title: OCT4-GFP negative somatic cells, saline control, biological rep 3, female

description:
SOMAsal3
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv

source_name: OCT4-GFP negative somatic cells sorted from E15.5 ovary

treatment_protocol: Pregnant dams were dosed by IP injection at E12.5, E13.5, E14.5 and E15.5 with either 10 μg dex (Sigma) per gram of body weight, or with an equal volume of saline vehicle control. Ovaries were collected at E15.5, and germ cells FACS sorted from somatic cells using OCT4-GFP transgene.

value: ovary

value: female


title: Blood_Platelets_TR5111-NSCLC-MAAS

status: Public on Jun 12 2023

type: SRA

city: Amsterdam

first: Mafalda

last: Antunnes

state: zuid holland

address: de boelelaan 1118

department: NRG

country: Netherlands

institute: Amsterdam UMC

library_source: transcriptomic

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Assembly: hg19
Supplementary files format and content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

molecule: total RNA

organism: Homo sapiens

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

tag: cell type

value: Thrombocytes

tag: cancer stage

tag: patient group

value: NSCLC


title: Blood_Platelets_TR5109-NSCLC-MAAS


title: HDR Pool 3 GL2 - Rep 1 gfp -

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 460 West 12th Ave

department: Department of Biomedical Informatics

country: USA

institute: The Ohio State University

library_source: genomic

data_processing:
For pool 3, the FASTQ files containing barcode variants and a barcode map were processed using Enrich2 software. Enrich2 calculates the functional score for each variant from its abundance in the GFP-positive and GFP-negative pools. The functional score is obtained by normalizing the slope of the line connecting the control and experimental conditions for each pool by the wild-type adjusted by log ratio. The functional score was reported in log2 for each variant tested with a value of 0 representing normal wild-type function.
The process of interpreting variant scores involved two steps. First, two subpopulations of variants containing synonymous and nonsense changes were identified and analyzed in a scatter plot to display the relationship between the variant read count and their functional scores for each subpopulation. Under control conditions, the endogenous BRCA1 present in every cell functioned normally and was used as a baseline for the DNA damage repair assay. Thus, it was anticipated that all variant scores in this condition would cluster around 0 on the scatter plot. The minimum-read count threshold was determined to be the highest point where the results for any variant deviated from this functionally normal value. To confirm this threshold, using the scatter plot from the conditions in which the endogenous BRCA1 was depleted by transfecting siBRCA1-3’UTR, nonsense variants were expected to exhibit negative functional scores indicative of loss of function, and the read-count threshold would be higher than any nonsense mutants that scored as functionally normal. If the read count values from the conditions were different, we selected the higher threshold. Data with lower read counts than this empirically defined value were discarded. To further refine the data, the mean variance across four replicates was calculated, and variants with variance greater than 1 were removed from the analysis. These two filters removed variants with low frequency of read counts and high variability of results. The remaining variants have high frequency of datapoints that were relatively consistent in score, and we used these to evaluate functional effects of the amino acid change for each variant.
After applying the minimum reads-count threshold, a histogram was generated to visualize the distribution of the variant library (Figure S1, bottom right). Three subpopulations, missense, nonsense, and synonymous, were analyzed separately for each condition. To determine the functional score thresholds, the population of missense variants in the control siRNA experimental condition was modeled as a Gaussian distribution, and the lowest 1% of values were selected as the threshold for loss of function. Similarly, using the distribution plot for the BRCA1 siRNA condition, the population of nonsense variants were modeled as a Gaussian distribution and the highest 1% was defined as functionally normal. Only variants that were observed in at least three replicates were included in the analysis.
Assembly: genome_build.txt
Supplementary files format and content: .h5 files with counts and scores. Columns names are descriptive, _- denotes noGFP, _+ denotes GFP samples.

molecule: genomic DNA

source_name: HeLa

growth_protocol: DMEM supplemented with 10% fetal bovine serum and hygromycin B at 550 ¬µg/mL.

extract_protocol:
Inverse PCR reactions of the plasmid encoding the BRCA1 cDNA generate full length product, but one of the codons in the PCR oligonucleotide contains NNK (where N = A, C, G, T and K = G, T) in place of the terminal codon encoded by the oligonucleotide. For the 97 codons analyzed in this study, 97 different inverted oligonucleotide pairs were separately prepared and subjected to PCR. The PCR reactions were then pooled and circularized by the action of DNA ligase. An oligonucleotide containing a 16 bp degenerate oligonucleotide barcode was inserted upstream of the BRCA1 coding sequence, and long-read sequencing using a PacBio Sequel paired each barcode with a different BRCA1 variant. The plasmid library for pools 3 was transfected along with the FLP-In recombinase into a HeLa derived cell line that contained in its genome a single FLP-In Recombinase Target (FRT) sequence  and a single DNA sequence for measuring homology directed repair (HDR) of DNA double-strand breaks.
The HDR assay is initiated by transfecting a plasmid encoding the I-SceI endonuclease, which generates a DNA cut in one of the defective GFP sequences, and if the cell is competent for HDR, recombination repairs the defective GFP coding sequence, and the cell becomes GFP-positive. We performed this HDR assay under two conditions. In the first condition, we have transfected a control siRNA, and the cells contain endogenously expressed wild-type BRCA1. In the second condition, we have transfected an siRNA targeting the 3’-UTR of the endogenously expressed BRCA1 mRNA, and the cell is then dependent on the BRCA1 variant expressed from the FRT site. GFP-positive cells were separated from GFP-negative cells using flow sorting, and the barcode in the genome of the cells was isolated by PCR and analyzed by short read sequencing. The frequency of the barcode in the GFP-positive cells (functional for HDR) is compared under the conditions of depletion of the endogenous BRCA1 protein using the siRNA targeting the BRCA1 3’-UTR to the condition of the control siRNA. From the abundances of the barcodes in the various samples, we calculated a functional score using the program Enrich2.

treatment_protocol: HDR reporter assays and FACS sorts were performed for the BRCA1 variant libraries in quadruplicate. A confluent 10 cm plate of HeLa BRCA1 variant cell line was trypsinized and resuspended in 10 mL of culture media. 65 ml of the suspension was plated in each of 48 wells across two 24-well tissue culture plates. 24 hours later, each well was transfected with 30 pmol of siRNA and 1.5 ml Oligofectamine (ThermoFisher). Oligofectamine was diluted with 6 ml Opti-MEM and siRNA was diluted with 25 ml Opti-MEM for 5 minutes. The dilutions were then combined and incubated for an additional 30 minutes. The transfection mixture was then applied directly to the cells. 24 hours later, the cells were trypsinized and transferred to four 6-well tissue culture plates, then incubated for another 24 hours. Each well was then transfected with 50 pmol of siRNA, 3 mg pCBASceI (for I-SceI expression), and 3 ml Lipofectamine 2000. Plasmid and siRNA were diluted in 125 ml Opti-MEM and Lipofectamine was diluted in 125 ml Opti-MEM, then incubated for 5 minutes. The dilutions were combined and incubated for an additional 20 minutes. The transfection mixture was then applied directly to cells. Four to six hours later, the culture media was replaced with fresh media. BRCA1 3‚ÄôUTR siRNA, BRCA1 coding sequence siRNA and control siRNA were used in both rounds of transfection. After 24 hours, one well of cells treated with each condition was analyzed for GFP expression using flow cytometry to confirm transfection efficiency. If cells treated with control siRNA and 3‚ÄôUTR siRNA fell within 7-9% and 4-7% GFP+ cells respectively, and cells treated with BRCA1 coding sequence siRNA were 1-2% GFP+, the experiment would proceed. 72 hours post-transfection, the cells were pooled according to treatment and sorted using fluorescent activated cell sorting (FACS) using an Aria IIu instrument. Cells were resuspended and pooled in filter-sterilized sorting buffer containing 1X Phosphate Buffered Saline (Ca2+/Mg2+¬†free), 5 mM EDTA, 25 mM HEPES pH 7.0, and 1% heat-inactivated fetal bovine serum dialyzed against Ca2+/Mg2+¬†PBS. A minimum of 500,000 GFP+ cells and a maximum of 2 million GFP- cells were collected per pool.

tag: cell line

value: HeLa

tag: condition

value: Control group

tag: treatment

value: GL2 siRNA


title: HDR Pool 3 GL2 - Rep 2 gfp -


title: TMA1_20221116 | 004 | Liver cells

city: Basel

first: Sarp

last: Uzun

address: Schönbeinstrasse 40

department: Pathology

country: Switzerland

institute: University Hospital Basel, Institute of Medical Genetics and Pathology

description:
DSP-1001660004682-C-C06
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

data_processing:
Novaseq-derived FASTQ files for each sample were compiled for each compartment using the bcl2fastq program of Illumina, and then demultiplexed and converted to digital count conversion (DCC) files using the GeoMx DnD pipeline version 2.0.0.16 of Nanostring according to manufacturer’s pipeline. DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.4.2.2 (Nanostring).  Probes were checked for outlier status. A probe is removed if the geometric mean of that probe’s counts from all segments divided by the geometric mean of all probe counts representing the target from all segments is less than 0.1 or if the probe is an outlier according to the Grubb’s test in at least 20% of segments.   The counts for all remaining probes for a given target were then collapsed into a single metric by taking the geometric mean of probe counts.   Segments and genes were filtered out with abnormal low signal. Segments and genes with less than 5% of gene or segments detected and below the limit of quantification (LOQ) set at 2 geometric standard deviation above the geometric mean were removed from the study.  Gene counts were normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI.
Supplementary files format and content: Excel file containing segment properties, target properties, Q3 normalized target count matrix

source_name: Liver

extract_protocol:
Three FFPE tissue sections of 5-µm from liver biopsy tissue microarray (TMA) with VILI (n=6) and AIH (n=8) were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Then, sections were deparaffinized in 3 xylol baths of 5 minutes and rehydrated in ethanol gradient from 100% EtOH 2 baths of 5 minutes, followed by 95% EtOH 5 minutes. Slides were then washed in 1X PBS. Antigen retrieval was carried out with Tris-EDTA pH 9.0 buffer at 100°C for 20 minutes at low pressure. Slides were first immersed into hot water for 10 seconds and then immersed into Tris-EDTA buffer. The cooker vent kept open during the procedure to ensure low pressure and it was allowed to reach 100°C. Slides were then washed with 1X PBS, and incubated in proteinase K containing PBS (1ug/ml) for 15 minutes at 37°C and washed again in 1X PBS. Tissue were post-fixed in 10% neutral-buffered formalin (NBF) for 5 minutes, washed two times 5 minutes in NBF stop buffer (0.1M Tris Base, 0.1M Glycine) and finally one time in 1X PBS. The mix of Whole Transcriptome Atlas probes (WTA, Nanostring) was dropped on each section and covered with HybriSlip Hybridization Covers. Slides were then incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced cell Diagnostics). The day after, HybriSlip covers were gently removed and 25 minutes stringent washes were performed twice in 50% formamide and 2X saline sodium citrate (SSC) at 37 °C. Tissues were washed for 5 min in 2× SSC, then blocked in Buffer W (Nanostring Technologies) for 30 min at room temperature in a humidity chamber. Next, 500 nM Syto83 and antibodies targeting CD3 (BioRad, clone CD3-12), CD20 (Novus, clone IGEL/773) and Arginase (Cell Signaling, clone D4E3M) in Buffer W were applied to each section for 1 h at room temperature. Slides were washed twice in fresh 2× SSC then loaded on the GeoMx DSP.  Entire slides were imaged at ×20 magnification and morphologic markers were used to select Region Of Interest (ROI) either using circle or organic shapes. Automatic segmentation of ROI based on Arginase+ markers were used to defined Area of Illumination (AOIs). This allowed to separate liver cells (Arginase+) and cells around liver. A total of 59 AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited in a 96-well plate for subsequent processing. The indexing oligonucleotides were dried down overnight and resuspended in 10 μl of DEPC-treated water.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow on an Illumina NovaSeq S4 instrument.

