title: Mouse 9, Visceral Adipose, C57BL/6J, Vegetarian

city: Charlottesville

first: Mete

last: Civelek

state: VA

address: Center for Public Health Genomics, PO Box 800717

institute: University of Virginia

data_processing:
Quality control with fastQC to identify problems
Trim adapters with trimGalore, illumina adapters specified
Align to GRCm39 using hisat2. Weaker alignment observed for A/J, DBA/2J, SJL when comparing to C57BL6 reference, therefore mismatch penalty relaxed.
Quantification using htseq, fractional counting method
Assembly: GRCm39
Supplementary files format and content: comma separated values (.csv) file contains processed counts for each sample
Supplementary files format and content: tab-delimited text file contains transcripts per million (TPMs) for each sample

source_name: Visceral Adipose

growth_protocol: Male mice were maintained on chow diet.

extract_protocol:
Frozen tissue homogenized via pulverization. TRIzol added to homogenized frozen tissue to extract RNA. After centifugation to remove lipid and cell debris, we followed the Qiagen Rneasy Micro Kit to isolate mRNA species. We verified the RNA integrity via Tape Station.
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: 12 week old male mice of various strains were switched from chow diet to a mouse version of a popular human diet. These diets are isocaloric and have the same macronutrient content, while the nutrient source differs to reflect the human diet. At 18 weeks old (6 week on diet), the mice were sacrificed and metabolic organs were harvested.

value: Visceral Adipose

value: male

value: 12 week old

tag: diet

value: Vegetarian


title: Mouse 8, Visceral Adipose, C57BL/6J, Mediterranean

status: Public on Mar 04 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: Sex

tag: age

value: Mediterranean


title: blood_ctrl_mRNA_EXP_anti_TIGIT_comboTx_batch2

city: South San Francisco

first: Xiangnan

last: Guan

state: California

address: 1 DNA WAY

institute: Genentech

description:
mouse_scSeq_anti-TIGIT_comboTx_blood_metadata.rds
mouse_scSeq_anti-TIGIT_comboTx_blood_metadata.rds

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to the mouse transcriptome (mm10) and UMI counts were quantified to generate a gene–barcode matrix using the Cell Ranger pipeline (10x Genomics, v.6.1.1).
ADT hashtag expression were generated using the Cell Ranger pipeline (10x Genomics, v.6.1.1).
Downstream analyses including demultiplexing ADT hashtags and single cell processing were performed using the R package Seurat (v.3.2.2).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Seurat and R output files in .rds format.

source_name: blood

extract_protocol:
Blood and tumours were collected from mice and processed for single-cell suspension preparation by enzymatic dissociation and/or red blood cell lysis as needed. Cells within each tissue and treatment group were hash-tagged (BioLegend TotalSeq C), pooled from different mice and labelled with fluorescent anti-CD45 antibodies and a viability dye.
Live CD45+ cells were sorted and processed according to the 10x Genomics’ protocol (CG000330_Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide_RevA) to generate 5′ single-cell RNA-seq and hashed libraries.
Single cell RNAseq + Hashing ADT (antibody-derived tag)

value: blood

tag: cell type

value: blood CD45+

tag: treatment

value: ctrl

tag: library type

value: mRNA


title: blood_ctrl_ADT_EXP_anti_TIGIT_comboTx_batch2

library_source: other

molecule: protein

value: ADT

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody, TotalSeq-C0302 anti-mouse Hashtag 2 Antibody, TotalSeq-C0303 anti-mouse Hashtag 3 Antibody, TotalSeq-C0304 anti-mouse Hashtag 4 Antibody, TotalSeq-C0305 anti-mouse Hashtag 5 Antibody


title: Mouse 63, Visceral Adipose, SJL, Vegan

value: SJL

value: Vegan


title: tumor_tigit2a_mRNA_EXP_anti_TIGIT_monoTx_batch1

description:
mouse_scSeq_anti-TIGIT_monoTx_tumor_myeloid_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_myeloid_RNA_raw_counts.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_T_NK_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_tumor_T_NK_RNA_raw_counts.rds

source_name: tumor

value: tumor

value: tumor CD45+


title: tumor_tigit2a_ADT_EXP_anti_TIGIT_monoTx_batch1


title: Mouse 57, Visceral Adipose, SJL, Vegetarian


title: Mouse 59, Visceral Adipose, SJL, Vegetarian


title: tumor_tigit2b_mRNA_EXP_anti_TIGIT_monoTx_batch1


title: Mouse 53, Visceral Adipose, SJL, Mediterranean


title: B5A, invasive

city: Beijing

first: Yu

last: Zhang

address: 119 South Fourth Ring Road West

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing:
SOAPnuke (v1.5.6)
The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6), which removed the following: 1) reads containing adapters (adapter contamination); 2) reads with an unknown base N content greater than 5%; and 3) low-quality reads.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GRCh38
Supplementary files format and content: gene.fpkm.txt

molecule: total RNA

organism: Homo sapiens

source_name: pituitary adenoma

extract_protocol:
2.1 Tissue Sample Fragmentation and Lysis 2.1.1 Grinding Machine 2.1.1.1 Transfer appropriate sample to corresponding grinding tube, 2.1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 2.1.2 Liquid Nitrogen Grinding and Crushing 2.1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 2.1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.  Stand flat for 5 min for the fully lysis of tissue cells. 2.1.3 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2.2 Sample Purification 2.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6), which removed the following: 1) reads containing adapters (adapter contamination); 2) reads with an unknown base N content greater than 5%; and 3) low-quality reads.

value: pituitary adenoma

value: ACTH-silent

tag: phenotype

value: invasive


title: blood_tigit2a_mRNA_EXP_anti_TIGIT_monoTx_batch1

description:
mouse_scSeq_anti-TIGIT_monoTx_blood_metadata.rds
mouse_scSeq_anti-TIGIT_monoTx_blood_RNA_raw_counts.rds


title: Mouse 50, Visceral Adipose, SJL, American

value: Visceral Adipose

value: male

value: American


title: B20A, invasive


title: blood_tigit2a_ADT_EXP_anti_TIGIT_monoTx_batch1


title: blood_tigit2b_ADT_EXP_anti_TIGIT_monoTx_batch1


title: B1A, invasive


title: Mouse 48, Visceral Adipose, DBA/2J, Vegan

value: 12 week old


title: B19A, invasive


title: Mouse 43, Visceral Adipose, DBA/2J, Vegetarian

value: Vegetarian


title: Mouse 7, Visceral Adipose, C57BL/6J, Mediterranean

value: Mediterranean


title: B18A, invasive


title: B16A, invasive


title: Mouse 39, Visceral Adipose, DBA/2J, Mediterranean


title: Mouse 34, Visceral Adipose, DBA/2J, American


title: tumor_ctrl_mRNA_EXP_anti_TIGIT_monoTx_batch1

value: ctrl


title: Mouse 32, Visceral Adipose, A/J, Vegan

value: A/J


title: B7A, invasive


title: Mouse 54, Visceral Adipose, SJL, Mediterranean


title: Mouse 45, Visceral Adipose, DBA/2J, Vegan


title: B6A, invasive


title: A7A, non-invasive

value: gonadotroph adenoma

value: non-invasive


title: B4A, invasive


title: Mouse 49, Visceral Adipose, SJL, American

value: SJL


title: Mouse 64, Visceral Adipose, SJL, Vegan

value: Vegan


title: Mouse 22, Visceral Adipose, A/J, Mediterranean


title: Mouse 42, Visceral Adipose, DBA/2J, Vegetarian


title: Mouse 40, Visceral Adipose, DBA/2J, Mediterranean


title: B15A, invasive


title: B14A, invasive


title: B3A, invasive


title: A20A, non-invasive


title: B13A, invasive


title: B12A, invasive


title: B10A, invasive


title: A18A, non-invasive


title: Mouse 30, Visceral Adipose, A/J, Vegan


title: Mouse 27, Visceral Adipose, A/J, Vegetarian


title: Mouse 25, Visceral Adipose, A/J, Vegetarian


title: A9A, non-invasive


title: Mouse 33, Visceral Adipose, DBA/2J, American


title: Mouse 20, Visceral Adipose, A/J, American


title: A17A, non-invasive


title: A6A, non-invasive


title: Mouse 24, Visceral Adipose, A/J, Mediterranean


title: Mouse 9, Subcutaneous Adipose, C57BL/6J, Vegetarian

source_name: Subcutaneous Adipose

value: Subcutaneous Adipose


title: A5A, non-invasive


title: A4A, non-invasive


title: A3A, non-invasive


title: Mouse 16, Visceral Adipose, C57BL/6J, Vegan


title: Mouse 2, Visceral Adipose, C57BL/6J, American


title: A2A, non-invasive


title: A13A, non-invasive


title: Mouse 64, Subcutaneous Adipose, SJL, Vegan


title: A1A, non-invasive


title: A19A, non-invasive


title: Mouse 13, Visceral Adipose, C57BL/6J, Vegan


title: Mouse 12, Visceral Adipose, C57BL/6J, Vegetarian


title: Mouse 59, Subcutaneous Adipose, SJL, Vegetarian


title: Mouse 1, Visceral Adipose, C57BL/6J, American


title: A16A, non-invasive


title: Mouse 50, Subcutaneous Adipose, SJL, American


title: Mouse 17, Visceral Adipose, A/J, American


title: Mouse 49, Subcutaneous Adipose, SJL, American


title: Mouse 7, Subcutaneous Adipose, C57BL/6J, Mediterranean


title: A15A, non-invasive


title: Mouse 8, Subcutaneous Adipose, C57BL/6J, Mediterranean


title: A12A, non-invasive


title: Mouse 63, Subcutaneous Adipose, SJL, Vegan


title: A11A, non-invasive


title: Mouse 57, Subcutaneous Adipose, SJL, Vegetarian


title: Mouse 43, Subcutaneous Adipose, DBA/2J, Vegetarian


title: Mouse 42, Subcutaneous Adipose, DBA/2J, Vegetarian


title: Mouse 55, Subcutaneous Adipose, SJL, Mediterranean


title: Mouse 45, Subcutaneous Adipose, DBA/2J, Vegan


title: Mouse 48, Subcutaneous Adipose, DBA/2J, Vegan


title: Mouse 34, Subcutaneous Adipose, DBA/2J, American


title: Mouse 30, Subcutaneous Adipose, A/J, Vegan


title: Mouse 39, Subcutaneous Adipose, DBA/2J, Mediterranean


title: Mouse 25, Subcutaneous Adipose, A/J, Vegetarian


title: Mouse 38, Subcutaneous Adipose, DBA/2J, Mediterranean


title: Mouse 53, Subcutaneous Adipose, SJL, Mediterranean


title: Mouse 24, Subcutaneous Adipose, A/J, Mediterranean


title: Mouse 33, Subcutaneous Adipose, DBA/2J, American


title: Mouse 17, Subcutaneous Adipose, A/J, American


title: Mouse 32, Subcutaneous Adipose, A/J, Vegan


title: Mouse 27, Subcutaneous Adipose, A/J, Vegetarian


title: Mouse 22, Subcutaneous Adipose, A/J, Mediterranean


title: Mouse 2, Subcutaneous Adipose, C57BL/6J, American


title: Mouse 18, Subcutaneous Adipose, A/J, American


title: Mouse 16, Subcutaneous Adipose, C57BL/6J, Vegan


title: Mouse 12, Subcutaneous Adipose, C57BL/6J, Vegetarian


title: Mouse 1, Subcutaneous Adipose, C57BL/6J, American


title: Mouse 13, Subcutaneous Adipose, C57BL/6J, Vegan


title: lymph node tissue (FFPE) from patient C32

type: genomic

city: Munich

first: Christof

last: Winter

address: Ismaninger Str. 22

country: Germany

institute: Technical University of Munich

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Normalized using single sample Noob (ssNoob) implemented in the R package minfi (PMID 28035024)

label: Cy3, Cy5

molecule: genomic DNA

source_name: lymph node tissue (FFPE)

label_protocol: Standard Illumina protocol

extract_protocol: From FFPE tissue samples, areas containing at least 50% tumor cells were identified and marked by a pathologist. After macrodissecting these marked areas, DNA was extracted using the Maxwell RSC Blood DNA Kit with the Maxwell RSC 48 instrument (Promega). For DNA quality control, fragmentation and integrity were evaluated using the 4200 TapeStation system (Agilent), and DNA levels were quantified with the Qubit 4 Fluorometer (Thermo Fischer Scientific).

