, rep 3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Multiome_Spen+/-_GEX_repl1

description: Library name: SpenLOF_1-2_RNA


title: Control TM70 postcapture, rep 1

description:
Library name: Control TM70 postcapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Dex TM62 postcapture, rep 3

description:
Library name: Dex TM62 postcapture, rep 3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: GM12878 ATAC-seq library, DMSO , 0.5h , replicate 1

description: Library name: GM12878_ATAC_DMSO_0p5h_rep1


title: Multiome_control_ATAC_repl2

description: Library name: Control_13_ATAC


title: Dex TM62 postcapture, rep 2

description:
Library name: Dex TM62 postcapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_020

city: Wuhan

first: fangyu

last: wang

state: Hubei

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan university

description:
Library name: ID_020
column name in raw_counts.txt:ID_020

data_processing:
RNAseq fastq files were pre-processed with fastp.
Gene count for each patient was obtained by using STAR (V2.7.11a) quantMode set with the ‘GeneCounts’ parameter
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample

source_name: Glioma

extract_protocol:
Separating one part of human GBM tissue, the RNA isolation was performed using the RNAiso Plus (TAKARA, 9109) according to the manufacturer’s instructions. RNA quality was evaluated spectrophotometrically, and the RNA integrity was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, no.E7775). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and sequenced with paired-end reads on an Illumina NovaSeq 6000 (Illumina).

value: Glioma

value: IDH wild-type grade IV


title: ID_017

description:
Library name: ID_017
column name in raw_counts.txt:ID_017


title: Control TM62 postcapture, rep 1

description:
Library name: Control TM62 postcapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Multiome_Spen+/-_ATAC_repl1

description: Library name: SpenLOF_1-2_ATAC


title: Control TM62 postcapture, rep 2

description:
Library name: Control TM62 postcapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Resource TM83 postcapture

description:
Library name: Resource TM83 postcapture
Control sample used for the the resource analysis (figure 1)


title: Multiome_control_GEX_repl2

description: Library name: Control_13_RNA


title: Resource TM62 postcapture

description:
Library name: Resource TM62 postcapture
Control sample used for the the resource analysis (figure 1)


title: Dex TM70 precapture, rep 2

description:
Library name: Dex TM70 precapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex TM70 precapture, rep 1

description:
Library name: Dex TM70 precapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_S018

description:
Library name: ID_S018
column name in raw_counts.txt:ID_S018


title: Dex TM71 precapture, rep 1

description:
Library name: Dex TM71 precapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Multiome_control_ATAC_repl1

description: Library name: Control_3_ATAC


title: Dex TM62 precapture, rep 3

description:
Library name: Dex TM62 precapture, rep 3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_008

description:
Library name: ID_008
column name in raw_counts.txt:ID_008


title: Multiome_Spen+/-_ATAC_repl2

description: Library name: SpenLOF_15_ATAC


title: Dex TM71 precapture, rep 2

description:
Library name: Dex TM71 precapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_S004

description:
Library name: ID_S004
column name in raw_counts.txt:ID_S004


title: Dex TM62 precapture, rep 2

description:
Library name: Dex TM62 precapture, rep 2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Resource TM71 postcapture

description:
Library name: Resource TM71 postcapture
Control sample used for the the resource analysis (figure 1)


title: Dex TM62 precapture, rep 1

description:
Library name: Dex TM62 precapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_S039

description:
Library name: ID_S039
column name in raw_counts.txt:ID_S039


title: Multiome_control_GEX_repl1

description: Library name: Control_3_RNA


title: Control TM71 precapture, rep 2

description:
Library name: Control TM71 precapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: male_SN2_RNAseq_repl2

description: Library name: Sample_10_male_SN2_RNAseq_repl2

data_processing:
RNA sequencing results were aligned to GRCm38.p6 using STAR (STAR_2.7.10b) and annotated to RefSeq (GCF_000001635.26) using the Rsubread package (Rsubread_2.16.1)
Assembly: GRCm38.p6
Supplementary files format and content: TPM

source_name: Lymphoma cells

extract_protocol:
Included as additional column of SAMPLES section
RNA was purified with Uneasy Mini Kit (Qiagen, 74104) and sent to Admera Health for library preparation and sequencing

value: Lymphoma cells


title: male_SN2_RNAseq_repl1

description: Library name: Sample_9_male_SN2_RNAseq_repl1


title: Control TM70 precapture, rep 2

description:
Library name: Control TM70 precapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: female_SN2_RNAseq_repl4

description: Library name: Sample_7_female_SN2_RNAseq_repl4


title: Dex TM62 postcapture, rep 1

description:
Library name: Dex TM62 postcapture, rep 1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_S006

description:
Library name: ID_S006
column name in raw_counts.txt:ID_S006


title: Control TM70 precapture, rep 1

description:
Library name: Control TM70 precapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: ID_S036

description:
Library name: ID_S036
column name in raw_counts.txt:ID_S036


title: Control TM62 precapture, rep 1

description:
Library name: Control TM62 precapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Resource TM62 precapture