tag: cohort

value: AIH

tag: label

tag: tissue

value: Liver

tag: molecule subtype

value: DSP Barcode


title: TMA1_20221116 | 009 | Full ROI

description:
DSP-1001660004682-C-C11
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

value: VILI


title: Blood_Platelets_TR5113-NSCLC-MAAS


title: Blood_Platelets_TR5107-NSCLC-MAAS


title: OCT4-GFP negative somatic cells, saline control, biological rep 1, female

city: San Francisco

first: Steven

middle: Anthony

last: Cincotta

state: California

address: 35 Medical Center Way

institute: UCSF

description:
SOMAsal1
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv

data_processing:
Raw fastq reads were processed to remove adapter sequences, reads containing poly-N, and low quality reads
Reads were aligned to mm10 reference genome using Hisat2 v2.0.5.
Counts of reads mapping to each gene were determined using featureCounts v1.5.0-p3, followed by calculation of FPKM values.
Pairwise differential expression analysis was performed using DESeq2 v1.20.0. P-values were adjusted using Benjamini and Hochber FDR.
Assembly: mm10
Supplementary files format and content: CSV file containing raw counts for each sample
Supplementary files format and content: CSV file containing FPKM normalized counts for each sample
Supplementary files format and content: CSV file containing pairwise differential gene expression output from DESeq2

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNA was harvested using RNeasy Micro Kit (QIAgen)
mRNA was purified from total RNA using poly-dT beads, fragmented, and then used for first strand cDNA sythesis with random hexamer primers (followed by second strand cDNA synthesis). Fragments were end repaired, A-tailed, ligated to sequencing adapters, size selected, PCR amplified, and libraries purified. Libraries were quantified on Qubit and QC'ed on Agilent Bioanalyzer for quality and size distribution.

value: OCT4-GFP negative somatic cells

tag: developmental stage

value: saline

tag: Sex

tag: mouse strain


title: TMA1_20221116 | 003 | Full ROI

description:
DSP-1001660004682-C-C05
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR5115-HD-MAAS

value: Control


title: TMA1_20221116 | 002 | Full ROI

description:
DSP-1001660004682-C-C04
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: OCT4-GFP negative somatic cells, saline control, biological rep 2, female

description:
SOMAsal2
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv


title: OCT4-GFP negative somatic cells, dexamethasone treated, biological rep 3, female

description:
SOMAdex3
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv

value: dexamethasone


title: HDR Pool 3 GL2 - Rep 3 gfp +


title: HDR Pool 3 GL2 - Rep 2 gfp +


title: Blood_Platelets_TR5105-NSCLC-MAAS


title: HDR Pool 3 GL2 - Rep 1 gfp +


title: TMA1_20221116 | 001 | Liver cells

description:
DSP-1001660004682-C-C03
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: OCT4-GFP negative somatic cells, dexamethasone treated, biological rep 2, female

description:
SOMAdex2
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv


title: Blood_Platelets_TR5106-NSCLC-MAAS


title: TMA2_20221115 | 020 | Liver cells

description:
DSP-1001660004682-C-C02
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR5090-NSCLC-MAAS


title: HDR Pool 3 BRCA1 - Rep 4 gfp

value: Experimental group

value: BRCA1 siRNA


title: TMA1_20221116 | 006 | Liver cells

description:
DSP-1001660004682-C-C08
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: OCT4-GFP negative somatic cells, dexamethasone treated, biological rep 1, female

description:
SOMAdex1
gene_count_female.csv
gene_fpkm_female.csv
DGE_SOMA_DEXvsSAL_female_ALL.csv

value: ovary


title: Blood_Platelets_TR5088-NSCLC-MAAS


title: HDR Pool 3 GL2 - Rep 4 gfp +


title: TMA2_20221115 | 019 | Full ROI

description:
DSP-1001660004682-C-C01
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR5018-HD-MAAS


title: OCT4-GFP positive germ cells, saline control, biological rep 2, female

description:
PGCsal2
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv

source_name: OCT4-GFP positive germ cells sorted from E15.5 ovary

value: OCT4-GFP positive germ cells

value: female


title: Blood_Platelets_TR5017-HD-MAAS

value: Thrombocytes


title: TMA2_20221115 | 017 | Full ROI

description:
DSP-1001660004682-C-B11
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: HDR Pool 3 BRCA1 - Rep 2 gfp -

value: HeLa


title: OCT4-GFP positive germ cells, saline control, biological rep 3, female

description:
PGCsal3
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv


title: HDR Pool 3 BRCA1 - Rep 1 gfp -


title: Blood_Platelets_TR5016-HD-MAAS


title: TMA2_20221115 | 016 | Full ROI

description:
DSP-1001660004682-C-B10
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: HDR Pool 3 BRCA1 - Rep 4 gfp +


title: OCT4-GFP positive germ cells, saline control, biological rep 1, female

description:
PGCsal1
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv


title: OCT4-GFP positive germ cells, dexamethasone treated, biological rep 3, female

description:
PGCdex3
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv


title: Blood_Platelets_TR5015-HD-MAAS


title: OCT4-GFP positive germ cells, dexamethasone treated, biological rep 2, female

description:
PGCdex2
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv


title: Blood_Platelets_TR4970-HD-MAAS


title: TMA2_20221115 | 014 | Full ROI

description:
DSP-1001660004682-C-B08
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: TMA2_20221115 | 015 | Liver cells

description:
DSP-1001660004682-C-B09
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: HDR Pool 3 BRCA1 - Rep 3 gfp +


title: Blood_Platelets_TR4968-NSCLC-MAAS

value: NSCLC


title: HDR Pool 3 BRCA1 - Rep 2 gfp +


title: TMA2_20221115 | 013 | Full ROI

description:
DSP-1001660004682-C-B07
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: OCT4-GFP positive germ cells, dexamethasone treated, biological rep 1, female

description:
PGCdex1
gene_count_female.csv
gene_fpkm_female.csv
DGE_GERM_DEXvsSAL_female_ALL.csv


title: TMA2_20221115 | 018 | Full ROI

description:
DSP-1001660004682-C-B12
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR4964-HD-MAAS


title: HDR Pool 3 BRCA1 - Rep 3 gfp -


title: HDR Pool 3 BRCA1 - Rep 1 gfp +


title: TMA2_20221115 | 012 | Liver cells

description:
DSP-1001660004682-C-B06
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: LungSIY

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Raw read processing of single-cell RNA sequencing reads was performed as previously described in Macosko et al. Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Correction for ambient RNA contamination was performed using SoupX v1.2.1.
Data was further analyzed in Seurat v2.3.4.
BulkRNA of 2C cells: Sequence alignment and .bam file generation were performed by the KI Genomics Core / MIT BioMicro Center. The resulting .bam files were sorted using Samtools. Differential gene expression analysis was performed on the sorted .bam files with Cufflinks.
Assembly: mm10
Supplementary files format and content: DGE: single-cell genes/cell count matricies
Supplementary files format and content: 2C_priming.txt.gz: Cufflinks output, comparing gene expression between the SQ (Flank 1-4) samples and the IV samples (Lung 1-3).

source_name: Tumor

growth_protocol: Tumor cell lines were cultured at 37°C and 5% CO2 in DMEM (Gibco) supplemented with 10% 782 FBS (Atlanta Biologicals), 1% penicillin/streptomycin (Gibco), and 1X HEPES (Gibco). Tumor cells were harvested by trypsinization (Gibco) and washed 2 times with 1X PBS (Gibco). Cells were resuspended in PBS, and 2.5x105 tumor cells were injected subcutaneously into the flanks of mice, or intravenously via the tail vein.

extract_protocol:
Tumor-bearing mice were injected retro-orbitally with fluorescently-labeled anti-CD45 antibodies (CD45-IV) 3 minutes prior to euthanasia to differentiate tumor- and lung-infiltrating immune cells from circulating immune cells. Spleens and lymph nodes were dissected from mice and physically dissociated through a 70 µm filter to generate single cell suspensions. Splenocyte suspensions were lysed with ACK lysis buffer (Gibco) for 3 minutes to deplete red blood cells. Subcutaneous tumors and tumor-bearing lungs were dissected from mice, weighed, and collected in 5 mL DMEM (Gibco) containing the human tumor dissociation kit (Miltenyi) enzymes. Tumors were dissociated using the gentleMACS Octo Dissociator (Miltenyi). Following the digestion, tumor or lung pieces were mashed through a 70 µm filter with a 1 mL syringe plunger to generate a single cell suspension. The dissociated cells were washed 2 times with PBS and were layered over Ficoll (GE). Cells were spun over Ficoll at 450 g for 30 minutes with the lowest settings of acceleration and brakes. The layer at the interface of Ficoll and PBS, which contained the majority of the live immune cells, was collected and washed with PBS.
Cell suspensions were washed twice with cold PBS + 0.5% BSA + 2mM EDTA and then enriched for tumor-resident immune cells by performing negative selection with anti-PE microbeads (Miltenyi Biotec) followed by positive or negative selection with anti-CD45 microbeads (Miltenyi Biotec).
2C T cells were adoptively transferred to tumor-bearing mice as described above. Seventy-two hours after transfer, TdLN cells were isolated and prepared for FACS. 2C T cells were FACS-sorted directly into TRIzol reagent and RNA-extracted. RNA library preparation and sequencing were performed at the KI Genomics Core / MIT BioMicro Center. Sequencing was performed using the HiSeq 2000 sequencing system (Illumina).

treatment_protocol: Mice were injected intraperitoneally with anti-CTLA-4 (clone UC10-4F10-11, Bio X Cell) and anti-PD-L1 (clone 10F.9G2, Bio X Cell) antibodies on days 7, 10, 13, and 16 post-tumor inoculation. Each mouse received 100 µg of each antibody per treatment.

value: Tumor

tag: genotype

value: Untreated


title: FlankSIY


title: Adult Adrenal 11 [AA11]

city: Nijmegen

first: Mariska

middle: AM

last: Schröder

address: Geert Grooteplein

department: Department of Pediatric Endocrinology and Department of Laboratory Medicine

institute: Radboud university medical center

description: barcode: IonXpress_021

data_processing: Mapping of read data was performing automatically on the Torrent Suite server, against a reference fasta file composed of the transcript sequences of the target genes, and total read counts per target gene were then tallied.

source_name: Adrenal

extract_protocol:
RNA was isolated from frozen tissue samples using the total RNA Purification Kit (Norgen Biotek)
RNA was reversed transcribed using Superscript VILO cDNA synthesis kit (Thermo Fisher Scientific) using a C1000 Thermal cycler (Biorad)
Libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermofisher)
Templating and (RNA) sequencing were performed with the Ion PI HiQ OT200 kit, and Ion PI HiQ sequencing kit using Ion PI V3 chips (Life Technologies) and a Proton Sequencer (Thermofisher).

tag: tissue type

value: Adrenal

tag: batch


title: TMA2_20221115 | 011 | Liver cells

description:
DSP-1001660004682-C-B05
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

value: AIH

value: Liver

value: DSP Barcode


title: Blood_Platelets_TR4963-HD-MAAS


title: TMA2_20221115 | 010 | Liver cells

description:
DSP-1001660004682-C-B04
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR4962-NSCLC-MAAS


title: Adult Adrenal 10 [AA10]

description: barcode: IonXpress_019


title: Blood_Platelets_TR4957-NSCLC-MAAS


title: Fetal Adrenal 12 [FA12]

description: barcode: IonXpress_012


title: TMA2_20221115 | 009 | Liver cells

description:
DSP-1001660004682-C-B03
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: TMA2_20221115 | 008 | Liver cells

description:
DSP-1001660004682-C-B02
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Adult Adrenal 8 [AA8]

description: barcode: IonXpress_007


title: TMA2_20221115 | 007 | Liver cells

description:
DSP-1001660004682-C-B01
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

value: VILI


title: Blood_Platelets_TR4894-NSCLC-MAAS


title: Spleen_PMN-MDSC_BCG2_Day3

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

description:
full-length gene expression
bulk RNA-Seq
Spleen_PMN-MDSC_Day3_GeneMatrix.tsv

data_processing:
For bulk RNA-seq: RNA-seq data were mapped on the mouse reference (mm10) sequence using STAR (version 2.7.9a), and the gene expression was then quantified with RSEM (version 1.2.28). DESeq2 (version 1.36.0) was used to estimate the significance of DEGs between the two experimental groups.
For scRNA-seq: the Cell Ranger Software Suite (version 6.1.2) was used to process scRNA-seq data based on the cell ranger count and a mouse reference dataset (refdata-gex-mm10-2020-A). For each scRNA-seq dataset of the BCG and PBS group, the cell ranger count outputs were loaded in the R-statistical environment (version 4.1.0) using the Read10X function from the Seurat package (version 4.0.4).
Assembly: mm10
Supplementary files format and content: tsv, gene expression matrix by cell in the tsv formattsv
Supplementary files format and content: tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
RNA were extracted from cells using RNAClean XP beads
For bulk RNA-seq: RNA-seq data were mapped on the mouse reference (mm10) sequence using STAR (version 2.7.9a).
For scRNA-seq: the Cell Ranger Software Suite (version 6.1.2) was used to process scRNA-seq data based on the cell ranger count and a mouse reference dataset (refdata-gex-mm10-2020-A). For each scRNA-seq dataset of the BCG and PBS group, the cell ranger count outputs were loaded in the R-statistical environment (version 4.1.0) using the Read10X function from the Seurat package (version 4.0.4).

