title: Hoxb5_Tom_7d_30e_32c_Tomneg [SLX-19800_SIGAA5_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19800_SIGAA5_filtered_feature_bc_matrix.h5


title: Hoxb5_Tom_7d_54f_56a_Tomneg [SLX-20391_SITTC4_10x]

status: Public on Jun 20 2023

type: SRA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20391_SITTC4_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

treatment_protocol: Mice were treated with tamoxifen to induce a persistent fluorescent label, cells were harvested at indicated time intervals

tag: tissue

value: bone marrow

tag: cell type

value: Lin-negative, (cKit OR Sca1)-positive

tag: genotype

value: WT

tag: treatment


title: CUT&RUN_IgG_Th1_Ets1-SE-KO_Rep1B_Rep1T

city: Philadelphia

first: Golnaz

last: Vahedi

state: PA

address: 421 Curie Blvd

department: Department of Genetics

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
ChIP-seq libraries were pair-end sequenced by Illumina NextSeq 550. BWA was used for alignment of ChIP-seq data. Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses.
Assembly: GRCm38
Supplementary files format and content: CUT&RUN peak bed file normalized by IgG data.

molecule: genomic DNA

source_name: Th1 cells

extract_protocol:
CUT&RUN was performed on in-vitro polarized Th1 cells using CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, Cat#14-1048), using manufacturer’s recommendation. Briefly, 4 × 105 cells live cells were sorted out and nuclei were extracted, washed, and allowed to adsorb onto activated ConA beads. Cells were then resuspended in recommended buffer, 0.5 mg of antibody was added, mixed well, and allowed to incubate at 4°C overnight on a nutator. Recommended antibodies were used, including anti-H3K27ac (Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb, CST, Cat #8173S), anti-ETS-1 (C-20, SantaCruz, Cat# sc-350X) and anti-CTCF (Millipore, Cat# 07-729), along with positive and negative controls. Subsequently, the reactions were washed with cell permeabilization buffer and incubated with pAG-MNase, and the DNA was isolated for the antibody-binding regions.
Libraries were prepared according to instructions accompanying the NEBNext Ultra II Library Prep Kit for Illuina (Part# E7645S). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+38 bp) was performed on a NextSeq 550 or 61bp+61bp on Novaseq 6000 (Illumina) following the manufacturer's protocol.

treatment_protocol: Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco).  For Th1 polarization, 0.2x106 naive CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C.

value: Spleen

tag: strain

tag: chip antibody

value: IgG (included with EpiCypher CUTANA kit, Cat# 14-1048)


title: Hoxb5_Tom_5mo_56e_58g_Tomneg [SLX-19739_SIGAF9_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19739_SIGAF9_filtered_feature_bc_matrix.h5


title: CUT&RUN_IgG_Th1_WT_Rep1B_Rep1T


title: CUT&RUN_ETS1_Th1_Ets1-SE-KO_Rep1B_Rep1T

value: ETS1 (Canra Cruz, Cat# sc-350X)


title: Patient SC005's tumor tissue [T5-6-6]

city: Houston

first: Xiuning

last: Le

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
Sequence reads were processed by Cell-ranger version 5.0
Genome_build: GRCH38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, and matrix.mtx.tsv

organism: Homo sapiens

source_name: head and neck squamous cell carcinoma

extract_protocol:
For biospecimens collected for single-cell analysis, fresh samples were first evaluated by clinical pathology and appropriate samples (tumor versus normal tonsil tissue) were allocated to research in 10% FBS RPMI 1640 media and transferred to the laboratory. The tissue was dissociated per single-cell suspension protocol
Fresh single-cell suspension was used for generation of transcriptome libraries per 10xGenomics 5’RNAseq (Chromium Single Cell 5’ Library and Gel Bead Kit v1).

tag: subject id

value: Patient SC005

value: head and neck squamous cell carcinoma

tag: tissue type

value: tumor


title: Patient SC006's tumor tissue [T6-6-6]

value: Patient SC006


title: CUT&RUN_ETS1_Th1_Ets1-SE-KO_Rep2B_Rep1T


title: Patient SC008's tumor tissue [T8-6-6]

value: Patient SC008


title: HA-ICP22+V5-ICP27 cells, no DOX, replicate 1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: DNA isolated with MinElute PCR Purification Kit

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph

source_name: Omni-ATAC-seq

growth_protocol: T-HF cells were cultured in DMEM supplements with 10% FBS and P/S. Expression of HA-ICP22 and HA-ICP22 + V5-ICP27 was induced by adding 5 μg/ml doxycycline for 48h. Salt stress was induced with the addition of 80 mM KCl. For the second experiment HFFF were cultured as described for THF cells. 100000 cells were infected at MOI 10 under PAA treatment for 8 h and harvested/processed according to the OMNI-ATAC-seq protocol

extract_protocol:
Samples were processed according to the Omni-ATAC-seq protocol (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396)
See Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
NextSeq 500 sequencing 35bp paired-end reads

treatment_protocol: 5 μg/mL DOX was added to indicated samples 48 hours prior to performing Omni-ATAC-seq. 80 mM KCl (salt stress) was added to indicated samples for 2 hours prior to Omni-ATAC-seq. No pre-treatment with doxycycline for the infections of HFFF cells was applied.

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: no treatment

tag: treatment 2


title: HA-ICP22+V5-ICP27 cells, DOX, replicate 2

value: DOX (5 μg/mL)


title: MDA-MB-231_parental_0_FBS_R3_S54

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

growth_protocol: WT and GIV-KO MDA-MB231 cells grown in 0% and 10% serum concentration in p10 dishes (Corning) for 16 h prior to harvest

extract_protocol:
RNA extraction was done  using a kit (R2052, Zymo Research) as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: 0% and 10% serum concentration

tag: cell line

value: parental

tag: agent


title: Hoxb5_Tom_9mo_30jd_Tomneg [SLX19552_SIGAG3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19552_SIGAG3_filtered_feature_bc_matrix.h5


title: CUT&RUN_ETS1_Th1_WT_Rep1B_Rep2T


title: HA-ICP22+V5-ICP27 cells, no DOX, replicate 2


title: Hoxb5_Tom_5mo_57a_58h_Tompos [SLX-19739_SIGAE9_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19739_SIGAE9_filtered_feature_bc_matrix.h5


title: HA-ICP22+V5-ICP27 cells, DOX, replicate 1


title: T-HF cells, with SSRP1 KD, infected with WT strain F, replicate 2

description: DNA isolated with Zymo DNA Clean & Concentrator

source_name: Omni-ATAC

growth_protocol: T-HFs were cultured in DMEM supplements with 10% FBS and P/S. To induce KD, cells were treated with DOX 72 hours prior to infection. Cells were infected with HSV-1 strain F or ICP22-null mutant at an MOI of 10.

treatment_protocol: Cells were infected with wild type HSV-1 for 15min or ICP22-null mutatn for 1 hours using an MOI of 10. After infection, cell culture media was replaced with fresh media in which the PAA was added. Samples were harvested at the indicated time points and all samples were processed according to the Omni-ATAC-seq protocol.

tag: time post infection

value: 8 hpi

value: PAA (350 microg/ml) + DOX (1 μg/mL)

value: Herpes simplex virus 1, strain F


title: Hoxb5_Tom_9mo_30ah_Tompos [SLX19552_SIGAF3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19552_SIGAF3_filtered_feature_bc_matrix.h5

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: Patient SC003's tumor tissue [T3-6-6]

value: Patient SC003


title: CUT&RUN_CTCF_Th1_Ets1-SE-KO_Rep2B_Rep1T

value: Spleen

value: CTCF (Millipore 07-729)


title: Hoxb5_Tom_9mo_30jd_Tompos [SLX19552_SIGAE3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19552_SIGAE3_filtered_feature_bc_matrix.h5

value: WT


title: Patient SC029's primary tumor tissue [T29Primer_6-6]

value: Patient SC029

value: head and neck squamous cell carcinoma


title: Chip-seq of Ell3

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

country: China

institute: Southeast University

data_processing:
For quantification of repetitive genomic regions, we allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Peak calling was performed with the MACS2 and TE-specific peaks were selected by overlapping with the RepeatMasker from UCSC (mm9.rmsk) using bedtools
Assembly: mm9

growth_protocol: Feeder-free Mouse V6.5 embryonic stem cells were cultured on 0.1% gelatin-coated plates. mESCs were cultured in N2B27 medium (50% DMEM/F12 and 50%Neurobasal medium, 1x N2 supplement, 1x B27 supplement ,1x Penicillin-Streptomycin, 0.1 mM mercaptoethanol, 2 mM L-glutamine) supplemented with Mek inhibitor (PD0325901, 2.5 M),Gsk3 inhibitor (CHIR99021, 7.5 M) and 5 units of LIF, at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit (0801-0303). NEBNext® DNA Library Prep Master Mix Set for Illumina.

value: mouse embryonic stem cells

value: ELL3 sgRNA

value: Homemade #615


title: Patient SC029's metastatic tumor tissue [T29Met_6-6]

value: tumor


title: CUT&RUN_CTCF_Th1_Ets1-SE-KO_Rep1B_Rep1T


title: CUT&RUN_CTCF_Th1_WT_Rep1B_Rep2T


title: STING KO - CINhigh_WT_shSTING2

city: NEW YORK

first: Ashley

middle: M

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics, and Systems Biology

institute: Weill Cornell Medicine

description: Barcoded single cells

data_processing:
CellRanger (v3.1.0) was utilized to construct a count matrix from raw reads, including sample demultiplexing, alignment to CellRanger’s mm10-3.0.0 reference, barcode processing, and the generation of a raw digital expression matrix by collapsing groups of reads with the same unique molecular identifier (UMI), cell barcode and gene annotation.
The count matrix was then loaded into python using scanpy (read_10x_h5) for subsequent pre-processing and downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Cell x gene unnormalized and unfiltered count matrices.
Supplementary_files_format_and_content: Anndata structure containing normalized and normalized-and-log transformed count matrices after cell and gene filtering described in manuscript.