description:
Library name: Resource TM62 precapture
Control sample used for the the resource analysis (figure 1)


title: Resource TM71 precapture

description:
Library name: Resource TM71 precapture
Control sample used for the the resource analysis (figure 1)


title: Resource TM83 precapture

description:
Library name: Resource TM83 precapture
Control sample used for the the resource analysis (figure 1)


title: ID_S041

description:
Library name: ID_S041
column name in raw_counts.txt:ID_S041


title: female_SN2_RNAseq_repl5

description: Library name: Sample_8_female_SN2_RNAseq_repl5


title: Control TM62 precapture, rep 2

description:
Library name: Control TM62 precapture, rep 2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: female_SN2_RNAseq_repl3

description: Library name: Sample_6_female_SN2_RNAseq_repl3


title: female_SN2_RNAseq_repl2

description: Library name: Sample_5_female_SN2_RNAseq_repl2


title: ID_S026

description:
Library name: ID_S026
column name in raw_counts.txt:ID_S026


title: ID_S025

description:
Library name: ID_S025
column name in raw_counts.txt:ID_S025


title: female_SN2_RNAseq_repl1

description: Library name: Sample_4_female_SN2_RNAseq_repl1


title: Control TM71 precapture, rep 1

description:
Library name: Control TM71 precapture, rep 1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control TM62 precapture, rep 3

description:
Library name: Control TM62 precapture, rep 3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 H3K36me3

description:
Library name: Control CUT_Tag TM71 H3K36me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons

data_processing:
CUT&Tag samples were processed using the nfcore cutandrun pipeline with peaks called using SEACR v1.3; for each mark, peaks called in at least two samples were retained for downstream analyses (except for CTCF, only one sample available).
Assembly: hg38
Supplementary files format and content: bigWig showing read alignment
Supplementary files format and content: bed file with SEACR peaks observed in at least 2 samples (except for CTCF, only one sample available)
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag was performed on 100,000-200,000 cells using CUT&Tag-IT® Assay Kit, Anti-Rabbit (Cat# 53171).
The libraries were sequenced on the NextSeq 2000 platform (Illumina, CA, USA) at a read length of 50 base pairs.


title: Dex CUT&Tag TM71 H3K36me3

description:
Library name: Dex CUT_Tag TM71 H3K36me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: ID_S005

description:
Library name: ID_S005
column name in raw_counts.txt:ID_S005


title: ID_S009

description:
Library name: ID_S009
column name in raw_counts.txt:ID_S009


title: MZB_RNAseq_repl3

description: Library name: Sample_3_MZB_RNAseq_repl3

source_name: Marginal zone B cells

value: Marginal zone B cells

value: WT


title: Dex CUT&Tag TM71 H3K27me3

description:
Library name: Dex CUT_Tag TM71 H3K27me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex CUT&Tag TM71 H3K27Ac

description:
Library name: Dex CUT_Tag TM71 H3K27Ac
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: MZB_RNAseq_repl2

description: Library name: Sample_2_MZB_RNAseq_repl2


title: MZB_RNAseq_repl1

description: Library name: Sample_1_MZB_RNAseq_repl1


title: Dex CUT&Tag TM71 H3K4me3

description:
Library name: Dex CUT_Tag TM71 H3K4me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 H3K27Ac

description:
Library name: Control CUT_Tag TM71 H3K27Ac
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: sgTRAPPC4-2

city: hefei

first: Wentao

last: Zhang

state: anhui

address: meishan road

institute: anhui medical university

description:
Library name: Sample 5
LIU-LSC-1, TRAPPC4 knockout, rep 2

data_processing:
Raw sequencing reads were generated using the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.
Raw reads were processed using in-house scripts to remove adapters, low-quality reads, and reads with N bases. Clean reads were assessed for Q20, Q30, and GC content.
Clean reads were aligned to the reference genome using HISAT2 (v2.0.5).
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix (FPKM) in CSV format

extract_protocol:
Total RNA was extracted using standard TRIzol-based methods (or as per sample-specific protocol). RNA quality was assessed via Agilent Bioanalyzer and quantified with Qubit 2.0.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed in First Strand Synthesis Reaction Buffer under elevated temperature. First strand cDNA was synthesized with random hexamer primers and M-MuLV reverse transcriptase. Second strand synthesis was performed using DNA Polymerase I and RNase H. After end repair and A-tailing, adapter ligation was done, followed by PCR amplification and size selection (~370–420 bp) using AMPure XP beads.

