title: sorted colonic lamina propria iNKT VJ9

city: St. Louis

first: Rodney

middle: D

last: Newberry

address: 660 S. Euclid Ave

department: Medicine

description:
Library name: LIB040318
PipSeq

data_processing:
The demultiplexed human fastq files were processed with the PIPseeker 3.0.5 software (Fluent Biosciences) to determine UMI for each cell for each sample.
The demultiplexed mouse fastq files were processed with the cellranger-6.0.1 software (10X Genomics) against mouse genome mm10 to determine UMI for each cell for each mouse sample.
Assembly: Mouse mm 10 2020
Assembly: Human  GRCh38-2022.04
Supplementary files format and content: Tab separated values and matrix file

source_name: colon lamina propria

extract_protocol:
Human colonic resections were stored in MACS storage solution prior to processing. For lamina propria isolation, white fatty muscularis layer was removed and tissues washed with 40ml Hank’s Balanced Salt solution (HBSS) containing 5mM of EDTA for 30 mins for 2 times at37°C in a shaking incubator.  Remaining tissues were cut into pieces and digested with Dispase (50U/ml stock) and Type VIII Collagenase Collagenase (10,000 U/ml) at 37°C under shaking conditions for 90 mins in R5 media. The digested tissues were filtered through 100-µm cell strainer and centrifuged at 1,500 rpm for 5 mins. The cells were and resuspended in PBS before performing the cell staining for flow cytometry staining. Cells were stained with CD45, TCRb, CD3, loaded CD1d tetramer and viability dye and sorted on a FACS Aria II.
For mouse lamina propria isolation, white fatty muscularis layer was removed and tissues washed with 20ml Hank’s Balanced Salt solution (HBSS) containing 5mM of EDTA for 15 mins for 3 times at 37°C in a shaking incubator. Remaining tissues were cut into pieces and digested with Dispase (50U/ml stock) and Type VIII Collagenase Collagenase (10,000 U/ml) at 37°C under shaking conditions for 90 mins in R5 media. The digested tissues were filtered through 100-µm cell strainer and centrifuged at 1,500 rpm for 5 mins. The cells were and resuspended in PBS before performing the cell staining for flow cytometry staining. Cells were stained with CD45, TCRb, CD3, loaded CD1d tetramer and viability dye before being sorted on a FACS Aria II.
Sorted human  iNKT cells were processed with the T2 PIPseq kit following manufacturer instructions prior to sequencing on Illumina NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol at the Genome Technology Access Center at Washington University School of Medicine in St. Louis
Sorted mouse iNKT cells were counted and 10,000 cells were loaded onto a 10X Genomics Chromium controller for 3’v3.1 library preparation as per the manufacturer’s recommendations.  The concentration of each library was determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library. Library preparation and sequencing was performed at the Genome Technology Access Center at Washington University in Saint Louis School of Medicine.

treatment_protocol: Mice were treated i.p. with 6.6ug of EGFRi for 4 days or vehicle control prior to LP isolation. Human samples were from healthy surgical resections.

value: colon lamina propria

tag: Sex

value: F

value: iNKT

value: Colon polyp

tag: age

value: 51 years

tag: resection

value: Healthy


title: sorted colonic lamina propria iNKT VJ6

status: Public on Feb 26 2026

type: SRA

country: USA

institute: Washington University School of Medicine

description:
Library name: LIB040317
PipSeq

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

value: M

tag: cell type

tag: disease state

value: Diverticulitis

value: 41 years


title: ryp1 hi MOI 24h 3

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: Ryp1_MOI_hi_24h_3_S69

library_source: transcriptomic

data_processing:
Transcript abundances were quantified based on the annotated C. posadasii Silveira genome, BioProject PRJNA664774. Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2. Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least nine samples.
Differentially expressed genes were identified by comparing replicates for contrasts of interest using the glmQLFit, glmQLFTest, and topTags functions in edgeR version 4.0.16. Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2X (absolute log2 fold change ≥ 1) for a given contrast.
Assembly: PRJNA664774
Supplementary files format and content: The results of the edgeR analysis are in processed data file S1_Table_JSAS03.txt, an Excel-compatible tab-delimited text conforming to JavatreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the C. posadassii Silveira systematic gene name from the PRJNA664774 reference genome. The NAME column gives short names taken from Table S1 of Mandel et al [cite: PMID35385558]. The next columns give edgeR BH-adjusted p-values for differential expression in each of the 7 contrasts. The next 6 columns give systematic names and annotations for related genomes as mapped by INPARANOID in Mandel et al [cite: PMID35385558]: previous C. posadasii Silveira annotation (CpV2 and Cp_anno), C. immitis RS  (CiRS and CiRS_anno) and H. ohiense G217B (HcG217B and HcG217B_anno). The next 24 columns give integer-rounded KALLISTO estimated counts for each transcript in each sample. The counts are followed by a GWEIGHT place-holder column for JavaTreeView compatibility. The final 7 columns give the edgeR fit log2 ratios for each contrast. The estimated counts in this file are sufficient to recapitulate the edgeR analysis.

organism: Coccidioides posadasii

source_name: fungal cell

growth_protocol: BMDM were seeded one day prior to the infection in 6-well plates.  On day of infection, WT and ryp1Δ arthroconidia were added to the wells at an MOI of 0.1 or 1 and the plates were spun at 550 g for 5 min to bring the arthroconidia proximal to the BMDM. At 1 h, the media was removed and replaced with fresh BMM, except for the Coccidioides alone wells.  At each timepoint, cells were washed twice with PBS, then QIAzol was added to each of 2 wells and and incubated for 5 min at room temperature. The contents of 2 wells were then combined for each sample, with three samples per condition and per timepoint.  Each sample underwent bead beating for 2 min to improve yield of fungal RNA. At this point samples were removed from the BSL3.

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo).
Libraries were made with the NEBNext polyA mRNA magnetic isolation module and NEBNext Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes as instructed.  Libraries were pooled and sequencing was performed by the Chan-Zuckerberg BioHub-San Francisco on one lane of Novaseq S4.

tag: genotype

tag: infection

value: hi MOI

tag: time

tag: replicate

value: fungal cell


title: RNA-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep2

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

country: China

institute: Tsinghua University

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep2
RNA-seq sample EMX1_dead_sgrna_rep2

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.

tag: cell line

tag: batch


title: WT lo MOI 48h 2

description: Library name: WT_MOI_lo_48h_2_S71

value: WT

value: lo MOI


title: Bronchoalveolar lavage, replicate 1

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10th Amistad Street

department: Department of Anesthesiology

institute: Yale University

description:
Library name: BAL_1
10X Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.1 (10x Genomics). Reads were aligned to the Rattus norvegicus reference transcriptome (Rnor_6.0, Ensembl release 95) with intronic reads included. Gene-barcode matrices were generated using the cellranger_count pipeline with default parameters. Further processing, including quality control, normalization, clustering, and downstream analysis, was performed in R using Seurat as described in the manuscript.
Assembly: Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6)
Supplementary files format and content: R objects (.Robj)

organism: Rattus norvegicus

source_name: Bronchoalveolar lavage (primary immune and epithelium)

growth_protocol: Primary rat lung-derived cells (from pulmonary dissociation and bronchoalveolar lavage) were maintained in organoid culture (in transwells) with a DMEM F12 supplemented with growth factors (Fgf10, Egf), small molecule inhibitors of TGFβ and GSK3 signaling, and antibiotics. Cultures were incubated at 37°C in a humidified atmosphere with 5% CO₂ for 10 days. Organoid cultures were seeded using three defined input ratios of primary cell suspensions: 100% pulmonary dissociation (PD_3D), 100% bronchoalveolar lavaage (BAL_3D), and a 50:50 mix (Mixed_3D).

extract_protocol:
Single-cell suspensions were prepared from dissociated organoids, bronchoalveolar lavage (BAL), and pulmonary dissociation (PD) samples using customized enzymatic or mechanical protocols, followed by filtration to achieve a single-cell suspension. Cells were resuspended in 0.1% BSA in PBS at 1 million cells/mL and processed for single-cell RNA-seq using the Chromium Next GEM Single Cell 3’ v3.1 platform (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol. Cell lysis and mRNA capture occurred within Gel Beads-in-emulsion (GEMs) using barcoded oligo(dT) primers. See manuscript for more detail.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol. Barcoded cDNA was amplified by PCR, purified with SPRIselect beads, and prepared for sequencing on an Illumina platform. See manuscript for more detail.


title: 25Leucine-3

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

description: Library name: Sample 13

data_processing:
FastQC 0.11.9 was used to evaluate quality of seqenced reads.
Gene abundance estimates were obtained for each sample using kallisto (version 0.50.1).
Transcript estimates are read into gene counts using tximport (version 1.32.0), then counts are normalized using DESeq2 (version 1.44.0).
Counts tables were generated for each amino acid. Leucine, isoleucine, and valine share the BCAA samples as their controls. All other amino acids have their own unique controls.
Assembly: GRCh38 (Release 45)
Supplementary files format and content: csv files include DESeq2 normalized counts for each sample

molecule: total RNA

source_name: Jurkat

extract_protocol:
RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1μg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jurkat

tag: treatment

value: 25% Leucine

tag: time-point

value: Day 3


title: sorted colonic lamina propria iNKT VJ10

description:
Library name: LIB040319
PipSeq

value: 45 years


title: WT lo MOI 24h 2

description: Library name: WT_MOI_lo_24h_2_S59


title: sorted colonic lamina propria iNKT VJ5

description:
Library name: LIB040316
PipSeq

value: colon lamina propria

value: Neuroendocrine carcinoma

value: 52 years


title: 25Leucine-4

description: Library name: Sample 14


title: Starting pulmonary dissociation, replicate 1

description:
Library name: PD_1
10X Genomics

source_name: Pulmonary dissociation (epi, endo, immune, mesenchyme) (primary)


title: Starting pulmonary dissociation, replicate 2

description:
Library name: PD_2
10X Genomics

value: Pulmonary dissociation (epi, endo, immune, mesenchyme) (primary)