molecule: polyA RNA

source_name: Triple Negative Breast Cancer

growth_protocol: 4T1 cell line was purchased from the American Type Culture Collection (ATCC) and cultured in RPMI supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). For orthotopic tumor implantation, 2.5 × 10^5 4T1 cells in 50 ul PBS were mixed 1:1 with Matrigel (BD Biosciences) and injected into the fourth mammary fat pad.

extract_protocol:
Primary tumors were resected under sterile conditions 14 days after orthotopic implantation in the mammary fat pad of BALB/c immune competent mice. The entire tumor was immediately place in RPMI media (Corning) on ice and dissociated using both mechanical and enzymatic digestion (Mouse Tumor Dissociation Kit #130-096-730 , Miltenyi Biotec) generally within 1 hour of surgical resection
10X Genomics, Single Cell 3′ V2 Reagent Kits User Guide PN-120233

tag: stage of tumor progression

value: Primary Tumor

value: Triple Negative Breast Cancer


title: T-HF cells, with no SSRP1 KD, infected with WT strain F, replicate 2

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: 8 hpi

value: PAA (350 microg/ml)


title: CUT&RUN_CTCF_Th1_WT_Rep1B_Rep1T


title: Patient SC027's tumor tissue [T27_6-6]

value: Patient SC027


title: STING KO - CINhigh_WT_shSTING1

description: Barcoded single cells


title: T-HF cells, with SSRP1 KD, infected with WT strain F, replicate 1

value: PAA (350 microg/ml) + DOX (1 μg/mL)

value: Herpes simplex virus 1, strain F


title: T-HF cells, with no SSRP1 KD, infected with WT strain F, replicate 1


title: CUT&RUN_ETS1_Th1_WT_Rep1B_Rep1T

value: Spleen

value: ETS1 (Canra Cruz, Cat# sc-350X)


title: T-HF cells, with SSRP1 KD, mock, replicate 2

value: no infection


title: High CIN - CINhigh_WT_shRenilla2

description: Barcoded single cells


title: Patient SC026's tumor tissue [T26_6-6]

value: Patient SC026


title: Patient SC025's tumor tissue [T25_6-6]

value: Patient SC025

value: head and neck squamous cell carcinoma


title: T-HF cells, with SSP1 KD, mock, replicate 1


title: CUT&RUN_H3K27ac_Th1_Ets1-SE-KO_Rep2B_Rep1T

value: H3K27Ac (Cell Signaling Technologies; Cat# 8173S)


title: High CIN - CINhigh_WT_shRenilla1

description: Barcoded single cells


title: CUT&RUN_H3K27ac_Th1_Ets1-SE-KO_Rep1B_Rep1T


title: High CIN - CINhigh_dnMCAK

description: Barcoded single cells


title: Patient SC022's tumor tissue [T22_6-6]

value: Patient SC022


title: Low CIN - CINlow_GFP_MCAK2

description: Barcoded single cells


title: T-HF cells, with no SSRP1 KD, mock, replicate 2


title: T-HF cells, with no SSRP1 KD, mock, replicate 1


title: T-HF cells, with SSRP1 KD, infected with ICP22-null mutant, replicate 2

value: ICP22-null mutant of herpes simplex virus 1, strain F


title: Patient SC019's tumor tissue [T19-6-6]

value: Patient SC019

value: tumor


title: CUT&RUN_H3K27ac_Th1_WT_Rep1B_Rep1T


title: Low CIN - CINlow_GFP_MCAK1

description: Barcoded single cells

value: Primary Tumor

value: Triple Negative Breast Cancer


title: T-HF cells, with SSRP1 KD, infected with ICP22-null mutant, replicate 1

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: 8 hpi


title: Low CIN - CINlow_GFP_KIF2B2

description: Barcoded single cells


title: Patient SC014's tumor tissue [T14-6-6]

value: Patient SC014


title: Patient SC013's tumor tissue [T13-6-6]

value: Patient SC013


title: T-HF cells, with no SSRP1 KD, infected with ICP22-null mutant, replicate 2

value: PAA (350 microg/ml)


title: ATAC-seq_Th1_ETS1-SE-KO_Rep2B_Rep2T

data_processing:
ATAC-seq libraries were pair-end sequenced by Illumina NextSeq 500. BWA was used for alignment. Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses. Additionally, Picard was used to mark and remove duplicates. Furthermore, for each ATAC-seq library the insert size was calculated by Picard.
Assembly: GRCm38
Supplementary files format and content: ATAC-seq peak bed file estimated from macs2

source_name: Th2 cells

extract_protocol:
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS, followed by treatment with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting nuclei, the pellets were resuspended in 50 μL transposition reaction with 2.5 μL Tn5 transposase (FC-121-1030; Illumina). The reaction was incubated in a 37°C water bath for 45 minutes. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen) and amplified with varying cycles, depending on the side reaction results. Libraries were purified using a QIAQuick PCR Purification Kit (Qiagen).
Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 550 (Illumina). Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent).

treatment_protocol: Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). A part of the isolated naive CD4+ T cells were used for ATAC-seq. For Th1/Th2 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, 0.2x106 naive CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C. Th2 polarization was induced by cultivating 0.2x106 naive CD4+ T cells in complete RPMI supplemented with 10 mg/mL of anti-IFN- (Clone: XMG1.2, BioXCell, Cat#BE0055), 50 ng/mL of recombinant IL-4 (BioLegend, Cat# 574302) and 1 mg/mL of soluble anti-CD28 for 6 days at 37°C. Purity was verified using flow cytometry.

value: Spleen


title: Low CIN - CINlow_GFP_KIF2B1

description: Barcoded single cells


title: ATAC-seq_Th1_ETS1-SE-KO_Rep1B_Rep2T


title: High CIN - CINhigh_GFP_KIF2A

description: Barcoded single cells


title: CUT&RUN_H3K27ac_Th1_WT_Rep1B_Rep2T


title: High CIN - CINhigh_GFP

description: Barcoded single cells


title: T-HF cells, with SPT6 KD, infected with WT strain F, replicate 2

value: PAA (350 microg/ml) + DOX (1 μg/mL)

value: Herpes simplex virus 1, strain F


title: ATAC-seq_Th2_WT_Rep1B_Rep1T


title: ATAC-seq_Th2_WT_Rep2B_Rep1T


title: T-HF cells, with no SSRP1 KD, infected with ICP22-null mutant, replicate 1


title: Patient SC006's normal tissue [N6-6-6]

source_name: normal tissue adjucent to head and neck squamous cell carcinoma

value: Patient SC006

value: normal


title: Patient SC005's normal tissue [N5-6-6]

value: Patient SC005

value: normal tissue adjucent to head and neck squamous cell carcinoma


title: High CIN - CINhigh_WT2

description: Barcoded single cells


title: ATAC-seq_Th1_ETS1-SE-KO_Rep2B_Rep1T


title: Patient SC001's tumor tissue [T1-6-6]

value: Patient SC001

value: head and neck squamous cell carcinoma


title: Patient SC003's normal tissue [N3-6-6]

value: Patient SC003


title: High CIN - CINhigh_WT1

description: Barcoded single cells

value: Primary Tumor


title: T-HF cells, with SPT6 KD, infected with WT strain F, replicate 1


title: T-HF cells, with no SPT6 KD, infected with WT strain F, replicate 2


title: ATAC-seq_Th1_ETS1-SE-KO_Rep1B_Rep1T


title: ATAC-seq_Th1_WT_Rep2B_Rep1T


title: Patient SC010's tumor tissue [T10-6-6]

value: Patient SC010

value: tumor


title: T-HF cells, with no SPT6 KD, infected with WT strain F, replicate 1

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: 8 hpi


title: ATAC-seq_Th1_WT_Rep1B_Rep1T


title: CDK9_2

city: Nanjing,China

first: kun

last: tian

address: School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing,  China.

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: ensembl_homo_sapiens_grch38_p12_gca_000001405_27

source_name: HepG2 cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 °C with 5% CO2 incubation. Cells were seeded into 6-well plates (Corning) 24 h prior to transfection at a density of 200,000 cells per well.

extract_protocol:
Total RNA was prepared from transfection experiments after 72 h using a RNA Isolation Reagent (R701-01, Vazyme). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Cells were transfected by using Lipofectamine 2000 (Life Technologies) following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg FEN1 plasmids were transfected and 500 pmoL of DNA probes were transfected 24 h later.

value: human liver carcinoma cell  line HepG2

value: hpDNAs targeting the mRNA of CDK9


title: 7596

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
Saline_vs_Plasma-ExpDiff.csv
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 24

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: Bulk Hippocampal Tissue

extract_protocol:
RNA extracted using TRIzol (Thermo FIsher)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

value: Bulk Hippocampal Tissue

tag: developmental stage

value: Aged mice

value: Saline treatment


title: CDK9_3

treatment_protocol: Cells were transfected by using Lipofectamine 2000 (Life Technologies) following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg FEN1 plasmids were transfected and 100 pmoL of DNA probes were transfected 24 h later.


title: T-HF cells, with SPT6 KD, mock, replicate 2

value: no infection

value: PAA (350 microg/ml) + DOX (1 μg/mL)


title: 7595

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 23

value: Young Platelet treatment


title: ATAC-seq_naive_CD4_ETS1-SE-KO_Rep1B_Rep2T

source_name: naive CD4+

value: Spleen


title: AFP_1

treatment_protocol: Cells were transfected by using Lipofectamine 2000 (Life Technologies) following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg FEN1 plasmids were transfected and 500 pmoL of other DNA probes were transfected 24 h later.