value: HNSCC cell line

value: TRAPPC4 knockout

value: KO TRAPPC4


title: sgTRAPPC4-3

description:
Library name: Sample 6
LIU-LSC-1, TRAPPC4 knockout, rep 3


title: Control CUT&Tag TM71 H3K27me3

description:
Library name: Control CUT_Tag TM71 H3K27me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 CTCF

description:
Library name: Control CUT_Tag TM71 CTCF
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 H3K4me3

description:
Library name: Control CUT_Tag TM71 H3K4me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: esg-GAL4/Luciferase RNAi (control), D2 (day2 adult), gut

city: Houston

first: Hongjie

last: Li

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: 9_LucRNAi_D2
10x Genomics

data_processing:
Raw snRNA-seq data, in the form of FASTQ files, underwent alignment to the Drosophila melanogaster reference genome (FlyBase release 6.31) using the Cell Ranger software (v8.0.0). Subsequent steps involved the removal of ambient RNA contamination via CellBender [PMID: 37550580] and the identification and exclusion of potential doublet cells using Scrublet [PMID: 30954476]. Quality control criteria necessitated the elimination of cells exhibiting fewer than 200 genes. Genes detected in fewer than 3 nuclei were removed from our analysis. Additionally, cells harboring over 5% of mitochondrial transcripts were eliminated.
Assembly: dm6.31
Supplementary files format and content: .h5ad matrix file

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: gut

growth_protocol: Flies were maintained on standard cornmeal-yeast-agar medium at 25°C

extract_protocol:
Single-nucleus suspensions were prepared following the protocol we described previously [PMID: 35620068], except that homogenization was limited to 15 strokes with a tight pestle. Next, we used the BD AriaIII FACS sorter to collect nuclei. Nuclei were stained by Hoechst-33342 on ice (1:1000; >5min). Hoechst+ nuclei were collected during sorting. Individual nuclei were collected into one 1.5ml RNase-free Eppendorf tube with 200µl 1x PBS with 0.5% BSA (RNase inhibitor added) as the receiving buffer.
For each sample, 100k nuclei were collected. Nuclei were spun down for 10 min at 950g at 4°C and then resuspended using 40µl or desired amount of 1x PBS with 0.5% BSA (RNase inhibitor added). 2µl of nucleus suspension was used for counting the nuclei with hemocytometers to calculate the concentration. 24K nuclei were loaded to the 10x Chromium Next GEM Chip G for each channel to target >10k nuclei. Next, we performed snRNA-seq using the 10x Genomics platform with the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) with the following settings. All PCR reactions were performed using the BioRad C1000 Touch Thermal cycler with a 96-deep Well Reaction Module. For cDNA amplification, 12 cycles were performed. Sample index PCR was conducted following the 10x Genomics protocol recommended cycle numbers. As per the 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on a bioanalyzer. The final library was sent to Admera Health, LLC for Illumina NovaSeq X plus 25B 2x150 lane sequencing with the dual index configuration Read 1 28 cycles, Index 1 (i7) 10 cycles, Index 2 (i5) 10 cycles, and Read 2 90 cycles. A PhiX control library was spiked in at 5% concentration. The sequencing depth is about 37-56K reads per nucleus.

treatment_protocol: Midgut samples were collected from females across each stage: wandering third instar larva (L3), white prepupa (P0), 18hr pupa (P18), 48hr pupa (P48), and day 2 adults (D2). Guts were dissected in cold Schneider medium. Crop, malpighian tubules, and hindgut were removed to enrich midgut cells during sequencing. Guts were placed into 1.5ml RNAase free Eppendorf tubes with a cold Schneider medium containing RNase Inhibitor (Promega, N2611), flash-frozen using liquid nitrogen and stored at -80°C until processing. Sample sizes for each stage are as follows: L3 midguts n=50 per genotype; P0 n=40 per genotype; P18 n=250 for control and n=360 for dTet RNAi; P48 n=120 per genotype; D2 n=50 per genotype

value: gut

tag: Sex

value: female

tag: developmental stage

value: day2 adult

value: esg-GAL4/Luciferase RNAi


title: ID_S038

description:
Library name: ID_S038
column name in raw_counts.txt:ID_S038


title: ID_S013

description:
Library name: ID_S013
column name in raw_counts.txt:ID_S013


title: esg-GAL4/dTet RNAi (dTet RNAi), P48 (48 hour pupa), gut

description:
Library name: 8_dTetRNAi_48h
10x Genomics

value: 48 hour pupa

value: esg-GAL4/dTet RNAi


title: Control CUT&Tag TM70 H3K27me3

description:
Library name: Control CUT_Tag TM70 H3K27me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons

value: Trabecular mehswork cells


title: Dex CUT&Tag TM70 H3K27me3

description:
Library name: Dex CUT_Tag TM70 H3K27me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex CUT&Tag TM71 H3K4me2

description:
Library name: Dex CUT_Tag TM71 H3K4me2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: sgTRAPPC4-1

description:
Library name: Sample 4
LIU-LSC-1, TRAPPC4 knockout, rep 1


title: esg-GAL4/dTet RNAi (dTet RNAi),  D2 (day2 adult), gut

description:
Library name: 10_dTetRNAi_D2
10x Genomics


title: Dex CUT&Tag TM71 H3K4me1

description:
Library name: Dex CUT_Tag TM71 H3K4me1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex CUT&Tag TM71 CTCF