value: lymph node tissue (FFPE)

tag: disease state

value: hnCUP

tag: methcup id

tag: gender (0 = male, 1 = female)

tag: age at diagnosis

tag: smoking (0 = no, 1 = yes, 2 = ex)

tag: alcohol abuse (0 = no, 1 = yes)

tag: p16 status (0 = negative (<70%), 1 = positive (>70%))

tag: t

tag: g


title: lymph node tissue (FFPE) from patient C28

tag: tissue

value: unknown


title: lymph node tissue (FFPE) from patient C24


title: lymph node tissue (FFPE) from patient C26


title: lymph node tissue (FFPE) from patient C03


title: lymph node tissue (FFPE) from patient C33


title: lymph node tissue (FFPE) from patient C25


title: Mouse 9, Quadriceps Muscle, C57BL/6J, Vegetarian

source_name: Quadriceps Muscle

value: Quadriceps Muscle

tag: strain

tag: Sex

tag: diet


title: lymph node tissue (FFPE) from patient C30


title: lymph node tissue (FFPE) from patient C22


title: lymph node tissue (FFPE) from patient C23


title: lymph node tissue (FFPE) from patient C27


title: lymph node tissue (FFPE) from patient C21


title: Mouse 7, Quadriceps Muscle, C57BL/6J, Mediterranean

tag: age


title: Mouse 63, Quadriceps Muscle, SJL, Vegan


title: p65 ChIP-seq WT KLA6h [re-analyzed]

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

state: CA

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
disuccinimidyl glutarate-formaldehyde cross-linked
processed data file:
BMDM_ChIP_p65_peaks.txt

library_source: genomic

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include peak text files (ChIP-Seq peak data, using default HOMER parameters). All genomic coordinates are relative to mm10 mouse assembly.

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

tag: genotype/variation

value: Srebp1 WT

tag: cell type

value: bone marrow derived macrophages

tag: treatment

value: KLA for 6 hours

tag: antibody

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# A0314)


title: lymph node tissue (FFPE) from patient C01

tag: disease state

tag: methcup id


title: Mouse 59, Quadriceps Muscle, SJL, Vegetarian

value: male

value: 12 week old

value: Vegetarian


title: KO, replicate 2, bulk RNAseq

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

data_processing:
Sequence reads were mapped to GRCz11/danrer11 using STAR (v2.7.10a)
Read count extraction were performed using RSEM (v1.3.1)
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.32.0)
Assembly: danrer11
Supplementary files format and content: tab-delimited text files include gene expression  for each Sample

organism: Danio rerio

source_name: embryo

extract_protocol:
RNA was extracted by TRNzol method, and 500ng of total RNA was used to construct sequencing library.
RNA libraries for RNA-Seq were prepared using the Vazyme RNA-Seq library kit according to the manufacturer's protocol.

value: embryo

value: 48 hpf

tag: genotype

value: tet2/3 double knock out


title: KO, replicate 1, bulk RNAseq


title: lymph node tissue (FFPE) from patient C17

tag: gender (0 = male, 1 = female)

tag: age at diagnosis

tag: smoking (0 = no, 1 = yes, 2 = ex)


title: p65 ChIP-seq WT noTx [re-analyzed]

value: none (control)


title: lymph node tissue (FFPE) from patient C19

tag: alcohol abuse (0 = no, 1 = yes)

tag: p16 status (0 = negative (<70%), 1 = positive (>70%))

tag: t


title: lymph node tissue (FFPE) from patient C20

tag: tissue

tag: g


title: p65 ChIP-seq WT KLA1h [re-analyzed]

tag: strain

value: KLA for 1 hours


title: Mouse 64, Quadriceps Muscle, SJL, Vegan

value: SJL

tag: Sex

tag: age

tag: diet

value: Vegan


title: Mouse 8, Quadriceps Muscle, C57BL/6J, Mediterranean

value: Mediterranean


title: WT, replicate 2, bulk RNAseq

value: wild type


title: lymph node tissue (FFPE) from patient C10

value: lymph node tissue (FFPE)

value: hnCUP


title: Mouse 54, Quadriceps Muscle, SJL, Mediterranean

value: Quadriceps Muscle


title: lymph node tissue (FFPE) from patient C11

value: unknown


title: lymph node tissue (FFPE) from patient C12


title: Mouse 53, Quadriceps Muscle, SJL, Mediterranean


title: lymph node tissue (FFPE) from patient C16


title: lymph node tissue (FFPE) from patient C18


title: lymph node tissue (FFPE) from patient C02


title: exponential growth 6H_WT6

city: Toulouse

first: Marta

last: Kwapisz

address: 118, route de Narbonne

department: MCD

country: France

institute: CNRS-UT

description: WT; ∆TERMP_00517

data_processing:
Qauality of each raw sequencing file (fastq) was verified with FastQC
Reads were aligned to the reference T.barophilus genome (GCA_000151105.2) using STAR aligner
Read count per sample was computed using HT-seq count
The raw count table was cleaned for lowly expressed genes, genes with an averaged raw read count per sample higher or equal to 5 were kept
Based on multivariate data exploration: PCA and hierarchical clustering with Euclidian distance, the sample WT2 was identified as outlier and removed from the analysis.
Differential analysis was then applied to compare 3 mutant samples against 5 WT samples using DESeq2 Bioconductor R-package
DESeq2 normalization was applied on the raw read counts, taking account of the type and the batch effect, and log2 fold change (log2FC) values were computed for each gene. P-values for the significance of each fold change were then computed and adjusted for multiple testing.
Assembly: GCA_000151105.2

organism: Thermococcus barophilus

growth_protocol: Cells were grown exponentially in standard growth conditions  (TRM with sulfur, 85°C under atmospheric pressure). For each experiment 50 mL of culture containing 1Ex10^7 of cells, 6h after incubation from over-night stationary culture were used.

extract_protocol:
Total RNAs were extracted from three independent exponentially grown cultures (50 mL of culture containing 1Ex107 of cells, 6h after incubation from over-night stationary culture) of ∆TERMP_00517 (UBOCC-M-3300) (Wild-Type reference) and ΔASH-Ski2 (UBOCC-M-3317) strains  (mean quantity of total RNAs were 280 ng/µL, RIN=8.8).
RNA libraries for RNA-seq were prepared using standard Ilumina Library Prep Kit following manufacturer's protocols.

treatment_protocol: no treatment

tag: cell line

value: WT; {delta}TERMP_00517


title: control morpholino, 5hmC-input

data_processing:
Sequence reads were mapped to GRCz11/danrer11 using Bowtie2 (v2.2.6) with default parameters
Mapped reads were removed PCR duplicates using sambamba (v0.8.2)
Peaks were called using MACS (v2.2.7.1) with the significance cut-off q-value <=0.01
bigWig files were generated using bamCoverage (depptools v2.30.0)
Supplementary files format and content: danrer11
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
After the zebrafish head genome was extracted, the chromatin was ultrasonographed with covaris.
Using the Vazyme DNA library building kit, all DNA samples after IP extraction and DNA before 100ng IP extraction were input, and 13 and 6 (input) cycles were used on the thermal cycler to amplify the library. Use DNA clear beads from Vazyme to select after-expansion beads in 150-250bp length. The library was verified using Q-seq.

value: control morpholino


title: Mouse 50, Quadriceps Muscle, SJL, American

value: male

value: 12 week old

value: American


title: exponential growth 6H_WT4

description: WT; ∆TERMP_00517


title: exponential growth 6H_WT5

description: WT; ∆TERMP_00517


title: Mouse 57, Quadriceps Muscle, SJL, Vegetarian

value: Vegetarian


title: exponential growth 6H_delta3

description: ΔASH-Ski2; ∆TERMP_00517

value: {delta}ASH-Ski2; {delta}TERMP_00517


title: lymph node tissue (FFPE) from patient C09


title: exponential growth 6H_delta2

description: ΔASH-Ski2; ∆TERMP_00517


title: exponential growth 6H_delta1

description: ΔASH-Ski2; ∆TERMP_00517


title: Mouse 48, Quadriceps Muscle, DBA/2J, Vegan


title: control morpholino, 5hmC-hMeDIPseq

value: embryo

value: 48 hpf


title: tet2/3 double morpholino, 5hmC-hMeDIPseq

value: tet2/3 double morpholino


title: Mouse 45, Quadriceps Muscle, DBA/2J, Vegan

value: Vegan


title: exponential growth 6H_WT3

description: WT; ∆TERMP_00517


title: lymph node tissue (FFPE) from patient C15


title: exponential growth 6H_WT2

description: WT; ∆TERMP_00517


title: exponential growth 6H_WT1

description: WT; ∆TERMP_00517


title: Bdnrpd1-2, rep3

city: Strasbourg

first: Todd

middle: L

last: Blevins

address: 12 Rue du Général-Zimmer

institute: CNRS

description:
Bd09_AFVA-91
featureCounts_genes.tsv
featureCounts_TEs.tsv

data_processing:
trim_galore --length 100 --fastqc --paired
hisat2 --max-intronlen 5000 --rna-strandness RF
samtools sort -O BAM
featureCounts -p -M
Assembly: Bdistachyon_314_v3.1
Supplementary files format and content: tab-delimited text file including count values for each Sample on each TE/gene annotation

organism: Brachypodium distachyon

source_name: leaves

growth_protocol: Brachypodium distachyon seeds (Bd21-3 background) were germinated 4 days on wet Whatman filter paper at room temperature, then the plants were grown on soil for 4 weeks in a walk-in growth chamber with a day/night cycle of 20 h/4 h at temperatures of 26°C/20°C under 6x OSRAM FQ 49W/965HO Lumilux de Lux Cool Daylight lighting (40 cm distance to light tubes).