value: hpDNAs targeting the mRNA of AFP


title: 7594

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 22

value: Young Plasma treatment


title: T-HF cells, with SPT6 KD, mock, replicate 1


title: T-HF cells, with no SPT6 KD, mock, replicate 2

value: PAA (350 microg/ml)


title: ATAC-seq_naive_CD4_ETS1-SE-KO_Rep1B_Rep1T


title: 7159

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 21


title: Rat #24 - no stress

city: Boulder

first: Serge

last: Campeau

state: Colorado

address: 2860 Wilderness Place

department: Psychology and Neuroscience

institute: University of Colorado Boulder

data_processing:
Sequence reads were trimmed for adaptor sequence (Illuminaclip adapters TruSeq3-PE-2) and 3 leading/trailing base sequences using Trimmomatic (v. 0.36) (slidingwindow:4:15; Minlen:36)
Hisat2 (v. 2.0.5) was employed to map the reads to the rn6 Rattus Norvegicus reference genome
Gene expression was estimated using the featureCount routine of the Subread module (v. 1.6.2) on sorted BAM files with the annotated rat genome (Rnor 6.0.100)
FeatureCount gene count estimations were then used independently as DESeq2 inputs (v. 1.28.1 (Love et al., 2014); run in R v. 4.0.2) for differential gene expression analyses to report significant log2 fold changes (lfc) with padj values (Wald statistic) of ≤ 0.05
Assembly: Rnor 6.0.100 (https://ftp.ensembl.org/pub/release-100/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.100.gtf.gz; downloaded June 2020)
Supplementary files format and content: The 'featurecounttrim24.txt' is a tab delimited text file that is a concatenated (matrix) file of all individual sample featurecount files obtained from the Subread module (v. 1.6.2)

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Total RNA was extracted with PureLink RNA Mini Kit #12183018A with TRIzol Reagent #15596026, Invitrogen
Paired-end (75 bp) libraries were prepared with a KAPA HyperPrep mRNA kit (#KK8580) according to the manufacturer's instructions; 1 ug total RNA was used for the construction of sequencing libraries.

treatment_protocol: All rats were euthanized on the same morning, with rats from each of the four groups euthanized sequentially, 24 hours after the last noise (or control) exposure. Euthanasia was performed via guillotine after minimal disturbances to the rats in their home cages. Within 2 min from retrieving each rat from its cage, brains were rapidly extracted and placed in an ice-cold large rat brain matrix (EMS #69083-C – coronal, 1.0 mm), and a 2-mm coronal brain slice between 2.5-4.5 mm posterior to bregma (including the rPH region bilaterally) was collected and submerged in 2 ml of RNAlater RNA Stabilization Solution  (Invitrogen) at 4oC. The brain slices were further dissected 24-hrs after collection on an ice-cold surface by excising a block of tissue bounded ventrally by a horizontal cut 0.5-mm ventral to the dorsal aspect of the 3rd ventricle, laterally by vertical cuts centered on the lateral edge of the mammillothalamic tracts, and dorsally by a horizontal cut centered on the dorsal edge of the mammillothalamic tracts; the tissue block was submerged in RNALater and stored at 4oC until RNA extraction (6 days later).

value: Sprague-Dawley, Envigo

tag: development

value: adult

value: brain

tag: brain region

value: rostral posterior hypothalamus

value: no stress


title: ATAC-seq_naive_CD4_WT_Rep1B_Rep1T


title: 7157

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 20


title: 7156

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 19


title: Rat #23 - no stress


title: C1

treatment_protocol: untreated

value: human liver carcinoma cell  line HepG2

value: untreated


title: 7155

description:
Saline_vs_Plasma-ExpDiff.csv
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 18

value: Bulk Hippocampal Tissue


title: T-HF cells, with SPT6 KD, infected with ICP22-null mutant, replicate 2

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: 8 hpi

value: ICP22-null mutant of herpes simplex virus 1, strain F


title: T-HF cells, with SPT6 KD, infected with ICP22-null mutant, replicate 1

value: PAA (350 microg/ml) + DOX (1 μg/mL)


title: T-HF cells, with no SPT6 KD, mock, replicate 1

value: no infection


title: Rat #22 - no stress


title: m2_actB_ctrl

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

source_name: spleen

extract_protocol: 10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Activated B cells were derived from cultures of naïve B cells that were stimulated for 72 hours with 20 mg/ml LPS, 5 ng/ml IL-5, and 20 ng/ml IL-2

value: spleen

value: activated B cell

tag: sorting markers

tag: mouse strain

value: LPS, IL-2, IL-5 for 72 hrs


title: m3_actB_ctrl

tag: tissue

tag: cell type


title: T-HF cells, with no SPT6 KD, infected with ICP22-null mutant, replicate 2

tag: treatment

value: PAA (350 microg/ml)


title: 7154

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 17

tag: strain

value: Aged mice

value: Young Platelet treatment


title: m1_actB_ctrl


title: 7152

description:
Saline_vs_Plasma-ExpDiff.csv
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 16

value: Saline treatment


title: T-HF cells, with no SPT6 KD, infected with ICP22-null mutant, replicate 1


title: IRF8.gRNA2.Thy1pos.C

description:
IRF8.gRNA2.Thy1pos.C.rpkm
IRF8_naiveB.geneRpkm.detected.csv

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Activated B cells and plasmablasts were derived from cultures of naïve B cells that were stimulated for 72 hours with 20 mg/ml LPS, 5 ng/ml IL-5, and 20 ng/ml IL-2

value: naive B cell

tag: genotype

value: IRF8 KO

tag: irf8 sgrna

value: sgRNA 2


title: HFFF cells infected with HSV-1 WT (8 hpi), treated with PAA, replicate 2

source_name: ATAC-seq

growth_protocol: HFFFs were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected with HSV-1 strain F or ICP22-null mutant at an MOI of 10.

extract_protocol:
Samples were processed according to the original ATAC-seq protocol by Buenrostro et al., Nature Methods 2013
Buenrostro et al., Nature Methods 2013
NextSeq 500 sequencing 35bp paired-end reads

treatment_protocol: Cells were infected with wild type HSV-1 for 15min or ICP22-null mutatn for 1 hour using an MOI of 10. After infection, cell culture media was replaced with fresh media in which the PAA was added. Samples were harvested at the indicated time points and all samples were processed according to the original ATAC-seq protocol.

value: Primary human fetal foreskin fibroblasts (HFFF)

value: PAA (350 µg/ml)

value: Herpes simplex virus 1, strain F


title: 7151

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 15

value: Bulk Hippocampal Tissue


title: ATAC-seq_naive_CD4_WT_Rep1B_Rep2T

value: Spleen


title: IRF8.gRNA2.Thy1pos.A

description:
IRF8.gRNA2.Thy1pos.A.rpkm
IRF8_naiveB.geneRpkm.detected.csv


title: Rat #18 - 1 day stress

value: Sprague-Dawley, Envigo

value: adult

value: brain

value: rostral posterior hypothalamus

value: 1 day stress


title: Rat #20 - no stress

value: no stress


title: Rat #19 - no stress


title: HFFF cells infected with HSV-1 WT (8 hpi), treated with PAA, replicate 1

value: 8 hpi


title: 7150

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 14

value: Aged mice

value: Young Plasma treatment


title: HFFF cells infected with HSV-1 WT (8 hpi), replicate 2

value: no treatment


title: IRF8.gRNA2.Thy1neg.B

description:
IRF8.gRNA2.Thy1neg.B.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: spleen

value: naive B cell

value: IRF8 WT


title: HFFF cells infected with HSV-1 WT (8 hpi), replicate 1

value: Primary human fetal foreskin fibroblasts (HFFF)


title: 7148

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 13

value: Young Platelet treatment


title: Rat #17 - 1 day stress


title: Rat #16 - 1 day stress


title: Rat #21 - no stress


title: 7147

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 12

value: Bulk Hippocampal Tissue


title: 7145

description:
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 10


title: HFFF cells infected with HSV-1 WT (12 hpi), treated with PAA, replicate 1

description: DNA isolated with MinElute PCR Purification Kit

value: 12 hpi

value: PAA (350 µg/ml)

value: Herpes simplex virus 1, strain F


title: Rat #15 - 1 day stress

value: Sprague-Dawley, Envigo

value: adult

value: brain


title: HFFF cells infected with HSV-1 WT (12 hpi), replicate 2


title: IRF8.gRNA1.Thy1pos.C

description:
IRF8.gRNA1.Thy1pos.C.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: IRF8 KO

value: sgRNA 1


title: HFFF cells infected with HSV-1 WT (12 hpi), treated with PAA, replicate 2


title: Rat #12 - 3 days repeated stress

value: rostral posterior hypothalamus

value: 3 days repeated stress


title: 7143

description:
Saline_vs_Plasma-ExpDiff.csv
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 8

value: Aged mice

value: Saline treatment


title: 7146

description:
Saline_vs_Plasma-ExpDiff.csv
Saline_vs_Platelet_enriched-ExpDiff.csv
Sample 11


title: IRF8.gRNA2.Thy1pos.B

description:
IRF8.gRNA2.Thy1pos.B.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: spleen

value: naive B cell

value: sgRNA 2


title: 7144

description:
Saline_vs_Plasma-ExpDiff.csv
Sample 9

value: Young Plasma treatment


title: IRF8.gRNA1.Thy1pos.B

description:
IRF8.gRNA1.Thy1pos.B.rpkm
IRF8_naiveB.geneRpkm.detected.csv


title: IRF8.gRNA1.Thy1pos.A

description:
IRF8.gRNA1.Thy1pos.A.rpkm
IRF8_naiveB.geneRpkm.detected.csv


title: HFFF cells infected with HSV-1 WT (12 hpi), replicate 1

value: Primary human fetal foreskin fibroblasts (HFFF)

value: no treatment


title: HFFF cells mock infected (8 hpi), treated with PAA, replicate 2

value: no infection

value: PAA (350 µg/ml)


title: Rat #11 - 3 days repeated stress

value: Sprague-Dawley, Envigo


title: IRF8.gRNA2.Thy1neg.C

description:
IRF8.gRNA2.Thy1neg.C.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: IRF8 WT