description:
Library name: Dex CUT_Tag TM71 CTCF
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 H3K4me1

description:
Library name: Control CUT_Tag TM71 H3K4me1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM71 H3K4me2

description:
Library name: Control CUT_Tag TM71 H3K4me2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: sgNTC-3

description:
Library name: Sample 3
LIU-LSC-1, control, rep 3

value: TRAPPC4 wild-type

value: NC


title: sgNTC-2

description:
Library name: Sample 2
LIU-LSC-1, control, rep 2


title: Dex CUT&Tag TM70 H3K27Ac

description:
Library name: Dex CUT_Tag TM70 H3K27Ac
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM70 H3K27ac

description:
Library name: Control CUT_Tag TM70 H3K27ac
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: esg-GAL4/dTet RNAi (dTet RNAi),  P18 (18 hour pupa), gut

description:
Library name: 6_dTetRNAi_18h
10x Genomics

value: 18 hour pupa


title: Dex CUT&Tag TM62 H3K36me3

description:
Library name: Dex CUT_Tag TM62 H3K36me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: esg-GAL4/Luciferase RNAi (control), P18 (18 hour pupa), gut

description:
Library name: 5_LucRNAi_18h
10x Genomics


title: Control CUT&Tag TM62 H3K36me3

description:
Library name: Control CUT_Tag TM62 H3K36me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM62 H3K27Ac

description:
Library name: Control CUT_Tag TM62 H3K27Ac
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control CUT&Tag TM62 H3K27me3

description:
Library name: Control CUT_Tag TM62 H3K27me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: esg-GAL4/Luciferase RNAi (control), P0 (0 hour pupa), gut

description:
Library name: 3_LucRNAi_0h
10x Genomics

value: 0 hour pupa


title: esg-GAL4/dTet RNAi (dTet RNAi), L3 (3rd instar larvae), gut

description:
Library name: 2_dTetRNAi_L3
10x Genomics

value: 3rd instar larvae


title: Dex CUT&Tag TM62 H3K27Ac

description:
Library name: Dex CUT_Tag TM62 H3K27Ac
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: sgNTC-1

description:
Library name: Sample 1
LIU-LSC-1, control, rep 1


title: esg-GAL4/dTet RNAi (dTet RNAi), P0 (0 hour pupa), gut

description:
Library name: 4_dTetRNAi_0h
10x Genomics


title: Control CUT&Tag TM62 H3K4me3

description:
Library name: Control CUT_Tag TM62 H3K4me3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Dex CUT&Tag TM62 H3K4me3

description:
Library name: Dex CUT_Tag TM62 H3K4me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Dex CUT&Tag TM62 H3K4me2

description:
Library name: Dex CUT_Tag TM62 H3K4me2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: esg-GAL4/Luciferase RNAi (control), P48 (48 hour pupa), gut

description:
Library name: 7_LucRNAi_48h
10x Genomics


title: Dex CUT&Tag TM62 H3K27me3

description:
Library name: Dex CUT_Tag TM62 H3K27me3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPEG + 30C, scRNA-seq

city: Chciago

first: Annisa

last: Dea

address: 929 E 57th St

institute: University of Chicago

description:
Library name: evo-ypeg-30
10x Genomics Chromium 3' v3.1

data_processing:
Raw sequencing data processed using Cell Ranger v7.1.0 (10x Genomics) with cellranger count. Reads aligned to Saccharomyces cerevisiae genome (sacCer3) with --expect-cells=2000.
Filtered count matrices exported as filtered_feature_bc_matrix.h5 per sample.
Assembly: sacCer3 (Saccharomyces cerevisiae, SGD R64-2-1)
Supplementary files format and content: Filtered feature-barcode matrix in HDF5 format (.h5) from Cell Ranger v7.1.0, one file per sample. Naming: {strain}_{condition}.h5 (strain = anc or evo).

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Saccharomyces cerevisiae (w303) cells were grown overnight to saturation in Yeast Peptone Dextrose (YPD) media and diluted to OD600 = 0.05 prior to treatment. For the evolved (derived) strain, continuous directed evolution was conducted using the eVOLVER system in synthetic dextrose complete (SDC) media containing 0.8M KCl over 9 months, with automated dilution at OD600=0.58 to OD600=0.08. The derived cells were grown overnight to saturation in YPD and diluted to OD600 = 0.05 prior to treatment.

extract_protocol:
Cells were pelleted, washed in PBS, and resuspended as single-cell suspension for loading onto the 10x Genomics Chromium controller according to the Chromium Next GEM Single Cell 3' v3.1 protocol.
scRNA-seq libraries prepared using 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 per manufacturer protocol. Libraries sequenced on Illumina NovaSeq X.