extract_protocol:
Total RNA from young emerging leaves (4-week-old) was extracted with TRIzol reagent, treated with DNaseI, and then purified again via phenol-chloroform extraction and ethanol precipitation.
DNAase-treated total RNA were subjected to poly(A)-tail selection, followed by library construction using Illumina TruSeq Stranded mRNA Library Prep kit.

value: leaves


title: tet2/3 double morpholino, 5hmC-input


title: Mouse 43, Quadriceps Muscle, DBA/2J, Vegetarian


title: IMM cells, 60 minute LPS Stimulation Rep 3

city: Bethesda

first: Matthew

middle: James

last: Marino

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description:
RawCountFile_rsemgenes.txt
DESeq2_60min_output.txt
9_R63

data_processing:
Basecalling was done using RTA 3.9.25
Demultiplexing was done using Bcl2fastq v2.20
Filtering (adaptor and quality) was done with Cutadapt 1.18
Alignment was performed using STAR 2.7.0f
RNAstatistics Picard 2.18.26
Duplication Statistics Picard 2.18.26
Quantification RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample
Supplementary files format and content: tab-delimited text file includes the DESeq2 normalized expression values for 0vs30 and 0vs60 minute comparisons

source_name: IMM

growth_protocol: IMM cells maintained in cDMEM. DMEM supplemented with heat inactivated 10% FBS and 0.02M HEPES in a humidified atmosphere with 5% CO2 and 37C.

extract_protocol:
RNA was harvested with the RNeasy mini plus kit (Qiagen), >500 ng was used for library construction.
RNA libraries were constructed by the NCI CCR Genomics core using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus.

treatment_protocol: After 5 passages following thaw from -80C in cDMEM, LPS (Enzo Life Sciences) was used to stimulate the cells (100 ng / mL in cDMEM) at the 0, 30, and 60 minute timepoints. After stimulation the plates (10 cm treated dishes) had the LPS containing media aspirated off the top and were immediately placed on ice. 2 washes with ice cold PBS were performed before the addition of lysis buffer.

value: IMM

tag: cell type

value: Immortalized mouse macrophages

value: WT

tag: treatment

value: LPS stimulation

tag: time point

value: 60 minute


title: lymph node tissue (FFPE) from patient C31

value: lymph node tissue (FFPE)

tag: disease state

value: hnCUP

tag: methcup id


title: Bdnrpd1-2, rep2

description:
Bd08_AFVA-90
featureCounts_genes.tsv
featureCounts_TEs.tsv

tag: genotype


title: IMM cells, 60 minute LPS Stimulation Rep 2

description:
RawCountFile_rsemgenes.txt
DESeq2_60min_output.txt
8_R62


title: Mouse 39, Quadriceps Muscle, DBA/2J, Mediterranean

value: Quadriceps Muscle

value: male

value: Mediterranean


title: lymph node tissue (FFPE) from patient C06

tag: gender (0 = male, 1 = female)

tag: age at diagnosis

tag: smoking (0 = no, 1 = yes, 2 = ex)


title: IMM cells, 60 minute LPS Stimulation Rep 1

description:
RawCountFile_rsemgenes.txt
DESeq2_60min_output.txt
7_R61


title: IMM cells, 30 minute LPS Stimulation Rep 3

description:
RawCountFile_rsemgenes.txt
DESeq2_30min_output.txt
6_R33

value: 30 minute


title: Bdnrpd1-2, rep1

description:
Bd07_AFVA-89
featureCounts_genes.tsv
featureCounts_TEs.tsv


title: Mouse 49, Quadriceps Muscle, SJL, American

value: SJL

value: 12 week old

value: American


title: Mouse 38, Quadriceps Muscle, DBA/2J, Mediterranean


title: Mouse 34, Quadriceps Muscle, DBA/2J, American


title: BdNRPD1_WT, rep2

description:
Bd05_AFVA-87
featureCounts_genes.tsv
featureCounts_TEs.tsv


title: IMM cells, 0 minute LPS stimulation Rep 1

description:
RawCountFile_rsemgenes.txt
1_R01


title: IMM cells, 0 minute LPS stimulation Rep 3

description:
RawCountFile_rsemgenes.txt
3_R03


title: IMM cells, 30 minute LPS Stimulation Rep 2

description:
RawCountFile_rsemgenes.txt
DESeq2_30min_output.txt
5_R32


title: BdNRPD1_WT, rep1

description:
Bd04_AFVA-86
featureCounts_genes.tsv
featureCounts_TEs.tsv


title: Mouse 42, Quadriceps Muscle, DBA/2J, Vegetarian

value: Vegetarian


title: lymph node tissue (FFPE) from patient C08

tag: alcohol abuse (0 = no, 1 = yes)

tag: p16 status (0 = negative (<70%), 1 = positive (>70%))

tag: t


title: IMM cells, 30 minute LPS Stimulation Rep 1

description:
RawCountFile_rsemgenes.txt
DESeq2_30min_output.txt
4_R31


title: Con_13wk_rep2

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

description: 10X Genomics

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification: Cell Ranger v6.1.2 (10X Genomics)
Clustering and gene expression analysis: Seurat v4.3
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone

extract_protocol:
Soft tissues and periosteum were removed from freshly collected femurs and tibiae. Bone marrow was flushed out by PBS with 1% BSA. Bones were reduced in fragments and digested with sequential incubations of LiberaseTM (1 Wunsch unit/mL) in HBSS buffer and 5 mM EDTA solution in Mg2+- and Ca2+-free PBS (4 times each for 20 min at 37 ºC). Cells were resuspended in sorting buffer (2 mM EDTA in PBS with 0.5% BSA) and passed through a 70 µm strain. Biotinylated antibodies against CD45, CD45R, CD71, TER-119, CD5, CD11b, Gr-1, Ly-6B.2, and CD3e, and anti-biotin magnetic beads were used to remove hematopoietic cells through columns containing ferromagnetic spheres. Eluted cells were resuspended in PBS with 0.5% BSA, counted and used for scRNA-sequencing assays.
Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) was used for library preparation according to manufactur's instructions. Libraries were sequenced using a NextSeq 2000 sequencer.

tag: tissue

value: Bone

value: Bone and bone marrow cells

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl

value: 13 weeks

value: Female


title: IMM cells, 0 minute LPS stimulation Rep 2

description:
RawCountFile_rsemgenes.txt
2_R02

value: IMM

value: Immortalized mouse macrophages

value: WT


title: SOXCOsxCre_13wk_rep2

description: 10X Genomics

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl OsxCre

tag: Sex


title: lymph node tissue (FFPE) from patient C05

value: lymph node tissue (FFPE)

value: hnCUP

tag: g


title: VCOV_s06_P3,scRNA-seq

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Research Hospital

description:
10x Genomics
Sample 28

data_processing:
The scRNA-seq demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Hierarchical Data Format 5 File (h5 files)

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats of HDs (n=6) or from 6 healthy vaccinated subjects through Lympholyte®-H Cell Separation density gradient solution (Cedarlane Laboratories, Burlington, North Carolina, USA) according to the manufacturer’s instruction. In vitro experiments were performed on freshly isolated PBMCs, with a viability greater than 95%, while single-cell ones on PBMCs previously frozen in Fetal Bovine Serum (FBS) supplemented with 10% of the cryoprotective Dimethyl Sulfoxide (DMSO).
Libraries for scRNA-seq were prepared using the Chromium Single Cell Platform with a Single-Cell 5′ Library and Gel Bead Kit (10X Genomics, PE-1000006). Thawed PBMC samples were evaluated for viability prior to scRNA-seq analysis, and all were ≥95% viable. Cells were resuspended in a volume equivalent to 10,000 target cells for each sample, and were individually loaded onto a Chromium single-cell controller (10X Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were then lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Complementary DNAs (cDNA) were generated and split to generate the additional  γδ scTCR-seq libraries. Complementary DNAs were amplified, and the quality was assessed using an Agilent 4200 Tapestation. The scRNA-seq libraries were sequenced using an Illumina Novaseq6000 sequencer with a paired-end 150-bp (PE150) reading strategy (performed by CapitalBio Technology).
scRNA-seq paired with γδTCR-seq

value: blood

value: PBMC

tag: age

value: 25-50 years old

tag: gender

value: Male


title: SOXCOsxCre_13wk_rep1

description: 10X Genomics

tag: cell type


title: Mouse 32, Quadriceps Muscle, A/J, Vegan

value: Quadriceps Muscle

tag: strain

value: A/J

value: male

value: 12 week old

tag: diet

value: Vegan


title: BdNRPD1_WT, rep3

description:
Bd06_AFVA-88
featureCounts_genes.tsv
featureCounts_TEs.tsv

value: leaves


title: Con_13wk_rep1

description: 10X Genomics

value: Bone

value: Bone and bone marrow cells

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl

value: 13 weeks

value: Female


title: VCOV_s06_P0,scRNA-seq

description:
10x Genomics
Sample 26

tag: treatment


title: Mouse 30, Quadriceps Muscle, A/J, Vegan


title: SOXCOsxCre_7wk_rep1

description: 10X Genomics

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl OsxCre

value: 7 weeks


title: SOXCOsxCre_7wk_rep2

description: 10X Genomics


title: Mouse 27, Quadriceps Muscle, A/J, Vegetarian

value: Vegetarian


title: Con_7wk_rep1

description: 10X Genomics


title: Con_7wk_rep2

description: 10X Genomics


title: WT, replicate 1, bulk RNAseq

value: embryo

value: 48 hpf

value: wild type


title: Mouse 33, Quadriceps Muscle, DBA/2J, American

value: Quadriceps Muscle

value: American


title: P5

city: Tampere

first: Kirsi

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere university

description: transcript_level_raw_counts_kallisto.txt

data_processing:
Tools provided by Babraham bioinformatics group (FastQC v0.11.7, TrimGalore! v0.5.0) were used in quality control for both RRBS and RNA-seq fastq-files
The trimmed RRBS files were mapped using Bismark v0.19.1 followed by the differential methylation calling in regional level ( 1000 bp tiles) in R-enviroment (version 3.5.2) using methylKit v1.8.1. Only CpG-sites with at least 10 reads coverage were included.
The trimmed RNA-seq files were mapped using using kallisto v0.44.0
Genome_build: hg38 (UCSC)
Supplementary_files_format_and_content: txt-files that contain feature matrices for the samples: 1) methylation percentage matrix for the 1000 bp regions ("tiles") produced by methylKit (for region level differential methylation analysis)  and 2) transcript-level raw count matrix from kallisto that is compatible with tximport and can be used to differential expression analysis in transcript level or gene level.