title: Starting pulmonary dissociation, replicate 3

description:
Library name: PD_3
10X Genomics


title: WT lo MOI 48h 1

description: Library name: WT_MOI_lo_48h_1_S70


title: Dataset 3: Isotype NMU tumor #4

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description: 10X Genomics

data_processing:
The sequenced reads were aligned to either the human reference genome hg18 or the rat reference genome Rn6. Demultiplexing, barcode calling, gene counting, and group aggregation were subsequently performed. These procedures were all carried out using the 10X Genomics Cell Ranger 7.0.1 and Cell Ranger Aggr. v7.0.1 on 10X Cloud (https://cloud.10xgenomics.com/)
For preprocessing and quality-control, the filtered count matrix files were processed in R using Seurat package. Stringent filtering parameters were set to filter out low-quality reads and dead cells (2000 <nCount < 60000 & percent mt < 20 & percent ribo RPS/RPL < 40). Doublets were identified and removed using DoubletFinder.
The data were normalized using SCTransform and integrated using SCTIntegration prior to decomposing into 30-dimension PCA, clustering and dimensional reduction by UMAP. Subclusters of immune, epithelial, stroma and subsequent T cells, myeloid, and fibroblast clusters were further subsetted and reclustered at same dimension but higher resolution.
DEGs of each seurat cluster at each step were computed using Seurat FindMarkers function. Cell identities were identified and annotated using up to a combination of three methods (1) DEGs of lineage markers, (2) gene modules from previous studies, (3) reference cell atlas such as Celltypist, ProjecTIL.
Downstream analyses relevant to the study include Milo neighborhood analysis, Trajectory analysis Monocle3, FCoEx, single-cell GSEA (Escape), ProjecTIL, CellChat, Gini index quantification, etc.
Assembly: hg18 (Dataset 1), rn6 (Dataset 2-3)
Supplementary files format and content: barcodes.tsv.gz (barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix), filtered_feature_bc_matrix.h5 (combined features, barcodes, matrix)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Rat mammary carcinoma

extract_protocol:
For dataset 1, clinical specimens were shipped in DMEM media via dry ice and digested immediately upon arrival to the lab. For dataset 2-3, rats were sacrificed and tumors were extracted and minced gently prior to tissue digestion protocol. For both human and rat tissues, the minced tissues were placed in 2 mg/mL collagenase 4, 2 mg/kg hyaluronidase, 2 mg/mL BSA (5-6 fold-greater than tissue volume) and incubated with shaking at 37*C for 60 min (human tumor tissues and rat mammary gland tissue) or 80-90 min (rat tumor tissues). The digested tumors were serially filtered from 500um and 100um strainers and centrifuged at 1700 rpm for 7 min and resuspended in DMEM. For dataset 1 and 2, tissues were stained with FACS markers (CD45+, EpCAM+, CD10+, Live/Dead Aqua, 30min), washed, and filtered, and were subjected to FACS sorting at low speed followed by single-cell library construction targeting 5000 cells/sample. For dataset 3, the entired tumor tissues were digested briefly with TryLE Express Enzyme (7 min) and submited for scRNAseq library construction targeting 5000 cells/sample.
For dataset 1-2, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 3' HT v3 protocol targeting 5000 cells per sample. For dataset 3, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 5' HT Reagent Kit v2 (Dual Index) protocol.
Equimolar libraries were sequenced on an Illumina NovaSeq6000 at the DFCI Molecular Biology Core Facility with at least 25000 reads per cells.

treatment_protocol: For dataset 2-3, tumor induction in Sprague-Dawley rats was performed via two injection of N-Nitroso-N-Methylurea(NMU, 50mg/kg, 7 days apart). Tumor volumes were measured daily following first detection of palpable tumors in the mammary areas.

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

tag: strain

value: Hsd:Sprague-Dawley SD

value: Female

value: NMU(50mg/kg, twice)+rat IgG isotype(2.5mg/kg & 10mg/kg)


title: 25Leucine-2

description: Library name: Sample 12


title: Dataset 3: Isotype NMU tumor #3

description: 10X Genomics

value: NMU(50mg/kg, twice)+mouse IgG isotype(10mg/kg)


title: 25Leucine-1

description: Library name: Sample 11


title: Pulmonary dissociation (PD) organoids, replicate 3

description:
Library name: PD_3D_3
10X Genomics

source_name: Pulmonary organoids (100% PD)

value: Pulmonary organoids (100% PD)


title: ryp1 lo MOI 24h 3

description: Library name: Ryp1_MOI_lo_24_3_S63

value: fungal cell


title: Dataset 3: anti-OX40+anti-PDL1 NMU tumor - Non-Responder #2

description: 10X Genomics

value: NMU(50mg/kg, twice)+anti-OX40(2.5mg/kg, every 48hr)+anti-PDL1(10mg/kg, every 7 day)


title: MCF10A PM shGFP 72h dox, biol rep 2

city: Toronto

first: Brandon

middle: Alexander

last: Cho

state: ON

address: 25 Orde Street, Room 6-1001 MRS

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
Library name: Sample 6
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC4_PM

library_source: genomic

data_processing:
read quality was assessed using FastQC (v0.12.1), and results summarized with MultiQC (v1.25.2). Pair-end reads were trimmed using Trim Galore (v0.6.6). Reads that passed the quality control and trimming steps were aligned to the human genome (hg38) using Bowtie2 (v2.4.1).Unaligned reads, mitochondrial reads, and duplicate reads were removed at this stage. Peak calling was performed with Macs3 (v3.0.3), using –nomodel and –nolambda parameters. Peaks overlapping with human blacklist regions were filtered out. As further validation steps, library was checked for Fraction of Reads in Peaks (FriP), enrichment of reads at promoters, fragment length distribution, and genome distribution
Assembly: hg38
Supplementary files format and content: xls top table of differentially accessible regions of MCF10A PM shCHD1 lines vs MCF10A PM shGFP cell lines

molecule: genomic DNA

source_name: Breast

growth_protocol: Cells were cultured in DMEM/F12 (Invitrogen #111330-032) supplemented with 5% horse serum (Invitrogen #16050-122), 20 ng/mL hEGF (Peprotech #AF-100-15), 500 ng/mL hydrocortisone (Sigma #H-0888), 100 ng/mL cholera toxin (Sigma #C8052-2MG), 10 μg/mL insulin (Sigma #I-1882), and 100 U/ml penicillin/streptomycin (Life Technologies #15140122) at 37˚C

extract_protocol:
50,000 live cells were sorted and then centrifuged at 500xg for 5 minutes at 4˚C. Cell pellets were then resuspended in 50 µL of cold resuspension buffer (RSB; 10 mMTris-HCl at pH 7.4, 10mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, to dissociate cell membrane. Samples were incubated on ice for 3 minutes and then washed with 1 mL of ATAC RSB with 0.1% NP-40 by inverting the tube. The nuclei were subsequently pelleted by centrifugation at 500xg for 10 minutes at 4˚C and then resuspended in 50 µL of transposition mixture (25 µL of 2x TD buffer, 2.5 µL of transposase [100nM final], 16.5 µL of 1x PBS, 0.5 µL of 1% digitonin, 05 µL of 10% Tween-20, 5 µL of nuclease-free water) for tagmentation. Tagmentation was performed at 37˚C for 30 minutes at 1000 RPM on a thermomixer. DNA clean-up was performed following the tagmentation using the Zymo DNA Clean and Concentrator 5 kit (Zymo #D4014) and DNA was eluted in 21 µL of elution buffer
Library amplification was performed as per the Omni-ATAC protocol52. After five initial amplification cycles, an additional qPCR surveillance step was included to determine the optimal number of extra PCR amplification cycles,  enough to generate sufficient material for library sequencing, without over-amplifying and introducing duplicate artifacts. Amplified libraries were then purified with AMPure XP beads (Beckman Coulter #A63880) using a double-sided bead purification approach, to remove smaller primer dimers as well as large >1000bp fragments. Finally, libraries were quantified using the Qubit dsDNA high-sensitivity kit (Invitrogen #Q32854) and pooled at equimolar concentrations to be sequenced paired-end on a single lane of an Illumina NovaSeqX 10B flow cell.

treatment_protocol: Cells were treated with doxycycline at 50ng/ml for 72h at 37˚C

value: Breast

value: MCF10A PM

value: Breast epithelial cell line

value: Control

value: 72h doxycycline


title: ryp1 lo MOI 48h 2

description: Library name: Ryp1_MOI_lo_48h_2_S74

value: lo MOI


title: sorted colonic lamina propria iNKT VJ3

description:
Library name: LIB040315
PipSeq

value: colon lamina propria

value: M

value: iNKT

value: Diverticulitis

value: 63 years

value: Healthy


title: ryp1 lo MOI 48h 3

description: Library name: Ryp1_MOI_lo_48h_3_S75


title: 25Isoleucine-4

description: Library name: Sample 9

value: Jurkat

value: 25% Isoleucine

value: Day 3


title: WT lo MOI 24h 1

description: Library name: WT_MOI_lo_24h_1_S58

value: WT

value: fungal cell


title: 25Isoleucine-5

description: Library name: Sample 10


title: MCF10A PM shCHD1 B 72h dox, biol rep 2

description:
Library name: Sample 5
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC4_PM_Chd1B

value: Breast

value: CHD1 KD


title: Dataset 3: anti-OX40+anti-PDL1 NMU tumor - Responder #2

description: 10X Genomics

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

value: Hsd:Sprague-Dawley SD

value: Female

value: NMU(50mg/kg, twice)+anti-OX40(2.5mg/kg, every 48hr)+anti-PDL1(10mg/kg, every 7 day)


title: Dataset 3: anti-OX40+anti-PDL1 NMU tumor - Non-Responder #1

description: 10X Genomics


title: ryp1 lo MOI 24h 2

description: Library name: Ryp1_MOI_lo_24_2_S62

value: lo MOI


title: MCF10A PM shCHD1 A 72h dox, biol rep 2

description:
Library name: Sample 4
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC4_PM_Chd1A

value: MCF10A PM

value: Breast epithelial cell line

value: 72h doxycycline


title: 25Isoleucine-3

description: Library name: Sample 8


title: sorted colonic lamina propria iNKT VJ1

description:
Library name: LIB040313
PipSeq

value: colon lamina propria

value: M

value: iNKT

value: Crohn's Disease

value: 20 years

value: Healthy


title: 25Isoleucine-2

description: Library name: Sample 7

value: Jurkat

value: 25% Isoleucine

value: Day 3


title: Dataset 3: anti-PDL1 NMU tumor - Non-Responder #2

description: 10X Genomics

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

value: NMU(50mg/kg, twice)+mouse anti-rat PDL1(10mg/kg, every 7 day)


title: ryp1 lo MOI 48h 1

description: Library name: Ryp1_MOI_lo_48h_1_S73

value: fungal cell


title: Dataset 3: anti-OX40+anti-PDL1 NMU tumor - Responder #1

description: 10X Genomics

value: Hsd:Sprague-Dawley SD

value: Female

value: NMU(50mg/kg, twice)+anti-OX40(2.5mg/kg, every 48hr)+anti-PDL1(10mg/kg, every 7 day)


title: MCF10A PM shGFP 72h dox, biol rep 1

description:
Library name: Sample 3
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC3_PM

value: Breast

value: MCF10A PM

value: Breast epithelial cell line

value: Control

value: 72h doxycycline


title: 25Isoleucine-1

description: Library name: Sample 6


title: MCF10A PM shCHD1 B 72h dox, biol rep 1

description:
Library name: Sample 2
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC3_PM_Chd1B