treatment_protocol: Saturated overnight cultures were diluted to OD600 0.05 in one of 20 environmental conditions (18 for the evolved strain): YPD at 30C, YPD at 37C, YPD+diamide, YPD+H2O2, YPD+KCl, YPD+sorbitol, YPD+KCl+diamide, YPD+KCl+H2O2, YPEG+30C, YPEG+37C (ancestral only), SDC, SDC+37C, SDC+diamide, SDC+H2O2, SDC+KCl, SDC+sorbitol, SDC+KCl+diamide, SDC+KCl+H2O2, SC+EG+30C, SC+EG+37C (ancestral only). Cells grown to log phase and harvested.

value: yeast

value: KCl-derived strain

value: YPEG + 30C

value: derived


title: Control CUT&Tag TM62 H3K4me2

description:
Library name: Control CUT_Tag TM62 H3K4me2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Atlas2024_IVR_64603_HPCLS_BCM_572_DMSO

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

description: Library name: HPCLS_BCM_572_DMSO

data_processing:
Aligningnment, cunatification and feature-barcode matrices generation done with Cell Ranger version 7.0.1
Assembly: human GRCh38
Supplementary files format and content: tab-separated values files and matrix files

source_name: lung

growth_protocol: slices were cultured in 24-well plates supplemented with DMEM/F12 media containing 1% FBS and antibiotics.

extract_protocol:
Enzymatic tissue digestion with Elastase, DNAse I and Liberase.
10X genomics protocol 5' version 3.1

treatment_protocol: Lung slices were incubated with or without EIPA (12.5 uM) for another 72 h. Culture media was changed after every 36 hours and treated with drugs or DMSO with total of 3 treatments.

value: lung

value: DMSO


title: Dex CUT&Tag TM62 H3K4me1

description:
Library name: Dex CUT_Tag TM62 H3K4me1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Atlas2024_IVR_64599_HPCLS_BCM_571_DMSO

description: Library name: HPCLS_BCM_571_DMSO


title: Atlas2024_IVR_65672_GEX_577_DMSO

description: Library name: 577_DMSO


title: esg-GAL4/Luciferase RNAi (control), L3 (3rd instar larvae), gut

description:
Library name: 1_LucRNAi_L3
10x Genomics

value: gut

value: female


title: S. cerevisiae derived strain, YPD + sorbitol, scRNA-seq

description:
Library name: evo-ypd-sorb
10x Genomics Chromium 3' v3.1

value: YPD + sorbitol


title: Atlas2024_IVR_65671_GEX_577_EIPA

description: Library name: 577_EIPA

value: EIPA


title: HPCLS_64852_BCM_572_EIPA

description: Library name: 572_EIPA


title: Control CUT&Tag TM62 H3K4me1

description:
Library name: Control CUT_Tag TM62 H3K4me1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Dex Total RNA TM72, Rep1

description:
Library name: Dex Total RNA TM72 Rep1
Dexamethasone-treated sample used for control vs dexamethasone comparisons

data_processing:
Reads were trimmed using Trimmomatic v0.36. Transcript level quantitation was performed using Kallisto v0.48.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from Ensembl v106. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.14.0 with using the lengthScaledTPM option. The gene level count values were TMM normalized and differential expression in the dexamethasone experiment was performed using edgeR v4.0.3. Enrichment of GO terms and KEGG pathways was performed using clusterProfiler v4.10.0.
Assembly: hg38
Supplementary files format and content: tab delimited file containing raw counts for each sample

extract_protocol:
We performed total RNA-sequencing on three samples each for the resource, dexamethasone control, and dexamethasone treatment experiments. For each experiment, primary TM cells were trypsinized, flash frozen and kept at -80°C. Total RNA was isolated using Qiagen RNeasy Mini Kit (Germantown, MD, USA; cat# 74104) and the quality of RNA was determined using Agilent TapeStation (Santa Clara, CA, USA).
Libraries were prepared from 10ng of total RNA using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (San Diego, CA, USA; cat# 20040525). Libraries were sequenced on an Illumina NextSeq 2000 platform.

treatment_protocol: TM cells with 80% confluency were maintained in medium containing 2% FBS for 2 hours before treating with 0.5 μM dexamethasone (cat#D4902) and ethanol as a vehicle control. The cells were treated for 7 days with media containing 2% FBS and dexamethasone changed every other day.

value: Dexamethasone


title: Control Total RNA TM72, Rep1

description:
Library name: Control Total RNA TM72 Rep1
Ethanol vehicle control sample used for control vs dexamethasone comparisons

value: Trabecular mehswork cells

value: Control


title: Control Total RNA TM70, Rep2

description:
Library name: Control Total RNA TM70 Rep2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Dex Total RNA TM70, Rep1

description:
Library name: Dex Total RNA TM70 Rep1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: Control Total RNA TM70, Rep1

description:
Library name: Control Total RNA TM70 Rep1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: HPCLS_62608_550_IPF_DMSO

description: Library name: 550_IPF_DMSO


title: S. cerevisiae derived strain, YPD + KCl + hydrogen peroxide, scRNA-seq

description:
Library name: evo-ypd-kcl-h2o2
10x Genomics Chromium 3' v3.1

value: YPD + KCl + hydrogen peroxide


title: S. cerevisiae derived strain, YPD + KCl + diamide, scRNA-seq

description:
Library name: evo-ypd-kcl-diam
10x Genomics Chromium 3' v3.1

value: YPD + KCl + diamide


title: HPCLS_64850_BCM_571_EIPA

description: Library name: 571_EIPA


title: Dex Total RNA TM70, Rep2

description:
Library name: Dex Total RNA TM70 Rep2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: PT9