source_name: Choroid plexus tumor

extract_protocol:
DNA was isolated with QIAMP DNA mini kit (QIAGEN). RNA was isolated using mirVana isolation kit (Invitrogen).
Library construction and sequencing were performed at the Beijing Genomics Institute (BGI), Hong Kong

value: Chroid Plexus tumor tissue

tag: subtype

value: Choroid plexus papilloma


title: VCOV_s05_P4,scRNA-seq

description:
10x Genomics
Sample 25

value: blood

value: PBMC

value: 25-50 years old


title: P3

value: Atypical choroid plexus


title: P4


title: Mouse 25, Quadriceps Muscle, A/J, Vegetarian

value: A/J

value: male

value: 12 week old


title: Mouse 24, Quadriceps Muscle, A/J, Mediterranean

value: Mediterranean


title: VCOV_s05_P3,scRNA-seq

description:
10x Genomics
Sample 24

value: Female


title: Mouse 22, Quadriceps Muscle, A/J, Mediterranean


title: M3

source_name: Medulloblastoma

value: Medulloblastoma tumor tissue

value: Classic medulloblastoma


title: VCOV_s05_P2,scRNA-seq

description:
10x Genomics
Sample 23


title: M2


title: VCOV_s05_P1,scRNA-seq

description:
10x Genomics
Sample 22


title: M1


title: Mouse 2, Quadriceps Muscle, C57BL/6J, American


title: VCOV_s06_P1,scRNA-seq

description:
10x Genomics
Sample 27

value: Male


title: VCOV_s05_P0,scRNA-seq

description:
10x Genomics
Sample 21


title: A1

source_name: ATRT

value: AT/RT tumor tissue


title: Mouse 18, Quadriceps Muscle, A/J, American

value: Quadriceps Muscle


title: VCOV_s04_P4,scRNA-seq

description:
10x Genomics
Sample 20


title: 5_DNA, P4

description: methylation_matrix_with_window_size_1000_read.thr10.txt


title: Mouse 17, Quadriceps Muscle, A/J, American

value: American


title: 16_DNA, P3

value: Chroid Plexus tumor tissue


title: 2_DNA, P2

value: Choroid plexus carcinoma


title: Mouse 16, Quadriceps Muscle, C57BL/6J, Vegan

value: Vegan


title: P1

value: Choroid plexus papilloma


title: VCOV_s04_P2,scRNA-seq

description:
10x Genomics
Sample 18

value: blood

value: PBMC

value: 25-50 years old


title: P2


title: Mouse 13, Quadriceps Muscle, C57BL/6J, Vegan

value: male


title: VCOV_s04_P1,scRNA-seq

description:
10x Genomics
Sample 17


title: 1_DNA, P1


title: 18_DNA, M1


title: 20_DNA, M2


title: 3_DNA, A2


title: VCOV_s04_P0,scRNA-seq

description:
10x Genomics
Sample 16


title: Mouse 12, Quadriceps Muscle, C57BL/6J, Vegetarian

value: 12 week old

value: Vegetarian


title: 4_DNA, A1


title: Mouse 1, Quadriceps Muscle, C57BL/6J, American


title: VCOV_s03_P4,scRNA-seq

description:
10x Genomics
Sample 15


title: A2


title: Mouse 9, Liver, C57BL/6J, Vegetarian

source_name: Liver

value: Liver


title: 21_DNA, P5


title: control/hifu, pooled replicate 2 [B1]

city: Los Angeles

first: Joshua

last: Berlind

address: 1425 San Pablo St

institute: University of Southern California

description: 10X Genomics

data_processing:
Data alignment and QC was conducted through the University of Southern California Center for Advanced Research Computing (CARC) using the Cell Ranger count Feature Barcode Analysis pipeline (10X Genomics) for concurrent UMI identification, reference genome (human hg38 genome) alignment, and HTO assignment. Samples were demultiplexed using the HTODemux pipeline in R version 4.0.1107. Data was further processed using Seurat v4.0 to remove cells with < 200 detectable genes and > 20% mitochondrial rate108. We retrieved roughly 2500 high quality cells with a depth of >10,000 reads/cell.
cell hash sequences for demultiplexing- sham: GTCCGACTAATAGCT; hifu: CAGGTTGTTGTCATT
Assembly: hg38
Supplementary files format and content: tab separated values files and matrix files

source_name: neural

extract_protocol:
Organoids were dissociated for single-cell RNA sequencing as described with minor modifications106. In brief, organoids were incubated in Papain (Worthington LK003176) with DNase1 (Worthington LK003170) reconstituted per manufacturer instructions for 60 minutes at 37⁰C with gentle shaking at 27 rpm with regular pipetting. Single-cell suspension was added to Earle’s Balanced Salt Solution (EBSS) with Ovomucoid Inhibitor (Worthington LK003182) and DNase1, pelleted, resuspended in ice-cold Neurobasal-A (Invitrogen) with 0.2% bovine serum albumin (BSA), and filtered through 40 µM Flowmi tips (Sigma BAH136800040-50EA). Cell count and viability was determined by Trypan Blue staining using a hemocytometer. Cells were labeled with hashtag-oligonucleotide (HTO) antibodies (Biolegend TotalSeq-B, 405287, 405289, 405291) and libraries were prepared following manufacturer protocols (10X Genomics, CG000206 Rev D).
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding for Cell Surface Protein); PN-1000128, PN-1000079, PN-1000127, PN-1000213

value: neural

tag: cell line

value: organoid

value: neurons, glia

tag: genotype

value: wildtype

value: sham/7d injured


title: control/hifu, pooled replicate 1 [A1]

description: 10X Genomics


title: VCOV_s03_P3,scRNA-seq

description:
10x Genomics
Sample 14

value: Male


title: hifu organoid replicate 3

description: hifu 3

data_processing:
Reads were aligned to the hg38 transcriptome using aligner STAR (v.2.5.3a)
Genes were annotated using the GENCODE29_v2 comprehensive gene annotation. Post-alignment quality control was performed in PartekFlow. To identify differentially expressed genes, the DESeq2 (v3.5) package in PartekFlow was used to estimate dispersion and size factors, fit the data to a local model, and generate differential statistics using the Wald hypothesis test.
Assembly: hg38
Supplementary files format and content: excel files of unfiltered non-normalized gene counts for each sample

extract_protocol:
RNA was extracted using QIAGEN RNeasy Kits according to the manufacturer's instructions.
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
Messenger RNA was extracted using NEBNext Poly(A) mRNA Magenetic Isolation Module according to the manufacturer’s protocol, and 3’ RNA-Seq library were prepared using the 3’-Digital Gene Expression RNAseq Library Kit (Amaryllis Nucleics). Libraries were sequenced on an Illumina NextSeq 500 machine (10-25M reads, single-end, 80 bp).

value: HIFU


title: VCOV_s04_P3,scRNA-seq

description:
10x Genomics
Sample 19

value: Female


title: Mouse 8, Liver, C57BL/6J, Mediterranean

value: Mediterranean


title: hifu organoid replicate 2

description: hifu 2


title: VCOV_s03_P2,scRNA-seq

description:
10x Genomics
Sample 13


title: sham organoid replicate 3

description: sham 3

value: sham


title: Mouse 64, Liver, SJL, Vegan

value: SJL

value: Vegan


title: VCOV_s03_P0,scRNA-seq

description:
10x Genomics
Sample 11

value: blood

value: PBMC

value: 25-50 years old


title: CD4T cells, rs6861(TT) genotyped donor 4, anti-CD3/CD28/IL-7

city: Amsterdam

first: Carla

last: Ribeiro

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Amsterdam UMC

data_processing:
During reverse transcription, each sample was tagged with a unique ID, and each RNA molecule was tagged with a unique molecular identifier (UMI). Samples were then pooled into one tube for downstream processing.
Quality control of the library preparationwas performed using capillary electrophoresis (Agilent DNA 7500 Chip) and libraries were quantified using qPCR. Based on quality of the inserts and concentration measurements, libraries were pooled in equimolar ratios and sequenced on a NextSeq 500 sequencing instrument (Illumina) with 100 bp read length for read 1 and 27 bp for read 2.
Raw data was demultiplexed  and fastq files generated using the bcl2fastq Conversion Software (Illumina). The Demultiplex QIAseq UPX 3' reads tool of Qiagen's CLC Genomics Workbench 21.0.1 was used to demultiplex raw sequencing reads according to sample indices and Quantify QIAseq UPX 3' workflow was used to process demultiplexed sequencing reads with default settings.
Reads were then mapped to the human genome (GRCh38) and annotated using the NCBI RefSeq GRCh38.p12 annotation.
Read count extraction and normalization were performed using the CLC Genomics Workbench 21.0.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes normalized counts per million for each sample

source_name: Primary cell

extract_protocol:
RNA was extracted and harvested using the miRNAeasy micro kit (Qiagen) according to manufacturers instructions. 10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the QIAseq UPX 3' Transcriptome kit according to manufacturer's instructions.

treatment_protocol: Fluorescence-activated cell sorted CD4T cells (from peripheral blood mononuclear cells; primary human material stored in liquid nitrogen) were plated at 250,000 cells/well/condition in 96-well round-bottom plates in 100 uL/well T-cell medium (Roswell Park Memorial Institute [RPMI; Sigma-Aldrich] medium containing 10% fetal bovine serum [FBS; Biological Industries] and 1% penicillin/streptomycinm [P/S; Invitrogen]) and left untreated (in T-cell medium) or stimulated for 16 hours with T-cell medium containing 0.06 ug/mL anti-CD3 (Sanquin), 1 ug/mL anti-CD28 (Sanquin), and 2 ng/mL IL-15 (PeproTech) 2 ng/mL IL-7 (PeproTech) where appropriate.

value: Primary cell

value: CD4T cell


title: Mouse 63, Liver, SJL, Vegan

value: Liver

value: male

value: 12 week old


title: sham organoid replicate 2

description: sham 2

value: neural

value: organoid

value: neurons, glia

value: wildtype


title: sham organoid replicate 1

description: sham 1


title: 15_DNA, M3

value: Medulloblastoma tumor tissue

value: Classic medulloblastoma


title: CD4T cells, rs6861(TT) genotyped donor 4, anti-CD3/CD28/IL-15


title: CD4T cells, rs6861(TT) genotyped donor 4, anti-CD3/CD28


title: VCOV_s02_P3,scRNA-seq

description:
10x Genomics
Sample 9

source_name: blood

value: Male


title: Mouse 59, Liver, SJL, Vegetarian

value: SJL

value: Vegetarian


title: CD4T cells, rs6861(TT) genotyped donor 3, anti-CD3/CD28/IL-7


title: Mouse 57, Liver, SJL, Vegetarian


title: CD4T cells, rs6861(TT) genotyped donor 3, anti-CD3/CD28/IL-15


title: Mouse 54, Liver, SJL, Mediterranean

value: Mediterranean


title: VCOV_s02_P1,scRNA-seq

description:
10x Genomics
Sample 7

value: blood

value: PBMC


title: Mouse 7, Liver, C57BL/6J, Mediterranean


title: hifu organoid replicate 1

description: hifu 1

value: HIFU


title: VCOV_s03_P1,scRNA-seq

description:
10x Genomics
Sample 12

value: 25-50 years old


title: Mouse 53, Liver, SJL, Mediterranean

value: Liver


title: VCOV_s02_P0,scRNA-seq

description:
10x Genomics
Sample 6


title: CD4T cells, rs6861(TT) genotyped donor 3, untreated

value: Primary cell

value: CD4T cell

value: untreated


title: Mouse 50, Liver, SJL, American

value: male

value: 12 week old

value: American


title: sample38_CT_MenACWY_+ve

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

data_processing:
The base calling and demultiplexing were performed live using original ONT software.
Reads were aligned to the reference transcriptome (version GRCh38) using minimap2 (secondary score ratio -p 0.99)
The transcript abundances were estimated from the output bam files using Salmon in alignment-based mode
Transcripts detected in less than 50 % of the samples from at least one of the study groups were removed. Ribosomal RNA (rRNA), mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (counts per million) for each transcript for each sample

