title: 11-Parenchyma-PBS.AIR (X126)

description: RNAseq (11 week PBS.AIR parenchyma)

source_name: Parenchyma

value: Parenchyma

tag: strain

value: Balb/C

value: 18-20 weeks


title: BLCa86 organoids

status: Public on Feb 01 2023

type: SRA

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

country: Switzerland

institute: UroGenus

library_source: transcriptomic single cell

data_processing:
Raw reads were mapped to the human reference genome GRCh38 (version 3.0.0 provided by 10X Genomics) using Cell Ranger (version 6.0.1).
The resulting gene count matrices were used to create a Seurat (version 4.1.1) object.
Cells with less than one detected feature and features found in less than one cell, were removed.
Heterotypic doublets were identified and removed with scDblFinder (version 1.6.0).
Low quality cells were removed using a median absolute deviation (MAD) threshold of 3 on the log10 transformed Feature and RNA counts per cell. Cells with above 50% mitochondrial reads were removed.
RNA expression was normalized using the NormalizeData function from Seurat with default parameters.
Assembly: GRCh38
Supplementary files format and content: data.matrix.h5, HDF5 feature-barcode matrix with normalized count (LogNormalized)

molecule: total RNA

organism: Homo sapiens

source_name: bladder

extract_protocol:
Organoids were collected in Basis medium (100g, 5min) and dissociated into single cells with 1ml TrypLE Express at 37°C for 10 min. Single-cell suspension was counted and cryopreserved in FBS/10%DMSO before scRNA sequencing. To obtain single cells from tumor tissue, tissues were digested as explained in the protocol for organoid derivation, and then cells were counted and cryopreserved in FBS/10%DMSO before analysis.  Slow-frozen single cell suspensions were shipped to the Genomics Facility Basel for scRNA-seq processing.
Cryovials were thawed and content transferred into 10 mL Basis medium and incubated for 10 min at room temperature to ensure complete removal of DMSO from the cells. Cells were collected (350g, 5 min), resuspended in 1 mL washing buffer consisting of PBS (Ca2+/Mg2+-free, Gibco, 10010-015) and 1% BSA (Sigma-Aldrich, A7906) and sequentially filtered through 100 µm (Falcon, 352360) and 40 µm cell strainers (Falcon, 352340). Apoptotic cells were removed by immunomagnetic cell separation using the Annexin Dead Cell Removal Kit (StemCell Technologies, 17899) and EasySepTM Magnet (StemCell Technologies, 18000). Whenever possible and required, repeat dead cell removal was performed to increase cell viability. Next, cells were washed with a resuspension buffer (PBS with 0.05% BSA), spin down and resuspended in a resuspension buffer. Cell numbers and viability were assessed at each step on a Cellometer K2 Image Cytometer (Nexcelom Bioscience, Cellometer K2) using ViaStain AOPI Staining Solution (Nexcelom Bioscience, CS2-0106-5mL) and PD100 cell counting slides (Nexcelom Bioscience, CHT4-PD100-003). Optimal cell concentrations were set according to 10x Genomics protocols (700-1200 cells/µL). Cells were loaded and processed using the 10x Genomics Chromium platform with the Next GEM Single Cell 3’ Reagent Kit v3.1 on 10x Genomics Chromium Single Cell Controller (10x Genomics, PN-120263). 4’000 cells were targeted per sample. Gene expression (GEX) libraries were amplified, pooled and sequenced on the Illumina NovaSeq 6000 platform with addition of 1% PhiX at recommended sequencing depth (20,000-50,000 reads/cell).

tag: tissue

value: bladder

tag: cell type

value: organoids from primary tissue

tag: tumor stage

tag: Sex

value: male

tag: treatment

value: naive


title: 17-2406-Month-6

city: Lebanon

first: Timothy

last: Sullivan

state: Grafton

address: 1 Medical Center Dr.

department: Biomedical Data Science

country: USA

institute: Dartmouth College

library_source: transcriptomic

data_processing:
First, we applied the cutadapt (version 1.15) to remove the adapter sequence (in our case it is “AGATCGGAAGAGC”) for the FASTQ files. Then, STAR (version 2.5.3a) was applied to align the reads to the hg19 human genome(17). Next, gene abundance was quantified using RSEM (version 3.3.9)(18). Lastly, normalized RPKM was calculated using TMM function (edgeR package)(19).
Supplementary files format and content: RNA-seq_20180810_normalizedRPKM_GeneSymbol_labelled_fixed.csv contains normalized RPKM values for all samples in the study.