treatment_protocol: Neonatal mice on day of life 3 to 4 were subcutaneously administered BCG (5×105 CFU) and or PBS. For bulk RNA-seq: about 5×105 PMN-MDSCs in the spleen were sorted from neonatal mice at day 1 or 3 after BCG vaccination. For scRNA-seq: CD3-CD19-CD11b+cells in the spleen were isolated.

value: Spleen

value: PMN-MDSCs

tag: strain

value: wild type

value: BCG vaccination

tag: time

value: Day 3


title: Spleen_PMN-MDSC_BCG_10x

description:
3'-end gene expression
scRNA-seq

library_source: transcriptomic single cell

tag: cell type

value: Myeloid cells


title: Spleen_PMN-MDSC_PBS2_Day3

value: PBS treatment


title: Spleen_PMN-MDSC_PBS_10x

description:
3'-end gene expression
scRNA-seq


title: TMA2_20221115 | 006 | Liver cells

description:
DSP-1001660004682-C-A12
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Fetal Adrenal 13 [FA13]

description: barcode: IonXpress_013


title: Blood_Platelets_VUMC-HC442-adap-HD-TR3438

value: Thrombocytes

tag: cancer stage

tag: patient group

value: Control


title: Spleen_PMN-MDSC_BCG1_Day3


title: Adult Adrenal 6 [AA6]

description: barcode: IonXpress_005


title: Spleen_PMN-MDSC_BCG1_Day1

description:
full-length gene expression
bulk RNA-Seq
Spleen_PMN-MDSC_Day1_GeneMatrix.tsv

value: Day 1


title: Adult Adrenal 4 [AA4]

description: barcode: IonXpress_003


title: Spleen_PMN-MDSC_BCG2_Day1


title: Adult Adrenal 7 [AA7]

description: barcode: IonXpress_006


title: Blood_Platelets_TR4040-HD-NKI


title: TMA2_20221115 | 004 | Liver cells

description:
DSP-1001660004682-C-A10
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: TMA2_20221115 | 005 | Full ROI

description:
DSP-1001660004682-C-A11
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Adult Adrenal 9 [AA9]

description: barcode: IonXpress_008


title: Blood_Platelets_TR3430-HD-NKI


title: Blood_Platelets_VUMC-HC425-adap-HD-TR3437


title: Adult Adrenal 5 [AA5]

description: barcode: IonXpress_004


title: Fetal Adrenal 11 [FA11]

description: barcode: IonXpress_026


title: Spleen_PMN-MDSC_PBS2_Day1


title: Blood_Platelets_VUMC-HC434-adap-HD-TR3435


title: TMA2_20221115 | 003 | Full ROI

description:
DSP-1001660004682-C-A09
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: TMA2_20221115 | 002 | Liver cells

description:
DSP-1001660004682-C-A08
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_NKI-107-005309-HD-TR3345


title: TMA2_20221115 | 001 | Liver cells

description:
DSP-1001660004682-C-A07
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Fetal Adrenal 10 [FA10]

description: barcode: IonXpress_025


title: Spleen_PMN-MDSC_PBS1_Day3


title: Spleen_PMN-MDSC_PBS1_Day1


title: Fetal Adrenal 9 [FA9]

description: barcode: IonXpress_024


title: Blood_Platelets_TR4955-NSCLC-MAAS

value: NSCLC


title: TMA2_20221116 | 005 | Full ROI

description:
DSP-1001660004682-C-A06
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_TR3296-HD-NKI


title: Fetal Adrenal 8 [FA8]

description: barcode: IonXpress_018


title: TMA2_20221116 | 004 | Liver cells

description:
DSP-1001660004682-C-A05
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Blood_Platelets_NKI-107-005448-HD-TR3290


title: TMA2_20221116 | 003 | Full ROI

description:
DSP-1001660004682-C-A04
geo_submission_spatial_transcriptomics_Q3_normalized_dataset


title: Fetal Adrenal 7 [FA7]

description: barcode: IonXpress_017


title: Blood_Platelets_NKI-107-005495-HD-TR3286


title: Blood_Platelets_VUMC-HC0056-DOT-HD-48h-TR3089


title: Fetal Adrenal 6 [FA6]

description: barcode: IonXpress_015


title: Blood_Platelets_VUMC-HC0139-DOT-HD-48h-TR3070


title: Fetal Adrenal 5 [FA5]

description: barcode: IonXpress_014


title: liver,staph_CD45_WT,replicate3

city: New York City

first: Ze

last: Chen

state: New York

address: 430 East 29th Street

institute: NYU Grossman School of Medicine

description: 10x Genomics

data_processing:
The sequenced data were processed using Cell Ranger (version 6.0) to demultiplex the libraries. The reads were aligned to Mus musculus mm10 and SCV2 (MN985325.1) genomes to generate count tables that were further analyzed using Seurat (version 4.1.2)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Livers were chopped and incubated in RPMI + 10% FBS with collagenase VIII (100U/mL; Sigma Aldrich) and DNase I (150 g/mL; Sigma Aldrich) for 45 minutes at 37 C and then passed through a 70-m cell strainer (Fisher Scientific). Leukocytes were enriched for by density-gradient centrifugation over a 40/80% Percoll (GE Healthcare) gradient, and remaining red blood cells were lysed with ACK lysis buffer (Lonza) and washed in PBS and used for cell sorting or flow cytometry analysis.
For each data set, cells isolated from 2-4 mice were pooled together, with equal numbers of cells pooled from each animal used. 12,000 cells from each group were loaded on a 10X Genomics Next GEM chip and single-cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate cDNA and sequencing libraries were performed following 10X Genomics’ protocol. Libraries were pooled and sequenced using Illumina NovaSeq SP 100 cycle as per 10X sequencing recommendations.

value: liver cells

value: liver


title: liver,staph_CD45_dTOX,replicate3

description: 10x Genomics


title: liver,staph_CD45_dTOX,replicate2

description: 10x Genomics


title: TMA2_20221116 | 001 | Full ROI

description:
DSP-1001660004682-C-A02
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

value: AIH


title: liver,staph_CD45_WT,replicate4

description: 10x Genomics


title: liver,staph_CD45_dTOX,replicate4

description: 10x Genomics


title: liver,staph_CD45_dTOX,replicate1

description: 10x Genomics


title: No Template Control

description:
DSP-1001660004682-C-A01
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

value: No Template Control

value: Liver


title: Adult Testis 10 [AT10]

description: barcode: IonXpress_005


title: E_LP_Sub, rep 1 [T93220_13345357]

city: Saint-Gilles

first: Mariana

last: Mescouto Lopes

address: 16 Le Clos Domaine de, La Prise

department: UMR Pegase

country: France

institute: INRAe

data_processing:
Dragen RNA v3.8.4 (Illumina) was used for mapping and annotation against Sus scrofa reference genome GCF_000003025.6.
The data was analyzed using the R software (v. 4.1.2; http://www.r-project.org). Normalization, filtration, and statistical analysis were performed using the DESeq2  package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: NCBI Sus scrofa reference genome sequence Sscrofa11.1
Supplementary files format and content: Tab-delimited text files containing the number of counts of the identified genes for each sample.

organism: Sus scrofa

source_name: Peripheral blood

extract_protocol:
RNA was isolated using NucleoSpin RNA Kit according to the manufacturer’s instructions. 500 ng of total RNA was used for library preparation.
RNA libraries were prepared following the QIAseq Stranded mRNA Library Kit (Qiagen) protocol, without modification, and using 12 cycles for amplification.

value: Peripheral blood

tag: housing condition

value: Enriched

tag: parity group

value: LP

tag: dominance status

value: Subordinate


title: liver,staph_CD45_WT,replicate2

description: 10x Genomics


title: HL60 cells, CYTDRN, biol rep 3

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

country: Germany

institute: University Medical Center, Johannes Gutenberg University of Mainz

data_processing:
Quality of raw sequencing reads was assessed using FastQC (version 0.11.9)
Transcripts were quantified using decoy-aware selective alignment mode of the Salmon (version 1.8.0) based on GRCh38 genome and transcriptome
The quantified transcript counts were summed to gene counts using tximeta package (version 1.14.0) in R
Differentially expressed genes between drug- and DMSO-treated cells were identified using edgeR package (version 3.38.1) in R
Assembly: hg38
Supplementary files format and content: Salmon output containing transcript read counts and TPM values

growth_protocol: All cell lines were cultured in respective enriched media (HL60 and MOLM13: RPMI + 10% FBS; OCIAML3: alpha-MEM + 20% FBS) and were maintained at 37^° C and 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol (Thermo Fisher Scientific) and purified using Monarch Total RNA Miniprep kit (New England Biolabs) according to manufacturer’s instructions.
Unstranded paired-end RNA libraries were prepared by Novogene (UK) Co. Ltd.

treatment_protocol: 1 X 10^6 cells per well were seeded in a 6 well plate containing 5 ml of the media. Cells were treated with DMSO, cytarabine, daunorubicin or the combination of cytarabine and daunorubicin for 24 hours.

tag: cell line

value: Acute myeloid leukemia cells

value: WT

tag: treatment

value: Cytarabine and Daunorubicin

value: 24 hours


title: HL60 cells, DRN, biol rep 3

value: Daunorubicin


title: E_LP_Int, rep 1 [T93287_13345358]

tag: tissue

value: Intermediate


title: Adult Testis 8 [AT8]

description: barcode: IonXpress_003


title: liver,staph_CD45_WT,replicate1

description: 10x Genomics


title: liver,schisto_CD45,replicate4

description: 10x Genomics


title: TMA2_20221116 | 002 | Liver cells

description:
DSP-1001660004682-C-A03
geo_submission_spatial_transcriptomics_Q3_normalized_dataset

tag: cohort

tag: label

tag: molecule subtype

value: DSP Barcode


title: HL60 cells, CYT, biol rep 3

tag: genotype

value: Cytarabine


title: HL60 cells, DMSO, biol rep 3

value: DMSO


title: liver,schisto_CD45,replicate3

description: 10x Genomics

value: liver cells

value: liver


title: HL60 cells, CYTDRN, biol rep 2


title: Leydig Cell Tumor 7 [LCT7]

description: barcode: IonXpress_020

source_name: LCT

tag: tissue type

value: LCT


title: Leydig Cell Tumor 6 [LCT6]

description: barcode: IonXpress_019

tag: batch


title: Fetal Testis 5 [FT5]

description: barcode: IonXpress_018


title: C_LP_Int, rep 2 [T93013_13345371]

value: Conventional


title: Adult Testis 9 [AT9]

description: barcode: IonXpress_004


title: liver,schisto_CD45,replicate2

description: 10x Genomics

tag: strain


title: C_LP_Sub, rep 1 [T93204_13345356]

value: Peripheral blood

tag: time


title: liver,schisto_CD45,replicate1

description: 10x Genomics

tag: cell type


title: C_LP_Sub, rep 2 [T92989_13345370]


title: Fetal Testis 4 [FT4]