value: CHD1 KD


title: ryp1 lo MOI 24h 1

description: Library name: Ryp1_MOI_lo_24_1_S61

value: lo MOI


title: Dataset 3: anti-PDL1 NMU tumor - Non-Responder #1

description: 10X Genomics


title: MCF10A PM shCHD1 A 72h dox, biol rep 1

description:
Library name: Sample 1
Column name in comparison_DAR_34_KOmerge_vs_PM.xlsx: BC3_PM_Chd1A


title: Dataset 3: anti-PDL1 NMU tumor - Responder #2

description: 10X Genomics


title: 25Histidine-4

description: Library name: Sample 4

value: Jurkat

value: 25% histidine


title: WT alone 48h 2

description: Library name: WT_alone_48h_2_S53

value: WT

value: alone


title: sorted colonic lamina propria iNKT VJ2

description:
Library name: LIB040314
PipSeq

value: colon lamina propria

value: F

value: iNKT

value: Diverticulitis

value: 70 years

value: Healthy


title: Dataset 3: anti-OX40 NMU tumor - Non-Responder #2

description: 10X Genomics

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

value: Hsd:Sprague-Dawley SD

value: Female

value: NMU(50mg/kg, twice)+rat anti-rat OX40(2.5mg/kg, every 48hr)


title: WT alone 48h 3

description: Library name: WT_alone_48h_3_S54

value: fungal cell


title: MCF10A PM shGFP 72h dox biol rep 4

description:
Library name: Sample 24
Column name in Final_count_hg38: sorted_PM_shGFP_4_S42.bam

data_processing:
Library quality was assessed using FastQC and trimmed of adaptor sequences with Trim Galore! v0.4.0
Alignment was then performed using hisat2 v2.2.1 to the GRCh38 reference genome
Gene counts were obtained using the featureCounts function on Rsubread (v1.22.3)
Assembly: hg38
Supplementary files format and content: space delimited raw counts for each sample

extract_protocol:
Total RNA was extracted from 200 000 cells with the RNeasy Mini Kit (Qiagen #74106) with on-column DNase digestion (Qiagen #79254)
The RNA-seq library was generated following the manufacturer’s instructions for the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S) and the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760L).

value: Breast

value: MCF10A PM

value: Breast epithelial cell line

value: Control

value: 72h doxycycline


title: 25Histidine-2

description: Library name: Sample 2

value: Jurkat

value: 25% histidine

value: Day 3


title: 25Histidine-3

description: Library name: Sample 3


title: 25Histidine-5

description: Library name: Sample 5


title: MCF10A PM shGFP 72h dox biol rep 2

description:
Library name: Sample 22
Column name in Final_count_hg38: sorted_PM_shGFP_2_S30.bam


title: WT alone 48h 1

description: Library name: WT_alone_48h_1_S52

value: WT

value: alone


title: Dataset 3: anti-OX40 NMU tumor - Non-Responder #1

description: 10X Genomics


title: Dataset 3: anti-PDL1 NMU tumor - Responder #1

description: 10X Genomics

value: NMU(50mg/kg, twice)+mouse anti-rat PDL1(10mg/kg, every 7 day)


title: 125His3-D9

description: Library name: Sample 25

data_processing:
FastQC 0.11.9 was used to evaluate quality of seqenced reads.
Gene abundance estimates were obtained for each sample using kallisto (version 0.50.1).
Transcript estimates are read into gene counts using tximport (version 1.32.0), then counts are normalized using DESeq2 (version 1.44.0).
Assembly: GRCh38 (Release 45)
Supplementary files format and content: csv files include DESeq2 normalized counts for each sample

value: 12.5% histidine media

tag: time point

value: Day 9


title: ryp1 alone 48h 1

description: Library name: Ryp1_alone_48h_1_S55


title: ryp1 alone 48h 3

description: Library name: Ryp1_alone_48h_3_S57


title: MCF10A PM shGFP 72h dox biol rep 3

description:
Library name: Sample 23
Column name in Final_count_hg38: sorted_PM_shGFP_3_S36.bam


title: ryp1 alone 48h 2

description: Library name: Ryp1_alone_48h_2_S56


title: 25Histidine-1

description: Library name: Sample 1


title: MCF10A PM shGFP 72h dox biol rep 1

description:
Library name: Sample 21
Column name in Final_count_hg38: sorted_PM_shGFP_1_S24.bam


title: Dataset 3: anti-OX40 NMU tumor - Responder #2

description: 10X Genomics

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

value: Hsd:Sprague-Dawley SD


title: 125His2-D9

description: Library name: Sample 24


title: MCF10A PM shCHD1 B 72h dox biol rep 4

description:
Library name: Sample 20
Column name in Final_count_hg38: sorted_PM_shCHD1_B_4_S44.bam

value: CHD1 KD


title: Dataset 3: Isotype NMU tumor #2

description: 10X Genomics

value: Female

value: NMU(50mg/kg, twice)+mouse IgG isotype(10mg/kg)


title: Dataset 3: anti-OX40 NMU tumor - Responder #1

description: 10X Genomics

value: NMU(50mg/kg, twice)+rat anti-rat OX40(2.5mg/kg, every 48hr)


title: MCF10A PM shCHD1 B 72h dox biol rep 3

description:
Library name: Sample 19
Column name in Final_count_hg38: sorted_PM_shCHD1_B_3_S38.bam

value: Breast

value: MCF10A PM

value: Breast epithelial cell line


title: CSC-A with no Rhodococcus/Timepoint2/Replicate3/Media=B4U (B4 with urea)

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description: Library name: CSC_A_No_Rhodo_Rep_C_TP_2_Run_1

data_processing:
fastq files were aligned to bacterial genomes using the Burrows Wheeler Aligner
resulting SAM files were converted to raw count files using HTSeq
raw count files were normalized using DESeq2, each timepoint was normalized separately
The gseKEGG from the clusterProfiler R package was used for set over-enrichment and GSEA analysis of KEGG pathways and modules.
Assembly: Assemblies were annotated using Bakta19, and life history traits were estimated using Microtrait20 with default parameters. Potential cross-feeding interactions between community members was estimated by generating genome scale models from genome assemblies using CarveMe21 and then estimating interactions in minimal and M9 media using SMETANA22.
Supplementary files format and content: Processed data files contain normalized gene expression values in a .csv format. Libraries are columns and genes are rows

organism:
Curtobacterium flaccumfaciens
Microbacterium foliorum
Bacillus toyonensis
Rhodococcus qingshengii

source_name: Bacteria

growth_protocol: Species were cultivated according to the needs of the experiment (described below) in media comprised of 4g/L of yeast extract and 5g/L of dextrose enriched with 20 g/L of calcium chloride (5% concentration of total volume) with DI water adjusted to 1L (B4 media), or media comprised of 4g/L of yeast extract and 5g/L of dextrose enriched with 20 g/L of calcium chloride and 20 g/L of urea (B4UZN media).

extract_protocol:
RNA extraction was performed using Zymo’s Quick-DNA/RNA Miniprep Kit (D7003) and sequenced by Azenta (South Plainfield, NJ) using Illumina technology. Bioconductor’s DESeq2 package (3.9)26 was used to analyze gene expression for each member of the CSC-A community under the different conditions tested (in the presence and absence of C. flaccumfaciens and R. qingshengii or in different media types).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Samples were either: CSC-A Complete which comprised of all 4 species, CSC-A without C. flaccumfaciens in B4 (no urea) media, CSC-A without C. flaccumfaciens in B4UZN (with urea), or CSC-A without R. qingshengii in B4UZN

value: Bacteria


title: MCF10A PM shCHD1 B 72h dox biol rep 2

description:
Library name: Sample 18
Column name in Final_count_hg38: sorted_PM_shCHD1_B_2_S32.bam

value: 72h doxycycline


title: 125His1-D9

description: Library name: Sample 23


title: CSC-A with no Rhodococcus/Timepoint1/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_A_No_Rhodo_Rep_C_TP_1_Run_1


title: 25His1-D9

description: Library name: Sample 20

value: 25% histidine media


title: 25His3-D9

description: Library name: Sample 22


title: Dataset 2: NMU-treated rat mammary tumor #7-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

source_name: Mammary carcinoma

value: Mammary carcinoma

value: Breast stromal cells

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: MCF10A PM shCHD1 B 72h dox biol rep 1

description:
Library name: Sample 17
Column name in Final_count_hg38: sorted_PM_shCHD1_B_1_S26.bam


title: CSC-A with no Rhodococcus/Timepoint2/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_A_No_Rhodo_Rep_B_TP_2_Run_1


title: CSC-A with no Rhodococcus/Timepoint1/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_A_No_Rhodo_Rep_B_TP_1_Run_1


title: MCF10A PM shCHD1 A 72h dox biol rep 4

description:
Library name: Sample 16
Column name in Final_count_hg38: sorted_PM_shCHD1_A_4_S43.bam


title: MCF10A PM shCHD1 A 72h dox biol rep 2

description:
Library name: Sample 14
Column name in Final_count_hg38: sorted_PM_shCHD1_A_2_S31.bam


title: MCF10A PM shCHD1 A 72h dox biol rep 3

description:
Library name: Sample 15
Column name in Final_count_hg38: sorted_PM_shCHD1_A_3_S37.bam


title: CSC-A with no Rhodococcus/Timepoint2/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_A_No_Rhodo_Rep_A_TP_2_Run_1


title: 50His1-D9

description: Library name: Sample 18

value: 50% histidine media

value: Day 9


title: 25His2-D9

description: Library name: Sample 21


title: Dataset 3: Isotype NMU tumor #1

description: 10X Genomics

value: Rat mammary carcinoma

value: Mixed:breast cancer, immune, stroma

value: NMU(50mg/kg, twice)+rat IgG isotype(2.5mg/kg & 10mg/kg)


title: 50His2-D9

description: Library name: Sample 19


title: CSC-A with no Rhodococcus/Timepoint1/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_A_No_Rhodo_Rep_A_TP_1_Run_1


title: Dataset 2: NMU-treated rat mammary gland #3-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

source_name: Mammary microlesions

value: Mammary microlesions

value: Hsd:Sprague-Dawley SD

value: Female


title: Dataset 2: NMU-treated rat mammary tumor #7-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast cancer epithelium


title: 100His3-D9

description: Library name: Sample 17

value: 100% histidine media


title: MCF10A PM shCHD1 A 72h dox biol rep 1

description:
Library name: Sample 13
Column name in Final_count_hg38: sorted_PM_shCHD1_A_1_S25.bam

value: Breast

value: MCF10A PM

value: Breast epithelial cell line

value: CHD1 KD


title: Dataset 2: NMU-treated rat mammary gland #3-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast epithelium


title: CSC-A /Timepoint2/Replicate2/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_B_TP_2_Run_1

value: Bacteria


title: 100His1-D9

description: Library name: Sample 15


title: CSC-A /Timepoint1/Replicate3/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_C_TP_1_Run_1


title: Dataset 2: NMU-treated rat mammary tumor #6-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Mammary carcinoma

