title: Resource CUT&Run TM83 H3K36me3

description:
Library name: Resource CUT_Run TM83 H3K36me3
Control sample used for the the resource analysis (figure 1)

data_processing:
Reads were processed using the nfcore cutandrun pipeline v3.2.2. Peaks were called using SEACR v1.3 and overlapped using bedtools v2.29.2; only peaks observed in at least two samples were retained for further analysis.
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
Supplementary files format and content: bed file with called cis regulatory elements (CREs)
Supplementary files format and content: bed file with called super enhancers (SEs)
Library strategy: CUT&Run

extract_protocol:
Three CUTU&RUN samples were prepared from 200,000-300,000 cells for CTCF (cat#13-2014), IgG (cat#13-0042K), and each of the following histone marks: H3K27ac (cat#13-0059, cat#ab4729), H3K27me3 (cat#13-0055), H3K4me1 (cat#13-0057), H3K4me2 (cat#13-0027), H3K4me3 (cat#13-0041K), H3K36me3 (cat#13-0058), and H3K9me3
Sample libraries were prepared using the CUTANA ChiC/CUT&RUN kit (cat#14-1048) and sequenced on the NextSeq 2000 platform (Illumina, CA, USA) at a read length of 50 base pairs.

value: Trabecular mehswork cells


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

status: Public on Apr 10 2026

type: SRA

city: Chciago

first: Annisa

last: Dea

state: IL

address: 929 E 57th St

country: USA

institute: University of Chicago

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

library_source: transcriptomic single cell

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).

molecule: polyA RNA

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.

tag: cell type

value: yeast

tag: genotype

value: wild-type

tag: treatment

value: YPEG + 30C

tag: batch

value: ancestral


title: MR14

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

country: France

institute: Gustave Roussy

description:
Library name: MR14
FFPE Visium V1

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Lymph node metastatic 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.

tag: tissue

value: Lymph node metastatic osteosarcoma


title: Resource CUT&Run TM83 H3K27me3

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: Resource CUT_Run TM83 H3K27me3
Control sample used for the the resource analysis (figure 1)

library_source: genomic

molecule: genomic DNA

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.


title: Resource CUT&Run TM83 H3K27Ac (Abcam)

description:
Library name: Resource CUT_Run TM83 H3K27Ac (Abcam)
Control sample used for the the resource analysis (figure 1)


title: MR15

description:
Library name: MR15
FFPE Visium V1

source_name: Lung metastatic osteosarcoma

value: Lung metastatic osteosarcoma


title: Control ATAC TM62 Rep1

description:
Library name: Control ATAC TM62 Rep1
Ethanol vehicle control 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).

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: Control


title: Resource CUT&Run TM83 H3K27Ac (Activemotif)

description:
Library name: Resource CUT_Run TM83 H3K27Ac (Activemotif)
Control sample used for the the resource analysis (figure 1)


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

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

value: YPD + sorbitol


title: PT3

description:
Library name: PT3
FFPE Visium V1

source_name: Primary bone osteosarcoma

value: Primary bone osteosarcoma


title: Resource CUT&Run TM83 H3K9me3

description:
Library name: Resource CUT_Run TM83 H3K9me3
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM83 IgG

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


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

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

value: YPD + KCl + hydrogen peroxide


title: Resource CUT&Run TM83 H3K4me3

description:
Library name: Resource CUT_Run TM83 H3K4me3
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM83 H3K4me2

description:
Library name: Resource CUT_Run TM83 H3K4me2
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM83 H3K4me1

description:
Library name: Resource CUT_Run TM83 H3K4me1
Control sample used for the the resource analysis (figure 1)


title: MR12

description:
Library name: MR12
FFPE Visium V1


title: MR11B

description:
Library name: MR11B
FFPE Visium V1


title: Resource CUT&Run TM71 IgG

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


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

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

value: YPD + KCl


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

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

value: YPD + KCl + diamide


title: MR13

description:
Library name: MR13
FFPE Visium V1


title: MR11A

description:
Library name: MR11A
FFPE Visium V1


title: Resource CUT&Run TM71 H3K27me3

description:
Library name: Resource CUT_Run TM71 H3K27me3
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM83 CTCF

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


title: Resource CUT&Run TM71 H3K27Ac (Activemotif)

description:
Library name: Resource CUT_Run TM71 H3K27Ac (Activemotif)
Control sample used for the the resource analysis (figure 1)


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

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

value: YPD + heat stress, 37C


title: Resource CUT&Run TM71 H3K4me3

description:
Library name: Resource CUT_Run TM71 H3K4me3
Control sample used for the the resource analysis (figure 1)


title: MR10A

description:
Library name: MR10A
FFPE Visium V1


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

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

value: YPD + hydrogen peroxide


title: LR5

description:
Library name: LR5
FFPE Visium V1

source_name: Soft-tissue local osteosarcoma relapse

value: Soft-tissue local osteosarcoma relapse


title: Resource CUT&Run TM71 H3K27Ac (Abcam)

description:
Library name: Resource CUT_Run TM71 H3K27Ac (Abcam)
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM71 H3K36me3

description:
Library name: Resource CUT_Run TM71 H3K36me3
Control sample used for the the resource analysis (figure 1)


title: MR10B

description:
Library name: MR10B
FFPE Visium V1


title: Resource CUT&Run TM71 H3K4me2

description:
Library name: Resource CUT_Run TM71 H3K4me2
Control sample used for the the resource analysis (figure 1)


title: MR1

description:
Library name: MR1
FFPE Visium V1


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

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

value: YPD + diamide


title: Resource CUT&Run TM71 H3K9me3

description:
Library name: Resource CUT_Run TM71 H3K9me3
Control sample used for the the resource analysis (figure 1)

value: Trabecular mehswork cells


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

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

value: yeast

value: YPD (rich media)


title: Resource CUT&Run TM71 H3K4me1

description:
Library name: Resource CUT_Run TM71 H3K4me1
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM71 CTCF

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


title: LR19

description:
Library name: LR19
FFPE Visium V1

source_name: Soft-tissue local periprosthetic osteosarcoma relapse


title: Resource CUT&Run TM62 IgG

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


title: Resource CUT&Run TM62 H3K27Ac (Abcam)

description:
Library name: Resource CUT_Run TM62 H3K27Ac (Abcam)
Control sample used for the the resource analysis (figure 1)


title: LR17

description:
Library name: LR17
FFPE Visium V1


title: Resource CUT&Run TM62 H3K27Ac (Activemotif)

description:
Library name: Resource CUT_Run TM62 H3K27Ac (Activemotif)
Control sample used for the the resource analysis (figure 1)


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

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

value: wild-type

value: SDC + sorbitol


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

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

value: SDC + KCl

value: ancestral


title: P1251L_Veh

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

description: Library name: P1251L_Veh

data_processing:
FASTQ files were aligned to GENCODE v45 using a STAR (v2.7.9) two-pass alignment and RSEM (v1.3.3).
Assembly: GENCODE v45
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes basic phenotype information for each sample

source_name: colon

growth_protocol: Biopsies were collected from endoscopically normal appearing colonic mucosa using forceps in subjects undergoing screening or surveillance colonoscopy at the Digestive Health Center of the UVA Health System during the period September 2017 to December 2023. Upon retrieval, biopsies were placed on ice in pre-chilled tubes containing DMEM/F12 media supplemented with 10% fetal bovine serum (FBS) and 1X Pen-Strep (Gibco #15140-122: (100 U/mL penicillin, 100μg/mL streptomycin)). Biopsies were immediately transported to the laboratory for further processing. Recruitment was performed in accordance with relevant guidelines and regulations and was consistent with those required by both the National Institutes of Health and UVA. For the present study, normal colon organoids were established from left colon biopsies of five African American and five European American subjects. Biopsies were washed 3x with DPBS (Gibco #14190-136) at room temperature. Following this, the supernatant was aspirated, and biopsies were incubated in 10mL of DPBS containing 9mM Ultra-Pure EDTA (Invitrogen #155750-038) for 20 minutes at room temperature. Manual inversions of the samples were carried out every 2-3 minutes. During incubation, all tubes, tips and pipets were conditioned with wash media (DMEM/F-12 (Gibco #12634-010), 10% FBS (Gibco #16000-044), 10 mM HEPES (Gibco #15630-080), 2mM L-glutamine (Cellgro #25-005-CI), 1X Pen-Strep, 1X Glutamax (Gibco # 35050-061)) to avoid crypt adhesion. DPBS/EDTA was subsequently removed following incubation. 10mL of DPBS without EDTA was added. This solution was then manually pipetted up and down performed 8-10x to agitate colon crypts from colon biopsies. Tissue was allowed to settle, and supernatant was collected in a 15mL tube. This process was repeated two more times. Collected supernatant was spun at 1200rpm at 4ºC for 5 minutes and all but 2mL of supernatants from each 15mL tube was then removed and combined in a clean 50mL tube, without disturbing the pellet. Using a conditioned 5mL pipet, the remaining 2mLs from each tube was then combined into one 15mL tube and spun at 1200rpm at 4ºC for 5 minutes. The resulting supernatant was carefully removed. Pellets containing intact colon crypts were then added to 10μL of complex media (45% Wash Media, 50% L-WRN conditioned media, 10nM Gastrin (Sigma #G9020), 10μM Y27632 Dihydrochloride (R&D #1254), 1X B27 Supplement (Gibco #17504-44), 1X N2 Supplement (Gibco #17502-048), 1mM n-Acetylcysteine (Sigma #A9165), 50ng/μL EGF (Life Technologies  #PHG0311L), 10mM Nicotinamide (Sigma  #N6636), 500nM A83 (R&D #2939), 10μM SB202190 (R&D  #1264)) was added. To reduce the clumping of the colon crypts, this mixture was then manually pipetted several times. 200μL of Matrigel (Corning #356237) was then added and mixed. 35-50μL of each sample was then plated at the center of wells of a 48-well plate and incubated at 37ºC for 15 minutes. 300-500μL of complex media was then added and samples were returned to the incubator. Organoids were checked and fed after 24hrs. Following this, they were passaged as needed (every 3-5 days) then frozen.

extract_protocol:
RNA isolation was carried out using the Macherey-Nagel RNA XS Kit
TruSeq Stranded Total RNA Gold kit

treatment_protocol: Cells were seeded at a density of 1x106 cells per 48 well and exposed daily to media containing metformin  (0.09mmol/L) or vehicle control (water) for three days

value: colon

tag: cell line

value: colon organoid

value: epithelial

value: Water


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

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

value: SDC + KCl + hydrogen peroxide


title: Resource CUT&Run TM62 H3K27me3

description:
Library name: Resource CUT_Run TM62 H3K27me3
Control sample used for the the resource analysis (figure 1)


title: Resource CUT&Run TM62 H3K9me3

description:
Library name: Resource CUT_Run TM62 H3K9me3
Control sample used for the the resource analysis (figure 1)