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

country: France

institute: Gustave Roussy

description:
Library name: PT9
FFPE Visium V1

data_processing:
Raw sequencing data was processed with the Real Time Analysis 3 software (Illumina) to obtain fastq files.
High resolution whole slide images of the Visium slide were obtained for each sample and together with the associated FASTQ files were input into the SpaceRanger v2.0.1 pipeline (10X Genomics) to be aligned with the standard GRCh38 reference genome using default settings. The resulting count matrices and imaging files are made available in thi submission.
Samples were individually pre-processed, merged and jointly analyzed using the CellsFromSpace workflow. This generated two matrices of independent component analysis (ICA): a S x N cell embeddings (or "Source signals") matrix and a N x F feature loadings (or "Mixing weights") matrix where N represents components, S represent spots, and F represent genes. These matrices are provided.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: Gene expression matrix in h5 format
Supplementary files format and content: aligned_fiducials.jpg: spatial alignment image using fiducial features.
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and identification of tissue-covering spots
Supplementary files format and content: scalefactors_json.json: image scale factors for high and low resolution images in json format
Supplementary files format and content: tissue_hires_image.png: high resolution sample image
Supplementary files format and content: tissue_lowres_image.png: low resolution sample image
Supplementary files format and content: tissue_positions.csv: list of spot spatial barcodes and their respective spatial coordinates.
Supplementary files format and content: ica.cell.embeddings.all.csv: Spots x Component matrix from joint ICA of all samples.
Supplementary files format and content: ica.feature.loadings.all.csv: Feature x Component matrix from joint ICA of all samples.
Library strategy: Spatial Transcriptomics

source_name: Primary bone osteosarcoma

extract_protocol:
ST on FFPE samples was perfomed using the 10X Genomics Visium Spatial Gene expression for FFPE protocol V1, using the human whole transcriptome probe set. Tissue areas up to 6.5 x 6.5 mm were pre-selected by a pathologist following H&E staining. 5 µm sections of the selected areas were sectioned, dehydrated and deposited on the Visium Gene Expression V1 chip as recommended by the manufacturer.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression for FFPE Slides & Reagent kit (GC000407) according to manufacturer's instructions. Captured sequences were hybridized with the human whole transcriptome probe kit (PN1000364 or PN1000363). Prepared libraries were sequenced on the NovaSeq 6000 system (Illumina) using S4 Flow Cells with a target minimal reads per covered spot of 50k.

value: Primary bone osteosarcoma


title: Dex Total RNA TM62, Rep4

description:
Library name: Dex Total RNA TM62 Rep4
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPD + hydrogen peroxide, scRNA-seq

description:
Library name: evo-ypd-h2o2
10x Genomics Chromium 3' v3.1

value: YPD + hydrogen peroxide


title: Dex Total RNA TM62, Rep1

description:
Library name: Dex Total RNA TM62 Rep1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPD + KCl, scRNA-seq

description:
Library name: evo-ypd-kcl
10x Genomics Chromium 3' v3.1

value: yeast

value: YPD + KCl


title: Dex Total RNA TM62, Rep3

description:
Library name: Dex Total RNA TM62 Rep3
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: PT8

description:
Library name: PT8
FFPE Visium V1


title: Dex Total RNA TM62, Rep2

description:
Library name: Dex Total RNA TM62 Rep2
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPD + diamide, scRNA-seq

description:
Library name: evo-ypd-diam
10x Genomics Chromium 3' v3.1

value: KCl-derived strain

value: YPD + diamide


title: PT7

description:
Library name: PT7
FFPE Visium V1


title: Control Total RNA TM62, Rep3

description:
Library name: Control Total RNA TM62 Rep3
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Control Total RNA TM62, Rep4

description:
Library name: Control Total RNA TM62 Rep4
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPD + heat stress, 37C, scRNA-seq

description:
Library name: evo-ypd-37
10x Genomics Chromium 3' v3.1

value: YPD + heat stress, 37C

value: derived


title: Control Total RNA TM62, Rep2

description:
Library name: Control Total RNA TM62 Rep2
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, YPD (rich media), scRNA-seq

description:
Library name: evo-ypd
10x Genomics Chromium 3' v3.1

value: YPD (rich media)


title: Resource Total RNA TM83, Rep1

description:
Library name: Resource Total RNA TM83 Rep1
Control sample used for the the resource analysis (figure 1)