description: barcode: IonXpress_017


title: E_HP_Int, rep 2 [T91675_13345369]

value: Enriched

value: HP


title: Fetal Testis 3 [FT3]

description: barcode: IonXpress_016


title: HL60 cells, DRN, biol rep 2


title: HL60 cells, CYT, biol rep 2


title: Adult Testis 7 [AT7]

description: barcode: IonXpress_015

source_name: Testis

value: Testis


title: liver, schisto_CD11b,replicate3

description: 10x Genomics


title: C_LP_Sub, rep 1 [T93157_13345355]

value: LP

value: Subordinate


title: E_HP_Dom, rep 2 [T91533_13345367]

value: Dominant


title: HL60 cells, CYTDRN, biol rep 1

value: Acute myeloid leukemia cells

value: WT

value: Cytarabine and Daunorubicin

value: 24 hours


title: HL60 cells, DMSO, biol rep 2


title: C_HP_Sub, rep 2 [T91645_13345368]


title: Adult Testis 6 [AT6]

description: barcode: IonXpress_014


title: E_LP_Int, rep 2 [T93120_13345372]

value: Intermediate


title: liver, schisto_CD11b,replicate2

description: 10x Genomics


title: HL60 cells, DRN, biol rep 1

value: Daunorubicin


title: Adult Testis 5 [AT5]

description: barcode: IonXpress_013


title: C_LP_Int, rep 1 [T91522_13345354]


title: HL60 cells, CYT, biol rep 1

value: Cytarabine


title: Testicular Adrenal Rest Tumor 14 [TART14]

description: barcode: IonXpress_012

source_name: TART

value: TART


title: HL60 cells, DMSO, biol rep 1

value: DMSO


title: liver, schisto_CD11b,replicate4

description: 10x Genomics

value: liver cells

value: liver


title: Testicular Adrenal Rest Tumor 13 [TART13]

description: barcode: IonXpress_011


title: OCIAML3 cells, CYTDRN, biol rep 3


title: Testicular Adrenal Rest Tumor 12 [TART12]

description: barcode: IonXpress_010


title: C_HP_Dom, rep 2 [T83888_13345366]

value: Peripheral blood

value: Conventional


title: E_LP_Dom, rep 1 [T91384_13345352]

value: Enriched


title: E_HP_Dom, rep 2 [T83868_13345365]

value: HP


title: OCIAML3 cells, DRN, biol rep 3


title: TS_D6_Veh_3

city: Aurora

first: Ben-Zheng

last: Li

state: CO

department: Department of Physiology and Biophysics

institute: University of Colorado Anschutz Medical Campus

description:
TS_D6_Veh_3__S36_L003
JID_PYC_RNAseq_TS.csv

data_processing:
RNA-seq reads were adaptertrimmed and clipped using BBDuk (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/).
Trimmed sequences were aligned to mouse genome GRCm38.p6 (release 96) with STAR(Dobin et al., 2013).
Raw counts of identified genes were quantified and referenced against gene stable IDs
Differential expression was calculated by fitting the negative binomial generalized log-linear model and conducting the likelihood ratio test(McCarthy et al., 2012) on the trimmed mean of M values (TMM) (Robinson and Oshlack, 2010) normalized count data using the R package edgeR(Robinson et al., 2010).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin

extract_protocol:
RNA was harvested using an RNA Plus mini Kit (Qiagen, 74136)  for the construction of sequencing libraries.
PolyA selection was used for library prep
Sequencing was performed on an Illumina NovaSEQ 6000 with 2×200 paired-end reads at a depth of 80 million reads per sample.

value: Skin

value: Tape stripping+Vehicle


title: TS_D6_PYC_3

description:
TS_D6_PYC_3__S40_L003
JID_PYC_RNAseq_TS.csv

value: Tape stripping+Tat-PYC-Smad7, 0.5µg


title: C_HP_Dom, rep 1 [T83859_13345351]

value: Dominant


title: Fetal Adrenal 4 [FA4]

description: barcode: IonXpress_009


title: TS_D6_Veh_1

description:
TS_D6_Veh_1__S33_L003
JID_PYC_RNAseq_TS.csv

value: WT


title: OCIAML3 cells, CYT, biol rep 3

value: Acute myeloid leukemia cells

value: 24 hours


title: TS_D6_Veh_2

description:
TS_D6_Veh_2__S34_L003
JID_PYC_RNAseq_TS.csv


title: Fetal Adrenal 3 [FA3]

description: barcode: IonXpress_008


title: TS_D6_PYC_2

description:
TS_D6_PYC_2__S39_L003
JID_PYC_RNAseq_TS.csv


title: E_HP_Dom, rep 1 [T83821_13345350]


title: OCIAML3 cells, DMSO, biol rep 3


title: TS_D6_PYC_1

description:
TS_D6_PYC_1__S38_L003
JID_PYC_RNAseq_TS.csv


title: Fetal Adrenal 2 [FA2]

description: barcode: IonXpress_007


title: Fetal Adrenal 1 [FA1]

description: barcode: IonXpress_006


title: E_HP_Dom, rep 1 [T83410_13345348]


title: C_LP_Int, rep 1 [T91403_13345353]

value: LP

value: Intermediate


title: AD_D6_Veh_2

description:
AD_D6_Veh_2__S26_L003
JID_PYC_RNAseq_AD.csv

value: DNFB+Vehicle


title: Adult Adrenal 3 [AA3]

description: barcode: IonXpress_005

value: Adrenal


title: AD_D6_Veh_3

description:
AD_D6_Veh_3__S25_L003
JID_PYC_RNAseq_AD.csv


title: E_HP_Dom, rep 1 [T83740_13345349]


title: liver, schisto_CD11b,replicate1

description: 10x Genomics

value: liver cells


title: OCIAML3 cells, DRN, biol rep 2

value: Daunorubicin


title: E_HP_Dom, rep 2 [T82157R2_13345364]

value: Peripheral blood


title: AD_D6_Veh_1

description:
AD_D6_Veh_1__S27_L003
JID_PYC_RNAseq_AD.csv


title: OCIAML3 cells, CYT, biol rep 2

value: Cytarabine


title: Adult Adrenal 2 [AA2]

description: barcode: IonXpress_004


title: OCIAML3 cells, DMSO, biol rep 2

value: DMSO


title: E_HP_Int, rep 1 [T82157_13345346]

value: Enriched

value: HP


title: Testicular Adrenal Rest Tumor 11 [TART11]

description: barcode: IonXpress_022

value: TART


title: Testicular Adrenal Rest Tumor 10 [TART10]

description: barcode: IonXpress_021


title: C_HP_Dom, rep 2 [T82133R2_13345363]

value: Conventional


title: AD_D6_PYC_3

description:
AD_D6_PYC_3__S31_L003
JID_PYC_RNAseq_AD.csv

value: Skin

value: DNFB+Tat-PYC-Smad7, 0.5µg


title: OCIAML3 cells, DRN, biol rep 1

value: Acute myeloid leukemia cells

value: WT


title: C_HP_Int, rep 1 [T82133_13345345]


title: AD_D6_PYC_1

description:
AD_D6_PYC_1__S32_L003
JID_PYC_RNAseq_AD.csv


title: OCIAML3 cells, CYTDRN, biol rep 1

value: Cytarabine and Daunorubicin

value: 24 hours


title: OCIAML3 cells, CYTDRN, biol rep 2


title: OCIAML3 cells, CYT, biol rep 1


title: Testicular Adrenal Rest Tumor 9 [TART9]

description: barcode: IonXpress_012


title: C_LP_Sub, rep 2 [T704_13345362]

value: LP

value: Subordinate


title: C_HP_Dom, rep 1 [T82166_13345347]

value: Dominant


title: OCIAML3 cells, DMSO, biol rep 1


title: Testicular Adrenal Rest Tumor 8 [TART8]

description: barcode: IonXpress_011


title: IMQ_D6_Veh_2

description:
IMQ_D6_Veh_2_L002
JID_PYC_RNAseq_IMQ.csv

value: IMQ+Vehicle


title: Adult Adrenal 1 [AA1]

description: barcode: IonXpress_003

value: Adrenal


title: Cushing- TART 2 [CT2]

description: barcode: IonXpress_026


title: C_LP_Sub, rep 2 [T619_13345361]

value: Peripheral blood


title: IMQ_D6_Veh_1

description:
IMQ_D6_Veh_1_L002
JID_PYC_RNAseq_IMQ.csv


title: IMQ_D6_Veh_3

description:
IMQ_D6_Veh_3_L002
JID_PYC_RNAseq_IMQ.csv


title: Cushing-TART 1 [CT1]

description: barcode: IonXpress_025


title: MOLM13 cells, DRN, biol rep 3

value: Daunorubicin


title: AD_D6_PYC_2

description:
AD_D6_PYC_2__S30_L003
JID_PYC_RNAseq_AD.csv


title: MOLM13 cells, CYTDRN, biol rep 3


title: MOLM13 cells, CYT, biol rep 3

value: Cytarabine


title: E_LP_Int, rep 2 [T454_13345360]

value: Enriched

value: Intermediate


title: Leydig Cell Tumor 5 [LCT5]

description: barcode: IonXpress_024

value: LCT


title: E_LP_Sub, rep 2 [T382_13345359]


title: IMQ_D6_PYC_1

description:
IMQ_D6_PYC_1_L002
JID_PYC_RNAseq_IMQ.csv

value: Skin

value: IMQ+Tat-PYC-Smad7, 0.5µg


title: E_LP_Int, rep 1 [T93287_10078651]


title: MOLM13 cells, DMSO, biol rep 3

value: Acute myeloid leukemia cells

value: DMSO


title: IMQ_D6_PYC_2

description:
IMQ_D6_PYC_2_L002
JID_PYC_RNAseq_IMQ.csv

value: WT


title: MOLM13 cells, CYTDRN, biol rep 2

value: Cytarabine and Daunorubicin

value: 24 hours


title: Testicular Adrenal Rest Tumor 7 [TART7]

description: barcode: IonXpress_010

value: TART


title: Testicular Adrenal Rest Tumor 6 [TART6]

description: barcode: IonXpress_009


title: WT_IMQ_D6_3

description:
WT_IMQ_D6_3_S16_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv

value: IMQ


title: E_LP_Sub, rep 1 [T93220_10078650]

value: LP

value: Subordinate


title: C_LP_Sub, rep 1 [T93204_10078653]

value: Peripheral blood

value: Conventional


title: MOLM13 cells, DRN, biol rep 2

value: Daunorubicin


title: Testicular Adrenal Rest Tumor 5 [TART5]

description: barcode: IonXpress_008


title: C_LP_Sub, rep 1 [T93157_10078649]


title: WT_IMQ_D6_2

description:
WT_IMQ_D6_2_S15_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv


title: MOLM13 cells, CYT, biol rep 2

value: Cytarabine


title: WT_IMQ_D6_1

description:
WT_IMQ_D6_1_S14_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv


title: Testicular Adrenal Rest Tumor 4 [TART4]

description: barcode: IonXpress_007


title: IMQ_D6_PYC_3

description:
IMQ_D6_PYC_3_L002
JID_PYC_RNAseq_IMQ.csv


title: E_LP_Int, rep 2 [T93120_10078660]

value: Enriched

value: Intermediate


title: MOLM13 cells, DMSO, biol rep 2


title: Testicular Adrenal Rest Tumor 3 [TART3]

description: barcode: IonXpress_006


title: IMQ_K5.Smad7_TG, Day 6_4

description:
TG_IMQ_D6_4_S13_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv

value: Skin


title: MOLM13 cells, CYTDRN, biol rep 1


title: C_LP_Int, rep 2 [T93013_10078659]


title: IMQ_K5.Smad7_TG, Day 6_3

description:
TG_IMQ_D6_3_S12_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv


title: Testicular Adrenal Rest Tumor 2 [TART2]

description: barcode: IonXpress_004


title: MOLM13 cells, DRN, biol rep 1


title: Testicular Adrenal Rest Tumor 1 [TART1]

description: barcode: IonXpress_003


title: IMQ_K5.Smad7_TG, Day 6_2

description:
TG_IMQ_D6_2_S11_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv


title: Leydig Cell Tumor 4 [LCT4]