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

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

value: SDC + hydrogen peroxide


title: ChIP_45_Input.Rx

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: ChIP_45_Input.Rx

data_processing:
Basecalls were performed using Illumina bcl2fastq v.2.19 for NextSeq2000 output
For samples with a spike-in normalization, reads were trimmed using Cutadapt v.4.1  with parameters --nextseq-trim=30 --minimum-length=20. Spike-in containing samples were aligned using Bowtie2 v.2.2.6 with parameters --sensitive --no-unal,  Non-spiked-in samples were aligned using Bowtie v.1.1.2 with parameters -m 1 -v 2.
bigWig files were generated using package deepTools v.3.5.1 and function bamCoverage, with a parameter to extend reads length -extLen=150. Normalization applied using parameter --scaleFactor, which was calculated from D.melanogaster spike-in reads (bigWig files tagged with "Rx)"
Assembly: hg38, dm6 spike-in
Supplementary files format and content: bigWig

source_name: Large intestine; Colon

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (Millipore Sigma, cat# D6429) supplemented with 10% fetal bovine serum (FBS) (Millipore Sigma, cat# F2442). DLD-1 cells were grown at 37°C in a humidified incubator with 5% CO₂ to maintain normoxic conditions.

extract_protocol:
Immunoprecipitated DNA was extracted using ChIP-DNA purification kit (Zymo Research, cat# D5205) following manufacturer’s instructions. DNA was eluted using in 10mM Tris-HCL pH 8 and quantified using qubit.
ChIP-seq libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes compatible with Illumina systems. DNA libraries were sequenced on Illumina NextSeq 2000 instruments as paired end 50b reads.

treatment_protocol: For hypoxic culture, cells were incubated at 37°C in a controlled atmosphere with 1% O₂.

value: Large intestine; Colon


title: V0179L_Veh

description: Library name: V0179L_Veh


title: Resource CUT&Run TM62 H3K4me1

description:
Library name: Resource CUT_Run TM62 H3K4me1
Control sample used for the the resource analysis (figure 1)


title: V0166L_Veh

description: Library name: V0166L_Veh


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

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

value: SDC + diamide


title: Resource CUT&Run TM62 H3K4me2

description:
Library name: Resource CUT_Run TM62 H3K4me2
Control sample used for the the resource analysis (figure 1)


title: P1266L_Veh

description: Library name: P1266L_Veh


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

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

value: SDC + heat stress, 37C


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

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

value: SDC + KCl + diamide


title: Resource CUT&Run TM62 H3K36me3

description:
Library name: Resource CUT_Run TM62 H3K36me3
Control sample used for the the resource analysis (figure 1)

value: Trabecular mehswork cells


title: Resource CUT&Run TM62 H3K4me3

description:
Library name: Resource CUT_Run TM62 H3K4me3
Control sample used for the the resource analysis (figure 1)


title: ChIP_42_HIF1A_gRNActrl_Normoxia.Rx

description: Library name: ChIP_42_HIF1A_gRNActrl_Normoxia.Rx

value: WT

value: normoxia

tag: antibody

value: HIF-1A (CST, cat# 36169S)


title: ChIP_44_HIF1A_HIF1B.KO1-Hypoxia.Rx

description: Library name: ChIP_44_HIF1A_HIF1B.KO1-Hypoxia.Rx

value: hypoxia


title: Resource CUT&Run TM62 CTCF

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


title: ChIP_43_HIF1A_gRNActrl_Hypoxia.Rx

description: Library name: ChIP_43_HIF1A_gRNActrl_Hypoxia.Rx


title: P1243L_Veh

description: Library name: P1243L_Veh


title: P1239L_Veh

description: Library name: P1239L_Veh


title: ChIP_41_BHLHE40_BHLHE40.KO1_Hypoxia.Rx

description: Library name: ChIP_41_BHLHE40_BHLHE40.KO1_Hypoxia.Rx

value: BHLHE40 (ThermoFisher, cat# PA1-16546)


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

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

value: yeast

value: wild-type

value: SDC (synthetic defined complete)

value: ancestral


title: ChIP_39_BHLHE40_gRNActrl_Hypoxia.Rx

description: Library name: ChIP_39_BHLHE40_gRNActrl_Hypoxia.Rx

value: epithelial


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

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

value: SC + ethanol/glycerol, 30C


title: S. cerevisiae ancestral strain, SC + ethanol/glycerol, 37C, scRNA-seq

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

value: SC + ethanol/glycerol, 37C


title: P1176L_Veh

description: Library name: P1176L_Veh

value: colon

value: colon organoid

value: Water


title: P1229L_Veh

description: Library name: P1229L_Veh


title: P1098L_Veh

description: Library name: P1098L_Veh


title: ChIP_38_BHLHE40_gRNActrl_Normoxia.Rx

description: Library name: ChIP_38_BHLHE40_gRNActrl_Normoxia.Rx

value: Large intestine; Colon


title: ChIP_35_BHLHE40_shctrl_Hypoxia.Rx

description: Library name: ChIP_35_BHLHE40_shctrl_Hypoxia.Rx


title: ChIP_40_BHLHE40_HIF1B.KO1_Hypoxia.Rx

description: Library name: ChIP_40_BHLHE40_HIF1B.KO1_Hypoxia.Rx


title: ChIP_32_Pol2_shBHLHE40_Hypoxia

description: Library name: ChIP_32_Pol2_shBHLHE40_Hypoxia

value: RPB1_NTD (CST, cat# D8L4Y)


title: ChIP_31_Pol2_shctrl_Hypoxia

description: Library name: ChIP_31_Pol2_shctrl_Hypoxia

value: WT


title: P1115L_Veh

description: Library name: P1115L_Veh


title: OE13-RNA-seq-1

city: Wuhan

first: feng

last: zhao

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: Library name: B1

data_processing:
The clean data were mapped against the rice reference genome (MSU 7.0, http://rice.plantbiology.msu.edu/) with the corresponding annotation by Hisat2 (version 2.2.1) using default parameters
FeatureCounts (version 2.0.0) and DESeq2 (version 1.38.3) were used to calculate DEGs with an adjusted P < 0.05 and Foldchange > 1.2
GO enrichment analysis of DEGs was performed on the ShinyGO website (version 0.77, http://bioinformatics.sdstate.edu/go/)
Assembly: IRGSP-1.0
Supplementary files format and content: The gene expression matrix was normalized using FPKM method

organism: Oryza sativa Japonica Group

source_name: leaves

extract_protocol:
For RNA-seq analysis, 14-d-old rice seedlings (OE13 and OE13-2KR/oswox13-1), with drought treatment for 6 h, were used to extract high quality total RNAs from the leaves using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions, followed by reverse transcription (1 µg RNA per reaction) using Vazyme Mix (R312-01).
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced (paired‐end, 2 × 150 bp) on an Illumina HiSeq 2000 instrument.

value: leaves

value: drought resistant type

value: drought stress


title: V0179L_Met

description: Library name: V0179L_Met

value: Met


title: ChIP_34_BHLHE40_shctrl_Normoxia.Rx

description: Library name: ChIP_34_BHLHE40_shctrl_Normoxia.Rx

value: normoxia

value: BHLHE40 (ThermoFisher, cat# PA1-16546)


title: ChIP_37_BHLHE40_Input.Rx

description: Library name: ChIP_37_BHLHE40_Input.Rx


title: ChIP_29_Pol2_shctrl_Normoxia

description: Library name: ChIP_29_Pol2_shctrl_Normoxia


title: ChIP_30_Pol2_shBHLHE40_Normoxia

description: Library name: ChIP_30_Pol2_shBHLHE40_Normoxia


title: ChIP_36_BHLHE40_shBHLHE40_Hypoxia.Rx

description: Library name: ChIP_36_BHLHE40_shBHLHE40_Hypoxia.Rx

value: hypoxia


title: V0166L_Met

description: Library name: V0166L_Met


title: OE13-RNA-seq-2

description: Library name: B2


title: ChIP_26_Pol2_TIMM13.TIMM8B_KO1_Normoxia

description: Library name: ChIP_26_Pol2_TIMM13.TIMM8B_KO1_Normoxia


title: P1266L_Met

description: Library name: P1266L_Met


title: ChIP_24_Pol2_TIMM13.TIMM8A_KO1_Normoxia

description: Library name: ChIP_24_Pol2_TIMM13.TIMM8A_KO1_Normoxia


title: Multiome, 24hr Flu, ATAC, Mouse

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: 10X-Zacharias-24hrSerumFlu-20240104-Multiv1-ATAC
Mouse_24hr_Flu_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger mkfastq then processed using the Cell Ranger Arc pipeline.
Assembly: Custom - GRCm39 with PR8 IAV / GRCh38 with PR8 IAV
Supplementary files format and content: Cell Ranger Arc output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: Seurat object: mouse_minseqe_submission_ready.rds, human_minseqe_submission_ready.rds

organism: Mus musculus

source_name: Lung

extract_protocol:
Nuclei isolated from flu-exposed and control AEOs at 8, 16, and 24hours were encapsulated in Gel-Beads-in emulsion (GEMs) using the Next-GEM Chromium Single Cell Multiome ATAC + Gene Expression Library & Gel Bead Kit v1 on the 10xChromium.
Standard institutional library preparation protocol for Illumina sequencing at CCMC

value: Lung

value: Organoid

value: Flu

tag: timepoint


title: OE13-2KR/oswox13-1-RNA-seq-1

description: Library name: A1

value: drought sensitive type


title: ChIP_25_Pol2_TIMM13.TIMM8A_KO2_Normoxia

description: Library name: ChIP_25_Pol2_TIMM13.TIMM8A_KO2_Normoxia

value: epithelial


title: ChIP_21_Pol2_TIMM8B_KO2_Hypoxia

description: Library name: ChIP_21_Pol2_TIMM8B_KO2_Hypoxia


title: P1243L_Met

description: Library name: P1243L_Met

value: colon

value: colon organoid


title: ChIP_23_Pol2_TIMM13_KO2_Hypoxia

description: Library name: ChIP_23_Pol2_TIMM13_KO2_Hypoxia

value: Large intestine; Colon


title: ChIP_28_Pol2_INPUT

description: Library name: ChIP_28_Pol2_INPUT


title: Multiome, 16hr Flu, ATAC, Mouse

description:
Library name: 10X-Zacharias-William-SAGM16Flu-20240209-Multiv1-ATAC
Mouse_16hr_Flu_filtered_feature_bc_matrix.h5


title: P1229L_Met

description: Library name: P1229L_Met


title: P1239L_Met

description: Library name: P1239L_Met


title: Multiome, 16hr Control, ATAC, Mouse

description:
Library name: 10X-Zacharias-William-SAGM16Con-20240209-Multiv1-ATAC
Mouse_16hr_Control_filtered_feature_bc_matrix.h5