source_name: Skin

extract_protocol:
Samples were stored in RNAlater and subsequently homogenized using a Qiagen Tissuelyser II.  RNA was purified using Qiagen’s RNeasy Fibrous Tissue minikit. Quality and concentration of RNA was assessed on a TapeStation 4400 (Agilent)
100ng of total RNA was used for library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were prepared manually or automated on an epMotion 5075t (Eppendorf, Hauppauge, NY). Libraries were assessed for size and concentration using the TapeStation 4400. Sequencing libraries were quantified on a Qubit fluorometer 3.0 (Thermo Fisher Scientific, Waltham, MA) prior to normalization for equimolar pooling.
Single-index paired-end sequencing was performed on Illumina’s NextSeq 500 to achieve >40 million reads per sample.

value: Skin

value: Abatacept

tag: timepoint

tag: patient

tag: escape

value: Y; 6mo

tag: intrinsic subtype

value: Proliferative


title: 11-Airway-PBS.AIR (X125)

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

description: RNAseq (11 week PBS.AIR airway)

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0  and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs  real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using STAR (v2.5.1b), followed by gene quantitation with RSEM (v1.2.31) and Kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: raw gene counts comma separated

organism: Mus musculus

source_name: Airway

extract_protocol:
RNA was prepared using TRizol (Invitrogen) extraction method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Experimental asthma: Some mice were sensitized and challenged intranasally with house dust mite (HDM) extract 5 days per week for 3 weeks. In other mice, this was HDM treatment 3 times/week from weeks 4-11. Controls received phosphate buffered saline (PBS).
Experimental chronic obstructive pulmonary disease (COPD): Mice were exposed to cigarette smoke (CS) twice per day, 5 days per week for 8 weeks. Control mice were exposed to normal air (AIR).
Experimental asthma-COPD overlap (ACO): Mice were sensitized and challenged intranasally with HDM or PBS. From weeks 4-11, mice were also exposed to CS or AIR.
Treatment with dexamethasone (DEX): Separate groups of mice were treated with DEX during week 11.

value: Airway

tag: age

value: Female

tag: exposure


title: THP-1_UT_UI_24 h_Rep 2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of PMA-differentiated untreated unifected-THP-1 cells at 24 h

hyb_protocol: Labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent  scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using Limma R Bioconductor package . Normalization of the data was done using Quantile normalization.

source_name: THP-1, Untreated, Uninfected, 24 h, Replicate 2

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: THP-1 cells were maintained in RPMI 1640 supplemented with 2 mM glutamine, HEPES and sodium bicarbonate with 10% fetal bovine serum and 1× Penicillin-Streptomycin solution. The cells were passaged at nearly 80% confluency. The experiment was performed at ~99% cell viability as determined by trypan blue exclusion method.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Nearly, 10 ×10^6 THP-1 cells were seeded in T-175 cm2 flasks in RPMI with 10% FBS. The cells were then differentiated with 30 nM PMA for 16-18 h. Following differentiation, the cells were allowed resting for 2-3 h. The cells were infected with Mtb H37Rv at a multiplicity of infection (MOI) of ~10:1 (Bacteria: THP-1 cells) for 4 h and then treated with 0.1 mM Vitamin C (Vit C). After 24 h of Vit C treatment, the cells were treated with 4 µg/ ml isoniazid (INH). THP-1 RNA was isolated from Mtb infected-untreated flasks, -Vit C treated flasks and -Vit C + INH treated flasks at different time-points (2 h, 24 h, 96 h) post-Vit C addition. A parallel set of uninfected and untreated THP-1 cells served as uninfected control samples.

value: PMA-differentiated THP-1 cells

value: Untreated

tag: infection

value: Uninfected

tag: time


title: 17-2403-Month-6

value: N


title: THP-1_UT_UI_0 h_Rep 2

description: Gene expression of PMA-differentiated untreated unifected-THP-1 cells at 0 h

source_name: THP-1, Untreated, Uninfected, 0 h, Replicate 2

value: 0 h


title: THP-1_UT_UI_0 h_Rep 3

source_name: THP-1, Untreated, Uninfected, 0 h, Replicate 3


title: 3-Parenchyma-HDM (X124)

description: RNAseq (3 week HDM parenchyma)

value: Parenchyma

value: Balb/C

value: HDM


title: BLCa77 parental tumor

value: bladder

value: primary tissue

value: Ta


title: 17-2403-Month-3

value: Skin


title: 3-Airway-HDM (X123)

description: RNAseq (3 week HDM airway)

value: 18-20 weeks


title: Triple_r1

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
Reads were demultiplexed using the the pyBarcodeFilter script from the pyCRACutility suite
Adaptor trimming  with cutadapt 1.15
Quality-trimming with trimmomatic
Mapping with bowtie2
Normalized coverage obtained with the bamCoverage tool of deepTools2 package. Normalization to  counts per 10^7 counts. Reads that are shorter than 20 nt and that are mapped to 37S rDNA unit (transcribed by RNAPI) were filtered out.
Genome_build: R64
Supplementary_files_format_and_content: bigwig files for each sample and for each strand (plus or minus)