source_name: Whole blood

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0) and at SARS-CoV-2 diagnosis (CT). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
PCR-cDNA libraries were prepared using the SQK-PCS110 PCR-cDNA-sequencing kit following the standard Oxford Nanopore Technologies (ONT) protocol. Samples were barcoded (#1-8) and sequenced on PromethION. 2 samples were loaded per flow cell (15 ng each), with the paired samples run together and the unpaired samples randomly split into pairs

value: Whole blood

tag: timepoint

value: CT

tag: vaccine

value: MenACWY

tag: naat result

value: +ve

tag: participant number


title: sample37_CT_MenACWY_+ve

value: Female


title: sample39_CT_MenACWY_+ve

value: Male


title: VCOV_s02_P4,scRNA-seq

description:
10x Genomics
Sample 10

value: blood


title: VCOV_s01_P4,scRNA-seq

description:
10x Genomics
Sample 5

value: PBMC


title: sample36_CT_MenACWY_+ve


title: CD4T cells, rs6861(CC) genotyped donor 4, anti-CD3/CD28/IL-7


title: Mouse 49, Liver, SJL, American

data_processing:
Quality control with fastQC to identify problems
Trim adapters with trimGalore, illumina adapters specified
Align to GRCm39 using hisat2. Weaker alignment observed for A/J, DBA/2J, SJL when comparing to C57BL6 reference, therefore mismatch penalty relaxed.
Quantification using htseq, fractional counting method
Assembly: GRCm39
Supplementary files format and content: comma separated values (.csv) file contains processed counts for each sample
Supplementary files format and content: tab-delimited text file contains transcripts per million (TPMs) for each sample

extract_protocol:
Frozen tissue homogenized via pulverization. TRIzol added to homogenized frozen tissue to extract RNA. After centifugation to remove lipid and cell debris, we followed the Qiagen Rneasy Micro Kit to isolate mRNA species. We verified the RNA integrity via Tape Station.
TruSeq Stranded mRNA Library Prep Kit

value: SJL


title: sample35_CT_ChAdOx1_+ve


title: CD4T cells, rs6861(CC) genotyped donor 4, anti-CD3/CD28/IL-15


title: Mouse 48, Liver, DBA/2J, Vegan

value: Vegan


title: VCOV_s01_P3,scRNA-seq

description:
10x Genomics
Sample 4

value: 25-50 years old


title: sample34_CT_MenACWY_+ve


title: VCOV_s01_P2,scRNA-seq

description:
10x Genomics
Sample 3


title: CD4T cells, rs6861(TT) genotyped donor 4, untreated

value: Primary cell


title: Mouse 45, Liver, DBA/2J, Vegan

value: Liver


title: VCOV_s02_P2,scRNA-seq

description:
10x Genomics
Sample 8


title: CD4T cells, rs6861(TT) genotyped donor 3, anti-CD3/CD28

value: CD4T cell


title: sample33_CT_ChAdOx1_+ve


title: CD4T cells, rs6861(CC) genotyped donor 4, untreated

value: untreated


title: Mouse 43, Liver, DBA/2J, Vegetarian

value: male

value: 12 week old

value: Vegetarian


title: VCOV_s01_P1,scRNA-seq

description:
10x Genomics
Sample 2


title: sample32_CT_MenACWY_+ve

value: Whole blood

value: CT


title: CD4T cells, rs6861(CC) genotyped donor 4, anti-CD3/CD28


title: Mouse 42, Liver, DBA/2J, Vegetarian


title: CD4T cells, rs6861(CC) genotyped donor 3, anti-CD3/CD28/IL-7


title: CD4T cells, rs6861(CC) genotyped donor 3, anti-CD3/CD28/IL-15


title: sample30_CT_MenACWY_+ve

value: MenACWY

value: +ve


title: Mouse 39, Liver, DBA/2J, Mediterranean

value: Mediterranean


title: sample31_CT_MenACWY_+ve

value: Female


title: VCOV_s01_P0,scRNA-seq

description:
10x Genomics
Sample 1

value: blood

value: PBMC


title: 47H1 treatment on collagen from patient 30214, sample 46

first: Lee

middle: Benjamin

last: Rivera

address: 333 Oyster Point Blvd.

department: Biology

institute: NGM Bio

data_processing:
For sequencing alignment, RNA-seq data raw reads were filtered using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Mapping of filtered reads to UCSC hg19 genome sequences was performed using STAR (v2.6.0a). Counts were created using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to generate normalized counts and execute DEG analysis.
Assembly: hg19
Supplementary files format and content: gene expression read counts in tabular format

source_name: monocyte-derived dendritic cells

extract_protocol:
RNA isolation - RNA isoloation was perfomed using the RNEasy mini kit following manufacturer's instructions (Qiagen).
Sequencing - Total RNA was prepared for sequencing using the Illumina stranded mRNA library prep kit and sequenced on an Illumina NovaSeq SP V1 (100bp single-end reads and an average of 25 million reads were generated for each sample).

treatment_protocol: Generation of monocyte derived dendritic cells - Dendritic cells were derived from monocytes, which were purified from PBMCs using a human pan monocyte isolation kit (Miltenyi). DCs were generated by culturing monocytes in X-VIVO 15 media (Lonza) containing 50 ng/mL recombinant human GM-CSF (Peprotech) and 50 ng/mL recombinant human IL-4 (Peprotech) for 5-6 days. 96-well tissue culture plates (Corning) were coated with 5 µg/mL human collagen type 1 (Millipore Sigma) in PBS overnight at 4° C, then washed in PBS. 1 x 105 DCs were added to the plates with anti-LAIR1 or an isotype control antibody at the listed concentrations then incubated for 2 days at 37° C. Conditioned media was collected the next day and analyzed using Luminex (ProcartaPlex, ThermoFisher)

value: monocyte-derived dendritic cells

tag: patientid


title: 47H1 treatment on collagen from patient 20961, sample 50


title: sample29_CT_MenACWY_-ve

tag: tissue

value: -ve


title: 47H1 treatment on collagen from patient 30214, sample 54


title: sample28_CT_MenACWY_-ve

tag: Sex

value: Male


title: Mouse 34, Liver, DBA/2J, American

value: Liver

value: American


title: CD4T cells, rs6861(CC) genotyped donor 2, anti-CD3/CD28/IL-7

value: Primary cell

value: CD4T cell


title: control isotype antibody treatment on collagen from patient 20961, sample 51

value: Isotype


title: Mouse 38, Liver, DBA/2J, Mediterranean

value: male

value: 12 week old


title: Mouse 32, Liver, A/J, Vegan

value: A/J

value: Vegan


title: CD4T cells, rs6861(CC) genotyped donor 3, untreated

value: untreated


title: control isotype antibody treatment on collagen from patient 30214, sample 47


title: sample27_CT_MenACWY_-ve

value: Whole blood

value: CT

value: MenACWY


title: CD4T cells, rs6861(CC) genotyped donor 3, anti-CD3/CD28


title: Mouse 33, Liver, DBA/2J, American


title: CD4T cells, rs6861(CC) genotyped donor 2, anti-CD3/CD28/IL-15


title: CD4T cells, rs6861(CC) genotyped donor 2, anti-CD3/CD28


title: Mouse 30, Liver, A/J, Vegan


title: sample25_CT_ChAdOx1_+ve

value: +ve


title: hiPSC induced neurons-15day-well2

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
see our paper in bioRxiv 2022.06.15.495952; doi: https://doi.org/10.1101/2022.06.15.495958
Assembly: hg19
Supplementary files format and content: matrix of gene expression for each cell

source_name: cells

value: cells

value: hiPSC induced neurons-15day


title: Mouse 27, Liver, A/J, Vegetarian

first: Mete

last: Civelek

address: Center for Public Health Genomics, PO Box 800717

institute: University of Virginia

value: Vegetarian


title: sample26_CT_ChAdOx1_+ve

value: Female


title: CD4T cells, rs6861(CC) genotyped donor 2, untreated


title: sample24_CT_ChAdOx1_+ve

value: Male


title: hiPSC induced neurons-15day-well1


title: Mouse 25, Liver, A/J, Vegetarian

value: Liver


title: CD4T cells, rs6861(TT) genotyped donor 2, anti-CD3/CD28/IL-7

value: Primary cell

value: CD4T cell


title: sample23_CT_ChAdOx1_-ve

value: -ve


title: hiPSC induced neurons-21day-astrocytes-co-culture-well2


title: Mouse 24, Liver, A/J, Mediterranean

value: male

value: 12 week old

value: Mediterranean


title: sample22_D0_ChAdOx1_-ve


title: hiPSC induced neurons-21day-astrocytes-co-culture-well1


title: sample21_CT_ChAdOx1_-ve


title: CD4T cells, rs6861(TT) genotyped donor 2, anti-CD3/CD28


title: Mouse 22, Liver, A/J, Mediterranean

value: A/J


title: control isotype antibody treatment on collagen from patient 20356, sample 55

value: monocyte-derived dendritic cells

value: Isotype


title: sample20_D0_ChAdOx1_-ve

value: Whole blood


title: CD4T cells, rs6861(TT) genotyped donor 2, untreated

value: untreated


title: Mouse 2, Liver, C57BL/6J, American

value: American


title: CD4T cells, rs6861(TT) genotyped donor 1, anti-CD3/CD28/IL-7


title: hiPSC induced astrocytes-well1

value: cells

value: hiPSC induced astrocytes


title: Mouse 18, Liver, A/J, American


title: hiPSC induced astrocytes-well2


title: hiPSC induced neurons-21day-well2

value: hiPSC induced neurons-21days


title: hiPSC induced neurons-21day-well1


title: Mouse 17, Liver, A/J, American


title: CD4T cells, rs6861(TT) genotyped donor 1, anti-CD3/CD28


title: sample18_CT_MenACWY_-ve

value: CT

value: MenACWY

value: Female


title: Mouse 16, Liver, C57BL/6J, Vegan

value: Liver

value: Vegan


title: sample19_CT_ChAdOx1_-ve

value: -ve

value: Male


title: sample17_CT_MenACWY_-ve


title: CRL-3038, positive control

data_processing:
*library strategy: CUT&RUN
TrimGalore! version 0.6.7 was used to trim adapter reads, discarding reads with a length of less than 25 bp.
Reads were aligned to hg38 using bowtie2 version 2.4.5 and the –dovetail flag.
Duplicated reads were removed using Picard MarkDuplicates version 2.27.1
Regions overlapping with the regions described by Nordin et al. (Nordin et al, 2023) were removed using bedtools intersect version 2.29.1.
Afterwards, the reads were divided in reads with a length shorter or equal to 120 bp and reads longer than 120 bp with samtools view (version 1.8).
MACS3 version 3.0.0.bl was used to call the peaks for both fragment lengths.
Peaks located outside of the canonical chromosomes as well as on chrX or chrY were filtered out.
Peaks that overlapped with peaks in the negative control samples (input DNA) were removed using bedtools intersect version 2.29.1. Positive and negative controls were only filtered for canonical chromosomes.
Assembly: hg38
Supplementary files format and content: narrowPeak files, peaks filtered as described above

growth_protocol: Cells were grown according to ATCC protocol for each cell line

extract_protocol:
Cells were harvested by removing the media with cells from flasks and centrifuging the media 175G for 7 minutes. Supernatant was removed and cells washed once with PBS followed by centrifugation in 175G for 7 minutes. Cells were counted and 100,000 cells were collected for each reaction.
CUT&RUN was performed using Cell Signaling Technology CUT&RUN assay kit #86652.