value: Control


title: P1176L_Met

description: Library name: P1176L_Met


title: P1251L_Met

description: Library name: P1251L_Met


title: ChIP_18_Pol2_TIMM8A_KO1_Hypoxia

description: Library name: ChIP_18_Pol2_TIMM8A_KO1_Hypoxia

value: RPB1_NTD (CST, cat# D8L4Y)


title: ChIP_19_Pol2_TIMM8A_KO2_Hypoxia

description: Library name: ChIP_19_Pol2_TIMM8A_KO2_Hypoxia


title: ChIP_17_Pol2_gRNActrl_Hypoxia

description: Library name: ChIP_17_Pol2_gRNActrl_Hypoxia

value: WT


title: ChIP_20_Pol2_TIMM8B_KO1_Hypoxia

description: Library name: ChIP_20_Pol2_TIMM8B_KO1_Hypoxia


title: Multiome, 8hr Flu, ATAC, Mouse

description:
Library name: 10X-Zacharias-William-SAGM8Flu-20240207-Multiv1-ATAC
Mouse_8hr_Flu_filtered_feature_bc_matrix.h5


title: Multiome, 8hr Control, ATAC, Mouse

description:
Library name: 10X-Zacharias-William-SAGM8Con-20240207-Multiv1-ATAC
Mouse_8hr_Control_filtered_feature_bc_matrix.h5


title: Multiome, 24hr Control, ATAC, Mouse

description:
Library name: 10X-Zacharias-24hrSerumControl-20240104-Multiv1-ATAC
Mouse_24hr_Control_filtered_feature_bc_matrix.h5


title: ChIP_15_Pol2_Input

description: Library name: ChIP_15_Pol2_Input


title: ChIP_13_Pol2_TIMM13.TIMM8B_KO2_Hypoxia

description: Library name: ChIP_13_Pol2_TIMM13.TIMM8B_KO2_Hypoxia


title: P1115L_Met

description: Library name: P1115L_Met


title: OE13-2KR/oswox13-1-RNA-seq-2

description: Library name: A2

value: leaves


title: Multiome, 24hr Flu, GEX, Mouse

description: Library name: 10X-Zacharias-24hrSerumFlu-20240104-Multiv1-GEX-mm

molecule: nuclear RNA


title: ChIP_12_Pol2_TIMM13.TIMM8B_KO1_Hypoxia

description: Library name: ChIP_12_Pol2_TIMM13.TIMM8B_KO1_Hypoxia


title: ChIP_16_Pol2_gRNActrl_Normoxia

description: Library name: ChIP_16_Pol2_gRNActrl_Normoxia


title: ChIP_14_Pol2_HIF1B_KO_Hypoxia

description: Library name: ChIP_14_Pol2_HIF1B_KO_Hypoxia


title: ChIP_10_Pol2_TIMM13.TIMM8A_KO1_Hypoxia

description: Library name: ChIP_10_Pol2_TIMM13.TIMM8A_KO1_Hypoxia


title: ChIP_09_Pol2_gRNActrl_Hypoxia

description: Library name: ChIP_09_Pol2_gRNActrl_Hypoxia


description: Library name: ChIP_06_pSer2_TIMM13.TIMM8B_KO2_Hypoxia.RPKM

value: pSer2 (Active motif, cat# 61083)


title: P1098L_Met

description: Library name: P1098L_Met

value: Met


title: ChIP_11_Pol2_TIMM13.TIMM8A_KO2_Hypoxia

description: Library name: ChIP_11_Pol2_TIMM13.TIMM8A_KO2_Hypoxia


title: Multiome, 16hr Flu, GEX, Mouse

description: Library name: 10X-Zacharias-William-SAGM16Flu-20240209-Multiv1-GEX-mm


title: GM00637, Wildtype, 10 µM PDS for 24h, RNAseq rep3

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

description:
Library name: Fib_K_PDS_3
Fib_K_PDS_3

data_processing:
RNAseq reads from fibroblasts samples were aligned to hg38 with gtf file (comprehensive gene annotation file for regions CHR from release 40 (GRCh38.p13), https://www.gencodegenes.org/human/release_40.html) and STAR (version 2.7.9a) with default parameters. RNAseq reads from lymphoblastoidsamples were aligned to a composite reference genome of human and EBV (hg38 + EBV) with the corresponding composite gtf files via STAR. Because of the directionality of RNAseq library preparation protocol, the count of reads mapping to the reverse strand was used for subsequent differential analysis in DESeq2 with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file of raw counts for each sample
Supplementary files format and content: tab-delimited txt file of TPM values for each sample
Supplementary files format and content: tab-delimited txt file of results of differential analysis

growth_protocol: Cell lines from Bloom Syndrome and healthy donors were obtained from Coriell Institute (lymphoblastoid cell lines, LCL: GM16375, AG14980; fibroblast cell lines: GM08505, GM00637). LCLs were cultured in RPMI 1640 medium (Gibco, Cat. #21875) supplemented with 15% fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) and 1% GlutaMAX-I (Gibco, UK, Cat. #35050).  Fibroblast lines were cultured in 1X DMEM (Gibco, UK, Cat. #11960) supplemented with, 1% minimum essential medium non-essential amino acids (MEM NEAA, Gibco, UK, Cat. #11140) and 1% P/S and 10% or 15% FBS, respectively. Cell passaging was performed according to recommendations by Coriell Institute. All cells were cultured at 37°C under 5% CO2.

extract_protocol:
The collected cells were lysed in 1 ml of Trizol at room temperature (RT) for 5 minutes. Subsequently, 200 μl of chloroform was added, and the samples were centrifuged at 12,000 g for 15 minutes at 4°C to separate the phases. Prior to centrifugation, the samples were vortexed for 15 seconds and incubated at RT for 3 minutes. The upper phase, containing RNA, was carefully transferred to a new tube and mixed with 500 μl of isopropanol. The RNA was then precipitated at -20°C for 2 hours and subsequently pelleted at 12,000 g for 30 minutes at 4°C. The supernatant was discarded, and the RNA pellet was washed with 1 ml of ice-cold 75% ethanol. After centrifugation at 9,000 g for 5 minutes at 4°C, the ethanol wash step was repeated, and residual ethanol was aspirated using a pipette. The RNA pellet was air-dried by leaving the tubes open on the counter for approximately 5 minutes.The air-dried RNA pellet was resuspended in 50 μl of DNase reaction mix (5 μl of 10X Reaction Buffer for Turbo DNase, 1 μl of TURBO™ DNase (Thermo Fisher Scientific, AM2238) , 0.5 μl of recombinant RNase inhibitors (Jena Bioscience, PCR-392S) , and 43.5 μl of RNase-free water). The samples were incubated at 37°C for 25 minutes with gentle agitation at 550 rpm to carry out DNAse treatment. For reextraction of RNA, 150 μl of H2O and 200 μl of Phenol/Chloroform/Isoamylalcohol were added. The samples were vortexed for 15 seconds and then centrifuged at 13,000 rpm for 2 minutes at 4°C. The upper phase was transferred to a new tube and mixed with 20 μl of 3M Na-acetate pH 5.5 and 200 μl of isopropanol. The samples were incubated at -20°C for 1 hour to allow for the second RNA precipitation. The RNA was then pelleted, and the washing procedure was repeated as described in the initial precipitation step. The RNA pellet obtained after the final precipitation steps was dissolved in H2O.
poly A mRNA enrichment kit (New England Biolabs, E7490) and RNAseq library preparation kit (New England Biolabs, E7760S), following the manufacturer's protocols

treatment_protocol: Pyridostatin (PDS, Sigma-Aldrich, Cat. #SML2690) stocks (2.5 mM) were prepared by dissolving it in DMSO (Sigma-Aldrich, Cat. #D2650). For LCLs, wildtype cells from cell line AG14980 were treated with 10 µM PDS vs. 0.4% DMSO (control) for 24 h at the concentration of 1 million cells per ml. Cells were then cultured with gentle rotation at 100 rpm to ensure the equal exposure of cells to the treatment. For fibroblasts, wildtype cells (GM00637) at 60% confluency were treated with 10 µM PDS vs. 0.4% DMSO for 24 h.

value: fibroblast

value: Wildtype

value: 10 µM PDS for 24h


title: GM00637, Wildtype, 10 µM PDS for 24h, RNAseq rep2

description:
Library name: Fib_K_PDS_2
Fib_K_PDS_2


title: ChIP_08_Pol2_gRNActrl_Normoxia

description: Library name: ChIP_08_Pol2_gRNActrl_Normoxia

value: normoxia


title: ChIP_07_pSer2_Input.Rx

description: Library name: ChIP_07_pSer2_Input.Rx


title: Multiome, 24hr Control, GEX, Mouse

description: Library name: 10X-Zacharias-24hrSerumControl-20240104-Multiv1-GEX-mm

value: Lung

value: Organoid


title: GM00637, Wildtype, 10 µM PDS for 24h, RNAseq rep1

description:
Library name: Fib_K_PDS_1
Fib_K_PDS_1


description: Library name: ChIP_04_pSer2_TIMM13.TIMM8A_KO2_Hypoxia.RPKM

value: hypoxia


title: Multiome, 16hr Control, GEX, Mouse

description: Library name: 10X-Zacharias-William-SAGM16Con-20240209-Multiv1-GEX-mm


title: Multiome, 8hr Flu, GEX, Mouse

description: Library name: 10X-Zacharias-William-SAGM8Flu-20240207-Multiv1-GEX-mm

value: Flu


title: GM00637, Wildtype, 0.4%DMSO for 24h, RNAseq rep3

description:
Library name: Fib_K_DMSO_3
Fib_K_DMSO_3

value: 0.4%DMSO for 24h


description: Library name: ChIP_03_pSer2_TIMM13.TIMM8A_KO1_Hypoxia.RPKM

value: epithelial


description: Library name: ChIP_05_pSer2_TIMM13.TIMM8B_KO1_Hypoxia.RPKM

value: Large intestine; Colon


title: Multiome, 8hr Control, GEX, Mouse

description: Library name: 10X-Zacharias-William-SAGM8Con-20240207-Multiv1-GEX-mm

value: Control


title: GM00637, Wildtype, 0.4%DMSO for 24h, RNAseq rep2

description:
Library name: Fib_K_DMSO_2
Fib_K_DMSO_2


title: H3K36me3 - E16 primary neuron CxB rep2

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: H3K36me3_CxB_2
CxB_4

library_source: other

data_processing:
Adapters sequences were automatically detected and trimmed using TrimGalore. Reads were mapped to CAST SNP-masked GRCm39 genome using bowtie2 --local -X 2000. PCR duplicates were removed using Picard MarkDuplicates. Allele-specific reads were parsed using SNPsplit (v 0.6.0). For visualization purposes, bam files were converted to bigwig files with CPM normalization.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: other

source_name: Cortical neurons

growth_protocol: Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use. / NPCs were plated onto Geltrex coated plates at a density of 50,000 cells/mL (e.g. in 12 well plates 50,000 cells with 1 mL media, and in 6 well plates 100,000 cells in 2 mL media), and incubated for 3-4 hours to allow cell adherence. Transduction was performed at 7500 genomic particles per cell. Next day, NPC media was fed to keep multipotent state of the NPCs. After 48h of transduction, cells were replated onto new Geltrex coated plates with blasticidin-supplemented media. The next day, neuron differentiation was induced by replating NPCs onto PDL coated plates with cortical neuron media with blasticidin. The following day, cell culture media was optionally replaced to fresh cortical neuron media to enhance neuronal differentiation.