description: barcode: IonXpress_023

value: LCT


title: E_HP_Int, rep 2 [T91919_10078665]

value: HP


title: MOLM13 cells, CYT, biol rep 1

value: Acute myeloid leukemia cells


title: IMQ_K5.Smad7_TG, Day 6_1

description:
TG_IMQ_D6_1_S10_L004
JID_PYC_RNAseq_K5Smad7_TG VS WT.csv


title: E_HP_Int, rep 2 [T91675_10078664]


title: H3K27Ac_rep

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

data_processing:
Raw reads were aligned to mouse genome version mm10 using Bowtie2.
Peak calling were performed using MACS2 with --BEDPE option.
Assembly: mm10
Supplementary files format and content: MACS2 callpeak output file

source_name: P0.5 total epidermis

extract_protocol:
P0.5 backskin was treated with dispase, then the epidermis is separated from the dermis and further trysinized to get single cell suspendsion for ChIPseq.
Cells were subjected to Cut&Run based protocol for genomic DNA pull down. Pull-downed DNA were constructed into library using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

value: P0.5 total epidermis

value: Wildtype

tag: chip antibody

value: Cell Signaling Technology, Acetyl-Histone H3 (Lys27) Antibody #8173


title: C_HP_Sub, rep 2 [T91645_10078666]


title: HepG2, mtDNA enriched

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.5.0) with default settings.
Then, the clean data were mapped to the rCRS (NC_012920.1) or ChrM of mm10 mouse reference genome using Bismark (v0.20.1) with the parameters -X 2000 --score_min L,0,-0.6 or BS-Seeker2 (v2.1.8) with the parameter -m 3.
Duplicates were removed using Picard (v2.22.4). Bigwig files were generated using bedGraphToBigWig and visualized in Integrative Genomics Viewer (IGV).
Since we regarded sequencing depth as a relative concept and the vast majority of cytosines in mtDNA was sequenced far more than 50 times, we intentionally did not set a depth cutoff.
Assembly: mm10 Hg38
Supplementary files format and content: bigwig files for levels and sequencing depths of mtDNA-5mC

source_name: human hepatocarcinoma cell

extract_protocol:
Total DNA was extracted from cells or tissues using Phenol-chloroform DNA extraction protocol. If needed, enrichment of mtDNA was performed using TIANprep Mini Plasmid Kit (TIANGEN) according to the manufacturer’s instructions.
Briefly, 200-1000 ng genomic DNA was used for WGBS library construction. DNA was sonicated to ~250 bp fragments with the Diagenode Bioruptor Pico. Then DNA was subjected to end-repair, A-tailing, and ligation using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) and methylated adaptor (Roche) according to the manufacturer’s instructions. DNA was purified with VAHTS DNA Clean Beads. Subsequently, library was bisulfite modified using QIAGEN EpiTect Fast DNA Bisulfite Kit (59824) and amplified with KAPA2G Robust HotStart PCR Kits with dNTPs (Sigma-Aldrich). Library was finally subjected to 150 bp paired-end sequencing using the Illumina Novaseq6000 instrument.

value: human hepatocarcinoma cell

value: WT


title: MOLM13 cells, DMSO, biol rep 1

value: DMSO

value: 24 hours


title: Leydig Cell Tumor 3 [LCT3]

description: barcode: IonXpress_018


title: E_HP_Dom, rep 2 [T91533_10078661]

value: Peripheral blood

value: Dominant


title: Leydig Cell Tumor 2 [LCT2]

description: barcode: IonXpress_017


title: C_LP_Int, rep 1 [T91522_10078648]

value: Conventional

value: LP


title: HepG2


title: Leydig Cell Tumor 1 [LCT1]

description: barcode: IonXpress_016


title: E15_MOFcKO5

description: 10x Genomics

data_processing:
Raw reads were aligned to mouse genome build mm10 using cellranger v6.1.2
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Filtered feature-barcode matrix from cellranger out with cell barcode as column name and gene feature as row name

source_name: E15.5 total backskin

extract_protocol:
E15.5 backskin samples were dissociated into single cell suspension with colleganase treatment, followed by trypsinization.
ScRNAseq libraries were coonstructed using 10x Genomics Single cell 3' v3.1 protocol.

value: E15.5 total backskin


title: E15_MOFcKO6

description: 10x Genomics


title: MCF7

source_name: human breast cancer cell

value: human breast cancer cell


title: Fetal Testis 2 [FT2]

description: barcode: IonXpress_013


title: C_LP_Int, rep 1 [T91403_10078645]

value: Intermediate


title: C_LP_Sub, rep 2 [T92989_10078658]

value: Subordinate


title: HEK293T

source_name: human embryonic kidney cell

value: human embryonic kidney cell


title: E15_Control3

description: 10x Genomics

value: Control


title: E_LP_Dom, rep 1 [T91384_10078647]

value: Enriched


title: Fetal Testis 1 [FT1]

description: barcode: IonXpress_012


title: PTCL tissue, post treatment (C1D1), sample PTCL6 PTCL6 C1D1 RNAseq

city: New York

first: Maria

middle: Victoria

last: Revuelta

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description:
PTCL tissue, post treatment (C1D1), sample PTCL6
PTCL6-C1D1

data_processing:
Processed data is kallisto pseudocounts, transcript-filtered similarly to (10.1158/2159-8290.CD-20-0839) calculated as TPMs and log2+1 transformed
hg19

source_name: PTCL tissue

extract_protocol:
Illumina RNA Prep with Enrichment
PE2x100 cycles

value: PTCL tissue

value: Post CC-486


title: Adult Testis 4 [AT4]

description: barcode: IonXpress_020

value: Testis


title: Adult Testis 3 [AT3]

description: barcode: IonXpress_008


title: C_HP_Dom, rep 2 [T83888_10078663]

value: HP


title: E_HP_Dom, rep 2 [T83868_10078667]


title: PTCL tissue, pre treatment (C1D-6), sample PTCL6 PTCL6 C1D-6 RNAseq

description:
PTCL tissue, pre treatment (C1D-6), sample PTCL6
PTCL6-C1D-6

value: Pre CC-486


title: Adult Testis 2 [AT2]

description: barcode: IonXpress_007


title: H3K4me3_rep

value: P0.5 total epidermis

value: Wildtype

value: Cell Signaling Technology, Tri-Methyl-Histone H3 (Lys4) Antibody #9751


title: N2a

source_name: neuroblastoma cell

value: neuroblastoma cell

value: WT


title: PTCL tissue, post treatment (C1D1), sample PTCL5 PTCL5 C1D1 RNAseq

description:
PTCL tissue, post treatment (C1D1), sample PTCL5
PTCL5-C1D1


title: PTCL tissue, pre treatment (C1D-6), sample PTCL5 PTCL5 C1D-6 RNAseq

description:
PTCL tissue, pre treatment (C1D-6), sample PTCL5
PTCL5-C1D-6


title: Adult Testis 1 [AT1]

description: barcode: IonXpress_006


title: E_HP_Dom, rep 1 [T83821_10078646]

value: Peripheral blood

value: Dominant


title: E16_MOFcKO_rep2

data_processing:
Raw reads were aligned to mouse genome version mm10 using Tophat2.
Gene count data were genrated using Htseq count.
Assembly: mm10
Supplementary files format and content: gene count data. First column is gene name; secoond column is raw reads count.

source_name: E16.5 sorted H2BGFP+ Epithelial cell

extract_protocol:
For E16.5 samples, epithelial cells were enriched from backskin by sorting K14-H2BGFP+ cells using FACS. For P0.5 samples, epidermis was separated from dermis after dispase treatment, then epidermis was floated on TRIzol to lyse the cells for RNA extraction and library construction.
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: E16.5 sorted H2BGFP+ Epithelial cell


title: PTCL tissue, post treatment (C1D1), sample PTCL4 PTCL4 C1D1 RNAseq

description:
PTCL tissue, post treatment (C1D1), sample PTCL4
PTCL4-C1D1


title: mESC

source_name: embryonic stem cell

value: embryonic stem cell


title: PTCL tissue, pre treatment (C1D-6), sample PTCL4 PTCL4 C1D-6 RNAseq

description:
PTCL tissue, pre treatment (C1D-6), sample PTCL4
PTCL4-C1D-6


title: LUAD

source_name: lung adenocarcinoma cell

value: lung adenocarcinoma cell


title: E16_MOFcKO_rep1


title: E15_Control2

description: 10x Genomics

value: E15.5 total backskin

value: Control


title: PTCL tissue, post treatment (C1D1), sample PTCL3 PTCL3 C1D1 RNAseq

description:
PTCL tissue, post treatment (C1D1), sample PTCL3
PTCL3-C1D1

value: PTCL tissue


title: E_HP_Dom, rep 1 [T83410_10078643]

value: Enriched


title: N2a, mtDNA enriched


title: C_HP_Dom, rep 1 [T82166_10078641]

value: Conventional


title: E_HP_Dom, rep 1 [T83740_10078652]

value: HP


title: E16_Control_rep1


title: E_HP_Int, rep 1 [T82157_10078642]

value: Intermediate


title: E16_Control_rep2


title: PTCL tissue, post treatment (C1D1), sample PTCL2 PTCL2 C1D1 RNAseq

description:
PTCL tissue, post treatment (C1D1), sample PTCL2
PTCL2-C1D1

value: Post CC-486


title: TAPS Tet TKO LUAD

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.5.0) with default settings.
The clean data were mapped to the ChrM of mm10 mouse reference genome using Bowtie2 (v2.2.5).
Duplicates were removed using Picard (v2.22.4).
Methylation levels were called using asTair (v 3.2.6).
Assembly: mm10
Supplementary files format and content: bigwig files for levels and sequencing depths of mtDNA-5mC
Library strategy: TAPS

source_name: lung adenocarcinoma cells

extract_protocol:
Total DNA was extracted from cells or tissues using Phenol-chloroform DNA extraction protocol.
Whole-genome TAPS libraries were constructed as previously described. In brief, 100 ng genomic DNA spiked with 1.0 % of fully CpG-methylated lambda DNA was sonicated in EB buffer and purified by DNA clean beads to select for the desired DNA fragment size. DNA fragments were oxidized by recombinant human TET2CD twice, and then reduced with pyridine borane. The library was amplified with KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit.

value: lung adenocarcinoma cells

value: Tet TKO


title: MOF

data_processing:
Raw reads were aligned to mouse genome version mm10 using Bowtie2.
Peak calling were performed using MACS2 with --broad option for MOF and -f BAMPE option for Rfx2.
Assembly: mm10
Supplementary files format and content: MACS2 callpeak output file

extract_protocol:
P0.5 backskin was treated with dispase, then the epidermis is separated from the dermis and further trysinized to get single cell suspendsion for ChIPseq.
For MOF ChIPseq, cells were fixed and DNA fragmented, then pulled down using MOF antibody. For others, cells were subjected to Cut&Run based protocol for genomic DNA pull down. Pull-downed DNA were constructed into library using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

value: P0.5 total epidermis

value: Wildtype

value: Bethyl Rabbit anti-MOF/MYST1 Antibody  # A300-992A


title: B16

source_name: melanoma cell

value: melanoma cell

value: WT


title: C_HP_Dom, rep 1 [T83859_10078644]

source_name: Peripheral blood

value: Peripheral blood

value: Dominant


title: PTCL tissue, pre treatment (C1D-6), sample PTCL2 PTCL2 C1D-6 RNAseq

description:
PTCL tissue, pre treatment (C1D-6), sample PTCL2
PTCL2-C1D-6

value: Pre CC-486


title: C_HP_Int, rep 1 [T82133_10078640]


title: TAPS mESC

source_name: embryonic stem cells

value: embryonic stem cells


title: Tet TKO mESC

value: embryonic stem cell


title: aPD-L1-treated PD-1+ Tregs rep3 [15_aPDL1_PD1pos_03]

city: Rotterdam

first: Anneloes

last: van Krimpen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Pulmonary Medicine

institute: Erasmus MC

data_processing:
Reads were aligned using HISAT2 v2.0.4. (RNA-seq) with default parameters.
SAMTools (Li et al., 2009) is used to sort and merge alignments from multiple flow cells
Raw and RPKM counts are generated using HOMER v3.12 (Heinz et al., 2010) with the settings -count exons - condenseGenes
Statistical analyses were performed using the R-package DESeq2 as implemented by HOMER v3.12 (Heinz et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: Raw and RPKM expression values

source_name: Subcutaneous tumor

growth_protocol: Female 8-12-week-old C57BL/6 mice were subcutaneously injected with AE17-OVA (3.05) in 300 µl PBS. Mice were randomly assigned to experimental groups.