value: Atypical Teratoid Rhabdoid Tumor cells

tag: antibody

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb 9751


title: CD4T cells, rs6861(TT) genotyped donor 1, untreated

value: Primary cell

value: CD4T cell


title: CD4T cells, rs6861(TT) genotyped donor 2, anti-CD3/CD28/IL-15


title: CRL-3021, negative control

value: Medulloblastoma cells

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CUT&RUN) 66362


title: Mouse 13, Liver, C57BL/6J, Vegan

value: male

tag: age

value: 12 week old


title: CD4T cells, rs6861(CC) genotyped donor 1, anti-CD3/CD28/IL-7


title: sample16_D0_MenACWY_-ve

value: Whole blood


title: Mouse 12, Liver, C57BL/6J, Vegetarian

value: Vegetarian


title: CRL-3021, positive control


title: sample15_CT_ChAdOx1_+ve

value: CT

value: +ve


title: CD4T cells, rs6861(CC) genotyped donor 1, anti-CD3/CD28/IL-15


title: CRL-3021, rep B, NEUROD1 (CUT&RUN)

value: NEUROD1 (#PA5-47381, Invitrogen)


title: sample14_D0_ChAdOx1_+ve


title: CD4T cells, rs6861(CC) genotyped donor 1, anti-CD3/CD28


title: CD4T cells, rs6861(TT) genotyped donor 1, anti-CD3/CD28/IL-15


title: sample13_CT_MenACWY_-ve

value: MenACWY

value: Female


title: CD4T cells, rs6861(CC) genotyped donor 1, untreated

value: untreated


title: CRL-3038, rep B, NEUROD1 (CUT&RUN)


title: Mouse 8, Brown Adipose, C57BL/6J, Mediterranean

source_name: Brown Adipose

value: Brown Adipose

value: Mediterranean


title: CRL-3021, rep A, NEUROD1 (CUT&RUN)


title: Mouse 7, Brown Adipose, C57BL/6J, Mediterranean


title: sample11_CT_ChAdOx1_-ve

value: -ve

value: Male


title: Mouse 64, Brown Adipose, SJL, Vegan

value: SJL

value: Vegan


title: WTCHG_900295_295_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

data_processing:
Alignments were performed using bowtie with up to 2 mismatches in best strata mode, and bowtie2 with 2 gaps permitted
Reads were first aligned to the non-coding transcriptome. The bowtie indexes for the non-coding RNAome were built by merging fasta files from the following databases: miRbase (miRNAs), SnOPY (snoRNAs), trRNA_db (tRNAs), RefSeq (snRNAs, yRNAs, vault RNAs, lncRNAs.
Non-aligned reads were then aligned to the mRNA transcriptome, and antisense to the non-coding and mRNA transcriptome
All other reads were collapsed using a "gene_union" approach like those employed in seqCluster and mmQuant.
sRNA features were removed if they did not have an abundance of at least 5 counts per million in at least 20% of samples.
Assembly: GRCh38
Supplementary files format and content: txt file containing raw read counts for each gene for each sample

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
Small RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina (catalog #E7330) and run on a single flow cell target of 300 million reads) on the NexTSeq platform using the 75SR configuration with the aim of achieving 5.2 million reads per sample.


title: sample10_CT_MenACWY_-ve


title: WTCHG_900295_296_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_900295_294_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: CRL-3036, rep B, NEUROD1 (CUT&RUN)

value: Atypical Teratoid Rhabdoid Tumor cells


title: Mouse 63, Brown Adipose, SJL, Vegan

value: male


title: sample09_D0_MenACWY_-ve


title: Mouse 59, Brown Adipose, SJL, Vegetarian

value: 12 week old


title: CRL-3038, rep A, NEUROD1 (CUT&RUN)


title: WTCHG_900295_293_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood


title: sample08_CT_MenACWY_-ve


title: CRL-3020, rep B, NEUROD1 (CUT&RUN)


title: Mouse 1, Liver, C57BL/6J, American

value: Liver

value: American


title: Mouse 57, Brown Adipose, SJL, Vegetarian

value: Vegetarian


title: Mouse 9, Brown Adipose, C57BL/6J, Vegetarian


title: CRL-3036, rep A, NEUROD1 (CUT&RUN)

value: NEUROD1 (#PA5-47381, Invitrogen)


title: sample07_D0_MenACWY_-ve

value: MenACWY


title: CRL-3020, rep A, NEUROD1 (CUT&RUN)


title: sample12_D0_MenACWY_-ve

value: Female


title: Mouse 54, Brown Adipose, SJL, Mediterranean


title: WTCHG_900295_290_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: +ve


title: WTCHG_900295_292_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: shSRSF1,nascent

city: Hefei

first: Yan

last: Yang

state: Anhui

address: No.373 Huangshan Road

institute: University of Science and Technology of China

data_processing:
Raw sequence reads were trimmed for adaptor using cutadapt.
Trimmed reads were mapped to GRCh38/hg38 using bowtie2 and only uniquely mapped reads were retained.
Density of GRO-seq was then calculated  for plus and minus strands and normalized using the total uniquely mapped reads using bamCoverage in deepTools.
Bedtools was then used to calculate the signal density of GRO-seq on genes.
Assembly: hg38
Supplementary files format and content: bigwig files displaying the normalized signal of GRO-seq along the genome

molecule: nuclear RNA

growth_protocol: cells were cultured with DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S).

extract_protocol:
The nascent RNA was extracted by Trizol reagent (Invitrogene), according to the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SRSF1 knockdown


title: sample06_CT_ChAdOx1_-ve

value: CT


title: Mouse 53, Brown Adipose, SJL, Mediterranean

city: Charlottesville

value: Brown Adipose

value: Mediterranean


title: sample05_D0_ChAdOx1_-ve

value: -ve


title: WTCHG_900295_289_CT_MenACWY_+ve

description:
small RNA
stage2

value: Male


title: sample04_CT_MenACWY_+ve


title: Mouse 50, Brown Adipose, SJL, American

value: SJL


title: PDO71 NKL54 rep3 [1740R-251-18]

city: Basel

first: Emanuela

last: Kerschbamer

state: Basel Stadt

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
llumina universal adapters were removed with fastx_clipper from FastQC
Transcripts were quantified with salmon and summarized at the gene level through Bioconductor package tximeta.
Genes with raw counts mean <10 between each condition replicates were removed from the analysis.
Differential expression analysis was performed using DESeq2 with Wald test for significance.
Assembly: GRCh38
Supplementary files format and content: TPMs from Salmon
Supplementary files format and content: Raw counts from Salmon

source_name: Colon cancer

growth_protocol: PDOs were cultured in DMEM/F12 advanced medium  (DMEM/F12 (Gibco), 100 U/mL penicillin/streptomycin (Gibco), Primocin (InvivoGen), 2 mM GlutaMAX (Gibco), 1x B27 (Gibco), 100 nM prostaglandin E2 (Tocris), 0.5 μg/mL R-spondin (Peprotech), 4mM nicotinamide (Sigma), 10 nM gastrin I (Sigma), 50 ng/ml EGF (Peprotech), 100 ng/ml Noggin (Peprotech)).

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit (Invitrogen) following the manufacturer’s instructions
NEBnext PolyA selection+Ultra II Directional library preparation kit

treatment_protocol: PDOs were treated with SAHA (5µM) or NKL54 (10µM) or with the same volume of DMSO for 6 hours

value: Colon cancer

value: patient-derived organoid

value: Patient 71

value: NKL54 10µM

tag: replicate

tag: time

value: 6 hours


title: sample03_D0_MenACWY_+ve

value: Whole blood


title: WTCHG_900295_288_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: Mouse 49, Brown Adipose, SJL, American

tag: strain

value: male

value: 12 week old

value: American


title: WTCHG_900295_287_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY

value: +ve

value: Female


title: PDO71 SAHA rep3 [1740R-251-17]

tag: cell type

value: SAHA 5µM


title: Mouse 48, Brown Adipose, DBA/2J, Vegan

value: Brown Adipose

tag: diet

value: Vegan


title: PDO71 (control) rep 3 [1740R-251-16]

tag: treatment

value: DMSO


title: WTCHG_900295_286_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Male


title: sample02_CT_ChAdOx1_+ve

value: CT


title: sample01_D0_ChAdOx1_+ve


title: Mouse 43, Brown Adipose, DBA/2J, Vegetarian

value: Vegetarian


title: WTCHG_900295_285_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: PDO19 SAHA rep3 [1740R-251-14]

value: Colon cancer

tag: cell line

value: patient-derived organoid

value: Patient 19


title: WTCHG_900295_284_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood


title: PDO19 NKL54 rep3 [1740R-251-15]

value: NKL54 10µM

value: 6 hours


title: WTCHG_900295_291_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: No Template Control (GeoMx)

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

description:
NTC
DSP-1001660005544-A-A01_RIA1443A1-1
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

data_processing:
FASTQ converted to DCC files through Nanostring's pipeline
Assembly: GeoMx NGS Barcode sequencing
Supplementary files format and content: DCC files generated through Nanostring's pipeline
Library strategy: Spatial Transcriptomics

molecule: other

organism: synthetic construct

extract_protocol:
FFPE GeoMx Digital Spatial Profiling on CD31+ AOIs
GeoMx NGS library preparation with SeqCode Dual Index Primers

tag: genotype


title: Mouse 42, Brown Adipose, DBA/2J, Vegetarian

value: male

value: 12 week old


title: PDO19 (control) rep 3 [1740R-251-13]


title: Mouse 39, Brown Adipose, DBA/2J, Mediterranean

value: Mediterranean


title: WTCHG_900295_283_CT_ChAdOx1_+ve

description:
small RNA
stage2

tag: timepoint

value: +ve

value: Female


title: EPIC-LNP DMSO

city: Shanghai

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
*library strategy: circSHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to  experimental barcodes.
Analyses by CIRCshapemapper v2 (https://github.com/YangLab/circSHAPEmapper)
Assembly: Target RNA sequence
Supplementary files format and content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

extract_protocol:
For in vitro SHAPE-MaP, RNA are purified. About 50-200 ng of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for EPIC. Mn2+ was removed using RNAClean XP (Beckman Coulter) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.
circSHAPE-MaP libraries were prepared from 1 ng DNAs for circular RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Library was prepared by KAPA Hyper Prep Kit. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NovaSeq.

treatment_protocol: For in vitro SHAPE-MaP, 50-200 ng RNAs were obtained under each treatment, and then used for SHAPE-MaP reverse transcription by adding 1 uL (200 U/uL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for EPIC. Mn2+ was removed using RNAClean XP (Beckman Coulter) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.