extract_protocol:
Cells were gently washed with PBS and scraped into 1 ml PBS. An aliquot equivalent of 600,000 cells were used for each CUT&Tag sample. Cells were collected by centrifugation for 4 min at 300xg and supernatant was discarded.
Cells were resuspended in lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5 mM spermidine, 1.5 mM MgCl, 0.1 mM EDTA, and 0.25% IGEPAL CA-630) and incubated for 5 min on ice. Lysis was assisted mechanically by gently pipetting up and down 10 times with 1000 μL tips. Successful lysis was confirmed by Typan blue staining and inspection under a light microscope. Nuclei were collected by centrifugation for 4 min at 800xg. Nuclei pellet was washed with CUT&Tag wash buffer and resuspended in 1.5 mL wash buffer. All the procedures were performed according to manufacturer’s guides. Concanavalin A beads were conditioned by washing with 1.6 mL 1X CUT&Tag binding buffer two times. Prepared beads were resuspended in binding buffer and slowly added to the nuclei suspension. For each sample, 20 μL of beads were used. Nuclei binding was performed for 10 min at room temperature in a rotator. Beads-bound nuclei were collected using a magnetic stand and clear supernatant was discarded. Beads were resuspended in 50 μL ice-cold CUT&Tag antibody buffer and desired amount of antibody was added. Suspension was gently mixed by vortexing. Primary antibody binding was performed overnight at 4°C. After a quick spin, beads were cleared on a magnetic stand and supernatant was discarded. Beads were resuspended in 100 μL of 1:100 diluted secondary antibody in CUT&Tag Dig-Wash buffer and incubated for 1h at room temp with rotation. After secondary antibody binding, three washes with 1 mL CUT&Tag Dig-Wash buffer were performed. Beads were resuspended in 1:100 diluted CUT&Tag transposomes in CUT&Tag Dig-300 buffer and incubated on an orbital rotator for 60 min at room temperature. After transposome binding, beads were washed three times with Dig-300 buffer. Tagmentation was induced by incubating beads in 125 μL of CUT&Tag tagmentation buffer for 1h at 37°C. After tagmentation, total DNA was extracted using columns. Purified DNA was PCR amplified using proper index primers. Then, the PCR reaction was purified using SPRI beads. Samples were pooled equimolar. Sequencing was performed PE150.

value: Cortical neurons

value: F1 CastxBL6


title: ChIP_02_pSer2_gRNActrl_Hypoxia.RPKM

description: Library name: ChIP_02_pSer2_gRNActrl_Hypoxia.RPKM

value: WT


title: H3K36me3 - E16 primary neuron BxC rep2

description:
Library name: H3K36me3_BxC_2
BxC_2

value: F1 BL6xCast


title: AG14980, Wildtype, 10 µM PDS for 24h, RNAseq rep2

description:
Library name: Lym_B_PDS_2
Lym_B_PDS_2

value: lymphoblastoid


title: H3K36me3 - E16 primary neuron BxC rep1

description:
Library name: H3K36me3_BxC_1
BxC_1


title: ChIP_01_pSer2_gRNActrl_Normoxia.RPKM

description: Library name: ChIP_01_pSer2_gRNActrl_Normoxia.RPKM

value: pSer2 (Active motif, cat# 61083)


title: AG14980, Wildtype, 10 µM PDS for 24h, RNAseq rep3

description:
Library name: Lym_B_PDS_3
Lym_B_PDS_3

value: Wildtype


title: BATF3 CD8+ T cell Day 14, Donor U2

city: Nagoya

first: Seitaro

last: Terakura

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Hematology and Oncology

country: Japan

institute: Nagoya University Graduate School of Medicine

description:
Library name: Sample_36
ATAC-seq of BATF3 CD8+ T cells at Day 14 from donor U2
12-Day14

data_processing:
Raw reads were processed using nf-core/atacseq pipeline (v2.1.2)
Alignment to GRCh38 human reference genome using STAR
Peak calling using MACS2 with default parameters
Consensus peaks called across all samples using BEDTools merge
Read counting at consensus peaks using featureCounts
Assembly: GRCh38
Supplementary files format and content: Tab-delimited peak count matrix
Supplementary files format and content: BED format peak coordinates
Supplementary files format and content: Tab-delimited peak-gene mapping

source_name: CD8+ T lymphocyte

growth_protocol: CD8+ T cells were isolated from human PBMCs and cultured in X-VIVO 15 medium supplemented with 5% human AB serum, IL-2 (50 IU/mL), and IL-15 (5 ng/mL).

extract_protocol:
ATAC-seq library preparation was performed using the Active Motif ATAC-seq kit (Cat#53150). Briefly, 50,000 cells were washed in cold PBS, lysed to isolate nuclei, and subjected to Tn5 transposase reaction for simultaneous DNA fragmentation and adapter insertion.
Following Tn5 transposition, DNA was purified and PCR amplified using Illumina-compatible primers. Library quality was confirmed by Bioanalyzer. Libraries were sequenced on Illumina NovaSeq X Plus (paired-end 150bp) at Macrogen Japan.

treatment_protocol: Cells were transduced with lentiviral vectors encoding BATF, BATF3, or left untransduced (control). Transduction was performed on Day 0 after isolation. Cells were collected at Day 0, Day 7, and Day 14 post-transduction.

tag: donor id

tag: transduction

value: Day 14

value: CD8+ T lymphocyte


title: Untransduced CD8+ T cell Day 14, Donor U2

description:
Library name: Sample_30
ATAC-seq of Untransduced CD8+ T cells at Day 14 from donor U2
10-Day14

value: Untransduced


title: BATF CD8+ T cell Day 14, Donor U2

description:
Library name: Sample_33
ATAC-seq of BATF CD8+ T cells at Day 14 from donor U2
11-Day14

value: BATF


title: Untransduced CD8+ T cell Day 0, Donor U2

description:
Library name: Sample_28
ATAC-seq of Untransduced CD8+ T cells at Day 0 from donor U2
10-Day0

value: Day 0


title: BATF3 CD8+ T cell Day 0, Donor U2

description:
Library name: Sample_34
ATAC-seq of BATF3 CD8+ T cells at Day 0 from donor U2
12-Day0


title: AG14980, Wildtype, 0.4%DMSO for 24h, RNAseq rep3

description:
Library name: Lym_B_DMSO_3
Lym_B_DMSO_3


title: BATF CD8+ T cell Day 0, Donor U2

description:
Library name: Sample_31
ATAC-seq of BATF CD8+ T cells at Day 0 from donor U2
11-Day0


title: BATF3 CD8+ T cell Day 7, Donor U2

description:
Library name: Sample_35
ATAC-seq of BATF3 CD8+ T cells at Day 7 from donor U2
12-Day7

value: Day 7


title: RiboTag, CA1, Control, 5min, IP, replicate 4

city: New York

first: Ruth

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

description: Library name: RiboTag_Control_5min_IP_Rep4

data_processing:
Illumina's bcl2fastq2 Conversion Software was used for basecalling. Salmon quantifications were derived using Salmon from raw FastQ against the mm10 transcriptome sequences. Differential expression analysis was performed directly from Salmon quantifications using Tximport and DESeq2
Assembly: mm10
Supplementary files format and content: Salmon transcript quantifications against the mm10 transcriptome sequences
Library strategy: RiboTag

source_name: CA1 hippocampus

extract_protocol:
After optogenetic activation, tissue was dissected from acute brain slices in HBSS with 0.1 mg/mL cycloheximide and then resuspended in 5% w/v ice-cold polysome buffer (20 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 0.5 mM DTT) freshly supplemented with 40 U/ml RNasin Plus (Promega), cOmplete protease inhibitors (Roche), 0.1 mg/mL cycloheximide, and 0.5 mM DTT) and homogenized by dounce homogenization (40 strokes type A pestle followed by 40 strokes type B pestle). NP-40 was added to 1% final concentration and lysate was incubated on ice for 10 min. Supernatant was subsequently centrifuged at 2000 x g for 10 min at 4°C followed by 20,000 x g for 10 min at 4°C. 10% of the resulting lysate was used as input and the remaining lysate was pre-cleared by rotation with 50 μl Protein G Dynabeads (Invitrogen) (washed in polysome buffer) for 45 min at 4°C. HA-tagged ribosomes were collected by indirect IP by adding mouse anti-HA (8 μl antibody per mL lysate; Biolegend; MMS-101R) antibody directly to the lysate, rotating the mixture at 4°C for 4 hours, and adding 150 μl Protein G dynabeads to the lysate + antibody followed by overnight rotation at 4°C. Beads were washed twice with polysome buffer containing 1% NP-40 and three times with high salt wash buffer (20 mM HEPES, 5 mM MgCl2, 350 mM KCl, 1% NP-40) freshly supplemented with 0.1 mg/mL cycloheximide, and 1 mM DTT. All washes were 5 minutes with rotation at 4°C. RNA was extracted from input and IP samples by incubation with 1 mL Trizol at room temperature for 5 minutes and then RNeasy Lipid Tissue Mini Kit (Qiagen) via the manufacturer’s protocol with on-column DNase treatment (Roche). RNA quantity and quality were obtained by the Agilent 2100 Pico Bioanalyzer system.
The libraries were prepared by Illumina Stranded Total RNA Prep with Ribo-Zero Plus following the manufacturer’s instructions. High-throughput sequencing was performed on NovaSeq (Illumina) to obtain 150 nucleotide paired-end reads.