value: Breast stromal cells

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: 100His2-D9

description: Library name: Sample 16

value: Day 9


title: MCF10A PE shGFP 72h dox biol rep 3

description:
Library name: Sample 11
Column name in Final_count_hg38: sorted_PE_shGFP_3_S33.bam

value: MCF10A PE

value: Control

value: 72h doxycycline


title: Dataset 2: NMU-treated rat mammary tumor #7-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Breast immune cells

value: Hsd:Sprague-Dawley SD


title: CSC-A /Timepoint1/Replicate2/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_B_TP_1_Run_1


title: Dataset 2: NMU-treated rat mammary tumor #6-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast cancer epithelium

value: Female


title: Dataset 2: NMU-treated rat mammary gland #3-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Mammary microlesions


title: MCF10A PE shGFP 72h dox biol rep 1

description:
Library name: Sample 9
Column name in Final_count_hg38: sorted_PE_shGFP_1_S21.bam

value: Breast


title: CSC-A /Timepoint2/Replicate1/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_A_TP_2_Run_1


title: CSC-A /Timepoint2/Replicate3/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_C_TP_2_Run_1


title: MCF10A PE shCHD1 B 72h dox biol rep 4

description:
Library name: Sample 8
Column name in Final_count_hg38: sorted_PE_shCHD1_B_4_S41.bam

value: Breast epithelial cell line


title: NoHis3-D6

description: Library name: Sample 12

value: No histidine media

value: Day 6


title: Dataset 2: NMU-treated rat mammary tumor #5-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics


title: MCF10A PE shCHD1 B 72h dox biol rep 3

description:
Library name: Sample 7
Column name in Final_count_hg38: sorted_PE_shCHD1_B_3_S35.bam

value: CHD1 KD


title: CSC-A /Timepoint1/Replicate1/Media=B4U Run 2 (B4 with urea)

description: Library name: CSC_A_Complete_Rep_A_TP_1_Run_1

value: Bacteria


title: NoHis1-D6

description: Library name: Sample 14


title: 125His1-D6

description: Library name: Sample 11

value: 12.5% histidine media


title: Dataset 2: NMU-treated rat mammary tumor #5-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Mammary carcinoma

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: MCF10A PE shCHD1 B 72h dox biol rep 2

description:
Library name: Sample 6
Column name in Final_count_hg38: sorted_PE_shCHD1_B_2_S28.bam

value: MCF10A PE


title: CSC-A /Timepoint2/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_2_R3_B4U


title: CSC-A /Timepoint2/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_2_R2_B4U


title: NoHis2-D6

description: Library name: Sample 13


title: Dataset 2: NMU-treated rat mammary tumor #6-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics


title: 125His2-D6

description: Library name: Sample 10


title: Dataset 2: NMU-treated rat mammary tumor #5-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics


title: CSC-A /Timepoint2/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_2_R1_B4U


title: CSC-A with no Curtobacterium/Timepoint2/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_2_R3_B4U


title: 25His2-D6

description: Library name: Sample 8

value: 25% histidine media


title: Dataset 2: NMU-treated rat mammary tumor #4-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Breast stromal cells


title: Dataset 2: NMU-treated rat mammary tumor #4-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics


title: MCF10A PE shCHD1 A 72h dox biol rep 3

description:
Library name: Sample 3
Column name in Final_count_hg38: sorted_PE_shCHD1_A_3_S34.bam

value: 72h doxycycline


title: 25His3-D6

description: Library name: Sample 7


title: CSC-A with no Curtobacterium/Timepoint2/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_2_R1_B4U


title: Dataset 2: NMU-treated rat mammary gland #2-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast epithelium

value: Hsd:Sprague-Dawley SD


title: CSC-A /Timepoint1/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_1_R3_B4U


title: 50His1-D6

description: Library name: Sample 6

value: 50% histidine media


title: MCF10A PE shCHD1 A 72h dox biol rep 2

description:
Library name: Sample 2
Column name in Final_count_hg38: sorted_PE_shCHD1_A_2_S29.bam


title: 125His3-D6

description: Library name: Sample 9


title: Dataset 2: NMU-treated rat mammary tumor #4-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Breast immune cells

value: Female


title: 50His2-D6

description: Library name: Sample 5


title: M46_Biol_Replicate_2

first: Carolina

last: Di Benedetto

address: 2340 Sutter Street, S371

institute: University of California, San Francisco

description: Library name: Sample_6

data_processing:
Fastq files were aligned to the hg38 reference genome using Bowtie2
SAM files were converted to BAM, sorted and indexed using Samtools
BAM files were filtered by proper pairs and indexed using Samtools, inferred duplicates were removed using Picard (http://broadinstitute.github.io/picard), and black-listed regions were removed using Bedtools
Bigwig files were generated with BPM normalization using Deeptools
Target accessible DNA regions were quantified on Bigwig files using Megadepth
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig files

source_name: breast

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% heat inactivated FBS, 100 units/mL Penicillin and 100 µg/mL Streptomycin. Cells were grown at 37°C in a humified atmosphere at 5% CO2.

extract_protocol:
ATAC-seq was performed in MCF7, M11 (MCF7Δ#1) and M46 (MCF7Δ#2) using the ATAC-Seq Kit (Active Motif, Catalog No. 53150), following manufacturer’s instructions. 10.000 fresh cells per sample in duplicates were used.
ATAC-Seq Kit (Active Motif, Catalog No. 53150)

treatment_protocol: The germline insertion variant rs58296163 was deleted by CRISPR. Clones with the desired DNA modification were identified by PCR and DNA sequencing.

value: breast

value: breast cancer cell

value: insertion-deleted


title: MCF10A PE shCHD1 A 72h dox biol rep 1

description:
Library name: Sample 1
Column name in Final_count_hg38: sorted_PE_shCHD1_A_1_S22.bam

value: Breast

value: Breast epithelial cell line

value: CHD1 KD


title: MCF10A PE shGFP 72h dox biol rep 4

description:
Library name: Sample 12
Column name in Final_count_hg38: sorted_PE_shGFP_4_S39.bam

value: Control


title: 25Methionine-5

description: Library name: Sample 20

value: Jurkat

value: 25% Methionine

value: Day 3


title: MCF10A PE shCHD1 B 72h dox biol rep 1

description:
Library name: Sample 5
Column name in Final_count_hg38: sorted_PE_shCHD1_B_1_S23.bam

value: MCF10A PE


title: Dataset 2: NMU-treated rat mammary gland #2-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Mammary microlesions

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: CSC-A /Timepoint1/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_1_R2_B4U

value: Bacteria


title: Dataset 2: NMU-treated rat mammary gland #1-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast epithelium

value: Hsd:Sprague-Dawley SD


title: MCF10A PE shCHD1 A 72h dox biol rep 4

description:
Library name: Sample 4
Column name in Final_count_hg38: sorted_PE_shCHD1_A_4_S40.bam

value: 72h doxycycline


title: CSC-A /Timepoint1/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_1_R1_B4U


title: M46_Biol_Replicate_1

description: Library name: Sample_5

value: breast


title: CSC-A with no Curtobacterium/Timepoint2/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_2_R2_B4U


title: Dataset 2: NMU-treated rat mammary gland #1-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Breast immune cells

value: Female


title: 100His1-D6

description: Library name: Sample 3

value: 100% histidine media

value: Day 6


title: MCF10A PE shGFP 72h dox biol rep 2

description:
Library name: Sample 10
Column name in Final_count_hg38: sorted_PE_shGFP_2_S27.bam

value: Breast

value: Breast epithelial cell line


title: M11_Biol_Replicate_2

description: Library name: Sample_4

value: breast cancer cell

value: insertion-deleted


title: 100His2-D6

description: Library name: Sample 2


title: 50His3-D6

description: Library name: Sample 4

value: 50% histidine media


title: M11_Biol_Replicate_1

description: Library name: Sample_3


title: CSC-A with no Curtobacterium/Timepoint1/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_1_R2_B4U


title: Dataset 2: NMU-treated rat mammary tumor #3-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Mammary carcinoma

value: Breast stromal cells


title: Dataset 2: NMU-treated rat mammary tumor #3-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast cancer epithelium

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: 100His3-D6

description: Library name: Sample 1


title: MCF7_Biol_Replicate_2

description: Library name: Sample_2

value: WT


title: CSC-A /Timepoint0/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_0_R3_B4U

value: Bacteria


title: CSC-A with no Curtobacterium/Timepoint1/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_1_R3_B4U


title: 12-5His-2-D6

description: Library name: Sample 25

data_processing:
FastQC 0.11.9 was used to evaluate quality of seqenced reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto (version 0.50.1).
Transcript estimates are read into gene counts using tximport (version 1.32.0), then counts are normalized using DESeq2 (version 1.44.0).
Assembly: GRCh38 (Release 45)
Supplementary files format and content: csv files include DESeq2 normalized counts for each sample

value: Jurkat

value: 12.5% histidine media


title: Dataset 2: NMU-treated rat mammary tumor #3-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Breast immune cells

value: Hsd:Sprague-Dawley SD


title: Dataset 2: NMU-treated rat mammary tumor #2-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Female


title: CSC-A with no Curtobacterium/Timepoint1/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_1_R1_B4U


title: DE_MEKi.d2_RNA_Rep2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: DE_MEKi_d2_RNA_r2

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: hg38 + dm6
Supplementary files format and content: Excel file containing read counts per human genes. Columns names matche with sample titles.

source_name: Definitive Endoderm

growth_protocol: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW) were obtained from the CCHMC Pluripotent Stem Cell Facility (PSCF) and cultured under feeder-free condition in mTeSR1 medium (85850, StemCell Technologies) on plates coated with either hESC-qualified Matrigel (354277, Corning) or Cultrex Stem Cell Qualified Reduced Growth Factor Basement Membrane Extract (3434-010-02, Biotechne). hPSCs were cultured in a humidified incubator at 37℃ with 5% CO2.

extract_protocol:
1.0x106 cultured cells were dissociated into single cells using Accutase and were mixed with 100,000 Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were lysed with Aurum Total RNA Lysis Solution (7326802, BioRad). Total RNA was extracted using Aurum™ Total RNA Mini Kit (7326820, BioRad).
The sequencing libraries were prepared by Novogene.

treatment_protocol: For Paraxial mesoderm (PM) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For mesendoderm (ME) differentiation, hPSCs were cultured in CDM2 medium supplemented with 33 ng/ml ActivinA (800-0, Shenandoah; or GFH6, Cell Guidance Systems), 4 uM CHIR99021 (SML1046-25MG, Sigma-Aldrich), 20 ng/ml bFGF (PHG0261, Thermo Fisher Scientific), and 100 nM PIK90 (528117, EMD Millipore) for 24 hours. For subsequent PM differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 1 uM A83-01 (SML0788-5MG, Sigma-Aldrich), 3 uM CHIR99021, 20 ng/ml bFGF, and 250 nM LDN193189 for 24 hours.  For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.  For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.  For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for two days during differentiation from hPSC into NE, PM, and DE.