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells grown on CSM-TRP to OD600= 0.4-0.6

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol.
RNA was reverse transcribed using the Reverse transcriptase IV (Invitrogen). The cDNA solution was used to perform multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per ml of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

value: W303-derived strain

tag: genotype

value: Rpc160-HTP expressing C128 Q476A, K479A, R481G


title: BLCa77 organoids

value: organoids from primary tissue

value: male

value: naive


title: 17-2403-Baseline

value: Abatacept

value: Baseline

value: Proliferative


title: THP-1_UT_UI_0 h_Rep 1

source_name: THP-1, Untreated, Uninfected, 0 h, Replicate 1

value: PMA-differentiated THP-1 cells

value: Untreated

value: Uninfected

value: 0 h


title: NonnaiveCD8, Post-pembro2_scTCRseq

city: Boston

first: Deepak

middle: A

last: Rao

state: MA

address: 60 Fenwood Road

department: Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital

data_processing:
Both RNA and TCR libraries were processed using the CellRanger workflow (v6.1.1)
For RNA libraries, BCL files from the sequencing output were used to generate FASTQ files using the cellranger mkfastq command. Reads were then aligned to a reference (GRCh38), filtered, and counts of barcodes and UMIs were generated using the cellranger count command.
For TCR libraries, BCL files were also used to generate FASTQ files using cellranger mkfastq, as above. Reads were then aligned to a TCR reference (vdj-GRCh38), productive contigs were filtered, and CDR3 regions were identified for each cell. Cells with the same V(D)J transcripts were then grouped into the same clonotype.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 files provide feature-barcode matrices for cell-associated barcodes
Supplementary files format and content: filtered_contig_annotations.csv files provide the TCR information identified for each high-confidence contig for cell-associated barcodes
Library strategy: scTCRseq

source_name: PBMC

extract_protocol:
PBMCs were thawed, and viable/CD3+/CD8+/non-[CD45RA+;CCR7+] cells were sorted. Cells were then encapsulated in oil droplets, and RNA was reverse-transcribed and amplified, according to the 10X Genomics protocol for 5' barcoded GEX and V(D)J TCR.
Libraries were prepared according to the 10X Genomics protocol for 5' barcoded GEX and V(D)J TCR.

value: PBMC

value: Non-naive CD8 T cells

value: Post-pembro 2

tag: single-cell or bulk

value: single-cell

tag: molecule type

value: T cell receptor RNA


title: 16-2256-Baseline

value: Skin

value: Placebo

value: N

value: Inflammatory


title: 3-Parenchyma-PBS (X122)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

tag: strain

value: Balb/C

value: 18-20 weeks

value: Female

value: PBS


title: NonnaiveCD8, Post-pembro2, scRNAseq

data_processing:
Both RNA and TCR libraries were processed using the CellRanger workflow (v6.1.1)
For RNA libraries, BCL files from the sequencing output were used to generate FASTQ files using the cellranger mkfastq command. Reads were then aligned to a reference (GRCh38), filtered, and counts of barcodes and UMIs were generated using the cellranger count command.
For TCR libraries, BCL files were also used to generate FASTQ files using cellranger mkfastq, as above. Reads were then aligned to a TCR reference (vdj-GRCh38), productive contigs were filtered, and CDR3 regions were identified for each cell. Cells with the same V(D)J transcripts were then grouped into the same clonotype.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 files provide feature-barcode matrices for cell-associated barcodes
Supplementary files format and content: filtered_contig_annotations.csv files provide the TCR information identified for each high-confidence contig for cell-associated barcodes

tag: tissue

value: total RNA


title: 11-Parenchyma-HDM.CS.DEX (X120)

description: RNAseq (11 week HDM.CS.DEX parenchyma)


title: R451V_r1

value: W303-derived strain

value: Rpc160-HTP expressing C128 R451V


title: R451V_r2


title: THP-1_UT_UI_24 h_Rep 1

source_name: THP-1, Untreated, Uninfected, 24 h, Replicate 1

tag: cell type

value: PMA-differentiated THP-1 cells

value: Untreated

value: Uninfected


title: Q199R_r2

value: Rpc160-HTP expressing C128 Q199R


title: 3-Airway-PBS (X121)

description: RNAseq (3 week PBS airway)

value: Airway


title: 16-2256-Month-6

value: Skin


title: Q199R_r1


title: 11-Airway-HDM.CS.DEX (X119)

description: RNAseq (11 week HDM.CS.DEX airway)