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA

value: AAV-Control

tag: time post_activation

tag: fraction

value: IP


title: BATF CD8+ T cell Day 7, Donor U2

description:
Library name: Sample_32
ATAC-seq of BATF CD8+ T cells at Day 7 from donor U2
11-Day7


title: BATF3 CD8+ T cell Day 14, Donor F2

description:
Library name: Sample_27
ATAC-seq of BATF3 CD8+ T cells at Day 14 from donor F2
9-Day14


title: GM00637, Wildtype, 0.4%DMSO for 24h, RNAseq rep1

description:
Library name: Fib_K_DMSO_1
Fib_K_DMSO_1

value: fibroblast

value: 0.4%DMSO for 24h


title: H3K36me3 - E16 primary neuron CxB rep1

description:
Library name: H3K36me3_CxB_1
CxB_3

value: Cortical neurons

value: F1 CastxBL6


title: BATF3 CD8+ T cell Day 7, Donor F2

description:
Library name: Sample_26
ATAC-seq of BATF3 CD8+ T cells at Day 7 from donor F2
9-Day7


title: BATF3 CD8+ T cell Day 0, Donor F2

description:
Library name: Sample_25
ATAC-seq of BATF3 CD8+ T cells at Day 0 from donor F2
9-Day0


title: AG14980, Wildtype, 0.4%DMSO for 24h, RNAseq rep2

description:
Library name: Lym_B_DMSO_2
Lym_B_DMSO_2

value: lymphoblastoid


title: Untransduced CD8+ T cell Day 7, Donor U2

description:
Library name: Sample_29
ATAC-seq of Untransduced CD8+ T cells at Day 7 from donor U2
10-Day7


title: AG14980, Wildtype, 0.4%DMSO for 24h, RNAseq rep1

description:
Library name: Lym_B_DMSO_1
Lym_B_DMSO_1


title: GM00637, Wildtype, none, RNAseq rep3

description:
Library name: Fib_WT_K3
Fib_WT_K3


title: BATF CD8+ T cell Day 7, Donor F2

description:
Library name: Sample_23
ATAC-seq of BATF CD8+ T cells at Day 7 from donor F2
8-Day7


title: RiboTag, CA1, Control, 5min, IP, replicate 1

description: Library name: RiboTag_Control_5min_IP_Rep1


title: RiboTag, CA1, Control, 5min, IP, replicate 3

description: Library name: RiboTag_Control_5min_IP_Rep3


title: Untransduced CD8+ T cell Day 14, Donor F2

description:
Library name: Sample_21
ATAC-seq of Untransduced CD8+ T cells at Day 14 from donor F2
7-Day14


title: AG14980, Wildtype, 10 µM PDS for 24h, RNAseq rep1

description:
Library name: Lym_B_PDS_1
Lym_B_PDS_1

value: 10 µM PDS for 24h


title: BATF CD8+ T cell Day 0, Donor F2

description:
Library name: Sample_22
ATAC-seq of BATF CD8+ T cells at Day 0 from donor F2
8-Day0


title: RiboTag, CA1, Opto, 5min, IP, replicate 4

description: Library name: RiboTag_ChR2_5min_IP_Rep4


title: Untransduced CD8+ T cell Day 7, Donor F2

description:
Library name: Sample_20
ATAC-seq of Untransduced CD8+ T cells at Day 7 from donor F2
7-Day7


title: RiboTag, CA1, Opto, 5min, IP, replicate 3

description: Library name: RiboTag_ChR2_5min_IP_Rep3


title: Untransduced CD8+ T cell Day 0, Donor F2

description:
Library name: Sample_19
ATAC-seq of Untransduced CD8+ T cells at Day 0 from donor F2
7-Day0


title: GM00637, Wildtype, none, RNAseq rep2

description:
Library name: Fib_WT_K2
Fib_WT_K2

value: Wildtype


title: RiboTag, CA1, Opto, 5min, IP, replicate 2

description: Library name: RiboTag_ChR2_5min_IP_Rep2


title: GM08505, BLM-/-, none, RNAseq rep2

description:
Library name: Fib_BS_D2
Fib_BS_D2

value: BLM-/-


title: Untransduced CD8+ T cell Day 14, Donor U1

description:
Library name: Sample_12
ATAC-seq of Untransduced CD8+ T cells at Day 14 from donor U1
4-Day14

value: Day 14

value: CD8+ T lymphocyte


title: GM08505, BLM-/-, none, RNAseq rep1

description:
Library name: Fib_BS_D1
Fib_BS_D1


title: RiboTag, CA1, Control, 5min, Input, replicate 2

description: Library name: RiboTag_Control_5min_Input_Rep2

value: Input


title: AG14980, Wildtype, none, RNAseq rep3

description:
Library name: Lym_WT_B3
Lym_WT_B3


title: BATF3 CD8+ T cell Day 14, Donor F1

description:
Library name: Sample_9
ATAC-seq of BATF3 CD8+ T cells at Day 14 from donor F1
3-Day14


title: BATF CD8+ T cell Day 14, Donor U1

description:
Library name: Sample_15
ATAC-seq of BATF CD8+ T cells at Day 14 from donor U1
5-Day14

value: BATF


title: GM00637, Wildtype, none, RNAseq rep1

description:
Library name: Fib_WT_K1
Fib_WT_K1


title: RiboTag, CA1, Opto, 5min, IP, replicate 1

description: Library name: RiboTag_ChR2_5min_IP_Rep1


title: Untransduced CD8+ T cell Day 7, Donor U1

description:
Library name: Sample_11
ATAC-seq of Untransduced CD8+ T cells at Day 7 from donor U1
4-Day7

value: Untransduced

value: Day 7


title: BATF3 CD8+ T cell Day 7, Donor U1

description:
Library name: Sample_17
ATAC-seq of BATF3 CD8+ T cells at Day 7 from donor U1
6-Day7


title: BATF3 CD8+ T cell Day 14, Donor U1

description:
Library name: Sample_18
ATAC-seq of BATF3 CD8+ T cells at Day 14 from donor U1
6-Day14


title: Untransduced CD8+ T cell Day 0, Donor U1

description:
Library name: Sample_10
ATAC-seq of Untransduced CD8+ T cells at Day 0 from donor U1
4-Day0

value: Day 0


title: BATF CD8+ T cell Day 0, Donor U1

description:
Library name: Sample_13
ATAC-seq of BATF CD8+ T cells at Day 0 from donor U1
5-Day0


title: RiboTag, CA1, Control, 5min, Input, replicate 4

description: Library name: RiboTag_Control_5min_Input_Rep4

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA

value: AAV-Control


title: BATF3 CD8+ T cell Day 0, Donor U1

description:
Library name: Sample_16
ATAC-seq of BATF3 CD8+ T cells at Day 0 from donor U1
6-Day0


title: BATF3 CD8+ T cell Day 7, Donor F1

description:
Library name: Sample_8
ATAC-seq of BATF3 CD8+ T cells at Day 7 from donor F1
3-Day7


title: RiboTag, CA1, Control, 5min, Input, replicate 3

description: Library name: RiboTag_Control_5min_Input_Rep3


title: AG14980, Wildtype, none, RNAseq rep2

description:
Library name: Lym_WT_B2
Lym_WT_B2


title: BATF CD8+ T cell Day 14, Donor F1

description:
Library name: Sample_6
ATAC-seq of BATF CD8+ T cells at Day 14 from donor F1
2-Day14


title: BATF CD8+ T cell Day 7, Donor F1

description:
Library name: Sample_5
ATAC-seq of BATF CD8+ T cells at Day 7 from donor F1
2-Day7


title: RiboTag, CA1, Opto, 5min, Input, replicate 4

description: Library name: RiboTag_ChR2_5min_Input_Rep4


title: Untransduced CD8+ T cell Day 14, Donor F1

description:
Library name: Sample_3
ATAC-seq of Untransduced CD8+ T cells at Day 14 from donor F1
1-Day14


title: Untransduced CD8+ T cell Day 0, Donor F1

description:
Library name: Sample_1
ATAC-seq of Untransduced CD8+ T cells at Day 0 from donor F1
1-Day0


title: Untransduced CD8+ T cell Day 7, Donor F1

description:
Library name: Sample_2
ATAC-seq of Untransduced CD8+ T cells at Day 7 from donor F1
1-Day7


title: RiboTag, CA1, Control, 5min, Input, replicate 1

description: Library name: RiboTag_Control_5min_Input_Rep1


title: BATF3 CD8+ T cell Day 0, Donor F1

description:
Library name: Sample_7
ATAC-seq of BATF3 CD8+ T cells at Day 0 from donor F1
3-Day0


title: SH-SY5Y human neuroblastoma cell treated with oleoylethanolamide after 24 hours, replication 1

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: OEA1

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

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: human neuroblastoma cell

value: WT

value: OEA


title: GM16375, BLM-/-, none, RNAseq rep3

description:
Library name: Lym_BS_A3
Lym_BS_A3

value: lymphoblastoid


title: AG14980, Wildtype, none, RNAseq rep1

description:
Library name: Lym_WT_B1
Lym_WT_B1


title: RiboTag, CA1, Opto, 5min, Input, replicate 2

description: Library name: RiboTag_ChR2_5min_Input_Rep2


title: RiboTag, CA1, Opto, 5min, Input, replicate 3

description: Library name: RiboTag_ChR2_5min_Input_Rep3


title: GM16375, BLM-/-, none, RNAseq rep2

description:
Library name: Lym_BS_A2
Lym_BS_A2


title: SH-SY5Y human neuroblastoma cell treated with oleoylethanolamide after 24 hours, replication 2

description: Library name: OEA2


title: GM16375, BLM-/-, none, RNAseq rep1

description:
Library name: Lym_BS_A1
Lym_BS_A1


title: RiboTag, CA1, Opto, 5min, Input, replicate 1

description: Library name: RiboTag_ChR2_5min_Input_Rep1


title: SH-SY5Y human neuroblastoma cell treated with butyrate after 24 hours, replication 3

description: Library name: BA3

value: BA


title: BATF CD8+ T cell Day 0, Donor F1

description:
Library name: Sample_4
ATAC-seq of BATF CD8+ T cells at Day 0 from donor F1
2-Day0


title: AG14980, Wildtype, biological replicate 2, Input, G4 ChIPseq rep3

description:
Library name: Lym_WT_B2_Input
ChIP_rep2_B_Input

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38 or composite genome of hg38 and EBV using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded. ATAC-seq peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAMPE --nomodel –min-length 100 narrowPeak parameters. For a given cell type, two types of ATACseq peak sets were generated. Using LCL as an example, to identify differentially accessible regions in each contrast (BS vs WT or PDS vs DMSO), a local peak set was called by pooling equal number reads from each sample. To identify peaks that are differentially accessible in BS and PDS-treated conditions, equal number of reads from WT, BS, DMSO- and PDS-treated samples from the same cell type was pooled to call a global peak set, which was further supplemented by unique peaks in the local peak sets from BS vs WT or PDS vs DMSO contrasts. The number of fragments in each ATACseq peak was quantified with htseq-count (HTSeq version 0.9.1). Subsequently, the count matrix was normalized and differential analysis was carried out in DESeq2 (version 1.30.1) to identify significantly differential signals (adjusted p-value <0.05). Loess normalization method in csaw (version 1.24.3) following differential analysis with edgeR (version 3.32.1) were employed to compare PDS- and DMSO-treated samples.
Assembly: hg38
Supplementary files format and content: narrowPeak, G4 peaks called for each biological replicate consisting of 3 technical replicates: IP1, IP2, and IP3
Supplementary files format and content: narrowPeak, G4 ChIPseq peaks for WT or BLM-/- sample after filtering on irreproducibility of the ChIPseq peaks in the two biological replicates using IDR with the threshold of FDR<0.05
Supplementary files format and content: bedgraph files generated from the filtered bamfile for each sample
Supplementary files format and content: tab-delimited txt file of results of differential analysis