title: PT5

description:
Library name: PT5
FFPE Visium V1


title: S. cerevisiae derived strain, SDC + KCl + hydrogen peroxide, scRNA-seq

description:
Library name: evo-sdc-kcl-h2o2
10x Genomics Chromium 3' v3.1

value: SDC + KCl + hydrogen peroxide


title: Resource Total RNA TM62, Rep3

description:
Library name: Resource Total RNA TM62 Rep3
Control sample used for the the resource analysis (figure 1)


title: Resource Total RNA TM83, Rep2

description:
Library name: Resource Total RNA TM83 Rep2
Control sample used for the the resource analysis (figure 1)


title: Resource Total RNA TM71, Rep2

description:
Library name: Resource Total RNA TM71 Rep2
Control sample used for the the resource analysis (figure 1)


title: Control Total RNA TM62, Rep1

description:
Library name: Control Total RNA TM62 Rep1
Ethanol vehicle control sample used for control vs dexamethasone comparisons


title: Resource Total RNA TM62, Rep2

description:
Library name: Resource Total RNA TM62 Rep2
Control sample used for the the resource analysis (figure 1)


title: Resource Total RNA TM71 Rep1

description:
Library name: Resource Total RNA TM71 Rep1
Control sample used for the the resource analysis (figure 1)


title: PT6

description:
Library name: PT6
FFPE Visium V1


title: Dexamethasone-treated ATAC TM70 Rep1

description:
Library name: Dexamethasone-treated ATAC TM70 Rep1
Dexamethasone-treated sample used for control vs dexamethasone comparisons

data_processing:
Reads were processed using the nf-core ATACseq pipeline using the default settings with peaks called using SEACR. We retained all replicate peaks identified in the conservative set by irreproducible discovery rate (IDR) analysis.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
We performed ATAC-seq on two samples each for the resource, control, and dexamethasone treatment experiment. For each, approximately 50,000 cells were used for cell lysis, nuclei extraction, tagmentation and DNA purification.
ATAC-seq and library preparation was performed using a commercial kit from Diagenode (cat#C01080001, cat# C01011034) following the manufacturer’s instructions. Pair-end sequencing with read length of 50 base pairs was done on the NextSeq 2000 platform (Illumina, CA, USA).


title: S. cerevisiae derived strain, SDC + KCl, scRNA-seq

description:
Library name: evo-sdc-kcl
10x Genomics Chromium 3' v3.1

value: SDC + KCl


title: S. cerevisiae derived strain, SDC + KCl + diamide, scRNA-seq

description:
Library name: evo-sdc-kcl-diam
10x Genomics Chromium 3' v3.1

value: SDC + KCl + diamide


title: PT1

description:
Library name: PT1
FFPE Visium V1


title: PT4

description:
Library name: PT4
FFPE Visium V1


title: Resource Total RNA TM62, Rep1

description:
Library name: Resource Total RNA TM62 Rep1
Control sample used for the the resource analysis (figure 1)


title: PT2

description:
Library name: PT2
FFPE Visium V1


title: S. cerevisiae derived strain, SDC + sorbitol, scRNA-seq

description:
Library name: evo-sdc-sorb
10x Genomics Chromium 3' v3.1

value: SDC + sorbitol


title: Control ATAC TM70 Rep1

description:
Library name: Control ATAC TM70 Rep1
Ethanol vehicle control sample used for control vs dexamethasone comparisons

value: Trabecular mehswork cells


title: MR4

description:
Library name: MR4
FFPE Visium V1

source_name: Lung metastatic osteosarcoma

value: Lung metastatic osteosarcoma


title: Dexamethasone-treated ATAC TM62 Rep2

description:
Library name: Dexamethasone-treated ATAC TM62 Rep2
Dexamethasone-treated sample used for control vs dexamethasone comparisons

value: Dexamethasone


title: Dexamethasone-treated ATAC TM62 Rep1

description:
Library name: Dexamethasone-treated ATAC TM62 Rep1
Dexamethasone-treated sample used for control vs dexamethasone comparisons


title: S. cerevisiae derived strain, SDC + hydrogen peroxide, scRNA-seq

description:
Library name: evo-sdc-h2o2
10x Genomics Chromium 3' v3.1

value: SDC + hydrogen peroxide


title: S. cerevisiae derived strain, SDC + diamide, scRNA-seq

description:
Library name: evo-sdc-diam
10x Genomics Chromium 3' v3.1

value: SDC + diamide


title: Resource ATAC TM71 Rep2

description:
Library name: Resource ATAC TM71 Rep2
Control sample used for the the resource analysis (figure 1)


title: Control ATAC TM62 Rep2

description:
Library name: Control ATAC TM62 Rep2
Ethanol vehicle control sample used for control vs dexamethasone comparisons

value: Control


title: Resource ATAC TM62 Rep3

description:
Library name: Resource ATAC TM62 Rep3
Control sample used for the the resource analysis (figure 1)