tag: sample type

value: in vitro cDNA

value: EPIC-LNP DMSO samples only treated with DMSO


title: WTCHG_900295_282_CT_ChAdOx1_+ve

description:
small RNA
stage2

tag: vaccine

tag: naat result


title: PDO71 NKL54 rep2 [1740R-251-12]

value: Patient 71


title: shCtrl,nascent

value: WT


title: Mouse 38, Brown Adipose, DBA/2J, Mediterranean

value: Brown Adipose


title: EPIC-LNP NAI,repeat2

value: EPIC-LNP NAI samples modified by NAI in DMSO


title: PDO71 SAHA rep2 [1740R-251-11]

value: Colon cancer

value: SAHA 5µM


title: EPIC-LNP DC

value: EPIC-LNP DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: Mouse 34, Brown Adipose, DBA/2J, American

value: American


title: PDO71 (control) rep 2 [1740R-251-10]

value: patient-derived organoid

value: DMSO


title: Mouse 45, Brown Adipose, DBA/2J, Vegan

value: male

value: Vegan


title: WTCHG_900295_280_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: CT

value: MenACWY

tag: participant number


title: WTCHG_900295_279_CT_MenACWY_+ve

description:
small RNA
stage2

tag: tissue

value: +ve

value: Female


title: PDO19 NKL54 rep2 [1740R-251-09]

value: Patient 19

value: NKL54 10µM

value: 6 hours


title: WTCHG_900295_281_CT_ChAdOx1_+ve

description:
small RNA
stage2

tag: Sex

value: Male


title: Mouse 33, Brown Adipose, DBA/2J, American

value: Brown Adipose

value: 12 week old


title: Mouse 32, Brown Adipose, A/J, Vegan

value: A/J


title: PDO19 SAHA rep2 [1740R-251-08]

value: Colon cancer

value: SAHA 5µM


title: WTCHG_900295_278_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: EPIC-Cy5 DMSO

value: in vitro cDNA

value: EPIC-Cy5 DMSO samples only treated with DMSO


title: EPIC-Cy5 NAI,repeat2

value: EPIC-Cy5 NAI samples modified by NAI in DMSO


title: Mouse 30, Brown Adipose, A/J, Vegan

value: male

value: Vegan


title: EPIC-Cy5 DC

value: EPIC-Cy5 DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: Mouse 27, Brown Adipose, A/J, Vegetarian

value: Vegetarian


title: WTCHG_900295_277_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood

value: +ve


title: PDO19 (control) rep 2 [1740R-251-07]

value: patient-derived organoid

value: Patient 19

value: DMSO


title: EPIC-Cy5 NAI,repeat1


title: PDO71 NKL54 rep1 [1740R-251-06]

value: Patient 71

value: NKL54 10µM

value: 6 hours


title: WTCHG_900295_276_CT_MenACWY_+ve

description:
small RNA
stage2

value: CT

value: MenACWY

value: Female


title: Mouse 25, Brown Adipose, A/J, Vegetarian

value: Brown Adipose

value: A/J

value: 12 week old


title: EPIC-3 DMSO

value: in vitro cDNA

value: EPIC-3 DMSO samples only treated with DMSO


title: WTCHG_900295_275_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: Mouse 24, Brown Adipose, A/J, Mediterranean

value: male

value: Mediterranean


title: WTCHG_900295_274_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood

value: +ve


title: EPIC-LNP NAI,repeat1

value: EPIC-LNP NAI samples modified by NAI in DMSO


title: Mouse 22, Brown Adipose, A/J, Mediterranean


title: PDO19 NKL54 rep1 [1740R-251-03]

value: Colon cancer

value: patient-derived organoid

value: Patient 19


title: WTCHG_900295_273_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: Mouse 2, Brown Adipose, C57BL/6J, American

value: American


title: EPIC-3 NAI,repeat1

value: EPIC-3 NAI samples modified by NAI in DMSO


title: WTCHG_900295_272_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Male


title: Mouse 18, Brown Adipose, A/J, American


title: PDO19 SAHA rep1 [1740R-251-02]

value: SAHA 5µM

value: 6 hours


title: PDO19 (control) rep 1 [1740R-251-01]

value: DMSO


title: WTCHG_900295_271_CT+7_ChAdOx1_+ve

description:
small RNA
stage2

value: Female


title: EPIC-2 DMSO

value: in vitro cDNA

value: EPIC-2/EPIC-PKR DMSO samples only treated with DMSO


title: PDO71 NKL54 ATAC-seq rep2

data_processing:
ATAC-seq data were analyzed using the Nextflow (v21.10.4) nf-core atacseq pipeline (v1.2.1) for the preliminary steps, alignment on GRCh38 and peak calling.
Peaks called by MACS2 (v2.2.7.1) within the nf-core pipeline, were loaded in R and normalized using the library size as reads in peaks (libRiP) normalization within DiffBind.
The reciprocal normalization factors for each sample were used in deepTools, bamCoverage to produce bigwig files.
Assembly: GRCh38
Supplementary files format and content: bigwig, normalized

extract_protocol: Extraction and library preparation protocol was based on “An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. M Ryan Corces et  al., Nature Methods, 2017”

value: Patient 71

value: NKL54 10µM


title: Mouse 17, Brown Adipose, A/J, American

value: Brown Adipose

value: A/J

value: male

value: 12 week old


title: WTCHG_900295_270_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: CT

value: MenACWY

value: +ve


title: EPIC-2 DC

value: EPIC-2/EPIC-PKR DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: Mouse 16, Brown Adipose, C57BL/6J, Vegan

value: Vegan


title: WTCHG_900295_269_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: Male


title: PDO71 SAHA ATAC-seq rep2

value: Colon cancer

value: patient-derived organoid

value: SAHA 5µM

value: 6 hours


title: PDO71 SAHA rep1 [1740R-251-05]

value: Patient 71


title: EPIC-PKR NAI,repeat2

value: in vitro cDNA

value: EPIC-PKR NAI samples modified by NAI in DMSO


title: Mouse 13, Brown Adipose, C57BL/6J, Vegan

value: Brown Adipose


title: PDO71 (control) ATAC-seq rep 2

value: DMSO


title: PDO71 (control) rep 1 [1740R-251-04]


title: EPIC-3 DC

value: EPIC-3 DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: EPIC-3 NAI,repeat2

value: EPIC-3 NAI samples modified by NAI in DMSO


title: WTCHG_900295_268_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: Female


title: PDO19 NKL54 ATAC-seq rep2

value: Patient 19

value: NKL54 10µM


title: Mouse 12, Brown Adipose, C57BL/6J, Vegetarian

value: male

value: 12 week old

value: Vegetarian


title: WTCHG_900295_267_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: CT

value: +ve


title: Mouse 1, Brown Adipose, C57BL/6J, American

value: American


title: EPIC-2 NAI,repeat1

value: EPIC-2 NAI samples modified by NAI in DMSO


title: PDO19 SAHA ATAC-seq rep 2

value: Colon cancer

value: patient-derived organoid

value: SAHA 5µM

value: 6 hours


title: WTCHG_900295_266_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY


title: PDO19 (control) ATAC-seq rep 2

value: DMSO


title: EPIC-1 DMSO

value: in vitro cDNA

value: EPIC-1 DMSO samples only treated with DMSO


title: EPIC-1 DC

value: EPIC-1 DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: MLH1-G11_2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

data_processing:
data was aligned using MapSplice2 and mm10 assembly as reference genome
The generated BAM files were post-processed to translate genomic to transcriptomic coordinates and used as input to RSEM for gene expression quantification employing GENCODE vM9 as transcript annotation
Assembly: mm10 assembly with GENECODE cM9 was used for trasncription annotation
Supplementary files format and content: gzipped text file with the gene quantification performed by RSEM for each sample in each column

source_name: KP cell line

extract_protocol:
Cell lines were harvested using Trpsin/EDTA (Gibco). Extraction was followed by Qiagen Rneasy Mini column clean-up accordingly to manifacturer instructions (Qiagen).
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Mlh1 knockout clones were generated by Crispr Cas9 based technology using 2 single guide RNAs (sgRNA) targeting Mlh1 exon 5 as described in36. Briefly, KP cells were transiently transfected with pZac2.1-U6sgRNA-CMV-ZsGreen and (pSpCas9(BB)(PX458) using Lipofectamine 3000 (Invitrogen), following the manufacturer´s instructions. ZsGreen+ cells were cell sorted and single clones were tested for Mlh1 expression. KPctrl cells derive from cells transiently transfected with only (pSpCas9(BB)(PX458)

value: C57BL/6 KP mice

value: KP cell line

value: sgRNA with MLH1 gene sequence

value: KP


title: EPIC-PKR NAI,repeat1

value: EPIC-PKR NAI samples modified by NAI in DMSO


title: WTCHG_900295_265_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood

value: CT

value: +ve

value: Male


title: WTCHG_900295_264_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: Female


title: MLH1-G11_1


title: PDO71 SAHA ATAC-seq rep1

value: Colon cancer

value: patient-derived organoid

value: Patient 71

value: SAHA 5µM


title: PDO71 NKL54 ATAC-seq rep1

value: NKL54 10µM

value: 6 hours


title: WTCHG_900295_263_CT_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY


title: EPIC-1 NAI,repeat 1

value: in vitro cDNA

value: EPIC-1 NAI samples modified by NAI in DMSO


title: PDO71 (control) ATAC-seq rep 1

value: DMSO


title: EPIC-1 NAI,repeat 2


title: WTCHG_900295_262_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: PDO19 NKL54 ATAC-seq rep1

value: Patient 19


title: MLH1_CAS9_2

value: C57BL/6 KP mice

value: KP cell line

value: sgRNA with control sequence

value: KP


title: WTCHG_900295_261_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: CT

value: +ve


title: FlnKO ROI 16

first: Yuanyi

last: Feng

address: 4301 Jones Bridge Road

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

description:
Experimental Slide 2022-08-18 | 076 | Full ROI
DSP-1001660012009-A-G05

data_processing:
Sequencing data were processed through GeoMx NGS Pipeline according to GeoMx DSP NGS Readout User Manual (MAN-10153-01).
Raw sequencing FASTQ files were converted to digital count conversion (DCC) files and further processed to obtain data for each target probe in each ROI by subtracting the mean of background and normalizing to Q3 of all targets.
Assembly: mm10
Supplementary files format and content: FlnKO CountMatrix.xlsx, DCC files
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Mouse brains were fixed by transcardial perfusion with nuclease-free PBS and 4% paraformaldehyde. Fixed brains were embedded in OCT, cut to 7-μm cryosections, and placed on a microscope slide.
GeoMx Mouse Whole Transcriptome oligonucleotide probes by NanoString

value: brain

value: 3 months

tag: region

value: PH

value: FlnKO


title: MLH1_CAS9_1


title: PDO19 SAHA ATAC-seq rep1

value: Colon cancer

value: patient-derived organoid

value: SAHA 5µM

value: 6 hours


title: FlnKO ROI 15

description:
Experimental Slide 2022-08-18 | 075 | Full ROI
DSP-1001660012009-A-G04

tag: age


title: WTCHG_900295_260_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY

value: Male


title: FlnKO VSVZ ROI 15

description:
Experimental Slide 2022-08-18 | 074 | Full ROI
DSP-1001660012009-A-G03

value: VSVZ


title: Mouse7, CTRL, Small-CTRL_5 (GeoMx)

description:
B022-B-mouseWTA-021
DSP-1001660005544-A-D07_RIA1443A43-43
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: mesenchymal glioma stem cell

value: ctrl


title: MLH1-G11_3

value: C57BL/6 KP mice

value: KP cell line

value: sgRNA with MLH1 gene sequence

value: KP


title: EPIC-2 NAI,repeat2

value: in vitro cDNA

value: EPIC-2 NAI samples modified by NAI in DMSO


title: WTCHG_900295_259_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: CT

value: +ve


title: PDO19 (control) ATAC-seq rep 1

value: Colon cancer

value: patient-derived organoid

value: Patient 19

value: DMSO

tag: replicate


title: Mouse7, CTRL, Small-CTRL_4 (GeoMx)

description:
B022-B-mouseWTA-020
DSP-1001660005544-A-D06_RIA1443A42-42
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: brain


title: FlnKO VSVZ ROI 14

description:
Experimental Slide 2022-08-18 | 073 | Full ROI
DSP-1001660012009-A-G02

value: 3 months

value: VSVZ

value: FlnKO


title: MOLM13_R3

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

institute: University of Arkansas for Medical Sciences

data_processing:
RNA-seq data was analyzed using the transcript aligner STAR (v2.5.1b) [15] and transcript level data were generated by Salmon (v0.7.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values of both the CD34+ HPSC and MOLM-13 replicates.