extract_protocol:
fibroblasts were first trypsinised (Sigma-Aldrich, Cat. #SLCH3385), pelleted at 300 g for 5 min and washed once with cold 1x Dulbecco's phosphate buffered saline (PBS, Gibco, Cat. #14190). Lymphoblastoid cells were pelleted at 300 g for 5 min and washed once with cold 1x PBS.
50, 000 cells were subjected to ATACseq preparation essentially as described in Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

value: Wildtype

tag: chip antibody


title: AG14980, Wildtype, biological replicate 2, IP rep3, G4 ChIPseq rep3

description:
Library name: Lym_WT_B2_IP3
ChIP_rep2_B_IP3

value: absolute antibody, cat.no. Ab00174-30.126


title: RiboTag, CA1, Control, 30min, IP, replicate 4

description: Library name: RiboTag_Control_30min_IP_Rep4

value: IP


title: SH-SY5Y human neuroblastoma cell treated with butyrate after 24 hours, replication 2

description: Library name: BA2


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 6

description: Library name: con_3

value: NC


title: AG14980, Wildtype, biological replicate 2, IP rep2, G4 ChIPseq rep2

description:
Library name: Lym_WT_B2_IP2
ChIP_rep2_B_IP2


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 4

description: Library name: con_1


title: RiboTag, CA1, Control, 30min, IP, replicate 3

description: Library name: RiboTag_Control_30min_IP_Rep3


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 5

description: Library name: con_2


title: SH-SY5Y human neuroblastoma cell treated with butyrate after 24 hours, replication 1

description: Library name: BA1


title: AG14980, Wildtype, biological replicate 1, Input, G4 ChIPseq rep3

description:
Library name: Lym_WT_B1_Input
ChIP_rep1_B_Input


title: SH-SY5Y human neuroblastoma cell treated with bacterial supernatant after 24 hours, replication 1

description: Library name: Law_1

value: LAW


title: RiboTag, CA1, Control, 30min, IP, replicate 1

description: Library name: RiboTag_Control_30min_IP_Rep1


title: AG14980, Wildtype, biological replicate 2, IP rep1, G4 ChIPseq

description:
Library name: Lym_WT_B2_IP1
ChIP_rep2_B_IP1


title: SH-SY5Y human neuroblastoma cell treated with oleoylethanolamide after 24 hours, replication 3

description: Library name: OEA3


title: RiboTag, CA1, Opto, 30min, IP, replicate 4

description: Library name: RiboTag_ChR2_30min_IP_Rep4


title: AG14980, Wildtype, biological replicate 1, IP rep3, G4 ChIPseq rep3

description:
Library name: Lym_WT_B1_IP3
ChIP_rep1_B_IP3


title: SH-SY5Y human neuroblastoma cell treated with bacterial supernatant after 24 hours, replication 3

description: Library name: Law_3


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 3

description: Library name: c3


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 1

description: Library name: c1


title: SH-SY5Y human neuroblastoma cell with no treatment after 24 hours, replication 2

description: Library name: c2


title: AG14980, Wildtype, biological replicate 1, IP rep2, G4 ChIPseq rep2

description:
Library name: Lym_WT_B1_IP2
ChIP_rep1_B_IP2


title: RiboTag, CA1, Opto, 30min, IP, replicate 3

description: Library name: RiboTag_ChR2_30min_IP_Rep3


title: S143P-corrected ATAC-seq 3

first: Asia

last: Owais

address: 840 S Wood Street

department: Cardiology

institute: University of Illinois at Chicago

description:
Library name: sample 9
DifferentialPeak.xlsx
GC3_S15_L005

data_processing:
detailed methods are found in the manuscript
Assembly: hg38
Supplementary files format and content: excel files, differential peak analysis

source_name: iPSC-derived atrial cardiomyocytes

growth_protocol: iPSC-aCMs were maintained in Cardiomyocyte maturation medium

extract_protocol:
Briefly, the Cell membrane was permeabilized with nuclear lysis buffer (10 mM tris, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL-630). Then, cells were resuspended in 50uL of transposase reaction mixture (22.5uL nuclease-free water, 25uL of TD buffer, and 2.5uL of TDE1 enzyme, Illumina #20034197). Transposition was carried out at 37°C for 22 min, followed by DNA purification with DNA Clean and Concentrator-5 (Zymo Research) according to the manufacturer’s recommendation.
Following purification, library fragments were PCR amplified with Nextera XT v2 adapter primers. Multiplexed and pooled library was sequenced on the Novaseq X Plus with paired ends of 50 nucleotides per the manufacturer’s instructions. The

value: iPSC-derived atrial cardiomyocytes

value: cardiomyocyte


title: RiboTag, CA1, Opto, 30min, IP, replicate 2

description: Library name: RiboTag_ChR2_30min_IP_Rep2


title: S143P-corrected ATAC-seq 2

description:
Library name: sample 8
DifferentialPeak.xlsx
GC2_S14_L005


title: AG14980, Wildtype, biological replicate 1, IP rep1, G4 ChIPseq rep1

description:
Library name: Lym_WT_B1_IP1
ChIP_rep1_B_IP1


title: S143P-corrected ATAC-seq 1

description:
Library name: sample 7
DifferentialPeak.xlsx
GC1_S13_L005


title: RiboTag, CA1, Opto, 30min, IP, replicate 1

description: Library name: RiboTag_ChR2_30min_IP_Rep1


title: RiboTag, CA1, Control, 30min, Input, replicate 4

description: Library name: RiboTag_Control_30min_Input_Rep4

value: Input


title: sgTRAPPC4-3

city: hefei

first: Wentao

last: Zhang

state: anhui

address: meishan road

institute: anhui medical university

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

data_processing:
Clean reads were aligned to the human reference genome (hg38) using Bowtie2. Low-quality alignments, PCR duplicates, and reads mapped to mitochondrial or organellar DNA were subsequently removed.
Differentially Accessible Regions (DARs) were identified by comparing ATAC-seq signal intensities between groups. We used the R package DiffBind to perform DAR analysis. First, peaks from all samples were overlapped to define a consensus peak set. To reduce noise caused by variable peak widths, the summit of each peak was determined, and each peak was redefined by extending 200 bp upstream and downstream of the summit.
Assembly: GRCh38
Supplementary files format and content: Differentially Accessible Region (DARs) in TSV format

extract_protocol:
Nuclei were extracted from fresh cells and lysed to release chromatin. Tn5 transposase was used to simultaneously fragment DNA and insert sequencing adapters. The resulting tagmented DNA fragments were purified using AMPure XP beads.
ATAC-seq libraries were constructed following the Omni-ATAC protocol. Briefly, 50,000–100,000 nuclei were isolated and incubated with Tn5 transposase (Illumina Nextera) in a reaction buffer to simultaneously fragment DNA and insert sequencing adapters. After purification, PCR amplification was performed with indexing primers, and libraries were size-selected (~150–700 bp) using AMPure XP beads. Final libraries were quantified by Qubit and quality-checked using a Bioanalyzer before sequencing.

value: HNSCC cell line

value: TRAPPC4 knockout

value: KO TRAPPC4


title: GM16375, BLM-/-, biological replicate 2, IP rep2, G4 ChIPseq rep2

description:
Library name: Lym_BS_A2_IP2
ChIP_rep2_A_IP2

value: BLM-/-


title: S143P-corrected 1

description:
Library name: sample 7
gene_fpkm (1).xlsx
DD-RS3-GC1_S1

data_processing:
Raw FASTQ files were uploaded to Biojupies (https://maayanlab.cloud/biojupies) for analysis.
Assembly: hg38
Supplementary files format and content: .xlsx files contain average fold change

growth_protocol: iPSC-aCMs were maintained in Cardiomyocyte maturation medium prior to RNA extraction

extract_protocol:
RNA was isolated using Trizol and QC-ed by bioAnalyzer (Agilent 2100)
RNA-seq libraries were generated using an Illumina TruSEQ-like protocol (provided by Illumina).


title: GM16375, BLM-/-, biological replicate 2, IP rep3, G4 ChIPseq rep3

description:
Library name: Lym_BS_A2_IP3
ChIP_rep2_A_IP3


title: RiboTag, CA1, Control, 30min, Input, replicate 3

description: Library name: RiboTag_Control_30min_Input_Rep3

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA

value: AAV-Control


title: S143P-corrected 3

description:
Library name: sample 9
gene_fpkm (1).xlsx
DD-RS3-GC3_S3


title: GM16375, BLM-/-, biological replicate 2, IP rep1, G4 ChIPseq rep1

description:
Library name: Lym_BS_A2_IP1
ChIP_rep2_A_IP1

value: lymphoblastoid


title: sgTRAPPC4-2

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


title: sgNTC-2

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

value: TRAPPC4 wild-type


title: GM16375, BLM-/-, biological replicate 1, Input, G4 ChIPseq

description:
Library name: Lym_BS_A1_Input
ChIP_rep1_A_Input


title: RiboTag, CA1, Opto, 30min, Input, replicate 4

description: Library name: RiboTag_ChR2_30min_Input_Rep4


title: sgNTC-1

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


title: sgTRAPPC4

description:
Library name: Sample 1
LIU-LSC-1, KO TRAPPC4

data_processing:
Clean reads were aligned to the human reference genome (hg38) using Bowtie2. Low-quality alignments, PCR duplicates, and reads mapped to mitochondrial or organellar DNA were subsequently removed.
Assembly: GRCh38
Supplementary files format and content: CUT&Tag Peaks in txt format
Library strategy: CUT&Tag

extract_protocol:
For CUT&Tag experiments targeting FOS, LIU-LSC-1 cells were harvested and washed with wash buffer. Intact nuclei were isolated using digitonin-based permeabilization and immobilized on concanavalin A-coated magnetic beads. Nuclei-bound cells were incubated overnight at 4°C with a primary antibody against FOS (1:50 dilution), followed by a secondary antibody incubation to amplify the signal. Protein A-Tn5 transposome was then added to bind the antibody complexes. After washing, tagmentation was performed by adding Mg²⁺ to activate Tn5, simultaneously fragmenting DNA and incorporating sequencing adapters. DNA was then extracted by reverse crosslinking, followed by purification using AMPure XP beads.
CUT&Tag libraries were constructed following the published protocol by Kaya-Okur et al. (2019, Nature Communications). Briefly, concanavalin A-coated magnetic beads were used to immobilize the nuclei. After digitonin permeabilization, samples were incubated overnight at 4°C with a primary antibody against the target protein (FOS), followed by incubation with a secondary antibody. Protein A-Tn5 fusion enzyme loaded with sequencing adapters was then added to bind the antibody complex. After tagmentation at 37°C for 1 hour, DNA was released by adding SDS and Proteinase K, followed by overnight incubation at 55°C. DNA fragments were purified using AMPure XP beads. Library amplification was performed by PCR using indexed primers, and libraries were size-selected (typically 300–700 bp) using magnetic beads. The final libraries were quantified and sequenced on the Illumina PE150 platform.