value: Definitive Endoderm

value: MEKi inhibitor


title: DE_MEKi.d2_RNA_Rep1

description: Library name: DE_MEKi_d2_RNA_r1


title: MCF7_Biol_Replicate_1

description: Library name: Sample_1

value: breast


title: CSC-A with no Curtobacterium/Timepoint0/Replicate3/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_0_R3_B4U


title: 25His-2-D6

description: Library name: Sample 22

value: 25% histidine media

value: Day 6


title: CSC-A /Timepoint0/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_0_R1_B4U


title: PM_MEKi.d2_RNA_Rep2

description: Library name: PM_MEKi_d2_RNA_r2

source_name: Paraxial Mesoderm

value: Paraxial Mesoderm


title: Dataset 2: NMU-treated rat mammary tumor #2-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Mammary carcinoma


title: CSC-A /Timepoint0/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_0_R2_B4U


title: 12-5His-1-D6

description: Library name: Sample 24


title: 25His-1-D6

description: Library name: Sample 21


title: 25His-3-D6

description: Library name: Sample 23


title: Dataset 2: NMU-treated rat mammary tumor #1-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Breast stromal cells


title: PM_MEKi.d2_RNA_Rep1

description: Library name: PM_MEKi_d2_RNA_r1


title: Dataset 2: NMU-treated rat mammary tumor #2-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics


title: CSC-A with no Curtobacterium/Timepoint0/Replicate2/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_0_R2_B4U


title: Dataset 2: NMU-treated rat mammary tumor #1-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

value: Breast cancer epithelium


title: 50His-3-D6

description: Library name: Sample 20

value: 50% histidine media


title: CSC-A with no Curtobacterium/Timepoint0/Replicate1/Media=B4U (B4 with urea)

description: Library name: CSC_NoCur_0_R1_B4U


title: DE_MEKi.d2_ChIP_Input_Rep2

description: Library name: DE_MEKiD2_Input_Rep2_Lib643

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
BigWig files were generated using reads aligned to hg38 using bedtools and UCSC toolkit in a RPM scale (*.rpm.bw). For ChIP samples, additional bigwig files were generated by normalizing by spike-in counts, i.e. read per 0.1 million spike-in count (*.rpsm.bw).
Assembly: hg38 + dm6
Supplementary files format and content: bigwig in RPM scale (*.rpm.bw); bigwig in spike-in normalized scale (*.rpsm.bw)

source_name: Definitive endoderm

extract_protocol:
Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was quenched by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 x g for 5 min at 4°C, and the supernatant was removed. The cell pellet was washed with ice-cold 1x PBS, centrifuged again at 600 x g for 5 min at 4°C, and the supernatant was aspirated. This wash step was repeated once more. The final cell pellet was frozen on dry ice and stored at -80°C until use.  Crosslinked human cells were resuspended in Lysis Buffer1 (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. For Drosophila S2 spike-in controls, crosslinked S2 cells were resuspended in 100 uL Lysis Buffer1 at a final concentration of 2.0x105 or 4.0x105 cells/uL, and 25% of the S2 cells were mixed with human cells. The mixed cell suspension was centrifuged at 665 x g for 5 min at 4℃, and the supernatant was removed. The cell pellet was then resuspended in Lysis Buffer2 (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. The cell lysate was then diluted in IP Dilution Buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA-free) and transferred to a milliTUBE ATA Fiber (Covaris). Chromatin was sonicated using a Covaris S220 (Covaris) for 5.5 min. Insoluble debris was removed by centrifugation at 12,000 x g for 5 min at 4℃. The supernatant containing sonicated chromatin was transferred to a new tube and stored at -80℃ until use.  Dynabeads Protein-G (10004D, Thermo Fisher Scientific) (25 - 80 uL) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). The desired amounts of H3K9me3 (ab8898, Abcam) antibodies were conjugated to washed Dynabeads by incubating for 2 to 6 hours at 4°C with rotation. Meanwhile, frozen sonicated chromatin was thawed on ice. A desired amount of chromatin (Table S3, based on DNA quantity) was diluted with IP dilution buffer at a 4:1 ratio. Antibody-conjugated Dynabeads were washed twice with IP Dilution Buffer (without protease inhibitor), resuspended in the diluted chromatin, and incubated overnight at 4°C with rotation. The next day, ChIPed beads were washed four times using the following washing buffers: (1) FA Lysis Buffer (50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA-free); (2) NaCl Buffer (50 mM HEPES-KOH [pH 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); (3) LiCl Buffer (100 mM Tris-HCl [pH 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); (4) 10 mM Tris-HCl [pH 8.0]. Following washing steps, chromatin was eluted with TES buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1,000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse-crosslinked by adding NaCl to a final concentration of 200 mM and incubating for 8 hours at 65°C. Samples were then treated with 50 ng/uL RNaseA (EN0531, ThermoFisher Scientific) for 30 min at 37°C, followed by treatment with 0.2 mg/mL Protease K (03115828001, Roche) for 2 hours at 37°C. DNA was purified using phenol-chloroform extraction, followed by ethanol precipitation. DNA concentration was measured using Quantus fluorometer (Promega).
Multiplexed libraries were prepared from ChIP and Input samples (two replicates) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB), following the manufacturer’s protocol with the following modifications. After adaptor ligation, cleanup was performed using AMPure XP Beads (A63880, Beckman Coulter), MagBind Magnetic Beads (M1378-01, Omega), or homemade Sera-mag beads (Rohland et al., Genome Res. 2012) without size selection. After RCR enrichment of the adaptor-ligated library, two rounds of size selection were performed using the AMPure XP Beads or MagBind Magnetic Beads.

value: Definitive endoderm


title: Dataset 2: NMU-treated rat mammary tumor #1-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: 50His-2-D6

description: Library name: Sample 19

value: Jurkat


title: DE_MEKi.d2_ChIP_Input_Rep1

description: Library name: DE_MEKiD2_Input_Rep1_Lib642


title: 50His-1-D6

description: Library name: Sample 18


title: CSC-A /Timepoint2/Replicate3/Media=B4

description: Library name: CSC_2_R3_B4

value: Bacteria

value: CSC-A /Timepoint2/Replicate3/Media=B4


title: CSC-A /Timepoint2/Replicate2/Media=B4

description: Library name: CSC_2_R2_B4

value: CSC-A /Timepoint2/Replicate2/Media=B4


title: Dataset 2: Untreated rat mammary gland #3-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics

source_name: Normal mammary tissues

value: Normal mammary tissues

value: Breast normal epithelium

value: Hsd:Sprague-Dawley SD

value: Female

value: ddH2O (pH6)


title: 100His-3-D6

description: Library name: Sample 17

value: 100% histidine media

value: Day 6


title: PM_MEKi.d2_ChIP_Input_Rep1

description: Library name: PM_MEKiD2_Input_Rep1_Lib640

source_name: Paramesoderm

value: Paramesoderm

value: MEKi inhibitor


title: PM_MEKi.d2_ChIP_Input_Rep2

description: Library name: PM_MEKiD2_Input_Rep2_Lib641


title: Dataset 2: Untreated rat mammary gland #3-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Breast immune cells


title: 100His-1-D6

description: Library name: Sample 15


title: NE_MEKi.d2_ChIP_Input_Rep2

description: Library name: NED2_MEKiD2_Input_Rep2_Lib639

source_name: Neuroectoderm

value: Neuroectoderm


title: 100His-2-D6

description: Library name: Sample 16


title: CSC-A with no Curtobacterium/Timepoint2/Replicate2/Media=B4

description: Library name: CSC_NoCur_2_R2_B4


title: DE_MEKi.d2_ChIP_H3K9me3_Rep2

description: Library name: DE_MEKiD2_H3K9me3_Rep2_Lib649

value: Definitive endoderm


title: Dataset 2: Untreated rat mammary gland #2-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics


title: NE_MEKi.d2_ChIP_Input_Rep1

description: Library name: NED2_MEKiD2_Input_Rep1_Lib638


title: CSC-A /Timepoint2/Replicate1/Media=B4

description: Library name: CSC_2_R1_B4

value: CSC-A /Timepoint2/Replicate1/Media=B4


title: Dataset 2: Untreated rat mammary gland #2-Stroma fraction (EpCAM- CD45-)

description: 10X Genomics

value: Breast stromal cells


title: CSC-A with no Curtobacterium/Timepoint2/Replicate3/Media=B4

description: Library name: CSC_NoCur_2_R3_B4

value: Bacteria


title: Dataset 2: Untreated rat mammary gland #2-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics


title: Dataset 2: Untreated rat mammary gland #1-Epithelium fraction (EpCAM+ CD45-)

description: 10X Genomics


title: DE_MEKi.d2_ChIP_H3K9me3_Rep1

description: Library name: DE_MEKiD2_H3K9me3_Rep1_Lib648


title: CSC-A with no Curtobacterium/Timepoint2/Replicate1/Media=B4

description: Library name: CSC_NoCur_2_R1_B4


title: NoHis-3

description: Library name: Sample 14

value: Jurkat

value: No histidine media

value: Day 3


title: Dataset 2: Untreated rat mammary gland #1-Immune fraction (CD45+ EpCAM-)

description: 10X Genomics

value: Normal mammary tissues


title: 12-5His-3

description: Library name: Sample 11

value: 12.5% histidine media


title: NoHis-2

description: Library name: Sample 13


title: CSC-A /Timepoint1/Replicate2/Media=B4

description: Library name: CSC_1_R2_B4

value: CSC-A /Timepoint1/Replicate2/Media=B4


title: PM_MEKi.d2_ChIP_H3K9me3_Rep1

description: Library name: PM_MEKiD2_H3K9me3_Rep1_Lib646


title: PM_MEKi.d2_ChIP_H3K9me3_Rep2

description: Library name: PM_MEKiD2_H3K9me3_Rep2_Lib647


title: NoHis-1

description: Library name: Sample 12


title: 12-5His-2

description: Library name: Sample 10


title: CSC-A /Timepoint1/Replicate3/Media=B4

description: Library name: CSC_1_R3_B4

value: CSC-A /Timepoint1/Replicate3/Media=B4


title: Amplicon long-read sequencing Tcf19_wt_rep2

description:
Library name: Tcf19_wt_rep2
Long-read amplicon sequencing for target Tcf19.

data_processing:
Raw FASTQ files were aligned to the mm10 reference genome using minimap2 (version 2.30) with options "-ax splice --splice-flank no -g 12000 -G 10000" to accommodate potential large deletion regions. Alignment outputs were sorted and indexed using samtools, and resulting BAM files were used for downstream coverage and indel analyses. Aligned reads were filtered to retain reads spanning the Cas9 cut site.
To reduce PCR bias from preferential amplification of shorter amplicons, deletions were grouped by start and end coordinates for deduplication-aware counting. Comparing total deletion counts versus unique deletion groups (keyed by start/end) showed an inflection point at 300 bp.For reads with deletion length > 300 bp, identical deletions sharing the same start and end coordinates were counted only once.
Assembly: mm10
Supplementary files format and content: Processed files are deduplicated bigWig tracks (*.dedup.bw).