extract_protocol:
PD-1- Treg cells, PD-1+ Treg cells and CD4-Th cells were FACS-purified based on CD4, CD25, RFP and PD1 expression from tumors of Foxp3Cre-RFP mice on day 13.
RNA-Seq: Smart-seq2 library construction (as described in Picelli et al. Nature Methods (2013))

treatment_protocol: Female 8-12-week-old C57BL/6 mice with established mesothelioma (AE17-OVA) were systemically treated with either 200 ug aPD-L1 antibodies (clone MIH5, provided by L. Boon, Polpharma Biologics) or isotype (clone 2A3, Bioxcell) in 300 uL PBS intraperitonally at day 10 and were sacrificed at day 13 after treatment.

tag: strain background

tag: genotype/variation

value: GATIR Foxp3Cre-rfp Gata3Cre-yfp

value: PD1+ Treg cell


title: C_LP_Sub, rep 2 [T704_10078657]

tag: housing condition

value: Conventional

tag: parity group

value: LP

value: Subordinate


title: PTCL tissue, post treatment (C1D1), sample PTCL6 PTCL6 C1D1 RRBS

data_processing:
Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark. CpG-context methylation call output files are in txt format and filtered for at least 10 covered cytosines per site.
hg19

extract_protocol:
RRBS
SRx100 cycles

value: PTCL tissue

value: Post CC-486


title: aPD-L1-treated PD-1+ Tregs rep2 [14_aPDL1_PD1pos_02]


title: C_LP_Sub, rep 2 [T619_10078662]

tag: dominance status


title: PTCL tissue, pre treatment (C1D-6), sample PTCL6 PTCL6 C1D-6 RRBS

tag: treatment


title: Brain

source_name: mouse brain

value: mouse brain


title: PTCL tissue, pre treatment (C1D-6), sample PTCL3 PTCL3 C1D-6 RNAseq

description:
PTCL tissue, pre treatment (C1D-6), sample PTCL3
PTCL3-C1D-6

tag: tissue


title: TAPS Heart

source_name: heart

value: heart


title: aPD-L1-treated PD-1+ Tregs rep1 [13_aPDL1_PD1pos_01]


title: scRNA-Seq E17_Control

description: 10x Genomics

data_processing:
For E16.5 data, raw reads were aligned to mouse genome build mm10 using cellranger v1.3.1; for E17.5 data, raw reads were aligned to mouse genome build mm10 using cellranger v6.1.2
Assembly: refdata-cellranger-mm10-1.2.0 for E16.5 data; refdata-gex-mm10-2020-A for E17.5 data
Supplementary files format and content: Filtered feature-barcode matrix from cellranger out with cell barcode as column name and gene feature as row name

source_name: E17.5 total backskin

extract_protocol:
E16.5 or E17.5 backskin samples were dissociated into single cell suspension with colleganase treatment, followed by trypsinization.
For E16.5 samples, scRNAseq libraries were coonstructed using 10x Genomics Single cell 3' v2 protocol; for E17.5 samples, scRNAseq libraries were constructed using 10x Genomics Single Cell 3' v3 protocol.

value: E17.5 total backskin

value: Control


title: C_LP_Int, rep 2 [T408_10078655]

value: Intermediate


title: scRNA-Seq E17_QPC_cKO

description: 10x Genomics


title: Isotype-treated PD-1+ Tregs rep1 [11_iso_PD1pos_01]

value: Isotype


title: E_LP_Int, rep 2 [T454_10078656]

value: Peripheral blood

value: Enriched


title: Isotype-treated PD-1+ Tregs rep2 [12_iso_PD1pos_02]


title: PTCL tissue, pre treatment (C1D-6), sample PTCL5 PTCL5 C1D-6 RRBS

value: Pre CC-486


title: PTCL tissue, post treatment (C1D1), sample PTCL5 PTCL5 C1D1 RRBS


title: 100316_T0

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Papio_anubis genome reference (PapAnu2.0) using STAR and per transcript reads were counted with  HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow, using DREAM methodology for multiple measures modeling.
Assembly: PapAnu2.0
Supplementary files format and content: tab-delimited text file includes ENSEMBL transcript id and raw read counts for each transcript, in each sample

organism: Papio ursinus

source_name: total leukocytes

extract_protocol:
[Leukocyte separation protocol]  Total leukocytes from baboon blood were isolated using Histopaque 1119 and 1077 density gradient [Sigma Aldrich, St Louis, MO, USA]. Leukocytes were washed with HBSS.
Purified leukocytes were lysed with Trizol reagent and RNA was extracted as per manufacturer's instruction [Ambion, Life Technologies, Carlsbad, CA, USA].
RNA-sequencing was performed on a NextSeq 500 Flowcell, High SR75 (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: [Bacteria challenge protocol]  Healthy Papio ursinus baboons (8-20.2 kg body weight) with a leukocyte count less than 13 000/µL were challenged with 1-3 x 10E10  live E. coli or heat-inactivated S aureus (both are lethal doses) by intravenous infusion over 2 hours. The time point at which the bacterial infusion began was designated as time 0 (T0). Blood samples were collected at 2, 4, 8 and 24 hours  after the start of the bacterial infusion

value: total leukocytes

tag: experiment id

value: control (no bacteria challenge)

value: 0 hours


title: scRNA-Seq E16_Control_rep2

description: 10x Genomics

source_name: E16.5 total backskin

value: E16.5 total backskin


title: PTCL tissue, post treatment (C1D1), sample PTCL4 PTCL4 C1D1 RRBS


title: Isotype-treated PD-1- Tregs rep2 [07_iso_PD1neg_02]

value: GATIR Foxp3Cre-rfp Gata3Cre-yfp

value: PD1- Treg cell


title: E_LP_Sub, rep 2 [T382_10078654]

value: LP

value: Subordinate


title: PTCL tissue, post treatment (C1D1), sample PTCL3 PTCL3 C1D1 RRBS

value: PTCL tissue

value: Post CC-486


title: aPD-L1-treated PD-1- Tregs rep1 [09_aPDL1_PD1neg_02]


title: scRNA-Seq E16_MOFcKO_rep2

description: 10x Genomics


title: scRNA-Seq E16_MOFcKO_rep1

description: 10x Genomics


title: PTCL tissue, pre treatment (C1D-6), sample PTCL4 PTCL4 C1D-6 RRBS


title: LDEC_101016_T8

value: lethal dose E. coli

value: 8 hours


title: scRNA-Seq E16_Control_rep1

description: 10x Genomics

value: Control


title: Isotype-treated PD-1- Tregs rep1 [06_iso_PD1neg_01]

value: Isotype


title: E16_MOFcKO

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw reads were aligned to mouse genome build mm10 using cellrange-atac v2.0.0
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Filtered_peak_bc_matrix from cellranger-atac output with cell barcode as column name and peak as row name.

source_name: Epithelial enriched backskin

extract_protocol:
Single cell were isolated from E16.5 backskin using Collagenase treatment, followed by trypsinization. K14-H2BGFP-positive epithelial cells and K14-H2BGFP-negative non-epithelial cells were sorted by FACS, and then re-combined at 5:1 ratio to enrich for epithelial cells.
scATAC libraries were constructed following 10x Genomics single cell ATAC v1 protocol.

value: Epithelial enriched backskin


title: PTCL tissue, pre treatment (C1D-6), sample PTCL3 PTCL3 C1D-6 RRBS


title: PTCL tissue, post treatment (C1D1), sample PTCL2 PTCL2 C1D1 RRBS


title: aPD-L1-treated CD4+ T cells rep3 [05_aPDL1_CD4_03]

value: CD4 T cell


title: E16_Control

description: 10x Genomics


title: LDEC_101016_T2

value: 2 hours


title: aPD-L1-treated CD4+ T cells rep2 [04_aPDL1_CD4_02]


title: PTCL tissue, pre treatment (C1D-6), sample PTCL2 PTCL2 C1D-6 RRBS

value: Pre CC-486


title: LDEC_101016_T0

value: total leukocytes


title: aPD-L1-treated PD-1- Tregs rep2 [10_aPDL1_PD1neg_03]


title: PTCL peripheral blood, post treatment (C1D1), sample PTCL1 PTCL1 C1D1 RRBS

source_name: PTCL peripheral blood

value: PTCL peripheral blood


title: LDEC_092916_T8


title: aPD-L1-treated CD4+ T cells rep1 [03_aPDL1_CD4_01]


title: P0_Kansl1cKO_rep1

source_name: P0.5 total epidermal cells

value: P0.5 total epidermal cells


title: LDEC_092916_T4

value: 4 hours


title: LDEC_101016_T4


title: PTCL peripheral blood, pre treatment (C1D-6), sample PTCL1 PTCL1 C1D-6 RRBS


title: LDEC_092916_T2


title: Isotype-treated CD4+ T cells rep2 [02_iso_CD4_02]

value: GATIR Foxp3Cre-rfp Gata3Cre-yfp


title: Isotype-treated CD4+ T cells rep1 [01_iso_CD4_01]


title: P0_Control_rep1


title: LDEC_092916_T0

value: 0 hours


title: 2C_Lung3

data_processing:
Raw read processing of single-cell RNA sequencing reads was performed as previously described in Macosko et al. Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Correction for ambient RNA contamination was performed using SoupX v1.2.1.
Data was further analyzed in Seurat v2.3.4.
BulkRNA of 2C cells: Sequence alignment and .bam file generation were performed by the KI Genomics Core / MIT BioMicro Center. The resulting .bam files were sorted using Samtools. Differential gene expression analysis was performed on the sorted .bam files with Cufflinks.
Assembly: mm10
Supplementary files format and content: DGE: single-cell genes/cell count matricies
Supplementary files format and content: 2C_priming.txt.gz: Cufflinks output, comparing gene expression between the SQ (Flank 1-4) samples and the IV samples (Lung 1-3).

source_name: Lymph node

extract_protocol:
Tumor-bearing mice were injected retro-orbitally with fluorescently-labeled anti-CD45 antibodies (CD45-IV) 3 minutes prior to euthanasia to differentiate tumor- and lung-infiltrating immune cells from circulating immune cells. Spleens and lymph nodes were dissected from mice and physically dissociated through a 70 µm filter to generate single cell suspensions. Splenocyte suspensions were lysed with ACK lysis buffer (Gibco) for 3 minutes to deplete red blood cells. Subcutaneous tumors and tumor-bearing lungs were dissected from mice, weighed, and collected in 5 mL DMEM (Gibco) containing the human tumor dissociation kit (Miltenyi) enzymes. Tumors were dissociated using the gentleMACS Octo Dissociator (Miltenyi). Following the digestion, tumor or lung pieces were mashed through a 70 µm filter with a 1 mL syringe plunger to generate a single cell suspension. The dissociated cells were washed 2 times with PBS and were layered over Ficoll (GE). Cells were spun over Ficoll at 450 g for 30 minutes with the lowest settings of acceleration and brakes. The layer at the interface of Ficoll and PBS, which contained the majority of the live immune cells, was collected and washed with PBS.
Cell suspensions were washed twice with cold PBS + 0.5% BSA + 2mM EDTA and then enriched for tumor-resident immune cells by performing negative selection with anti-PE microbeads (Miltenyi Biotec) followed by positive or negative selection with anti-CD45 microbeads (Miltenyi Biotec).
2C T cells were adoptively transferred to tumor-bearing mice as described above. Seventy-two hours after transfer, TdLN cells were isolated and prepared for FACS. 2C T cells were FACS-sorted directly into TRIzol reagent and RNA-extracted. RNA library preparation and sequencing were performed at the KI Genomics Core / MIT BioMicro Center. Sequencing was performed using the HiSeq 2000 sequencing system (Illumina).