title: RiboTag, CA1, Control, 30min, Input, replicate 2

description: Library name: RiboTag_Control_30min_Input_Rep2


title: GM16375, BLM-/-, biological replicate 2, Input, G4 ChIPseq rep3

description:
Library name: Lym_BS_A2_Input
ChIP_rep2_A_Input


title: LMNA3

description: Library name: sample 6

data_processing:
Read alignments were first adjusted to account for TAC transposon binding: +4 bp for + strand alignments, -5 bp for - strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov55, then converted to bigWig using the UCSC tool bedGraphToBigWig 56. Tracks were normalized by the sum of alignment lengths of over 1 billion. The start position track was generated by taking just the first base of the alignment for + strand alignments or the last base of the alignment for - strand alignments, then creating bedGraph and bigWig tracks as for the open chromatin; tracks were normalized to the alignment count over 1 million. Open chromatin peaks were called using MACS257 with --nomodel set and no background provided; peaks with a score >5 were retained.
Assembly: hg38
Supplementary files format and content: normalized ATAC sequencing reads in xls format

extract_protocol:
Briefly, the Cell membrane was permeabilized with nuclear lysis buffer. Then, cells were resuspended in 50uL of transposase reaction mixture. Transposition was carried out at 37°C for 22 min, followed by DNA purification with DNA Clean and Concentrator-5 (Zymo Research) according to the manufacturer’s recommendation.
Following purification, library fragments were PCR amplified with Nextera XT v2. adapter primers. Multiplexed and pooled library was sequenced on the Novaseq X. Plus with paired ends of 50 nucleotides per the manufacturer’s instructions

value: atrial cardiomyocyte diffferentiation


title: SH-SY5Y human neuroblastoma cell treated with bacterial supernatant after 24 hours, replication 2

description: Library name: Law_2

value: human neuroblastoma cell

value: WT


title: S143P-corrected 2

description:
Library name: sample 8
gene_fpkm (1).xlsx
DD-RS3-GC2_S2


title: RiboTag, CA1, Control, 30min, Input, replicate 1

description: Library name: RiboTag_Control_30min_Input_Rep1


title: sgTRAPPC4-1

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


title: LMNA2

description: Library name: sample 5


title: RiboTag, CA1, Control, 30min, IP, replicate 2

description: Library name: RiboTag_Control_30min_IP_Rep2

value: IP


title: BATF CD8+ T cell Day 7, Donor U1

description:
Library name: Sample_14
ATAC-seq of BATF CD8+ T cells at Day 7 from donor U1
5-Day7

value: BATF

value: Day 7

value: CD8+ T lymphocyte


title: GM16375, BLM-/-, biological replicate 1, IP rep3, G4 ChIPseq

description:
Library name: Lym_BS_A1_IP3
ChIP_rep1_A_IP3

value: absolute antibody, cat.no. Ab00174-30.126


title: sgNTC-3

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

value: HNSCC cell line

value: NC


title: GM16375, BLM-/-, biological replicate 1, IP rep2, G4 ChIPseq

description:
Library name: Lym_BS_A1_IP2
ChIP_rep1_A_IP2


title: RiboTag, CA1, Control, 5min, IP, replicate 2

description: Library name: RiboTag_Control_5min_IP_Rep2


title: RiboTag, CA1, Opto, 30min, Input, replicate 2

description: Library name: RiboTag_ChR2_30min_Input_Rep2

value: Input


title: WT2

description: Library name: sample 2

value: iPSC-derived atrial cardiomyocytes

value: cardiomyocyte


title: BATF CD8+ T cell Day 14, Donor F2

description:
Library name: Sample_24
ATAC-seq of BATF CD8+ T cells at Day 14 from donor F2
8-Day14

value: Day 14


title: GM00637, Wildtype, 10 µM PDS for 24h, ATACseq rep3

description:
Library name: Fib_K_PDS3
K_PDS3

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38 or composite genome of hg38 and EBV using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded. ATAC-seq peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAMPE --nomodel –min-length 100 narrowPeak parameters. For a given cell type, two types of ATACseq peak sets were generated. Using LCL as an example, to identify differentially accessible regions in each contrast (BS vs WT or PDS vs DMSO), a local peak set was called by pooling equal number reads from each sample. To identify peaks that are differentially accessible in BS and PDS-treated conditions, equal number of reads from WT, BS, DMSO- and PDS-treated samples from the same cell type was pooled to call a global peak set, which was further supplemented by unique peaks in the local peak sets from BS vs WT or PDS vs DMSO contrasts. The number of fragments in each ATACseq peak was quantified with htseq-count (HTSeq version 0.9.1). Subsequently, the count matrix was normalized and differential analysis was carried out in DESeq2 (version 1.30.1) to identify significantly differential signals (adjusted p-value <0.05). Loess normalization method in csaw (version 1.24.3) following differential analysis with edgeR (version 3.32.1) were employed to compare PDS- and DMSO-treated samples.
Assembly: hg38
Supplementary files format and content: narrowPeak, ATAC-seq peaks for each pair of samples called by macs2, which were used in downstream differential anlaysis.
Supplementary files format and content: bedgraph files generated from the filtered bamfile.
Supplementary files format and content: tab-delimited txt file, number of fragments in each peak quantified by Htseq.
Supplementary files format and content: tab-delimited txt file of results of differential analysis

value: fibroblast

value: Wildtype

value: 10 µM PDS for 24h


title: GM16375, BLM-/-, biological replicate 1, IP rep1, G4 ChIPseq

description:
Library name: Lym_BS_A1_IP1
ChIP_rep1_A_IP1

value: lymphoblastoid

value: BLM-/-


title: WT1

description: Library name: sample 1

value: WT

value: atrial cardiomyocyte diffferentiation


title: RNA from tonsil, donor 2

city: Rennes

first: Samuel

last: Bastos Serra Trinca

address: 2 avenue du professeur Léon Bernard

institute: University of Rennes

description:
Library name: T2_SMRT
PacBio Revio

data_processing:
The Fastq sequences were sent to IMGT/HighV-QUEST for alignment with the IGH reference V(D)J database (IMGT/V-QUEST program version: 3,6,3). Sequences with a productive and usable VDJ were retained.
Assembly: IMGT/V-QUEST reference directory release: 202416-4
Supplementary files format and content: Table of clone counts after hierarchical clustering performed on IMGT outputs using the Scoper package (version 1.3.0)

source_name: tonsil

extract_protocol:
RNA extracted from memory B cells obtained by magnetic enrichment from a human tonsil
For classical RNA-seq libraries, 1200 ng of total RNA (with RIN over 7) were used for polyA selection and reverse transcription using the Truseq stranded mRNA library kit (Illumina). Sequencing (2x150 bp paired ends) was run on a Novaseq Illumina platform (Macrogen) in order to acquire 15 Gb of throughput per sample.

value: tonsil

value: memory B cells


title: RNA from tonsil, donor 1

description:
Library name: T1_SMRT
PacBio Revio


title: GM00637, Wildtype, 10 µM PDS for 24h, ATACseq rep2

description:
Library name: Fib_K_PDS2
K_PDS2


title: LMNA1

description: Library name: sample 4


title: RiboTag, CA1, Opto, 30min, Input, replicate 3

description: Library name: RiboTag_ChR2_30min_Input_Rep3

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA


title: SN2_1

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

description: Library name: bc2076

data_processing:
Data was aligned using pbmm2 to mm10 genome
Methylation values were extracted using pb-CpG-tools
Assembly: mm10
Supplementary files format and content: PacBio bam files with methylation calls and kinetics

source_name: spleen

extract_protocol:
DNA was extracted following the manufacturers protocol
libraries were constructed following the manufacturers protocol (SMRT-Seq, PacBio)

value: spleen

tag: Sex

value: female

value: CD19+ enriched B cells

value: Spen+Notch2 (CD19Cre+/-, SPENfl/wt, ICN2+/- )


title: Humanized Fed

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Library name: Humanized

data_processing:
Raw sequencing data were processed using Space Ranger (v2.0.0 for normal chow and high-fat diet studies, v3.1.0 for humanized liver studies, 10x Genomics) to align reads to the reference genome and generate spatial gene expression matrices.
Assembly: For normal chow and high-fat diet studies: mm10-2020-A. For humanized liver studies: GRCh38-2020-A.
Supplementary files format and content: barcode.tsv.gz: list of spatial barcodes
Supplementary files format and content: feature.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: table of Moran's I values for each gene
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: cytassist_image.tiff: CytAssist image
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
For high-fat diet studies, fresh frozen mouse livers were embedded in Neg-50 and stored at -80 °C until sectioning. After sectioned at 10 μm thickness, sections were adhered to capture areas by brief warming onto Visium v1 slides (10x Genomics). For humanized liver studies, livers were fixed in 4% paraformaldehyde (PFA) for 3 hours, cryoprotected in PFA + 30 % sucrose for overnight, embedded in OCT, and tissue blocks were kept at -80 °C until sectioning. After sectioned at 10 μm thickness, Visium v2 (prepared with CytAssist) was performed using the CytAssist instrument.
For both studies, the sample preparation was performed according to the manufacturer’s guidelines. Briefly, tissue sections were stained with hematoxylin and eosin (H&E), imaged using a brightfield microscope for histological reference and spatial registration. RNA capture, reverse transcription, second-strand synthesis, cDNA amplification, and library construction were performed. Libraries were indexed, quality-controlled, and sequenced on an Illumina platform using paired-end sequencing.

treatment_protocol: NCD mice were fed laboratory mouse chow diet (LabDiet, 5053) whereas 3MHFD mice were fed a 60% fat diet (Research Diets, D12492) beginning at 6 weeks of age for 3 months. uPA SCID-based humanized liver chimeric mice were generated as previously described and maintained with vitamin C containing chow diet (modified LabDiet 5053 containing 130 ppm vitamin C).

value: Liver

value: Humanized liver


title: WT3

description: Library name: sample 3

value: iPSC-derived atrial cardiomyocytes

value: cardiomyocyte


title: SN2_2

description: Library name: bc2084


title: Mac_L04:scRNA-seq CRISPR interference screen of CD14-positive monocyte,  pooled: untreated, LPS treated