organism: Mus musculus

source_name: embryo

extract_protocol:
For SMRT sequencing, 1 × 10^6 GFP-positive mESCs were isolated by FACS, and genomic DNA was extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102-01) following the manufacturer's protocol.
For long-amplicon PCR, 30 ng of genomic DNA was combined with 1 µL each of 10 µM forward and reverse primers, 12.5 µL of 2 × LongAmp enzyme mix (NEB, M0287S), and nuclease-free water to a final volume of 25 µL. PCR products were purified using DNA purification beads, and approximately 1 µg of amplicon was used for SMRTbell library preparation and subsequent SMRT sequencing.

value: embryo

value: mESC

value: embryonic stem cell

value: wild type control


title: Amplicon long-read sequencing Tcf19_wt_rep1

description:
Library name: Tcf19_wt_rep1
Long-read amplicon sequencing for target Tcf19.


title: 12-5His-1

description: Library name: Sample 9


title: CSC-A /Timepoint1/Replicate1/Media=B4

description: Library name: CSC_1_R1_B4

value: CSC-A /Timepoint1/Replicate1/Media=B4


title: NE_MEKi.d2_ChIP_H3K9me3_Rep1

description: Library name: NED2_MEKiD2_H3K9me3_Rep1_Lib644

value: Neuroectoderm

value: MEKi inhibitor


title: Amplicon long-read sequencing Tcf19_edit_rep3

description:
Library name: Tcf19_edit_rep3
Long-read amplicon sequencing for target Tcf19.

value: CRISPR-Cas9 editing


title: CSC-A with no Curtobacterium/Timepoint1/Replicate2/Media=B4

description: Library name: CSC_NoCur_1_R2_B4


title: 25His-2

description: Library name: Sample 7

value: 25% histidine media


title: hSTR2_association_Element

city: La Jolla

first: Alon

last: Goren

address: 9500 Gilman Drive

institute: University of California San Diego

description:
Library name: hSTR2_association_Element
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.

library_source: other

data_processing:
The FASTQ reads from the MPRA library were first subjected to quality control and adaptor trimming using Cutadapt, ensuring that low-quality bases and residual adaptor sequences were removed.
Following this preprocessing step, the cleaned reads were aligned to the appropriate variant reference library using BWA (Burrows-Wheeler Aligner), allowing accurate mapping of reads to their corresponding designed variants.
After alignment, read counts were computed for each variant to quantify their abundance in the library, forming the basis for downstream expression analysis.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file or CSV containing raw read counts for each variant in each sample.
Supplementary files format and content: A barcode-to-variant association table should be provided in TSV format.

molecule: other

growth_protocol: HEK293T cells were cultured in DMEM, high glucose, supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC. HeLa S3 cells were cultured in DMEM, high glucose, pyruvate supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC.

extract_protocol:
After 40-42 hours post-transfection, RNA and DNA were harvested using the AllPrep DNA/RNA mini Kit (Qiagen, 80204).
RNA was converted to cDNA using Superscript  Libraries were prepared using two rounds of PCR to attach Illumina barcodes and adaptors. Libraries were amplified using XX cycles on the thermocycler.

treatment_protocol: Cells were transfected using Lipofectamine 3000 to deliver the expression plasmid.

value: plasmid

value: Untreated


title: dpSTR_association_Element

description:
Library name: dpSTR_association_Element
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.


title: 25His-3

description: Library name: Sample 8

value: Jurkat


title: Amplicon long-read sequencing Tcf19_edit_rep1

description:
Library name: Tcf19_edit_rep1
Long-read amplicon sequencing for target Tcf19.


title: 25His-1

description: Library name: Sample 6

value: Day 3


title: NE_MEKi.d2_ChIP_H3K9me3_Rep2

description: Library name: NED2_MEKiD2_H3K9me3_Rep2_Lib645


title: CSC-A with no Curtobacterium/Timepoint1/Replicate3/Media=B4

description: Library name: CSC_NoCur_1_R3_B4

value: Bacteria


title: Amplicon long-read sequencing Tcf19_edit_rep2

description:
Library name: Tcf19_edit_rep2
Long-read amplicon sequencing for target Tcf19.


title: Amplicon long-read sequencing NanogSE_wt_rep2

description:
Library name: NanogSE_wt_rep2
Long-read amplicon sequencing for target NanogSE.


title: 50His-3

description: Library name: Sample 5

value: 50% histidine media


title: hSTR1_association_Element

description:
Library name: hSTR1_association_Element
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.


title: CSC-A with no Curtobacterium/Timepoint1/Replicate1/Media=B4

description: Library name: CSC_NoCur_1_R1_B4


title: CSC-A /Timepoint0/Replicate3/Media=B4

description: Library name: CSC_0_R3_B4

value: CSC-A /Timepoint0/Replicate3/Media=B4


title: CSC-A /Timepoint0/Replicate2/Media=B4

description: Library name: CSC_0_R2_B4

value: CSC-A /Timepoint0/Replicate2/Media=B4


title: Nuclei isolated from bone marrow, ID 37 May

city: Bethesda

first: P'ng

last: Loke

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: Library name: Sample 4

data_processing:
The analysis of our 4 single-nucleus RNA-seq samples was performed with the Cell Ranger 9.0.1 software. After assessing the UMI counts vs. barcodes graphs, the number of cells captured ranged from 1,250 to 1,400 and the mean reads per cell ranged from 84,790 to 214,143. Cells with low numbers of UMI counts were filtered out. The results from Cell Ranger were processed in R 4.5.0 with the Seurat (v5.3.0) package.
Assembly: Mmul_10
Supplementary files format and content: comma-separated values and columns are individual cells, identified by a unique cell barcode

molecule: nuclear RNA

organism: Macaca mulatta

source_name: Bone marrow

extract_protocol:
Nuclei were isolated from 4 frozen BM samples (10X Protocol: Isolation of Nuclei for Single Cell RNA Sequencing & Tissues for Single Cell RNA Sequencing)
Using the Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns (1000269, 10X Genomics), Chromium Next GEM Single Cell 3ʹ Gel Bead Kit v3.1, 16 rxns (PN-1000122) and Chromium Next GEM Chip G Single Cell Kit (PN-1000120, 10X Genomics), nuclei isolated from 4 frozen BM samples (10X Protocol: Isolation of Nuclei for Single Cell RNA Sequencing & Tissues for Single Cell RNA Sequencing) were processed to generate single-cell Gel Beads-in-emulsion (GEMs) according to the manufacturer’s protocol. Approximately 2,000 cells nuclei sample were loaded onto a Chromium Single Cell Controller to create GEMs. Cells were lysed, and poly(A) RNA was barcoded during reverse transcription using a Thermo Fisher Veriti 96-well thermal cycler at 53°C for 45 minutes, followed by 85°C for 5 minutes. The resulting cDNA was generated and amplified. Quality control and quantification of the cDNA were performed using the Agilent Genomic DNA ScreenTape Analysis kit (5067-5366 for Genomic DNA Reagents and 5067-5365 for Genomic DNA ScreenTape) in the TapeStation system. Single-cell RNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Library Kit v3.1 (PN-1000158, 10X Genomics) and sequenced on a NovaSeq Xplus platform. The sequencing run was configured as a 28:10:10:90 cycle run, targeting 10,000 cells with 25,000 reads per cell.

value: Bone marrow

value: Male

value: 1 year


title: Amplicon long-read sequencing NanogSE_wt_rep1

description:
Library name: NanogSE_wt_rep1
Long-read amplicon sequencing for target NanogSE.

value: embryo

value: mESC

value: embryonic stem cell

value: wild type control


title: CSC-A /Timepoint0/Replicate1/Media=B4

description: Library name: CSC_0_R1_B4

value: CSC-A /Timepoint0/Replicate1/Media=B4


title: CSC-A with no Curtobacterium/Timepoint0/Replicate3/Media=B4

description: Library name: CSC_NoCur_0_R3_B4


title: 50His-2

description: Library name: Sample 4

source_name: Jurkat


title: 50His-1

description: Library name: Sample 3


title: Nuclei isolated from bone marrow, ID 26 May

description: Library name: Sample 2


title: Nuclei isolated from bone marrow, ID 37 April

description: Library name: Sample 3


title: CSC-A with no Curtobacterium/Timepoint0/Replicate2/Media=B4

description: Library name: CSC_NoCur_0_R2_B4


title: 100His-3

description: Library name: Sample 2

value: 100% histidine media


title: Amplicon long-read sequencing NanogSE_edit_rep2

description:
Library name: NanogSE_edit_rep2
Long-read amplicon sequencing for target NanogSE.

value: CRISPR-Cas9 editing


title: Amplicon long-read sequencing NanogSE_edit_rep3

description:
Library name: NanogSE_edit_rep3
Long-read amplicon sequencing for target NanogSE.


title: Nuclei isolated from bone marrow, ID 26 April

description: Library name: Sample 1


title: Amplicon long-read sequencing NanogSE_edit_rep1

description:
Library name: NanogSE_edit_rep1
Long-read amplicon sequencing for target NanogSE.


title: CSC-A with no Curtobacterium/Timepoint0/Replicate1/Media=B4

description: Library name: CSC_NoCur_0_R1_B4


title: scRNA-seq of E11 to E13.5 sheep embryos

city: Madrid

first: Priscila

last: Ramos-Ibeas

address: Avda. Puerta de Hierro, 12, local 10

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC

description:
Library name: in_vivo
Two Parse sublibraries. Sublibrary 1 contains E11 (A4) and E11.5 (A5, A6) samples; sublibrary 2 contains E12.5 (A7, A9, A10) and E13.5 (A8, A11, A12) samples.