title: IRF8.gRNA1.Thy1neg.B

description:
IRF8.gRNA1.Thy1neg.B.rpkm
IRF8_naiveB.geneRpkm.detected.csv


title: Rat #10 - 3 days repeated stress

value: adult

value: brain


title: Rat #14 - 1 day stress

value: 1 day stress


title: IRF8.gRNA2.Thy1neg.A

description:
IRF8.gRNA2.Thy1neg.A.rpkm
IRF8_naiveB.geneRpkm.detected.csv


title: Rat #13 - 1 day stress

value: rostral posterior hypothalamus


title: HFFF cells mock infected (8 hpi), replicate 2


title: Saline-3

description:
Saline_vs_PF4-ExpDiff.csv
Sample 6

source_name: Isolated Hippocampal Microglia

value: Isolated Hippocampal Microglia

value: Saline control treatment


title: Rat #8 - 3 days repeated stress

value: 3 days repeated stress


title: Saline-2

description:
Saline_vs_PF4-ExpDiff.csv
Sample 5

value: Aged mice


title: Rat #9 - 3 days repeated stress


title: PF4-4

description:
Saline_vs_PF4-ExpDiff.csv
Sample 4

value: PF4 treatment


title: IRF8.gRNA1.Thy1neg.A

description:
IRF8.gRNA1.Thy1neg.A.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: spleen

value: naive B cell


title: HFFF cells mock infected (12 hpi), treated with PAA, replicate 1

value: Primary human fetal foreskin fibroblasts (HFFF)


title: HFFF cells mock infected (12 hpi), replicate 1

value: no treatment


title: PF4-3

description:
Saline_vs_PF4-ExpDiff.csv
Sample 3


title: HFFF cells mock infected (12 hpi), treated with PAA, replicate 2

value: no infection


title: PF4-2

description:
Saline_vs_PF4-ExpDiff.csv
Sample 2


title: HFFF cells mock infected (12 hpi), replicate 2


title: Rat #7 - 3 days repeated stress


title: Rat #6 - 7 days repeated stress

value: 7 days repeated stress


title: YF13plus_III

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Raw reads were mapped to the Staphylococcus aureus LAC genome assembly GCF_015475575.1 using Bowtie2.
featureCounts was used to generate a read count table.
Assembly: GCF_015475575.1
Supplementary files format and content: gene_counts.tsv - tab separated table of read counts per gene

organism: Staphylococcus aureus

growth_protocol: Grown in Tryptic Soy Broth media with shaking (180rpm), at 37 C, for 1 h and 40 min after subculture. Cultures labelled 'plus' were additionaly treated with 10 mM H2O2 and 2.5 mM H2O2 for BS1302 and YF13, respectively. After 30 min of treatment cultures were spun down and washed.

extract_protocol: Cells were spun down, treated with ice-cold Trizol and homogenized by bead beating using Lysing Matrix B tubes. Upon centerifugation and treatment with chloroform and isopropanol, aquos phase was transferred to RNeasy spin column, washed, and eluted to DEPC treated water.

value: LAC agr KO


title: HFFF cells infected with ICP22-null mutant (8 hpi), treated with PAA, replicate 2

value: 8 hpi

value: PAA (350 µg/ml)

value: ICP22-null mutant of herpes simplex virus 1, strain F


title: Saline-4

description:
Saline_vs_PF4-ExpDiff.csv
Sample 7


title: YF13_untreated_III

value: untreated


title: Rat #4 - 7 days repeated stress

value: Sprague-Dawley, Envigo

value: adult

value: brain

value: rostral posterior hypothalamus


title: PF4-1

description:
Saline_vs_PF4-ExpDiff.csv
Sample 1

value: Isolated Hippocampal Microglia

value: Aged mice


title: HFFF cells infected with ICP22-null mutant (8 hpi), treated with PAA, replicate 1


title: WT_AML_LIC_ip_rep_4

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University

data_processing:
The reads from mRNA input samples’ raw sequencing data were preprocessed using Trim_galore, and Kallisto was used to quantify the read counts for each transcripts (GRCm38, cDNA sequences). The read counts of input were used as mRNA level.
The reads from mRNA input and m6A IP sequencing libraries were aligned to mm10 mouse reference genome with HISAT2 (v2.2.1).
The m6A peaks were called by exomePeak2 (v1.0.0).
The distribution m6A peaks over different regions on the transcript was depicted with annotations generated by Guitar (v2.4.0).
For calculating the relative m6A level for each gene, we used the mean of log2 Fold-change for all peaks annotation to genes. We further calculated the Z-score of adjusted fold-change in each cell type, and this Z-score represents the relative m6A level.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files
Library strategy: MeRIP-Seq

source_name: bone marrow leukemia cells

extract_protocol:
Bone marrow cells were extracted from wild-type (WT) AML mice. Blast cells and LICs were sorted from BM leukemia cells. Total RNA were extracted with Trizol, and mRNA were isolated with Oligo dT beads.
Briefly, total RNA was extracted, and poly (A) mRNA was purified from 10 μg total RNA using the mRNA Capture Beads. RNA samples were fragmented into 100 bp-long fragments by fragmentation buffer. The fragmentation reaction was stopped with 0.05 M EDTA. 1mg of affinity purified anti-m6A polyclonal antibody was incubated with protein-A beads in IP buffer for 2 h at 4 °C. Fragmented RNA was incubated with protein A beads-antibody at 4 °C for an additional 2 h. The beads were washed with 1x IP buffer twice, low salt buffer twice and high salt buffer twice before eluted. The eluates were purified with RNA Clean and Concentrator. The purified mRNA fragments were used to construct libraries with TruSeq Stranded mRNA Library Prep Kit. Sequencing was carried out on Illumina HiSeq X Ten.

value: bone marrow leukemia cells

tag: cell population

value: LIC

value: WT

tag: antibody

value: anti-m6A polyclonal antibody


title: Rat #3 - 7 days repeated stress


title: YF13_untreated_II

tag: cell line


title: WT_AML_LIC_ip_rep_3


title: HFFF cells infected with ICP22-null mutant (12 hpi), treated with PAA, replicate 2

value: Primary human fetal foreskin fibroblasts (HFFF)

value: 12 hpi

tag: agent


title: YF13plus_II

value: LAC agr KO


title: IRF8.gRNA1.Thy1neg.C

description:
IRF8.gRNA1.Thy1neg.C.rpkm
IRF8_naiveB.geneRpkm.detected.csv

value: spleen

value: naive B cell

value: IRF8 WT


title: YF13_untreated_I

value: untreated


title: YF13plus_I


title: BS1302plus_III

value: LAC agr KO rot KO


title: Rat #2 - 7 days repeated stress

value: Sprague-Dawley, Envigo

value: adult

value: 7 days repeated stress


title: HFFF cells infected with ICP22-null mutant (8 hpi), replicate 2

tag: time post infection

value: 8 hpi

value: no treatment

value: ICP22-null mutant of herpes simplex virus 1, strain F


title: HFFF cells infected with ICP22-null mutant (12 hpi), treated with PAA, replicate 1

value: PAA (350 µg/ml)


title: Rat #1 - 7 days repeated stress

value: brain

value: rostral posterior hypothalamus


title: WT_AML_LIC_ip_rep_1

value: bone marrow leukemia cells

value: LIC

value: WT

value: anti-m6A polyclonal antibody


title: Rat #5 - 7 days repeated stress


title: HFFF cells infected with ICP22-null mutant (8 hpi), replicate 1

value: Primary human fetal foreskin fibroblasts (HFFF)


title: HFFF cells infected with ICP22-null mutant (12 hpi), replicate 2

value: 12 hpi


title: WT_AML_blast_cell_ip_rep_4

value: blast cell


title: BS1302plus_I

value: LAC agr KO rot KO


title: WT_AML_blast_cell_ip_rep_3


title: Eucalypt_Ctrl_JW27

city: Richmond

first: Jonathan

middle: Michael

last: Plett

state: NSW

address: Bourke St. Entrance, Building L9

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

description: Biol Rep 3

data_processing:
Paired-end Illumina reads were quality trimmed using the CLC Genomics Workbench tool version 11.0 (CLC Bio/Qiagen) removing ambiguous nucleotides as well as low quality read ends. The quality cutoff (error probability) was set to 0.05, corresponding to a Phred score of 13. Trimmed reads of >40 bases were mapped using the RNA-Seq Analysis 2.16 package in CLC requiring >80% sequence identity over >80% of the read length; strand specificity was omitted.
Genes with at least two-fold expression change and FDR value ≤<=0.05 were considered significant. Multidimensional scaling (“plotMDS” function in edgeR) was applied to visualize gene expression profiles. Expression heatmaps were generated by hierarchically clustering based on average linkage of FPKM values with heatmap.2 function from gplots package
To check reliability of both expression data, we used the superSeq package which uses a subsampling approach to simulate and predict the number of differentially expressed genes at lower read depths and random sampling points from the original dataset. These subsampled reads are then extrapolated to predict the relationship between statistical power and read depth.
Genes from the time-series in planta assay from both fungal and the plant side were clustered into co-expression based modules using STEM (v1.3.11)
N/A
Assembly: https://phytozome-next.jgi.doe.gov/info/Egrandis_v2_0; https://mycocosm.jgi.doe.gov/Armlut1/Armlut1.home.html
Supplementary files format and content: Normalised read counts of all genes across all samples for E. grandis
Supplementary files format and content: Normalised read counts of all genes across all samples for A. luteobubalina

organism: Eucalyptus grandis

source_name: Root tissue (axenic)

growth_protocol: Plants and fungus were grown on half-strength MMN medium ((pH 5.5; 1 g l−1 glucose) at 22–30°C night/day temperature with a 16 h light cycle.

extract_protocol:
ISOLATE II Plant miRNA kit (Bioline, Sydney, Australia)
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration

treatment_protocol: Once the E. grandis seedlings were two months old and the fungal cultures had grown for one month, the plants were separated into one of three treatment categories: (1) fungal-free controls whereby the seedlings were transferred onto new half-strength MMN medium; (2) ‘pre-symbiosis’ which involved the transfer of seedlings onto new half-strength MMN medium in indirect contact with fungal mycelium for 24 h by separating the two organisms by a permeable cellophane membrane; (3) ‘physical contact’ seedlings were transferred onto new half-strength MMN medium and then placed into direct contact with the active growing edge of a fungal colony and then samples were harvested at 24 h, 48 h, 1 week, and 2 week post-contact. These plates were then closed using micropore tape to allow for gas exchange with the external environment.