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: Library name: Mac_L04_GEX_lib

data_processing:
Raw data from pooled samples were processed by Cell Ranger v9.0.1 using the 2024-A probe set reference. UMI counts were demultiplexed back to each treatment condition using the barcodes in the sample_name: sample_probe_barcode metadata column.
raw_matrix_genome_annotation:Chromium Human Transcriptome Probe Set v1.1.0: 2024-A , raw_matrix_value_units:UMI, raw_matrix_assays: scRNA-seq, CRISPR interference, raw_matrix_feature_keys:gene symbol for scRNA-seq, guide_id for CRISPR interference guides, raw_matrix_background_barcodes_included:False
Assembly: GRCh38
Supplementary files format and content: h5, count matrix: scRNA-seq and crispr guide UMI

source_name: blood

extract_protocol:
Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology) supplemented with appropriate cytokines at a density of 1x106 cells/ml and seeded in TC-treated 24-well plate (for most experiments; 0.5x106 cells per well) or 12-well plates (for pooled screens; 2x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF or GM-CSF. Media was replenished every 24 - 72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2. 180x106 cells from were plated in 12-well plates (2.5x106 cells in 2 ml of media per well) in SF macrophage media + 20 ng/ml M-CSF. Additional culture media was either added or changed every 48 hours. Macrophages were transduced on day 3 with a lentiVPX lentiviral sgRNA library targeting 583 myeloid-relevant genes (same genes as sgRNAs as for TNF screen described above) in a CROP-seq vector encoding GFP. Cells were spinfected with 4 ul of lentivirus in 1 ml of fresh media + 20 ng/ml M-CSF for 1 h at 32 °C and 1250 × g. On day 4, Cas9 ribonucleoproteins were delivered using Cas9-eVLPs. eVLP-containing media (70 ul of eVLPs per well in 1 ml of media) was applied to macrophages followed by spinfection for 1 h at 32 °C and 1250 × g. Cells were subsequently maintained in macrophage differentiation media until stimulation. On day 11 isolation, macrophages were stimulated with 50 ng/ml ultrapure LPS (Enzo) for 5 h, while parallel wells were maintained in fresh media as unstimulated controls. Cells were harvested using Accutase (BD), stained with a viability dye (GhostDye Red 780), and fixed using the Chromium Flex fixation protocol (10x Genomics). GFP-positive single cells were sorted by fluorescence-activated cell sorting on a FACSARIA cell sorter at the Gladstone Institutes Flow Cytometry Core Facility to enrich for sgRNA-expressing cells. Approximately 2.7 million unstimulated cells and 3.3 million LPS-stimulated cells were recovered after sorting.
GEM-X Flex Sample Preparation v2 Kit (10x genomics, catalog no. 1000781) per the manufacturer’s instructions

value: blood

value: CD14-positive monocyte

value: pooled:na, 50 ng/ml lipopolysaccharide

tag: experimental perturbation_timepoint

value: 5 hours

tag: donor ids

tag: donor age

value: 27 years

tag: source

value: STEMCELL technologies

tag: donor sex

value: male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: n/a (fresh)

tag: donor ethnicity

value: European American

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: transient

tag: suspension enriched_cell_types

tag: suspension depletion_factors

value: EasySep™ Human Monocyte Enrichment Kit without CD16 Depletion

tag: library protocol

value: 10X GEM-X Flex

tag: sample name


title: GM00637, Wildtype, 0.4%DMSO for 24h, ATACseq rep3

description:
Library name: Fib_K_DMSO3
K_DMSO3

tag: cell line

tag: cell type

value: fibroblast

tag: genotype

value: Wildtype

tag: treatment

value: 0.4%DMSO for 24h


title: RiboTag, CA1, Opto, 30min, Input, replicate 1

description: Library name: RiboTag_ChR2_30min_Input_Rep1

tag: tissue

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA

tag: time post_activation

tag: fraction

value: Input


title: RNA from tonsil, donor 3

description:
Library name: T3_SMRT
PacBio Revio

value: tonsil

value: memory B cells


title: Mac_L03:scRNA-seq CRISPR interference screen of CD14-positive monocyte,  pooled: untreated, LPS treated

description: Library name: Mac_L03_GEX_lib

value: blood

value: CD14-positive monocyte

value: pooled:na, 50 ng/ml lipopolysaccharide

tag: experimental perturbation_timepoint

value: 5 hours

tag: donor ids

tag: donor age

value: 27 years

tag: source

value: STEMCELL technologies

tag: donor sex

value: male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor body_mass_index


title: WT528

city: London

first: Emir

last: Turkes

address: Gower St

department: UK Dementia Research Institute

country: United Kingdom

institute: University College London

description:
Library name: S2
Fresh frozen Spatial transcriptome sequencing

data_processing:
Single Cell 3' v3.1 Dual Index libraries were sequenced on a NovaSeq SP instrument by Edinburgh Genomics using parameters recommended by 10X Genomics.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: filtered list of spatial barcodes
Supplementary files format and content: features.tsv.gz: filtered list of gene IDs
Supplementary files format and content: matrix.mtx.gz: filtered gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissues and spots
Supplementary files format and content: scalefactors_json.json: scalefactors
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Coronal sections including dorsal hippocampi

extract_protocol:
The Visium Spatial Tissue Optimization Reagents Kit (10X Genomics) was used to determine an optimal tissue permeabilization time of 12 minutes when performed on 10 m sections. Samples were mounted directly onto the Visium Gateway Gene Expression Slide and incubated at 37 oC on a thermocycler (T100 Thermal Cycler, Bio-Rad) for one minute, followed by methanol (>99.9%, 34860, Sigma-Aldrich) fixation at -20 oC for 30 minutes. Sections were blocked and stained with DAPI before coverslipping and imaging at 20x magnification using a Zeiss Axioscan 7 microscope.
Tissue permeabilization was performed as previously to release polyadenylated mRNA for capture by poly(dT) primers on the slide. Steps for reverse transcription, second strand synthesis and denaturation were followed according to the manufacturer’s kit to produce cDNA fragments, from which spatially-barcoded Illumina-compatible libraries were constructed using the dual Index Kit TT Set A (10X Genomics) to add unique i7 and i5 indexes for barcoding.

value: WT:CRISPR-Cas9 edited isogenic control


title: WT527

description:
Library name: S1
Fresh frozen Spatial transcriptome sequencing

value: Coronal sections including dorsal hippocampi

value: WT:C57BL/6J control


title: N2_4

description: Library name: bc2050

value: spleen

tag: Sex

value: female

value: CD19+ enriched B cells

value: Notch2 ( CD19Cre+/-, SPENwt/wt, ICN2+/- )


title: GM00637, Wildtype, 0.4%DMSO for 24h, ATACseq rep2

description:
Library name: Fib_K_DMSO2
K_DMSO2

tag: cell line

value: fibroblast

value: Wildtype

value: 0.4%DMSO for 24h


title: Mac_L02:scRNA-seq CRISPR interference screen of CD14-positive monocyte,  pooled: untreated, LPS treated

description: Library name: Mac_L02_GEX_lib

value: blood

tag: cell type

value: CD14-positive monocyte

value: pooled:na, 50 ng/ml lipopolysaccharide

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: n/a (fresh)

tag: donor ethnicity

value: European American

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: transient

tag: suspension enriched_cell_types

tag: suspension depletion_factors

value: EasySep™ Human Monocyte Enrichment Kit without CD16 Depletion

tag: library protocol

value: 10X GEM-X Flex

tag: sample name


title: 3-Month High-Fat Diet Fed

description: Library name: 3MHFD

tag: tissue

value: Liver

tag: genotype

tag: treatment

value: 3-month high-fat diet


title: Normal Chow Diet Fed

description: Library name: NCD

value: normal chow diet


title: N2_3

description: Library name: bc2090

value: spleen

value: female

value: CD19+ enriched B cells

value: Notch2 ( CD19Cre+/-, SPENwt/wt, ICN2+/- )


title: Mac_L01:scRNA-seq CRISPR interference screen of CD14-positive monocyte,  pooled: untreated, LPS treated

description: Library name: Mac_L01_GEX_lib

value: blood

value: CD14-positive monocyte

tag: experimental perturbation_timepoint

value: 5 hours

tag: donor ids

tag: donor age

value: 27 years

tag: source

value: STEMCELL technologies

tag: donor sex

value: male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection


title: GM00637, Wildtype, 10 µM PDS for 24h, ATACseq rep1

description:
Library name: Fib_K_PDS1
K_PDS1

tag: cell line

tag: cell type

value: fibroblast

value: Wildtype

value: 10 µM PDS for 24h


title: AG14980, Wildtype, 0.4%DMSO for 24h, ATACseq rep3

description:
Library name: Lym_B_DMSO3
B_DMSO3

value: lymphoblastoid

value: 0.4%DMSO for 24h


title: GM08505, BLM-/-, none, RNAseq rep3

description:
Library name: Fib_BS_D3
Fib_BS_D3

data_processing:
RNAseq reads from fibroblasts samples were aligned to hg38 with gtf file (comprehensive gene annotation file for regions CHR from release 40 (GRCh38.p13), https://www.gencodegenes.org/human/release_40.html) and STAR (version 2.7.9a) with default parameters. RNAseq reads from lymphoblastoidsamples were aligned to a composite reference genome of human and EBV (hg38 + EBV) with the corresponding composite gtf files via STAR. Because of the directionality of RNAseq library preparation protocol, the count of reads mapping to the reverse strand was used for subsequent differential analysis in DESeq2 with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file of raw counts for each sample
Supplementary files format and content: tab-delimited txt file of TPM values for each sample
Supplementary files format and content: tab-delimited txt file of results of differential analysis

value: BLM-/-


title: Xenium_normal

type: RNA

first: Peng

last: Ji

state: Illinois

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

hyb_protocol: A total of 500 genes were included in the analysis. Gene panel probe hybridization was performed  according to 10x protocol.

scan_protocol: Imaging, processing, decoding, quality control, and data generation were performed on the Xenium Analyzer system.

data_processing: Analysis was performed using Xenium Onboard Analysis

label: Xenium probe set

source_name: normal human bone marrow

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE tissue sections were cut at a thickness of 5 µm and placed onto a Xenium slide.

value: Bone marrow

tag: tissue preservation method

value: FFPE


title: Mouse 2

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

description: Library name: Mouse 2

data_processing:
SAW pipeline version V7.0.0
Deepcell cell segmentation
Assembly: mm10
Supplementary files format and content: Cell segmented .gef file
Library strategy: Spatial Transcriptomics

source_name: brain coronal hemisphere

extract_protocol:
Fresh frozen and mounted in OCT
STOMICS Gene Expression kit

value: brain coronal hemisphere

value: brain

value: WT

value: Injected


title: N2_2

description: Library name: bc2082

value: spleen

tag: Sex

value: female

value: CD19+ enriched B cells

value: Notch2 ( CD19Cre+/-, SPENwt/wt, ICN2+/- )