title: Resource ATAC TM62 Rep2

description:
Library name: Resource ATAC TM62 Rep2
Control sample used for the the resource analysis (figure 1)


title: Resource ATAC TM71 Rep1

description:
Library name: Resource ATAC TM71 Rep1
Control sample used for the the resource analysis (figure 1)


title: MR2

description:
Library name: MR2
FFPE Visium V1


title: S. cerevisiae derived strain, SC + ethanol/glycerol, 30C, scRNA-seq

description:
Library name: evo-sceg-30
10x Genomics Chromium 3' v3.1

value: yeast

value: SC + ethanol/glycerol, 30C


title: MR18

description:
Library name: MR18
FFPE Visium V1


title: MR16

description:
Library name: MR16
FFPE Visium V1

source_name: Heart metastatic osteosarcoma

value: Heart metastatic osteosarcoma


title: S. cerevisiae derived strain, SDC (synthetic defined complete), scRNA-seq

description:
Library name: evo-sdc
10x Genomics Chromium 3' v3.1

value: KCl-derived strain

value: SDC (synthetic defined complete)


title: Resource ATAC TM62 Rep1

description:
Library name: Resource ATAC TM62 Rep1
Control sample used for the the resource analysis (figure 1)


title: S. cerevisiae derived strain, SDC + heat stress, 37C, scRNA-seq

description:
Library name: evo-sdc-37
10x Genomics Chromium 3' v3.1

value: SDC + heat stress, 37C

value: derived


title: ENU54156B6G310_G5_neuro2110_S63_R1_001

status: Public on Apr 11 2026

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: ENU54156B6G310_G5_neuro2110_S63_R1_001

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38 using GSNAP 74. Only uniquely mapping reads were carried forward to downstream analysis. Sample quality was further assessed on a per-plate basis based on total read counts, percentage of reads mapping to the reference genome, and percentage of reads mapping to exons. Reads predominantly mapped to transcript 3’ ends, as expected from the library preparation method.
Assembly: GRCm38

source_name: Whole brain

growth_protocol: Founder C57BL/6NCrl males were treated with 3 x 100 mg/kg ENU (Sigma) and mutations bred to homozygosity in three generations. Generation 3 mice were collected usually between 8-12 weeks old, and an ear notch for DNA and brain samples were collected. Typically, 12 siblings from each pedigree were screened.

extract_protocol:
To homogenize the tissue, RNAlater was removed, and a 5 mm stainless steel bead (Qiagen) and 1.6 mL of Qiazol (Qiagen) was added. The tissue was homogenized using a Tissue Lyser II (Qiagen) for at least 30 minutes until a homogenous solution was confirmed. 400 µL of the homogenate solution was transferred into a new tube and allowed to sit for 5 minutes before adding 100 µL of chloroform (Sigma). The homogenate-chloroform mixture was shaken vigorously, allowed to stand for 2 minutes before centrifugation for 5 minutes at 4°C and 1000 x g. The top clear layer was removed and stored at -80 °C. For RNA extraction, 120 µL was transferred into a QIAgen S-block and processed on the QIAcube using the RNeasy 96 QIAcube HT Kit.
cDNA fragment libraries were constructed using the SMART-Seq® v4 3’ DE Kit (Takara Bio) following manufacturer’s recommendations, with minor modifications. Total RNA samples were processed in batches of 1152, distributed across twelve 96-well plates. For each sample, 4 ng total RNA was used as input for cDNA synthesis, then amplified for 8 cycles, with each sample in a row receiving a unique in-line index. Amplified cDNAs within a row were then combined into a 12-plex pool, cleaned up with Ampure XP beads (Beckman Coulter) and quantified using the Qubit HS DNA assay kit (Thermo Fisher Scientific). For each of the 96 cDNA pools generated from 12 plates, 400 pg were carried into Nextera XT library preparations (Illumina Inc.), each assigned with one of the 96 unique combinations of Forward and Reverse HT Index Primers included in the SMART-Seq® v4 3’ DE kit. After Ampure XP clean up and Qubit quantification, the 96 pools were combined in an equimolar manner to generate a 1152-plex Illumina library.  This library was concentrated with Ampure XP beads, quantified with Qubit and assessed on the TapeStation with the High Sensitivity D1000 assay (Agilent Technologies).

treatment_protocol: Mice were euthanized by cervical dislocation, then whole brains were collected. Each cerebellum was removed and the remaining brain matter was transferred to RNAlater and stored at 4C for up to 5 days.

value: Whole brain

tag: partofsubset

value: FALSE


title: Resource ATAC TM71 Rep3

description:
Library name: Resource ATAC TM71 Rep3
Control sample used for the the resource analysis (figure 1)


title: MR3

description:
Library name: MR3
FFPE Visium V1


title: S. cerevisiae ancestral strain, YPEG + heat stress, 37C, scRNA-seq

description:
Library name: anc-ypeg-37
10x Genomics Chromium 3' v3.1

value: wild-type

value: YPEG + heat stress, 37C

value: ancestral