value: Root tissue (axenic)

value: Root

value: Axenic control


title: Eucalypt_Ctrl_JW28

description: Biol Rep 4


title: BS1302_untreated_III

value: untreated


title: Eucalypt_Ctrl_JW26

description: Biol Rep 2


title: WT_AML_blast_cell_ip_rep_2


title: HFFF cells infected with ICP22-null mutant (12 hpi), replicate 1

value: no treatment


title: BS1302_untreated_II


title: Eucalypt_Ctrl_JW25

description: Biol Rep 1


title: WT_AML_blast_cell_ip_rep_1


title: HSV-1 lacking expression of UL41, replicate 2

description: followed ATACseq protocol

source_name: human fetal foreskin fibroblasts

growth_protocol: Human fetal foreskin fibroblasts were cultured in DMEM supplemented with 10% FBS, non-essential amino acids and P/S. Cells were infected at 60-80% confluency 24h after seeding (100000 cells/condition).

extract_protocol:
Infected cells were harvested by scraping at the indicated time points, washed, lysed with mild lysis buffer according to the published ATAC-seq protocol, incubated with Tn5 transposase (tagmentase) for 30 minutes, lysed in Qiagen's PB buffer, DNA purified according to the MinElute protocol.
12 PCR cycles according to the Illumina Nextera protocol using barcoded Nextera Primers.
35bp paired-end, NextSeq 500 (Illumina)

treatment_protocol: HFFF cells were inoculated for 15 minutes with an MOI of 10 and the time of the experiment started after the inoculum was removed. 300 µg/ml PAA was added to indicated samples for the full duration of the experiment.

tag: infection status

value: 8 hpi

tag: virus strain

value: strain 17


title: WT_AML_LIC_ip_rep_2


title: BS1302plus_II


title: BS1302_untreated_I


title: WT_AML_LIC_input_rep_4


title: HSV-1 lacking expression of UL41, replicate 1

description: followed ATACseq protocol


title: YF13 isolate 2

growth_protocol: Grown in Tryptic Soy Broth media  with shaking (180rpm), at 37 C, for 5 h.

treatment_protocol: Not treateted

value: LAC agr KO


title: YF13 isolate 3


title: KO-3

city: shenyang

first: Yang

last: Meng

address: Wenhua street num 11

department: College of Life and Health Sciences

institute: Northeastern University

data_processing:
The adaptor sequences and low-quality sequence reads were removed from the data sets. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: Cryptococcus neoformans var. grubii H99 .
Supplementary files format and content: tab-delimited text files include reads values for each Sample.

organism: Cryptococcus neoformans

source_name: Fungal cells

growth_protocol: WT and isw1∆ strains were inoculated into 50 ml of YPD broth and cultured overnight at 30°C in a shaking incubator. Cells were subcultured in 50 ml fresh YPD broth at OD600=0.2 until the OD600 reached 0.6 to 0.8. Three independent cultures for each strain were prepared. Every culture was washed three times with PBS and placed in a liquid nitrogen tank for RNA-seq.

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Fungal cells

value: Cryptococcus neoformans var. grubii H99


title: WT_AML_LIC_input_rep_3

value: bone marrow leukemia cells

value: LIC


title: HSV-1 lacking expression of ICP27, KOS, replicate 1

description: followed ATACseq protocol

value: strain KOS, 27LacZ


title: KO-2


title: WT_AML_LIC_input_rep_2

value: WT


title: KO-1


title: YF13 isolate 1


title: H99-3

value: wild type


title: H99-2


title: LAC isolate 3

source_name: LAC

value: LAC

value: LAC Wild Type


title: WT_AML_LIC_input_rep_1


title: H99-1


title: LAC isolate 2


title: WT_AML_blast_cell_input_rep_4

value: blast cell


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, +PAA, replicate 1

description: followed ATACseq protocol

value: 12 hpi

value: PAA 300ug/ml

value: strain F, R325


title: LAC isolate 1


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 4

description: followed ATACseq protocol


title: WT_AML_blast_cell_input_rep_2


title: WT_AML_blast_cell_input_rep_3


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 3

description: followed ATACseq protocol


title: Δsisfha-NQO, biol rep 3

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

description: The Sisfha deletion strain treated with NQO for 6 h, biol rep 3

data_processing:
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the whole genome of S. islandicus REY15A (Guo, et al., 2011) using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010.
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Saccharolobus islandicus

source_name: microbial cells

growth_protocol: S. islandicus strains were grown in MTSUV medium (Basic mineral medium+Typtone+Sucrose+Uracil+Vatamin) at 75 oC.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures were treated with 3 μM NQO when their OD(600nm) reached 0.2.

value: microbial cells

value: Sisfha knockout

value: NQO treatment


title: HSV-1 lacking expression of ICP27, KOS, replicate 2

description: followed ATACseq protocol

value: 8 hpi


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 2

description: followed ATACseq protocol


title: WT_AML_blast_cell_input_rep_1


title: Δsisfha-NQO, biol rep 2

description: The Sisfha deletion strain treated with NQO for 6 h, biol rep 2


title: Rat_APAP_24h_5

type: RNA

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

institute: University of Liverpool

description: Gene expression data from liver of rats treated with 1000 mg/kg APAP at 24h after administration

hyb_protocol: Following fragmentation, 30 µg of cRNA were hybridized for 16h at 45°C on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array or GeneChip™ Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control and low level analysis of raw fluorescence intensities was performed using the affy package (v1.64.0) in R v3.6.1. Raw data were processed using RMA normalization and a custom chip-definition file (CDF version 24 for mouse and version 19 for rat) from the BrainArray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated microarray probes to 18,180 and 13,877 genes for mouse and rat, respectively. Differential expression analyses were carried out using the limma package (v3.42.2) in R.

label: biotin

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

extract_protocol: Frozen liver samples were homogenised in Qiazol Lysis Reagent (Qiagen), and total RNA was purified following the manufacturer’s instructions.

value: liver

value: Sprague-Dawley

tag: Sex

value: male

value: 1000 mg/kg acetamnophen (o.g.)

tag: hours after treatment


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 1

description: followed ATACseq protocol


title: Leukemia cells-Prmt6-/-_rep3

description:
KO-3
p6_lgmp.3

data_processing:
All raw sequencing data were preprocessed using Trim_galore.
Kallisto was used to quantify the read counts for each transcripts (GRCm38, cDNA sequences).
The reads count for genes were assessed by R packages tximport.
Used HOMER (getDiffExpression.pl) to analysis differential genes.
Assembly: GRCm38
Supplementary files format and content: Prmt6_KO.vs.WT_expr.txt: Tab-delimited text file includes normalized reads for each Sample.

extract_protocol:
Bone marrow cells were extracted from 8- to 10-week-old Prmt6-/- and wild-type (WT) AML mice. L-GMP cells were sorted from WT and Prmt6-/- BM leukemia cells. Total RNA were extracted with Trizol, and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer, cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends, add A-tail, and connection connector. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: bone marrow leukemia cells

value: L-GMP cells

value: prmt6 KO


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, +PAA, replicate 2

description: followed ATACseq protocol

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph


title: Δsisfha-NQO, biol rep 1

description: The Sisfha deletion strain treated with NQO for 6 h, biol rep 1


title: Rat_APAP_24h_4


title: HSV-1 lacking expression of ICP0, replicate 2

description: followed ATACseq protocol

value: strain 17, dl1403


title: Leukemia cells-Prmt6-/-_rep2

description:
KO-2
p6_lgmp.2


title: Δsisfha, biol rep 3

description: The Sisfha deletion strain mock-treated for 6 h, biol rep 3

value: no treatment


title: Leukemia cells-Prmt6-/-_rep1

description:
KO-1
p6_lgmp.1


title: Leukemia cells-WT_rep3

description:
WT-3
wt_lgmp.3

value: WT


title: Rat_APAP_24h_2


title: Rat_APAP_24h_3


title: Leukemia cells-WT_rep2

description:
WT-2
wt_lgmp.2


title: HSV-1 wt, strain 17, +PAA, replicate 2

description: followed ATACseq protocol

value: strain 17


title: HSV-1 wt, strain 17, +PAA, replicate 1

description: followed ATACseq protocol

value: PAA 300ug/ml


title: Δsisfha, biol rep 2

description: The Sisfha deletion strain mock-treated for 6 h, biol rep 2


title: E233S-NQO, biol rep 3

description: The wild type strain E233S treated with NQO for 6 h, biol rep 3


title: Δsisfha, biol rep 1

description: The Sisfha deletion strain mock-treated for 6 h, biol rep 1


title: Leukemia cells-WT_rep1

description:
WT-1
wt_lgmp.1


title: E233S-NQO, biol rep 2

description: The wild type strain E233S treated with NQO for 6 h, biol rep 2


title: HSV-1 wt, strain 17, replicate 2

description: followed ATACseq protocol


title: E233S-NQO, biol rep 1

description: The wild type strain E233S treated with NQO for 6 h, biol rep 1


title: HSV-1 wt, strain 17, replicate 1

description: followed ATACseq protocol


title: HSV-1 lacking expression of ICP0, replicate 1

description: followed ATACseq protocol

value: 12 hpi


title: E233S, biol rep 3

description: The wild type strain E233S mock-treated for 6 h, biol rep 3

value: microbial cells


title: Rat_APAP_24h_1


title: Rat_APAP_09h_3

description: Gene expression data from liver of rats treated with 1000 mg/kg APAP at 9h after administration


title: Rat_APAP_09h_5


title: Rat_APAP_09h_4


title: Bulk 7, HC, Sigmoid colon, Female, 32

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

data_processing:
Quality filtering and adapter trimming was performed using Skewer version 2.2.8
Reads were mapped against the human reference genome using the STAR aligner version 2.5.2a.
Read counts per gene were obtained using RSEM version 1.2.31 and the Ensembl GTF annotation file (EMBL-EBI, Hinxton, UK).
Assembly: The genome used was GRCh38.p10, and gene annotation was based on Gencode version 27 (EMBL-EBI, Hinxton, UK)
Supplementary files format and content: tab delimited RSEM.genes.results, include the following columns:
Supplementary files format and content: gene_id: gene id
Supplementary files format and content: transcript_id(s): transcript id
Supplementary files format and content: length: gene length
Supplementary files format and content: effective_length: the abundance-weighted mean effective length of its isoforms
Supplementary files format and content: expected_count
Supplementary files format and content: TPM: transcripts per million
Supplementary files format and content: FPKM: fragments per kilobase of transcript per million fragments mapped

source_name: colon biopsy

extract_protocol:
RNA was isolated using an RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions and sequenced for bulk RNA-seq.
Barcoded RNAseq libraries were prepared from total RNA using a TruSeq stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were subjected to single-end sequencing (100 bp) on a HighSeq-3000 platform (Illumina, CA, USA) at the Translational Medicine and Genomics group (Boehringer-Ingelheim GmbH & Co, Biberach, Germany).