data_processing:
Data were processed with the Parse Biosciences pipeline (v1.3.1) with default settings. Expression matrices were loaded with the ReadParseBio function, and Seurat objects were generated for each of the 9 samples, which were independently processed. Cells with more than 20,000-60,000 detected reads, fewer than 1,000-3,000 or more than 5,000-9,000 detected genes were excluded from analyses. Cells were not filtered based on mitochondrial transcript content, given the heterogeneity embryonic cell types; however, mitochondrial gene percentages were on average lower than 1% in all samples, except for E11 (∼2%).
Assembly: Sequencing reads were aligned to the ovine genome (ARS-UI_Ramb_v2.0, Ensembl release 113)
Supplementary files format and content: RDS object containing all in vivo embryos from E11 to E13.5

organism: Ovis aries

source_name: Embryo

extract_protocol:
Embryos were digested and fixed right after flushing to avoid RNA degradation. Embryos were chopped and dissociated into single cells by incubation in TrypLE in 4-well dishes in an orbital shaker at 150 rpm, for 20 min at 38.5 °C. During this time, embryos were pipetted every 3 to 5 minutes and finally washed with ice-cold Euroflush medium (IVM Technologies) to quench TrypLE activity. Cells were filtered through Flowmi 40 µm cell strainers, collected in BSA-coated Falcon tubes and centrifuged at 300 G at 4 °C for 8 min. Then, cells were fixed using the EvercodeTM Cell Fixation kit v2 (ECF2101, Parse Biosciences) following the manufacturer instructions. Briefly, cells were suspended in Cell Prefixation Buffer, stained with Trypan Blue to assess cell viability and counted using a haemocytometer. Then, Cell Fixation Solution was added and cells were incubated on ice for 10 minutes. Next, Cell Permeabilization Solution was added, and after 3 min incubation on ice, Cell Neutralization Buffer was added to block the reaction. Then, cells were centrifuged at 300 G at 4 °C for 8 min, suspended in Cell Buffer and frozen in a Mr. FrostyTM freezing container at -80 °C until libraries preparation.
Single-cell RNA sequencing libraries were prepared using the Evercode Whole Transcriptome Mini v2 kit (Parse Biosciences) following the manufacturer’s protocol. Cells were barcoded using Parse Biosciences’ combinatorial barcoding strategy, and two sublibraries with around 12,000 cells each were prepared for paired-end sequencing.

value: Embryo

tag: developmental stage


title: 100His-1

description: Library name: Sample 1

value: Jurkat


title: Syngeneic graft  K5.6-2

status: Public on Feb 25 2026

type: RNA

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

institute: CIEMAT

hyb_protocol: Following fragmentation, 5.5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: RMA

label: Biotin

source_name: Tumor tissue from a syngeneic graft in a mouse injected with K5.6 cells

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Total RNA was extracted from FFPE tissue sections using the miRNeasy FFPE kit (Qiagen), or from fresh tissue/cells using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.

tag: mouse tissue

value: Syngeneic graft tumor tissue

tag: type of sample

value: Fresh

tag: mouse strain

value: QKO

tag: targeted cell (adenovirus)

value: Basal cells (Ad5-Krt5-Cre)


title: Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc) 2

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

description:
Gene expression data of hipoocampus microvessels from Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc)
Clariom D mouse
HGD + Curc_2

hyb_protocol: Fragmented and labeled sscDNA (5.5 ug) samples were hybridized in the GeneChip Hybridization Oven 645 and then washed and stained with the GeneChip™ Fluidics Station 450.

scan_protocol: The GeneGhip microarrays were scanned with the GeneChip™ Scanner 3000 7G

data_processing: Analyses of gene expression levels were performed with Transcriptome Analysis Console (TAC) software

source_name: Male mice brain hippocampus microvessels

label_protocol: Extracted total RNA (122.3 pg/mouse) was utilized for preparation of cRNA with the GeneChip®WT Pico Kit. The sscDNA (5.5 µg) obtained from 20 µg cRNA and labeled by terminal deoxynucleotidyl transferase (TdT) with the biotin-linked DNA Labeling Reagent.

growth_protocol: Male mice were housed (n=1/cage) in a temperature- and humidity-controlled environment with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from laser-captured hippocampal microvessels (300 microvessels/mouse) via the Arcturus PicoPure™ RNA Isolation Kit following the manufacturer’s instructions

treatment_protocol: Twenty week-old male C57BL/6J mice were fed HGD (34% sucrose) with 0.2% curcumin (HGD + Curc) for 12 weeks.

tag: Sex

tag: tissue

value: Hippocampus microvessels

value: High glycemic diet and 0.2% curcumin (w/w) (HGD + Curc)


title: Syngeneic graft  4K5-2

source_name: Tumor tissue from a syngeneic graft in a mouse injected with 4K5 cells

value: DKO


title: Syngeneic graft  4K5-3


title: Tumor QKO K20 3

source_name: Bladder tumor tissue from a QKO-K20 mouse

value: Bladder tumor tissue

value: FFPE

value: Suprabasal cells (Ad5-Krt20-Cre)


title: Tumor QKO K20 5


title: Syngeneic graft  K5.6-1


title: Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc) 3

description:
Gene expression data of hipoocampus microvessels from Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc)
Clariom D mouse
HGD + Curc_3

value: Male


title: Tumor QKO K20 1


title: Syngeneic graft  4K5-1


title: Tumor QKO K20 4


title: Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc) 1

description:
Gene expression data of hipoocampus microvessels from Male WT mice fed with high glycemic diet (34% sucrose) and 0.2% curcumin (w/w) (HGD + Curc)
Clariom D mouse
HGD + Curc_1


title: Tumor QKO K5 2

source_name: Bladder tumor tissue from a QKO-K5 mouse


title: Tumor QKO K5 1


title: Tumor DKO K20 4

source_name: Bladder tumor tissue from a DKO-K20 mouse


title: Tumor DKO K20 3


title: Tumor QKO K5 4


title: Tumor QKO K5 3


title: Tumor DKO K20 1


title: Tumor DKO K5 5

source_name: Bladder tumor tissue from a DKO-K5 mouse


title: Tumor DKO K5 3


title: Tumor DKO K20 2


title: Tumor QKO K20 2


title: Syngeneic graft  K5.6-3


title: Tumor DKO K5 1


title: Tumor DKO K5 2


title: Tumor DKO K20 5


title: CTRL URO QKO 5

source_name: Urothelial cells harvested from the bladder of QKO mice

value: Control urothelium


title: epi33_A

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were mapped to Arabidopsis reference genome (TAIR10 version) by TopHat2 (Kim et al., 2013).
Picard tools (available from http://broadinstitute.github.io/picard/) was used to discard duplicated reads.
Mapped reads from TopHat2 analysis were subsequently counted using htseq-count (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes between control and Tenofovir-treated samples using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed
Assembly: TAIR 10
Supplementary files format and content: For each genotype, the rawcount file is provided, generated with htseq-count (Anders et al., 2015).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown in plates on ½ MS media (1% sucrose and 0.8% agar, pH5.7) at 20°C under 12h light conditions (12h light/12h dark)

extract_protocol:
Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer's instructions. The RNA quality and integrity were assessed on the Agilent 2200 Tape Station.
Libraries for RNA expression analysis were prepared in tripicate from 1 µg of  high-integrity total RNA (RIN>8) using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA)  following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.

value: seedlings

tag: ecotype

tag: genotype


title: Tumor QKO K5 5


title: epi31_B


title: epi34_A


title: epi33_B


title: epi31_A


title: Tumor DKO K5 4


title: epi32_A


title: epi32_B


title: CTRL URO DKO 4

source_name: Urothelial cells harvested from the bladder of DKO mice


title: CTRL URO DKO 3


title: CTRL URO DKO 1


title: CTRL URO DKO 2


title: epi28_A


title: epi28_B


title: epi26_A


title: epi30_B


title: epi24_A


title: epi23_B


title: epi24_B


title: CTRL URO QKO 2


title: epi26_B


title: epi23_A


title: epi22_A


title: epi21_B


title: epi21_A


title: epi20_B


title: epi19_A


title: epi18_B


title: epi18_A


title: epi17_A


title: epi16_A


title: epi17_B


title: epi20_A


title: epi14_A


title: CTRL URO QKO 3


title: CTRL URO DKO 5


title: epi14_B


title: epi15_A


title: epi13_B


title: epi13_A


title: epi16_B


title: epi19_B


title: epi15_B


title: epi10_B


title: epi10_A


title: epi08_A


title: epi12_A


title: epi08_B


title: epi07_B


title: epi12_B


title: epi09_A


title: epi07_A


title: epi06_A


title: epi09_B


title: epi04_B


title: epi05_A


title: epi06_B


title: epi04_A


title: epi30_A


title: epi03_B


title: epi02_B


title: epi01_A


title: Col_B

value: wt


title: Col_A


title: epi01_B


title: epi05_B


title: epi02_A


title: epi69

data_processing:
Whole genome bisulfite sequencing (WGBS) datasets (fastq files) were trimmed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences
High-quality trimmed sequences were aligned against the Arabidopsis TAIR10 reference genome using Bismark (Krueger & Andrews, 2011). Duplicated reads were collapsed into one read.
Chloroplast sequences was used to estimate the bisulfite conversion.
To account for non-converted DNA, we applied a correction according to Catoni and Zabet 2021 (https://doi.org/10.1007/978-1-0716-1134-0_21). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Assembly: TAIR 10
Supplementary files format and content: For each genotype, the CX_Report generated by Bismark is provided (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.

source_name: leaves

growth_protocol: Plants were grown in single pots under long-day conditions (21°C, 16 h light, 8 h dark). Samples were collected from four weeks old plants.

extract_protocol:
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen), starting from leaves obtained from a single plant.
Bisulphite-converted DNA libraries  were performed starting from 0.5 to 1 lg of genomic DNA using the NEBNext DNA Sample PrepReagentSet1 (New England Biolabs), following the Illumina Genomic Sample Prep Guide (Illumina), as described in Becker et al (2011). The libraries for the epi62 samples were prepared by Novogene.

treatment_protocol: no treatment was applied

value: leaves


title: epi71


title: epi03_A


title: epi68


title: epi67


title: epi65


title: epi70


title: epi64


title: epi62EF


title: epi61


title: epi60_rep2


title: epi60


title: epi59


title: epi57


title: epi72


title: epi66


title: epi53


title: epi52


title: epi54


title: epi63


title: epi58


title: epi55


title: epi51


title: epi40_rep2


title: epi49


title: epi62EF_rep2


title: epi50


title: epi48


title: epi45


title: epi46


title: epi12_rep2


title: epi44


title: epi33_rep2


title: epi47


title: epi40


title: epi38


title: epi43


title: epi41


title: epi42


title: epi36


title: epi35


title: epi39


title: epi34


title: epi33


title: epi37


title: epi32


title: epi31


title: epi27


title: epi26


title: epi23


title: epi25


title: epi24


title: epi22


title: epi28


title: epi30


title: epi21


title: epi16


title: epi17


title: epi15


title: epi19


title: epi12


title: epi18


title: epi09


title: epi07


title: epi20


title: epi10


title: epi05


title: epi04


title: epi06


title: epi03


title: epi14


title: epi01


title: met13b


title: met1_B


title: epi13


title: epi01_rep2


title: met1_A


title: col


title: epi08


title: epi02


title: epi62_A


title: epi43_A


title: epi42_A


title: epi43_B


title: epi62_B


title: epi41_A


title: epi39_A


title: epi41_B


title: epi39_B


title: epi37_A


title: epi35_B


title: epi37_B


title: epi34_B


title: MCF10CA1a, RNA-seq, biological replicate 3

first: Kathleen

middle: Shaindel Metz

last: Reed

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

description:
Library name: MCF10CA1a_R3
MCF10CA1a_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq

data_processing:
Adapter and quality trimming was performed with Trim Galore
Reads were aligned to the hg38 reference genome using STAR
Gene expression was quantified using Salmon
Reads were summarized to a gene level using txImport
Differentially expressed genes were called using DESeq2
Assembly: hg38
Supplementary files format and content: *quant.sf: tab-delimited file of transcript-level quantifications including transcript ID, length, effective length, TPM, and NumReads, output from Salmon; .bw: bigwig files of signal tracks; .tsv: tab-delimited text file containing information on gene-summarized information for all genes including chromosome, start and end coordinates, ENSEMBL and HGNC IDs, DESeq2 output for each pairwise comparison, raw counts, differential cluster, variance-stabilize transformed counts, and Z-scored VST counts

growth_protocol: Cells were grown in DMEM/F12 supplemented with 1.05 mM CaCl2, 5% horse serum, and 10mM HEPES. Media for MCF10A and MCF10AT1 cells was additionally supplemented with 10 ug/ml insulin, 20ng/ml EGF, 0.5 ug/ml hydrocortisone, and 0.1 ug/ml cholera enterotoxin. Cells were grown to ~70% confluence in 15cm plates.