value: Lymph node

value: Lung


title: PA14_L_1

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

description:
start OD600 of 0.075; treated with 0.1% arabinose from OD1 to OD 2
rpg_table_PA14_terminator_constructs.csv

data_processing:
Pseudomonas aeruginosa UCBPP-PA14
Reads were mapped using bowtie2 (--very-sensitive-local --no-mixed --no-discordant --fr )
Reference genome: NC_008463.1
Files were converted into bam format using samtools
reads per gene from Pseudomonas aeruginosa UCBPP-PA14 were extracted using featureCounts (-Q 20 --fracOverlap 0.5)
Supplementary_files_format_and_content: reads per gene include antisense mapped reads of lasR and rsaL (using featureCounts options -s 1/2), antisense reads were selected using R environent

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 pJN105::PBAD_lasR_rsaL_PrsaL treated with 0.1% arabinose from OD1 to OD 2

growth_protocol: Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking. For cells harboring plasmid pJN105, medium was supplemented with gentamicin (50 µg/ml). For cells harboring plasmids pSEVA224 and pSEVA644, medium was supplemented with gentamicin (40 µg/ml) and kanamycin (200 µg/ml).

extract_protocol:
Bacterial cell pellets were resuspended in RNAprotect. RNA extraction was done as previously described (Schinner et al., 2020)
NEBNext Ultra II Directional RNA Library Prep

treatment_protocol: Cells harboring plasmid pJN105 were treated with 0.1 % arabinose at OD600 of 1 and harvested at OD600 of 2. Cells harboring plasmids pSEVA224 and pSEVA644 were treated with 0.1 mM IPTG at OD600 of 0.5-0.7 and harvested 2 h later at OD600 of 1.1-1.6.

tag: cell line/strains

value: PA14 pJN105::PBAD_lasR_rsaL_PrsaL


title: 2C_Lung2


title: Rfx2

source_name: P0.5 total epidermis

value: P0.5 total epidermis

value: Wildtype

value: Sigma-Aldrich Anti-Rfx2 antibody #HPA048969


title: LDEC_092616_T24

value: lethal dose E. coli

value: 24 hours


title: PA14_L_2


title: H3K27Ac

value: Cell Signaling Technology, Acetyl-Histone H3 (Lys27) Antibody #8173


title: 2C_Lung1


title: 2C_Flank4

value: Flank


title: LDEC_092616_T4


title: LDEC_092616_T8

value: 8 hours


title: P0_Kansl1cKO_rep2


title: PA14_LT_2

source_name: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 pJN105::PBAD_lasR_terminator_rsaL_PrsaL treated with 0.1% arabinose from OD1 to OD 2


title: PA14_LT_1


title: H3K4me1

value: Cell Signaling Technology, Mono-Methyl-Histone H3 (Lys4) Antibody #9723


title: 2C_Flank3


title: LDEC_092616_T2

value: total leukocytes

value: 2 hours


title: P0_Control_rep2

value: P0.5 total epidermal cells

value: Control


title: PA14_R_1

source_name: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 pJN105::PBAD_rsaL_lasR_PlasR treated with 0.1% arabinose from OD1 to OD 2

value: PA14 pJN105::PBAD_rsaL_lasR_PlasR


title: LDEC_092616_T0

value: 0 hours


title: 2C_Flank2

value: Lymph node


title: 2C_Flank1


title: H4K16Ac

description: Data were pooled from three sequencing run.

value: Sigma-Aldrich Anti-acetyl-Histone H4 (Lys16) Antibody # 07-329


title: Dnmt3a(+/-)-BM experimental CH, colon tumor 4

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were trimmed with trimmomatic, QC performed with FastQC
Reads were mapped to the transcriptome with the STAR aligner, and gene expression was quantified with RSEM.
Differential gene expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: RawGeneCounts.csv: tab-delimited file containing raw counts for all genes in all samples
Supplementary files format and content: NormalizedGeneCounts.xlsx: Excel file containing normalized counts for all genes in all samples

source_name: primary colon

extract_protocol:
RNeasy Micro kit (QIAGEN); 100ng of total RNA (RIN>7.0) was used for library preparation
poly(A)-enrichment (NEBNext Poly(A) mRNA Magnetic Isolation Module) and library preparation (NEBNext Ultra II Directional RNA Library Prep Kit)

treatment_protocol: bone marrow transplantation into wt C57BL6/J recipients (8 weeks), followed by CAC induction by a single injection of 10mg/kg AOM followed by 3 cycles of 3% (w/v) DSS in sterile drinking water for 1 week with 2 weeks off in between

value: primary colon

tag: disease state

value: whole colon tumor

tag: biological replicate

value: Dnmt3a(+/-) in BM

value: BMT, then AOM/DSS


title: LDSA_091916_T8

value: lethal dose Staph aureus


title: PA14_RT_1

source_name: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 pJN105::PBAD_rsaL_terminator_lasR_PlasR treated with 0.1% arabinose from OD1 to OD 2


title: LDSA_091916_T4

value: 4 hours


title: Dnmt3a(+/-)-BM experimental CH, colon tumor 3

tag: genotype


title: Dnmt3a(+/-)-BM experimental CH, colon tumor 2


title: PA14_RT_2


title: PA14_WT_1

source_name: RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 treated with 0.1% arabinose from OD1 to OD 2

value: PA14 WT


title: Dnmt3a(+/-)-BM experimental CH, colon tumor 1


title: H3K4me3

value: P0.5 total epidermis

value: Wildtype

value: Cell Signaling Technology, Tri-Methyl-Histone H3 (Lys4) Antibody #9751


title: S. coelicolor FLAG_vnz_CutR, no glucose, rep 2

city: Norwich

first: Ainsley

last: Beaton

address: Norwich Research Park

country: United Kingdom

institute: John Innes Centre

description: Sequencing performed by Novogene

data_processing: Alignment of reads to reference genome (NC_003888.3) using bowtie2 (bowtie2-2.2.3) options [bowtie2 -x reference_genome -S output.sam -U read_file]  conversion to .bam format and sorting using samtools (version 1.2). Commands: samtools view -bS [input.sam] > [output.bam]. Samtools sort [input.bam] [output.sortedbam]  Conversion of sorted bam file to a bedgraph format using bedtools. Command: genomeCoverageBed -ibam sorted.bam -g reference_genome.fna -scale -bga file.bedgraph.   Additional visual inspection was carried out using IGB to validate target peaks.

organism: Streptomyces coelicolor

growth_protocol: Growth media used were DNA (4 g/L Difco Nutrient Broth powder, 10 g/L agar), DNAD(DNA + 4% glucose), Streptomyces were inoculated onto cellophane covered agar plates as triplicate 5 μl  colonies and grown for 3 days at 30°C.

extract_protocol:
To cross-link proteins to DNA the cellophane disks were removed and submersed in 10 ml fresh 1% (v/v) formaldehyde solution at room temperature for 20 minutes. After a 5-minute incubation in 10 ml 0.5 M glycine the mycelium was harvested and washed twice with 25 ml ice-cold PBS pH 7.4 before being flash frozen in liquid nitrogen and stored at -80°C. For lysis the pellets were resuspended in 2 ml lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 10 mg/ml lysozyme, EDTA-free protease inhibitor) before 750 μl was transferred to a 2 ml microcentrifuge and samples incubated at 37°C for 30minutes. For fragmentation 750 μl IP buffer (100 mM Tris-HCl pH 8.0, 250 mM NaCl, 0.5% v/v Triton X-100, 0.1% SDS, EDTA-free protease inhibitor) was added and samples sonicated on ice at 50 Hz for 20 cycles of 10 seconds with at least 1 minute of rest between each cycle. 25 μl of the crude lysate was combined with 75 μl TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) and extracted with 100 μl phenol:chloroform. 2 μl 1mg/ml RNase A was mixed with 25 μl of the resulting extract, incubated at 37°C for 30 minutes and run on a 1% agarose gel to confirm a smear centred at 500 bp. The remaining crude lysate was centrifuged for 15 minutes at 13000 rpm, 4°C and supernatant saved. To prepare for binding 750 μl of Anti-FLAG M2 magnetic beads (Sigma Aldrich) were washed in 3.75 ml 0.5 IP buffer. The bead slurry was then mixed with 40 μl clarified lysate and incubated overnight on a vertical rotator  The lysate was removed, and the beads washed 4 times with 500 μl 0.5 IP buffer including 10 minutes vertical rotation at 4°C each cycle. Washed beads were incubated in 100 μl elution buffer (50 mM Tris-HCl pH 7.6, 10 mM EDTA, 1% SDS) overnight at 65°C. Elutant was removed and saved before an additional 50 μl elution  buffer was added and incubated at 65°C for a further 5 minutes. Once removed 3 μl 10mg/ml proteinase K was added to the combined eluants and incubated at 55°C for 2 hours. DNA was extracted with 200 μl phenol:chloroform and purified using a QIAquick PCR Purification Kit (QIAGEN) following the manufacturer’s instructions. DNA was eluted in 50 μl Buffer EB (10 mM Tris-HCl pH 8.5) and 47 μl snap frozen in liquid nitrogen and stored at -80°C. The remaining 3 μl of sample was used to determine the DNA concentration and quality. The Qubit Fluorometer 2.0 with the high-sensitivity kit was used for DNA concentration whilst DNA purity was quantified using a Nanodrop™ 2000 UV-Vis Spectrophotometer.
Carried out by Novogene

value: S. coelicolor deltacutRS +  pSS170-Cterm3xFLAG-vnzCutRS

value: no glucose (DNA media)


title: S. coelicolor FLAG_vnz_CutR, glucose, rep 1

description: Sequencing performed by Novogene

value: Glucose (DNAD media)


title: LDSA_091916_T0

value: total leukocytes


title: LDSA_091516_T8

value: 8 hours


title: Dnmt3a(+/+)-BM control, colon tumor 3

value: Dnmt3a(+/+) in BM


title: S. coelicolor FLAG_vnz_CutR, no glucose, rep 1

description: Sequencing performed by Novogene


title: Aged, 7 days post-injury snRNA-seq

city: Boulder

first: Jesse

middle: Vigoda

last: Kurland

state: Colorado

address: 1925 Colorado Avenue

department: MCDB

institute: University of Colorado Boulder

data_processing:
FastQC (v0.11.8) was used for initial quality control of Fastq files
nuclear RNA reads were mapped with the CellRanger Software Suite (10x Genomics, v3.0.1) using a pre-mRNA mm10 reference package
For uninjured technical replicates, files were integrated using cellranger aggregate
Genome_build: mm10 pre-mRNA (Millay, 2020)
Supplementary_files_format_and_content: paired-end fastq files from the Illumina Nextseq500
Supplementary_files_format_and_content: raw_bc_matrix files from cellranger count

source_name: TA muscle

growth_protocol: Mouse food - individually or grouped housed?

extract_protocol:
Methods paragraph
nuclear RNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ protocol, accessories and kits
single-nucleus RNA-seq, paired end, Illumina Nextseq500

treatment_protocol: For mice listed as injured, BaCl2 injection to the left TA and EDL

value: TA muscle

tag: condition

value: 7 days post-injury

tag: age

tag: gender

value: male


title: PA14_WT_2


title: Dnmt3a(+/+)-BM control, colon tumor 2

value: primary colon

tag: strain

value: whole colon tumor


title: S. coelicolor FLAG_CutR, glucose, rep 2

description: Sequencing performed by Novogene

value: S. coelicolor deltacutRS +  pSS170-Cterm3xFLAG-CutRS


title: LDSA_091516_T4

tag: cell type

value: lethal dose Staph aureus

tag: time

value: 4 hours


title: S. coelicolor FLAG_vnz_CutR, glucose, rep 2

description: Sequencing performed by Novogene


title: Dnmt3a(+/+)-BM control, colon tumor 1

value: BMT, then AOM/DSS


title: LDSA_091516_T2

value: 2 hours


title: S. coelicolor WT, glucose, rep 2

description: Sequencing performed by Novogene

value: WT


title: PA14_R_2

value: PA14 pJN105::PBAD_rsaL_lasR_PlasR


title: Aged, 4 days post-injury snRNA-seq

value: 4 days post-injury


title: S. coelicolor FLAG_CutR, glucose, rep 1

description: Sequencing performed by Novogene

value: Glucose (DNAD media)


title: LDSA_091516_T0

value: total leukocytes

value: 0 hours


title: Adult, 7 days post-injury snRNA-seq


title: LDSA_091916_T2


title: Blood smoke [Collection_E12]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Single-cell data were demultiplexed using bcl2fastq v2.19.0.316.
cellranger -v (3.1.0)
Normalization using Seurat
Assembly: GRCm38
Supplementary files format and content: raw seurat input matrices

source_name: Blood smoke

extract_protocol:
Single cell suspensions were stained with anti-mouse CD45 antibody and/or DAPI dye (live/dead exclusion), filtered with 70 um filters and sorted
10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1
10X Genomics Library Construction Kit
NovaSeq600 system: 28 bp (Read 1), 91 bp (Read 2) and 8 bp index read

treatment_protocol: Mice were exposed to normal air or cigarette smoke through custom-designed and purpose-built nose-only exposure system. The smoke of up to twelve 3R4F reference cigarettes was administered twice per day, 5 days a week for 3 months.