treatment_protocol: Biopsies were placed in RNAlater RNA Stabilization Reagent (QIAGEN, Hilden, Germany) and stored at –80ºC until RNA isolation.

value: colon biopsy

value: Female

tag: disease

value: HC

tag: tissue collection

value: Sigmoid colon

tag: disease type

tag: age

tag: publication id

value: Bulk 7

tag: batch

value: batch 3


title: E233S, biol rep 2

description: The wild type strain E233S mock-treated for 6 h, biol rep 2

tag: tissue

tag: strain

tag: cell type

tag: genotype

tag: treatment


title: mock infection, replicate 1

description: followed ATACseq protocol


title: mock infection, replicate 2

description: followed ATACseq protocol


title: E233S, biol rep 1

description: The wild type strain E233S mock-treated for 6 h, biol rep 1


title: Rat_APAP_09h_2

value: liver

value: Sprague-Dawley

value: male

value: 1000 mg/kg acetamnophen (o.g.)


title: Bulk 6, HC, Sigmoid colon, Female, 49

value: Bulk 6


title: Rat_APAP_06h_5

description: Gene expression data from liver of rats treated with 1000 mg/kg APAP at 6h after administration


title: Bulk 8, HC, Sigmoid colon, Female, 52

value: Bulk 8


title: Rat_APAP_09h_1


title: Bulk 5, HC, Sigmoid colon, Male, 27

value: Male

value: Bulk 5


title: Rat_APAP_06h_4


title: Armillaria_Ctrl_JW4

description: Biol Rep 4

organism: Armillaria luteobubalina

source_name: Free living mycelium

value: Free living mycelium

value: Mycelium

value: Axenic control


title: Bulk 3, HC, Sigmoid colon, Male, 68

value: colon biopsy

value: Bulk 3

value: batch 2


title: Armillaria_Ctrl_JW2

description: Biol Rep 2


title: Rat_APAP_06h_2


title: Bulk 2, HC, Sigmoid colon, Male, 51

value: HC

value: Sigmoid colon

value: Bulk 2


title: Armillaria_Ctrl_JW3

description: Biol Rep 3


title: Rat_APAP_06h_1

value: liver


title: Bulk 43, UC, ascending, male, 19

value: UC

value: ascending

value: Pancolitis

value: Bulk 43


title: Armillaria_Ctrl_JW1

description: Biol Rep 1


title: Bulk 1, HC, Sigmoid colon, Female, 52

value: Female

value: Bulk 1


title: Steatotic liver macrophage_CC_2 [B000918]

city: Nagoya

first: Michiko

last: Itoh

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
Low-quality reads and adapter sequences were trimmed using fastp software (doi: 10.1093/bioinformatics/bty560).
The reads were mapped to the mm10 reference genome using HISAT2 (doi: 10.1038/s41587-019-0201-4) followed by transcript assembly and quantification using StringTie (doi:10.1038/nbt.3122).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

growth_protocol: Hepatic macrophages were seeded on collagen-coated plates and maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was purified using RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
RNA-seq libraries were constructed by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB) and MGIEasy RNA Directional Library Prep Set (MGI), according to the manufacturer’s instruction.

treatment_protocol: Macrophages treated with cholesterol crystals (500 ug/ml) with or without β-cyclodextrin polyrotaxane (1mM) for 24 hours.

tag: strain background

value: macrophage

value: cholesterol crystals


title: Bulk 4, HC, Sigmoid colon, Female, 51

value: Bulk 4

value: batch 3


title: Rat_APAP_06h_3

value: Sprague-Dawley

value: male

value: 1000 mg/kg acetamnophen (o.g.)


title: Steatotic liver macrophage_veh_2 [B000916]

value: vehicle


title: Bulk 42, UC, rectum, female, 37

value: colon biopsy

value: female

value: rectum

value: proctitis

value: Bulk 42

value: batch 2


title: Steatotic liver macrophage_CC_1 [B000917]

value: liver


title: Bulk 22, CD, Rectum, Female, 56

value: Female

value: CD

value: Rectum

value: Ileocolonic

value: Bulk 22


title: Bulk 21, CD, Transverse colon, Male, 42

value: Male

value: Transverse colon

value: Bulk 21


title: Rat_APAP_03h_4

description: Gene expression data from liver of rats treated with 1000 mg/kg APAP at 3h after administration

value: Sprague-Dawley

value: male

value: 1000 mg/kg acetamnophen (o.g.)


title: Rat_APAP_03h_3


title: De-HA-3

city: Chengdu

first: Bo

last: Yuan

address: Jiuyanqiao Wangjiang Road

institute: Sichuan University

description: Gene expression after 3 days cultured with De-HA scaffold

hyb_protocol: The RNA was diluted using hybridization buffer after heating at 60 C for 30 min. A volume of 100 μL of hybridization solution was dispensed into the gasket slide. The gasket slide was further assembled into the gene expression microarray slide.

scan_protocol: After being incubated at 65 C for 17 hours, the hybridized arrays were washed and scanned using an Agilent DNA microarray Scanner (Agilent Technology, USA).

data_processing: The acquired array images were analyzed using Agilent Feature Extraction software (version 11.0.1.1). The GeneSpring GX v12.1 software package (Agilent Technology, USA) was used for quantile normalization and data processing.

source_name: MC3T3-E1 cell cultured with De-HA scaffold

label_protocol: Total RNA was linearly amplified and labeled with Cy3-UTP for each sample. After purifying, the labeled RNA was fragmented by adding blocking agent and fragmentation buffer.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions described in the protocol. RNA quality and quantity were assessed using a NanoDrop ND-1000. Then, RNA integrity was evaluated by denaturing agarose gel electrophoresis.

treatment_protocol: MC3T3-E1 were seeded on each scaffold at a density of 1 × 105 per/well in 24-well plates and then cultured for 3 days.

tag: cell line

value: De-HA scaffold


title: HCC-OC-23

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

data_processing:
raw data was converted to fasta file at http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/fastq2fasta/. Obtained fasta file was processed with miRDeep* v3.1  with using h19 genome and miRBase v19
Genome_build: h19
Supplementary_files_format_and_content: miRDeep* result file

source_name: HCC patient 42

extract_protocol:
Total RNA from 200 ul of serum was prepared using miRNeasy mini kit (Qiagen, Hilden Germany) according to the manufacturer’s instruction. Exosome rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 ul of serum was mixed with 250 ul of Exoquick and incubated for 12 hr at 4℃. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved with 200 ul of PBS with vigorous vortex. RNA was extracted using miRNeasy mini kit (Qiagen).
1) Filter Small RNA Separate RNA segment of different size by PAGE gel,　select 18-30nt stripe and recycle. 2) Adaptor ligation Prepare connection system，blend and centrifuge，connect warmly for a period of time. 3) RT-PCR Prepare reverse transcription system，connect warmly for a period on PCR instrument，then PCR amplification. 4) Purify PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recycled products in EB solution. Finally, label to finish the library construction. 5) Purify PCR products: Use Agilent 2100 Bio-analyzer and the ABI StepOnePlus Real-Time PCR System to test quality and production of the prepared library.

treatment_protocol: Peripheral blood was collected from all subjects directly into serum tubes before anti-viral treatment. The tubes were centrifuged at 1,500 g for 10 min at 4℃, sera were aliquoted and additionally centrifuged at 2,000 g to completely remove any remaining cells. Sera were stored at -80℃ until use.

tag: disease state

value: HCC patient

value: peripheral blood

tag: gender

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp

tag: cea


title: FeMnSi-2

description: Gene expression after 3 days cultured with FeMnSi scaffold

source_name: MC3T3-E1 cell cultured with FeMnSi scaffold

value: FeMnSi scaffold


title: Bulk 19, CD, Sigmoid colon, Female, 56

value: colon biopsy

tag: Sex

tag: disease

tag: tissue collection

value: Sigmoid colon

tag: disease type

value: Colonic

tag: age

value: Bulk 19

value: batch 2


title: Steatotic liver macrophage_veh_1 [B000915]

tag: tissue

value: liver

tag: cell type

value: macrophage

value: vehicle


title: De-HA-2

tag: treatment


title: Rat_APAP_03h_2

tag: strain

tag: hours after treatment


title: Rat_APAP_03h_5


title: FeMnSi-3

tag: cell line


title: FeMnSi-1


title: Normal liver macrophage_CC_1 [B000913]

tag: strain background

tag: genotype

value: WT

value: cholesterol crystals


title: Bulk 18, CD, Sigmoid colon, Male, 33

value: Male

value: CD

tag: publication id

value: Bulk 18

tag: batch


title: Rat_APAP_03h_1

value: Sprague-Dawley

value: male

value: 1000 mg/kg acetamnophen (o.g.)