growth_protocol: CD34+ HPSC were grown in SFEM II media (STEMCELL Technologies) in the presence of TPO (50 ng/uL), EPO (5 ng/uL), SCF (100 ng/uL), IL-3 (10 ng/uL), IL-6 (10 ng/ uL), and FLT3-L (10 ng/ uL). MOLM-13 cells were grown in RPMI 1640 in the presence of 20% FBS.

extract_protocol:
The total RNA was extracted from the HPSC and MOLM-13 cells using the AllPrep DNA/RNA Mini kit (Qiagen).
RNA-seq was performed using 100 ng total RNA with genomic DNA removal using the TURBO DNA-free kit (Ambion). RNA was prepared using the TruSeq stranded total RNA Ribo-zero gold kit (Illumina)
Libraries were sequenced using 150 bp paired-end reads on a NextSeq500 (Illumina).

value: Cancer cells


title: WTCHG_900295_258_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: Female


title: MLH1_CAS9_3

value: C57BL/6 KP mice

value: KP cell line

value: sgRNA with control sequence


title: Mouse7, CTRL, Large-CTRL_2 (GeoMx)

description:
B022-B-mouseWTA-019
DSP-1001660005544-A-D05_RIA1443A41-41
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: mesenchymal glioma stem cell

value: ctrl


title: Mouse6, KO, Outside_2 (GeoMx)

description:
B022-B-mouseWTA-018
DSP-1001660005544-A-D04_RIA1443A40-40
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: EGFR-KO


title: WTCHG_900295_257_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: MenACWY

value: +ve


title: Mouse6, KO , Outside_1 (GeoMx)

description:
B022-B-mouseWTA-017
DSP-1001660005544-A-D03_RIA1443A39-39
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_221_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: MOLM13_R1


title: Ctrl Cx ROI 15

description:
Experimental Slide 2022-08-18 | 070 | Full ROI
DSP-1001660012009-A-F11

value: Upper Cx

value: Ctrl


title: WTCHG_900295_220_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl Cx ROI 14

description:
Experimental Slide 2022-08-18 | 069 | Full ROI
DSP-1001660012009-A-F10

value: brain


title: CD34+ HPSC_R3

source_name: CD34+ HPSC

value: CD34+ HPSC

value: Primary cells


title: WTCHG_900295_219_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: CT

value: Male


title: Mouse5, WT, Outside_3 (GeoMx)

description:
B022-B-mouseWTA-015
DSP-1001660005544-A-D01_RIA1443A37-37
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: EGFR-WT


title: CD34+ HPSC_R2


title: CD34+ HPSC_R1


title: Ctrl Cx ROI 13

description:
Experimental Slide 2022-08-18 | 068 | Full ROI
DSP-1001660012009-A-F09

value: 3 months


title: WTCHG_900295_218_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: Mouse5, WT, Outside_2 (GeoMx)

description:
B022-B-mouseWTA-014
DSP-1001660005544-A-C12_RIA1443A36-36
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: MOLM13 cells replicate 3

data_processing:
Reads trimmed for adapter sequence
Reads mapped to rn6 genome using Bowtie2
Aligned reads shifted to accommodate Tn5 footprint
Peaks called by macs
Differential accessibility done in DiffBind
Assembly: hg38
Supplementary files format and content: Normalized read count table generated

source_name: MOLM13 cells

extract_protocol: ATAC-seq libraries were prepared in 3 experimental replicates according to the OMNI-ATAC protocol by Corces et al.  Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 2017; 14: 959-962.

value: MOLM13 cells


title: Ctrl VSVZ ROI 16

description:
Experimental Slide 2022-08-18 | 067 | Full ROI
DSP-1001660012009-A-F08

value: VSVZ


title: MOLM13 cells replicate 2


title: Ctrl VSVZ ROI 15

description:
Experimental Slide 2022-08-18 | 066 | Full ROI
DSP-1001660012009-A-F07


title: MOLM13_R2

value: Cancer cells


title: WTCHG_900295_216_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Female


title: Ctrl Cx ROI 16

description:
Experimental Slide 2022-08-18 | 071 | Full ROI
DSP-1001660012009-A-F12


title: Mouse7, CTRL, Large-CTRL_1 (GeoMx)

description:
B022-B-mouseWTA-012
DSP-1001660005544-A-C10_RIA1443A34-34
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: mesenchymal glioma stem cell

value: ctrl


title: MOLM13 cells replicate 1


title: WTCHG_900295_215_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: MenACWY


title: Mouse7, CTRL, Small-CTRL_3 (GeoMx)

description:
B022-B-mouseWTA-011
DSP-1001660005544-A-C09_RIA1443A33-33
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: CD34 cells replicate 3

source_name: CD34 cells

value: CD34 cells


title: FlnKO VSVZ ROI 13

description:
Experimental Slide 2022-08-18 | 072 | Full ROI
DSP-1001660012009-A-G01

value: FlnKO


title: Ctrl VSVZ ROI 13

description:
Experimental Slide 2022-08-18 | 064 | Full ROI
DSP-1001660012009-A-F05

value: brain

value: Ctrl


title: WTCHG_900295_214_CT_MenACWY_+ve

description:
small RNA
stage2

value: +ve


title: Ctrl VSVZ ROI 14

description:
Experimental Slide 2022-08-18 | 065 | Full ROI
DSP-1001660012009-A-F06


title: Mouse6, KO, Outside_1 (GeoMx)

description:
B022-B-mouseWTA-016
DSP-1001660005544-A-D02_RIA1443A38-38
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: EGFR-KO


title: Mouse6, KO, Small_2 (GeoMx)

description:
B022-B-mouseWTA-010
DSP-1001660005544-A-C08_RIA1443A32-32
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Ctrl VSVZ ROI 12

description:
Experimental Slide 2022-08-18 | 063 | Full ROI
DSP-1001660012009-A-F04


title: Ctrl Cx ROI 12

description:
Experimental Slide 2022-08-18 | 062 | Full ROI
DSP-1001660012009-A-F03

value: Upper Cx


title: CD34 cells replicate 1


title: Mouse6, KO, Large-KO_2 (GeoMx)

description:
B022-B-mouseWTA-009
DSP-1001660005544-A-C07_RIA1443A31-31
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_213_CT_MenACWY_+ve

description:
small RNA
stage2

value: CT


title: Mouse6, KO, Large-KO_1 (GeoMx)

description:
B022-B-mouseWTA-008
DSP-1001660005544-A-C06_RIA1443A30-30
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: CD34 cells replicate 2


title: WTCHG_900295_217_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: Mouse5, WT, Outside_1 (GeoMx)

description:
B022-B-mouseWTA-013
DSP-1001660005544-A-C11_RIA1443A35-35
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: EGFR-WT


title: E-In,low-GFP

data_processing:
Sequence reads were trimmed for adaptor sequence and sequencing primer using custom python scripts.
Trimmed reads were mapped to sgRNA library using bowtie allowing one mismatch (-v 1).
Read counts for each sgRNA were obtained using custom python scripts.
sgRNA read count was analyzed for enrichment of sgRNAs using MAGeCK test.
Assembly: Brunello sgRNA library
Supplementary files format and content: tab-delimited text file includes raw counts of each sgRNA for each sample

extract_protocol:
The genomic DNA were extractd with QIAGEN DNeasy kit according to the manufacturer’s instructions.
sgRNAs were amplified with PCR and PCR products were subjected to standard DNA-seq.

treatment_protocol: Cells were infeted with the lentivirus human CRISPR knockout pooled library. The 4x 10^6 were collected for control, after seven days of puromycin selection. The 4 x 10^7 cells were sorted for collecting the highest GFP fluorescence as experiment grop.


title: Ctrl Cx ROI 11

description:
Experimental Slide 2022-08-18 | 061 | Full ROI
DSP-1001660012009-A-F02

value: 3 months


title: Mouse6, KO, Small_1 (GeoMx)

description:
B022-B-mouseWTA-007
DSP-1001660005544-A-C05_RIA1443A29-29
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_211_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: Ctrl Cx ROI 10

description:
Experimental Slide 2022-08-18 | 060 | Full ROI
DSP-1001660012009-A-F01


title: Mouse5, WT, Small-WT_3 (GeoMx)

description:
B022-B-mouseWTA-006
DSP-1001660005544-A-C04_RIA1443A28-28
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_210_CT_MenACWY_+ve

description:
small RNA
stage2

value: Male


title: Ctrl Cx ROI 09

description:
Experimental Slide 2022-08-18 | 059 | Full ROI
DSP-1001660012009-A-E12


title: WTCHG_900295_209_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_900295_208_CT_MenACWY_+ve

description:
small RNA
stage2


title: P-In,low-GFP


title: Mouse5, WT, Large_3 (GeoMx)

description:
B022-B-mouseWTA-004
DSP-1001660005544-A-C02_RIA1443A26-26
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: P-In,high-GFP


title: Ctrl Cx ROI 08

description:
Experimental Slide 2022-08-18 | 058 | Full ROI
DSP-1001660012009-A-E11


title: WTCHG_900295_212_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: Mouse5, WT, Small-WT_2 (GeoMx)

description:
B022-B-mouseWTA-005
DSP-1001660005544-A-C03_RIA1443A27-27
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Ctrl Cx ROI 06

description:
Experimental Slide 2022-08-18 | 056 | Full ROI
DSP-1001660012009-A-E09


title: Mouse5, WT, Large_2 (GeoMx)

description:
B022-B-mouseWTA-002
DSP-1001660005544-A-B12_RIA1443A24-24
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_206_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_900295_207_CT_MenACWY_+ve

description:
small RNA
stage2