value: BALB/c

tag: Sex

value: female

value: 7-8 weeks

value: Live CD45-enriched whole blood cells from smoke-exposed mice


title: Blood air [Collection_E11]

source_name: Blood air


title: Adult, 4 days post-injury snRNA-seq

value: TA muscle

value: male


title: S. coelicolor WT, glucose, rep 1

description: Sequencing performed by Novogene


title: LDSA_090816_T24

value: 24 hours


title: S. coelicolor FLAG_CutR, no glucose, rep 2

description: Sequencing performed by Novogene

value: S. coelicolor deltacutRS +  pSS170-Cterm3xFLAG-CutRS

value: no glucose (DNA media)


title: Aged, uninjured, rep2 snRNA-seq

value: uninjured


title: Bone marrow smoke [Collection_E10]

source_name: Bone marrow smoke

value: Live CD45-enriched bone marrow cells from smoke-exposed mice


title: Aged, uninjured, rep1 snRNA-seq


title: Bone marrow air [Collection_E9]

source_name: Bone marrow air

value: Live CD45-enriched bone marrow cells from air-exposed mice


title: S. coelicolor FLAG_CutR, no glucose, rep 1

description: Sequencing performed by Novogene


title: LDSA_090816_T8

source_name: total leukocytes

value: lethal dose Staph aureus

value: 8 hours


title: LDSA_090816_T2

value: 2 hours


title: Bronchoalveolar smoke [Collection_E8]

source_name: Bronchoalveolar smoke

value: Live bronchoalveolar cells from smoke-exposed mice


title: S. coelicolor WT, no glucose, rep 2

description: Sequencing performed by Novogene

value: WT


title: S. coelicolor WT, no glucose, rep 1

description: Sequencing performed by Novogene


title: Adult, uninjured, rep1 snRNA-seq


title: Bronchoalveolar air [Collection_E7]

source_name: Bronchoalveolar air

value: BALB/c

value: Live bronchoalveolar cells from air-exposed mice


title: Adult, uninjured, rep2 snRNA-seq


title: LDSA_090816_T4

value: total leukocytes

value: 4 hours


title: LDSA_090816_T0

value: 0 hours


title: 41558

status: Public on Jun 11 2023

type: RNA

city: Heidelberg

first: Chang

last: Lu

address: Im Neuenheimer Feld 130

institute: Heidelberg University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.50.0).

source_name: LPS stimulated momocytes from CAD patients

label_protocol: Standard Illumina protocol

extract_protocol: total RNA was isolated using Illumina TotalPrep RNA Amplification Kit (Illumina, San Diego, CA, USA) and cDNA was produced.Quality control was performed with GenomeStudio.

value: monocytes

value: male


title: 20629


title: 20557

value: female


title: 41518


title: 10025


title: 10100


title: 41503


title: 20548


title: 10122


title: 20628


title: 31031


title: 20527


title: 41526


title: 31026


title: 20530


title: 10066


title: 10044


title: 10125


title: 10056


title: 41550


title: 10055


title: 20607


title: 10144


title: 10019


title: 41524


title: 10032


title: 10142


title: 20633


title: 10108


title: 41530


title: 10046


title: 41520


title: HAP1 Dux4ko, RNA-seq, HSV-1 GFP 8h.p.i., Replicate 2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For CUT&Tag, sequencing reads were mapped to the hg19 genome using bowtie2 (Langmead et al., 2012). The bigWig tracks were created by extending reads to 200, collapsing them into pileups, and normalizing to reads per million. Peaks were called using MACS2, using a cut off q-value<0.05, and IgG samples as control files. Filtering peaks using Bedtools to subtract peaks of 2h.p.i timepoint and subsequent filtering for peaks occuring in two or more consecutive timepoints.
For RNA-seq, Sequencing reads were aligned to hg19 and the HSV-1 strain 17 genome (the fasta file is part of this GEO entry) separately using hisat2 (Kim et al, 2015). Readcounts per gene were quantified using quasR (Gaidatzis et al, 2015) using a RefSeq gtf file for hg19, and the gtf file that is part of this GEO entry. For the HSV-1 gene counting, the bam and gtf files were both strand-separaed before counting.
Assembly: hg19, HSV1
Supplementary files format and content: bigwig, fasta, gtf, tsv

growth_protocol: DMEM, 10% fetal bovine serum, 1mM GlutaMAX, 1mM HEPES and 1x penicillin/streptomycin. Cells were cultured at 37°C / 5% CO2.

extract_protocol:
For CUT&Tag, we used the CUT&Tag Assay Kit (Active Motif) using 2.5ug Dux4 antibody (E5-5 Abcam) or 2.5ug rabbit IgG antibody (Cell Signalling Technology)
For RNA-seq, cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Infections were done in PBS, 0.1% Glucose, 1% fetal bovine serum. After 1h remaining virus was washed away with low pH Wash buffer (40mM Citic acid, 10mM KCl, 135 mM NaCl, pH 3).

tag: cell line

value: DUX4 KO

value: HSV-1 infection

tag: timepoint


title: HAP1 Dux4ko, RNA-seq, HSV-1 GFP 8h.p.i., Replicate 1


title: HAP1 DUX4ko, RNA-seq, Mock, Replicate 2

value: mock infection


title: HAP1 DUX4ko, RNA-seq, Mock, Replicate 1


title: HAP1wt, RNA-seq, Mock, Replicate 1

value: wt


title: 10040


title: HAP1wt, RNA-seq, Mock, Replicate 2


title: 10179


title: 20616


title: HFF-1, DUX4, CUT&Tag, Mock, Replicate2

data_processing:
For CUT&Tag, sequencing reads were mapped to the hg19 genome using bowtie2 (Langmead et al., 2012). The bigWig tracks were created by extending reads to 200, collapsing them into pileups, and normalizing to reads per million. Peaks were called using MACS2, using a cut off q-value<0.05, and IgG samples as control files. Filtering peaks using Bedtools to subtract peaks of 2h.p.i timepoint and subsequent filtering for peaks occuring in two or more consecutive timepoints.
For RNA-seq, Sequencing reads were aligned to hg19 and the HSV-1 strain 17 genome (the fasta file is part of this GEO entry) separately using hisat2 (Kim et al, 2015). Readcounts per gene were quantified using quasR (Gaidatzis et al, 2015) using a RefSeq gtf file for hg19, and the gtf file that is part of this GEO entry. For the HSV-1 gene counting, the bam and gtf files were both strand-separaed before counting.
Assembly: hg19, HSV1
Supplementary files format and content: bigwig, fasta, gtf, tsv
Library strategy: Cut & Tag


title: HAP1wt, RNA-seq, HSV-1 GFP 8h.p.i., Replicate 1


title: HAP1wt, RNA-seq, HSV-1 GFP 8h.p.i., Replicate 2


title: 41543


title: 41527


title: 41551


title: 10013


title: 20619


title: 10017


title: 31008


title: 20583


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 10h.p.i., Replicate2


title: 20630


title: 20569


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 10h.p.i., Replicate1


title: 20503


title: 41535


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 6h.p.i., Replicate2


title: HFF-1, IgG, CUT&Tag, HSV-1 GFP 12h.p.i., Replicate1


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 6h.p.i., Replicate1


title: HFF-1, IgG, CUT&Tag, HSV-1 GFP 12h.p.i., Replicate2


title: Pelvic cavity FFPE sample of Ovarian cancer [ST_HZ_20230215_9_18]

city: Shanghai

first: Leiqin

last: Liu

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

data_processing:
Approximately eight gigabases of RRBS data were obtained for each library. Adapter and inline barcode sequences were removed using Trim Galore (version 0.6.2).
The trimmed reads were mapped to the human genome version hg19 using BSMAP, with options “-q 20 -f 5 -r 0 -v 0.05 -s 16 -S 1”.
The resulting BAM files were converted to mHap files using the mHapTools.
CpG methylation metrics were extracted using the tool MethylDackel developed by Devon Ryan (https://github.com/dpryan79/MethylDackel).
We filtered out samples with low bisulfite conversion rates (< 99%), low mapping ratios (< 50%), and insufficient numbers of CpGs (< 0.8 million) at 10x coverage.
Assembly: hg19
Supplementary files format and content: The bedGraph contains the following 6 columns: 1) The chromosome. 2) The start coordinate. 3) The end coordinate. 4) The methylation percentage rounded to an integer. 5) The number of alignments/pairs reporting methylated bases. 6) The number of alignments/pairs reporting unmethylated bases.
Supplementary files format and content: The mhap contains the following 6 columns: 1) The chromosome. 2) The start coordinate, also the first CpG site position. 3) The end coordinate, also the last CpG site position. 4) The haplotype status with 1 for methylated sites, 0 for unmethylated ones. 5) Number of DNA methylation haplotypes. 6) Strand.

source_name: Pelvic cavity

extract_protocol:
Genomic DNA was isolated from FF tissues and FFPE sections using the TIANamp Genomic DNA kit (TIANGEN, Beijing, China) and TIAamp FFPE DNA kit (TIAGEN, Beijing, China), respectively, per the manufacture's recommendations.
Genomic DNA (10-50 ng) of FFPE samples was treated with shrimp alkaline phosphatase (New England Biolabs, USA), and the dephosphorylated DNA was used for subsequent MspI digestion, end-repair, and Illumina adapter ligation in "the same tube" without DNA purification. After sodium bisulfite conversion and PCR enrichment, the FFPE-RRBS libraries were subjected to 150 cycles of paired-end sequencing runs on a NovaSeq 6000 platform (Illumina, USA) with 15% of PhiX spike-in. For FF tissues, RRBS libraries were constructed utilizing 10-20 ng DNA without the SAP treatment, but the libraries were sequenced as described above.

value: Pelvic cavity

value: F

tag: clinical prognosis

value: Ovarian cancer

tag: specimen type

value: Formalin fixed paraffin-embedded tissue

tag: dataset

value: wgbs


title: HFF-1, DUX4, CUT&Tag, Mock, Replicate1

tag: treatment


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 12h.p.i., Replicate1


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 8h.p.i., Replicate1


title: Liver FFPE sample of Lung cancer [ST_HZ_20230215_8_15]

source_name: Liver

tag: tissue

value: Liver

value: M

value: Lung cancer


title: Hydrothorax FFPE sample of Stomach cancer [ST_HZ_20230215_8_14]

source_name: Hydrothorax

value: Hydrothorax

value: Stomach cancer


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 8h.p.i., Replicate2


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 4h.p.i., Replicate2


title: Lymphnode FFPE sample of Thyroid cancer [ST_HZ_20230215_6_7]

source_name: Lymphnode

value: Lymphnode

value: Thyroid cancer


title: Liver FFPE sample of Colon and rectum cancer [ST_HZ_20230215_6_12]

value: Colon and rectum cancer


title: Liver FFPE sample of Colon and rectum cancer [ST_HZ_20230215_7_13]


title: lymph node FFPE sample of Lung cancer [22M000192]

source_name: lymph node

value: lymph node

value: Test set