title: Normal liver macrophage_CC_2 [B000914]


title: HCC-OC-20

source_name: HCC patient 39

tag: disease state

value: HCC patient

value: peripheral blood

tag: gender

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp


title: Rat_Vehicle_24h_5

description: Gene expression data from liver of rats treated with vehicle at 24h after administration

tag: Sex

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)


title: De-HA-1

value: De-HA scaffold


title: Rat_Vehicle_24h_3

tag: tissue


title: HCC-OC-19

source_name: HCC patient 38

tag: age

tag: cea


title: HCC-OC-22

source_name: HCC patient 41


title: HCC-OC-21

source_name: HCC patient 40


title: HCC-OC-14

source_name: HCC patient 36


title: HCC-OC-17

source_name: HCC patient 37


title: Bulk 41, UC, rectum, male, 48

value: colon biopsy

tag: disease

value: UC

tag: tissue collection

value: rectum

tag: disease type

value: Proctitis

value: Bulk 41


title: Bulk 15, CD, Sigmoid colon, Female, 64

value: Female

value: Sigmoid colon

value: Ileocolonic

value: Bulk 15

value: batch 2


title: HCC-OC-10

source_name: HCC patient 34


title: Rat_Vehicle_24h_2

value: liver

tag: strain

value: Sprague-Dawley

tag: treatment

tag: hours after treatment


title: Rat_Vehicle_24h_1

value: male


title: Bulk 14, CD, Descending colon, Female, 35

value: CD

value: Descending colon

tag: publication id

value: Bulk 14

tag: batch


title: HCC-OC-08

source_name: HCC patient 32

tag: disease state

value: HCC patient

value: peripheral blood

tag: gender


title: Bulk 38, UC, sigmoid, male, 28

value: colon biopsy

value: UC

value: sigmoid

value: Pancolitis

value: Bulk 38


title: Bulk 39, UC, sigmoid, female, 29

value: female

value: Bulk 39


title: Bulk 13, CD, Sigmoid colon, Male, 67

value: Male

value: Sigmoid colon

value: Colonic

value: Bulk 13


title: Bulk 17, CD, Descending colon, Female, 31

value: Female

value: Bulk 17

value: batch 2


title: HCC-OC-06

source_name: HCC patient 31

value: male

tag: hbsag

tag: anti-hcv


title: Rat_Vehicle_09h_5

description: Gene expression data from liver of rats treated with vehicle at 9h after administration

value: liver

value: Sprague-Dawley

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)


title: Rat_Vehicle_09h_2


title: Rat_Vehicle_09h_1


title: Rat_Vehicle_09h_3


title: HCC-OC-05

source_name: HCC patient 30

value: HCC patient

value: peripheral blood

tag: afp

tag: dcp


title: HCC29

source_name: HCC patient 28

tag: tissue

value: NT


title: Normal liver macrophage_veh_1 [B000911]

tag: strain background

tag: cell type

value: macrophage

tag: genotype

value: WT

value: vehicle


title: HCC30

source_name: HCC patient 29

tag: age

value: female

tag: cea


title: Rat_Vehicle_09h_4

source_name: Liver

tag: strain

tag: Sex


title: Bulk 36, UC, sigmoid, male, 62

source_name: colon biopsy

value: colon biopsy

tag: disease

value: UC

tag: tissue collection

value: sigmoid

tag: disease type

value: Left-sided colitis

value: Bulk 36


title: Bulk 12, CD, Descending colon, Female, 39

value: Female

value: CD

value: Descending colon

value: Ileocolonic

tag: publication id

value: Bulk 12

tag: batch

value: batch 2


title: HCC28

source_name: HCC patient 27

tag: disease state

value: HCC patient

value: peripheral blood

tag: gender

tag: hbsag


title: Rat_Vehicle_06h_3

description: Gene expression data from liver of rats treated with vehicle at 6h after administration

value: liver

value: Sprague-Dawley

value: male

tag: treatment

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)

tag: hours after treatment


title: HCC26

source_name: HCC patient 25

tag: tissue

tag: anti-hcv

tag: afp

tag: dcp

value: NT


title: Bulk 34, UC, descending, female, 61

value: colon biopsy

value: female

value: UC

value: descending

tag: age

value: Bulk 34


title: Rat_Vehicle_06h_4

tag: strain


title: Rat_Vehicle_24h_4

tag: Sex


title: Rat_Vehicle_06h_2


title: Bulk 33, UC, sigmoid, male, 56

tag: disease

value: sigmoid

value: Pancolitis

value: Bulk 33


title: Bulk 37, UC, sigmoid, male, 44

tag: tissue collection

value: Bulk 37

value: batch 3


title: HCC11

source_name: HCC patient 15

value: HCC patient

tag: cea


title: Bulk 11, CD, Rectum, Female, 53

value: Female

value: CD

value: Rectum

tag: disease type

value: Ileocolonic

tag: publication id

value: Bulk 11

value: batch 2


title: HCC13

source_name: HCC patient 17

tag: disease state

value: peripheral blood

value: male

value: NT


title: HCC06

source_name: HCC patient 10

tag: gender

tag: alp

tag: cgtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: t-chol

tag: hbalc


title: Bulk 32, UC, sigmoid, male, 43

tag: tissue

value: colon biopsy

value: UC

tag: age

value: Bulk 32

tag: batch


title: NL108

value: normal

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil


title: Bulk 56, UC, sigmoid, female, 27

tag: Sex

value: female

tag: disease

tag: tissue collection

value: sigmoid

tag: disease type

value: Pancolitis

tag: publication id

value: Bulk 56


title: Rat_Vehicle_03h_2

description: Gene expression data from liver of rats treated with vehicle at 3h after administration

tag: tissue

value: liver

tag: strain

value: Sprague-Dawley

tag: treatment

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)

tag: hours after treatment


title: NL91

tag: disease state

tag: age

tag: gender

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: cea

tag: alp

tag: cgtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: t-chol

tag: hbalc


title: Rat_Vehicle_03h_1

tag: tissue

tag: strain

tag: Sex

tag: treatment

tag: hours after treatment


title: Rat_Vehicle_03h_4


title: NL89

tag: disease state

tag: age

tag: gender

tag: date

tag: afp

tag: dcp

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil


title: Rat_Vehicle_03h_3


title: Rat_Vehicle_06h_1


title: Bulk 53, UC, sigmoid, male, 50

tag: disease

tag: tissue collection

tag: disease type

tag: publication id

value: Bulk 53

tag: batch

value: batch 1


title: NL85

tag: tissue

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: cea

tag: alp

tag: cgtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: t-chol

tag: hbalc


title: NL78

tag: disease state

tag: age

tag: gender

tag: date

tag: afp

tag: dcp

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil


title: NL98

tag: tissue

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: cea

tag: alp

tag: cgtp

tag: hb


title: Rat_Baseline_0h_4

description: Gene expression data from liver of untreated rats (baseline 0h controls)

tag: strain

tag: Sex

tag: treatment

value: Untreated

tag: hours after treatment


title: Bulk 54, UC, sigmoid, female, 40

tag: disease

tag: tissue collection

tag: disease type

value: Left-sided colitis

tag: age

tag: publication id

value: Bulk 54

tag: batch


title: Bulk 52, UC, sigmoid, female, 39

tag: tissue

value: Bulk 52


title: Rat_Baseline_0h_3

value: male


title: Rat_Baseline_0h_5


title: Bulk 10, CD, Descending colon, Male, 47

value: colon biopsy

value: Male

value: CD

value: Descending colon

value: Colonic

value: Bulk 10

value: batch 2


title: Bulk 29, CD, Sigmoid colon, Male, 48

value: Sigmoid colon

value: Ileocolonic

value: Bulk 29


title: NL67

tag: disease state

value: normal

value: peripheral blood

tag: gender

value: female

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: afp

value: NT

tag: dcp

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil

tag: alb

tag: bs

tag: tg

tag: t-chol

tag: hbalc


title: Bulk 55, UC, rectum, female, 59

tag: tissue

tag: Sex

tag: disease

value: UC

tag: tissue collection

value: rectum

tag: disease type

value: Pancolitis

tag: age

tag: publication id

value: Bulk 55

tag: batch


title: Bulk 30, CD, Rectum, Male, 41

value: colon biopsy

value: Male

value: Rectum

value: Bulk 30

value: batch 1


title: NL50

tag: disease state

tag: gender

tag: date

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp

tag: cea

tag: ast

tag: alt

tag: alp

tag: cgtp

tag: hb


title: HCC-OC-09

source_name: HCC patient 33

value: HCC patient

tag: tissue


title: Eucalypt+Armillaria_2wk_JW24

description: Biol Rep 4

organism:
Eucalyptus grandis
Armillaria luteobubalina

source_name: Symbiotic tissue

value: Symbiotic tissue

tag: cell type

value: Root and mycelium

tag: genotype

value: HWK-2 and 2068

tag: treatment

value: 2 week symbiosis


title: HCC-OC-13

source_name: HCC patient 35

tag: disease state

value: peripheral blood

tag: age

value: male


title: Rat_Baseline_0h_2

value: liver

tag: strain

value: Sprague-Dawley

tag: Sex

value: Untreated

tag: hours after treatment


title: Bulk 51, UC, sigmoid, male, 41

tag: disease

value: UC

tag: tissue collection

value: sigmoid

tag: disease type

value: proctitis

tag: publication id

value: Bulk 51

tag: batch


title: NL44

value: normal

tag: gender

value: female

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: afp

value: NT

tag: dcp

tag: cea

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil

tag: alp

tag: alb

tag: bs

tag: t-chol

tag: hbalc


title: Rat_Baseline_0h_1

tag: tissue

tag: strain

tag: Sex

tag: treatment

tag: hours after treatment


title: Eucalypt+Armillaria_2wk_JW23

description: Biol Rep 3

tag: cell type

tag: genotype


title: Bulk 50, UC, sigmoid, male, 50

value: colon biopsy

tag: disease

tag: tissue collection

tag: disease type

value: Pancolitis

tag: age

tag: publication id

value: Bulk 50

tag: batch

value: batch 1


title: Eucalypt+Armillaria_2wk_JW22

description: Biol Rep 2

value: Symbiotic tissue

value: Root and mycelium

value: HWK-2 and 2068

value: 2 week symbiosis


title: Bulk 49, UC, sigmoid, male, 38

value: male

value: Left-sided colitis

value: Bulk 49


title: NL41

tag: disease state

value: healthy

value: peripheral blood

tag: gender

tag: date

tag: height

tag: weight

tag: bmi

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp

tag: cea

tag: ast

tag: alt

tag: wbc

tag: plt

tag: t-bil

tag: alp

tag: cgtp

tag: hb

tag: alb


title: Eucalypt+Armillaria_2wk_JW21

description: Biol Rep 1

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Bulk 28, CD, Ascending colon, Male, 29