extract_protocol:
Total RNA was isolated from cells using Trizol (Life Technologies) and purified using the Direct-zol RNA kit (Zymo Research, Irvine, CA, USA: R2050). RNA quality and quantity were assessed using the RNA 6000 Nano Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA quantity was further assessed using a Nanodrop2000 (Thermo Scientific, Lafayette, CO) and Qubit HS RNA assay (Thermo Fisher Scientific).
Total RNA was depleted of ribosomal RNA (New England Biolabs, NEB #7400), reverse transcribed using a random hexamer strategy, and strand-specific adapters were added following the NEBNext Ultra II RNA-seq library prep kit (New England Biolabs, E7770).

tag: cell type

value: epithelial (metastatic)


title: epi42_B


title: MCF10CA1a, RNA-seq, biological replicate 1

description:
Library name: MCF10CA1a_R1
MCF10CA1a_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: epi35_A


title: MCF10AT1, RNA-seq, biological replicate 3

description:
Library name: MCF10AT1_R3
MCF10AT1_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq

value: epithelial (pre-malignant)


title: MCF10CA1a, RNA-seq, biological replicate 2

description:
Library name: MCF10CA1a_R2
MCF10CA1a_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: MCF10A, RNA-seq, biological replicate 3

description:
Library name: MCF10A_R3
MCF10A_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq

value: epithelial (normal-like)


title: MCF10AT1, RNA-seq, biological replicate 1

description:
Library name: MCF10AT1_R1
MCF10AT1_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: MCF10AT1, RNA-seq, biological replicate 2

description:
Library name: MCF10AT1_R2
MCF10AT1_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: MCF10A, RNA-seq, biological replicate 1

description:
Library name: MCF10A_R1
MCF10A_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: MCF10CA1a, ATAC-seq, biological replicate 2

description:
Library name: MCF10CA1a_R2
OMNI ATAC-Seq

data_processing:
Read trimming and quality filtering was performed using FastQC and TrimGalore
The filtered fastq were then downsampled to approximately 50 million reads per replicate.
Reads were aligned to the hg38 reference genome using Bowtie2
Mitochondrial, Multi-mapped, and low quality reads, and duplicates were removed using samtools
MACS2  was used to call narrowPeaks, followed by IDR to generate sample level peak sets.
Assembly: hg38
Supplementary files format and content: .narrowPeak: tab-delimited file peak calls, output from MACS2; .bw: bigwig files of signal tracks; .bam: alignment files, output from Bowtie2; .tsv: tab-delimited text file containing list of all peaks called across all samples, including peak coordinates and raw ATAC-Seq counts from each cell type

extract_protocol:
Cells were treated with DNAse at a concentration of 200 U/mL and incubated at 37°C for 30m, then washed three times with PBS. Nuclei were then isolated using RSB-Lysis buffer incubation for 10m on ice. Cells were scraped from plates and entrifuged at 500xG for 5m at 4°C. Supernatant was removed, cell nuclei were washed in RSB-Wash buffer, and cells were spun again as before.
Libraries were prepared according to the omniATAC protocol (CITE). Nuceli are first incubated with Tn5 transposase, then DNA is purified using Zymo DNA Clean and Concentrator kit. Transposed DNA is then amplified to add Illumina adapters using NEBNext High-Fidelity PCR kit. Libraries are assessed for fragment size using TapeStation and quantified on a fluorometer.


title: MCF10CA1a, ATAC-seq, biological replicate 1

description:
Library name: MCF10CA1a_R1
OMNI ATAC-Seq


title: MCF10A, RNA-seq, biological replicate 2

description:
Library name: MCF10A_R2
MCF10A_RNA.bw
Paired-end, ribosomal RNA depleted RNA-Seq


title: MCF10A, ATAC-seq, biological replicate 2

description:
Library name: MCF10A_R2
OMNI ATAC-Seq


title: MCF10AT1, ATAC-seq, biological replicate 2

description:
Library name: MCF10AT1_R2
OMNI ATAC-Seq


title: MCF10AT1, ATAC-seq, biological replicate 1

description:
Library name: MCF10AT1_R1
OMNI ATAC-Seq


title: MCF10A, ATAC-seq, biological replicate 1

description:
Library name: MCF10A_R1
OMNI ATAC-Seq


title: rnp-6(G281D), E. coli BW25113 diet, rep4

city: Cologne

first: Jonathan

last: Kölschbach

address: Joseph-Stelzmann-Straße 9B

department: Antebi

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: Library name: rnp6_BW.Rep_4

data_processing:
rRNA transcripts were removed from the annotation file (Ensembl C. elegans release 105/ce11) by depleting all lines with 'rrna' tag.
cDNA fasta was generated using cufflinks (v2.2.1). cDNA index was build using kallisto (v0.46.1).
Strandness was determined by pseudoalignment of 4 million reads to reference transcriptome using kallisto (v0.46.1). Mapping strand was identified via RSeQC (v4.0).
Reads were pseudoaligned to reference transcriptome (WBcel235_89) and quantified using kallisto (v0.46.1).
Normalized read counts were created by standard median-ratio for estimation of size factors using DESeq2 (v1.24)
Assembly: ce11
Supplementary files format and content: fpkm csv file includes fpkm-normalized counts for all samples
Supplementary files format and content: median-of-ratios csv file includes median-of-ratios-normalized counts for all samples

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strains were maintained at 20°C on nematode growth medium (NGM) 10 cm plates seeded with standard E. coli OP50.

extract_protocol:
C. elegans samples were lysed using QIAzol lysis reagent (Quiagen). RNA was isolated by chloroform extraction and samples were purified using Rneasy mini plus kit (Quiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
The Illumina Tru-Seq stranded RiboZero protocol was used for RNA preparation. After purification and validation via TapeStation (Agilent Technologies), libraries were pooled for quantification using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems).

treatment_protocol: C. elegans strains were synchronized by egg-laying and grown on NGM 10 cm plates seeded with E. coli OP50 or BW25113. After 3 days of growth, D1 adult worms were harvested for subsequent RNA extraction.

value: whole animal

value: E. coli BW25113 diet


title: rnp-6(G281D), E. coli BW25113 diet, rep2

description: Library name: rnp6_BW.Rep_2


title: rnp-6(G281D), E. coli BW25113 diet, rep3

description: Library name: rnp6_BW.Rep_3


title: rnp-6(G281D), E. coli BW25113 diet, rep1

description: Library name: rnp6_BW.Rep_1


title: N2(wt), E. coli BW25113 diet, rep4

description: Library name: wt_BW.Rep_4


title: N2(wt), E. coli BW25113 diet, rep1

description: Library name: wt_BW.Rep_1


title: rnp-6(G281D), E. coli OP50 diet, rep1

description: Library name: rnp6_OP50.Rep_1

value: E. coli OP50 diet


title: rnp-6(G281D), E. coli OP50 diet, rep2

description: Library name: rnp6_OP50.Rep_2


title: rnp-6(G281D), E. coli OP50 diet, rep4

description: Library name: rnp6_OP50.Rep_4


title: rnp-6(G281D), E. coli OP50 diet, rep3

description: Library name: rnp6_OP50.Rep_3


title: N2(wt), E. coli OP50 diet, rep2

description: Library name: wt_OP50.Rep_2


title: N2(wt), E. coli OP50 diet, rep3

description: Library name: wt_OP50.Rep_3


title: N2(wt), E. coli BW25113 diet, rep2

description: Library name: wt_BW.Rep_2


title: P108, HCC, tumour and background liver tissues, Tconv, GEX

city: London

first: Alberto

last: Sanchez-Fueyo

address: Denmark Hill

department: James Black Centre

institute: Kings College London University

description:
Library name: Patient P108_Tconv_mrna
polyA RNA

data_processing:
Sequence reads from all samples were processed and aggregated using Cell Ranger (10X Genomics, v7.2).
Assembly: hg38  (GRCh38 )
Supplementary files format and content: CellRanger output files: Liver_and_PBMC_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Supplementary files format and content: CellRanger output files: HCC_tumour_and_background_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Library strategy: CITE-seq

source_name: HCC and background liver

extract_protocol:
PBMCs were isolated from heparinised blood by density centrifugation using Ficoll-Paque PLUS (Sigma-Aldrich). Tissue samples obtained from different surgical liver resections (HCC and paired non-tumoral background tissues from HCC resections; and histologically healthy liver tissue from liver metastasis resections) were collected in cold DMEM medium (Life Technologies) and processed within 2 hours. Tumour and tissue single cell suspensions were obtained by enzymatic digestion with the BD HorizonTM Dri Tumour & Tissue Dissociation Reagent (TTDR) (BD Biosciences) as per manufacturer instructions.
scRNAseq libraries (5´ gene expression library GEX, T cell receptor enriched library VDJ, and surface protein library containing the TotalSeq-C CITE-seq antibodies) were prepared using the Chromium Single Cell Immune Profiling kit (10x Genomics, v1.1) according to the manufacturer’s instructions. The generated scRNAseq libraries were sequenced using a total of 100 cycles (paired end reads) with a NovaSeq 6000 S2 flow cell (Illumina).

value: HCC and background liver

value: CD4+ T cells

tag: library type

value: mRNA


title: P108, HCC, tumour and background liver tissues, Treg, VDJ

description:
Library name: Patient P108_Treg_vdj
polyA RNA

value: TCR


title: N2(wt), E. coli OP50 diet, rep4

description: Library name: wt_OP50.Rep_4


title: P108, HCC, tumour and background liver tissues, Treg, GEX

description:
Library name: Patient P108_Treg_mrna
polyA RNA


title: P108, HCC, tumour and background liver tissues, Tconv, VDJ

description:
Library name: Patient P108_Tconv_vdj
polyA RNA