tag: Sex

value: Male

tag: disease

value: CD

tag: tissue collection

value: Ascending colon

tag: disease type

value: Colonic

tag: age

tag: publication id

value: Bulk 28

tag: batch

value: batch 3


title: ccc-24

source_name: ICC patient 24

tag: disease state

value: ICC

tag: gender

value: female

tag: hbsag

tag: anti-hcv

tag: afp

value: NT

tag: dcp

tag: cea


title: Eucalypt+Armillaria_1wk_JW20

description: Biol Rep 4

tag: tissue

value: Symbiotic tissue

tag: cell type

value: Root and mycelium

value: 1 week symbiosis


title: ccc-23

source_name: ICC patient 23

value: male


title: Eucalypt+Armillaria_1wk_JW19

description: Biol Rep 3

tag: genotype

value: HWK-2 and 2068

tag: treatment


title: Bulk 27, CD, Transverse colon, Female, 60

value: colon biopsy

tag: Sex

value: Female

tag: disease

value: Transverse colon

value: Bulk 27

value: batch 1


title: Bulk 48, UC, sigmoid, female, 25

value: UC

tag: tissue collection

value: sigmoid

tag: disease type

value: Pancolitis

value: Bulk 48


title: ccc-22

source_name: ICC patient 22

value: ICC

value: peripheral blood

tag: age


title: Eucalypt+Armillaria_1wk_JW18

description: Biol Rep 2


title: ccc-20

source_name: ICC patient 20

value: NT


title: Bulk 26, CD, Sigmoid colon, Female, 24

value: CD

value: Sigmoid colon

value: Colonic

tag: publication id

value: Bulk 26

tag: batch


title: Eucalypt+Armillaria_1wk_JW17

description: Biol Rep 1

value: Symbiotic tissue

value: Root and mycelium

value: HWK-2 and 2068

value: 1 week symbiosis


title: Bulk 47, UC, sigmoid, male, 69

value: colon biopsy

value: male

value: Left-sided colitis

value: Bulk 47


title: ccc-19

source_name: ICC patient 19

tag: disease state

tag: gender

value: female


title: Eucalypt+Armillaria_48h_JW16

description: Biol Rep 4

value: 48 hour symbiosis


title: Eucalypt+Armillaria_48h_JW15

description: Biol Rep 3


title: Bulk 46, UC, sigmoid, male, 35

value: UC

value: sigmoid

value: Bulk 46

value: batch 1


title: ccc-17

source_name: ICC patient 17

value: ICC

value: peripheral blood

tag: hbsag

tag: anti-hcv

value: NT


title: Bulk 45, UC, rectum, female, 37

value: rectum

value: Bulk 45


title: Eucalypt+Armillaria_48h_JW14

description: Biol Rep 2

value: Symbiotic tissue

value: Root and mycelium

value: HWK-2 and 2068


title: Bulk 44, UC, sigmoid, male, 31

value: colon biopsy

value: male

value: Pancolitis

value: Bulk 44


title: ccc-16

source_name: ICC patient 16

value: female

tag: afp

tag: dcp


title: ccc-15

source_name: ICC patient 15

tag: tissue

tag: cea


title: Eucalypt+Armillaria_24h_presymbiosis_JW12

description: Biol Rep 4

source_name: Presymbiosis root and mycelium

value: Presymbiosis root and mycelium

tag: cell type

tag: genotype

value: 24 hour pre-symbiosis


title: OCU.CCC14

source_name: ICC patient 14


title: Bulk 25, CD, Rectum, Male, 20

source_name: colon biopsy

tag: Sex

value: Male

value: CD

value: Rectum

value: Colonic

value: Bulk 25

value: batch 3


title: OCU.CCC11

source_name: ICC patient 11

value: ICC

value: peripheral blood

value: NT


title: Bulk 24, CD, Ascending colon, Male, 37

tag: disease

value: Ascending colon

value: Ileocolonic

value: Bulk 24

value: batch 1


title: Eucalypt+Armillaria_24h_presymbiosis_JW11

description: Biol Rep 3

value: Root and mycelium

value: HWK-2 and 2068

tag: treatment


title: Bulk 23, CD, Rectum, Female, 44

value: colon biopsy

value: Female

tag: tissue collection

tag: disease type

value: Bulk 23


title: Eucalypt+Armillaria_24h_presymbiosis_JW10

description: Biol Rep 2

value: Presymbiosis root and mycelium

value: 24 hour pre-symbiosis


title: Bulk 20, CD, Descending colon, Male, 22

value: Male

value: CD

value: Descending colon

value: Colonic

tag: age

tag: publication id

value: Bulk 20


title: ccc-18

source_name: ICC patient 18

tag: disease state

value: ICC

value: peripheral blood

value: male

value: NT


title: Eucalypt+Armillaria_24h_JW8

description: Biol Rep 4

value: Symbiotic tissue

value: 24 hour symbiosis


title: Bulk 16, CD, Ascending colon, Male, 35

value: Ascending colon

value: Ileocolonic

value: Bulk 16

tag: batch

value: batch 1


title: OCU.CCC09

source_name: ICC patient 9

tag: gender

value: female

tag: hbsag


title: OCU.CCC07

source_name: ICC patient 7

tag: anti-hcv

tag: afp


title: OCU.CCC08

source_name: ICC patient 8

tag: tissue

tag: dcp


title: Bulk 31, UC, sigmoid, female, 57

value: colon biopsy

value: UC

value: sigmoid

value: Pancolitis

value: Bulk 31


title: Eucalypt+Armillaria_24h_JW7

description: Biol Rep 3

source_name: Symbiotic tissue

tag: cell type

value: Root and mycelium

value: HWK-2 and 2068


title: Eucalypt+Armillaria_48h_JW13

description: Biol Rep 1

tag: genotype

value: 48 hour symbiosis


title: Eucalypt+Armillaria_24h_JW6

description: Biol Rep 2


title: Bulk 9, CD, Sigmoid colon, Male, 33

tag: Sex

value: Male

value: CD

value: Sigmoid colon

value: Colonic

value: Bulk 9


title: Eucalypt+Armillaria_24h_JW5

description: Biol Rep 1

value: Symbiotic tissue

value: 24 hour symbiosis


title: OCU.CCC04

source_name: ICC patient 4

value: ICC

value: peripheral blood

value: male

tag: cea


title: APC-2Rapa

status: Public on Jun 19 2023

city: Philadelphia

first: Peter

middle: S

last: Klein

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

data_processing:
Raw data was counted against the transcriptome described in Ensembl build 91 for the GRCz10 genome using Salmon
Assembly: GRCz10
Supplementary files format and content: raw counts per gene per sample - comma separated values

organism: Danio rerio

source_name: whole embryo

growth_protocol: standard zebrafish embryo development

extract_protocol:
Triazol/DNaseI/RNeasy/polyA selected
NEB Next Ultra RNA Library Kit

treatment_protocol: control vs 100nM rapamycin

value: whole embryo

value: embryo 48hpf

value: apc-mcr

tag: treatment

value: Rapamycin


title: APC-1Rapa


title: APC-3Rapa


title: OCU.CCC10

source_name: ICC patient 10

value: female

value: NT


title: WT-3Rapa

value: WT


title: Eucalypt+Armillaria_24h_presymbiosis_JW9

description: Biol Rep 1

value: Presymbiosis root and mycelium

value: Root and mycelium

value: HWK-2 and 2068

value: 24 hour pre-symbiosis


title: WT-2Rapa


title: WT-1Rapa


title: APC-3

value: Control


title: APC-2


title: APC-1


title: WT-3


title: Bulk 40, UC, sigmoid, male, 55

value: colon biopsy

tag: disease

value: UC

tag: tissue collection

value: sigmoid

value: Pancolitis

value: Bulk 40

value: batch 1


title: WT-1

value: whole embryo

tag: age

value: embryo 48hpf


title: WT-2


title: OCU.CCC05

source_name: ICC patient 5

value: ICC

value: peripheral blood

value: male


title: Normal liver macrophage_veh_2 [B000912]

source_name: liver

value: liver

tag: strain background

value: macrophage

value: WT

value: vehicle


title: WT + AntiA_rep1

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Assembly: Mus_musculus.GRCm38.95
Supplementary files format and content: xlsx file with counts per gene per sample

source_name: MEFs

growth_protocol: Mouse embryonic fibroblasts (MEFs) were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment

treatment_protocol: mouse embryonic fibroblasts (MEFs) pretreated with DMSO control or v-ATPase inhibitor Concanamycin A (ConA) (200 nM) for 1 h, and then co-treated with or without Dox (30 μg/ml), AntiA (2 μM) or FCCP (2 μM) for 24 h

value: MEFs

value: AntiA


title: WT + FCCP_rep1

value: FCCP


title: WT + FCCP_rep3


title: WT + ConA + FCCP_rep1

value: ConA and FCCP


title: WT + ConA + AntiA_rep2

value: ConA and AntiA


title: WT + FCCP_rep2


title: WT + ConA + FCCP_rep2


title: WT + AntiA_rep3


title: WT + ConA + AntiA_rep3


title: WT + ConA + Dox_rep3 [R3]

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: xlsx file with counts per gene per sample

source_name: WT + ConA + Dox_rep3

treatment_protocol: mouse embryonic fibroblasts (MEFs) pretreated with DMSO control or v-ATPase inhibitor Concanamycin A (ConA) (200 nM) for 1 h, and then co-treated with or without Dox (30 μg/ml) for 24 h

value: ConA and Dox


title: WT + AntiA_rep2


title: WT + ConA + AntiA_rep1


title: WT + ConA + Dox_rep2 [R2]

source_name: WT + ConA + Dox_rep2


title: WT + ConA + Dox_rep1 [R1]

source_name: WT + ConA + Dox_rep1


title: WT + Dox_rep1 [P1]

source_name: WT + Dox_rep1

value: Dox


title: WT + Dox_rep2 [P2]

source_name: WT + Dox_rep2


title: WT + ConA_rep3 [O3]

source_name: WT + ConA_rep3

value: ConA