title: NonnaiveCD8, Post-pembro1, scRNAseq

value: PBMC

value: Non-naive CD8 T cells

value: Post-pembro 1

value: single-cell


title: 16-2256-Month-3

value: Placebo

value: N

value: Inflammatory


title: Triple_r2

value: Rpc160-HTP expressing C128 Q476A, K479A, R481G


title: 16-2253-Month-6

value: Y; 6mo


title: 11-Parenchyma-HDM.CS (X118)

description: RNAseq (11 week HDM.CS parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks

value: Female


title: MLR, Post-pembro2, scTCRseq

data_processing:
Both RNA and TCR libraries were processed using the CellRanger workflow (v6.0.1)
For RNA libraries, BCL files from the sequencing output were used to generate FASTQ files using the cellranger mkfastq command. Reads were then aligned to a reference (GRCh38), filtered, and counts of barcodes and UMIs were generated using the cellranger count command.
For TCR libraries, BCL files were also used to generate FASTQ files using cellranger mkfastq, as above. Reads were then aligned to a TCR reference (vdj-GRCh38), productive contigs were filtered, and CDR3 regions were identified for each cell. Cells with the same V(D)J transcripts were then grouped into the same clonotype.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 files provide feature-barcode matrices for cell-associated barcodes
Supplementary files format and content: filtered_contig_annotations.csv files provide the TCR information identified for each high-confidence contig for cell-associated barcodes
Library strategy : scTCR-seq

extract_protocol:
After co-culture, the cells were stained with fixable viability dye, CD3, CD4 and CD8. Viable/violet-/CD3+/CFSE low cells were sorted. Cells were then encapsulated in oil droplets, and RNA was reverse-transcribed and amplified, according to the 10X Genomics protocol for 5' barcoded GEX and V(D)J TCR.
Libraries were prepared according to the 10X Genomics protocol for 5' barcoded GEX and V(D)J TCR.

treatment_protocol: Donor splenocytes were gamma-irradiated (30 Gy) and were loaded with CellTrace Violet dye to be able to distinguish donor and recipient cells. 1 x10^6 recipient PBMCs were loaded with CFSE and co-cultured with 4 x10^6 irradiated donor splenocytes for 5 days in 10% FCS-RPMI, supplemented with recombinant human IL-2 (20 units/ml) and anti-CD28 (1 µg/ml) at 37C and 5% CO2.

value: Post-pembro 2

value: T cell receptor RNA


title: MLR, Post-pembro2, scRNAseq

data_processing:
Both RNA and TCR libraries were processed using the CellRanger workflow (v6.0.1)
For RNA libraries, BCL files from the sequencing output were used to generate FASTQ files using the cellranger mkfastq command. Reads were then aligned to a reference (GRCh38), filtered, and counts of barcodes and UMIs were generated using the cellranger count command.
For TCR libraries, BCL files were also used to generate FASTQ files using cellranger mkfastq, as above. Reads were then aligned to a TCR reference (vdj-GRCh38), productive contigs were filtered, and CDR3 regions were identified for each cell. Cells with the same V(D)J transcripts were then grouped into the same clonotype.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 files provide feature-barcode matrices for cell-associated barcodes
Supplementary files format and content: filtered_contig_annotations.csv files provide the TCR information identified for each high-confidence contig for cell-associated barcodes

value: total RNA


title: WT_r2

value: W303-derived strain

value: Rpc160-HTP expressing C128


title: WT_r1


title: 11-Airway-HDM.CS (X117)

description: RNAseq (11 week HDM.CS airway)

value: Airway


title: NonnaiveCD8, Post-pembro1_scTCRseq

value: PBMC

value: Non-naive CD8 T cells

value: Post-pembro 1


title: 16-2253-Baseline

value: Skin

value: Placebo

value: Baseline


title: 16-2253-Month-3

value: Y; 6mo


title: Muscle_ALS5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Assembly: hg19
Supplementary files format and content: text files containing counts

source_name: muscle

extract_protocol:
Tissue samples were homogenized in TRIzol reagent and RNA was isolated with the RNAspin Mini Columns (GE Healthcare)
Sequencing libraries were prepared with using Illumina TruSeq Stranded Total RNA Library prep kit following the manufacturer’s instructions.

value: muscle

value: F

tag: age (years)

tag: disease state

value: ALS


title: Biopsy_829_1H

city: Toronto

first: Mingyao

last: Liu

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used Affymetrix Human Genome U133 Plus 2.0 Array annotation data (hgu133plus2.db package in R)

label: biotin

source_name: Biopsy, time point: H

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

value: lung

tag: evlp type

value: Non-EVLP


title: 11-Parenchyma-PBS.CS.DEX (X116)

description: RNAseq (11 week PBS.CS.DEX parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks

tag: Sex

value: Female


title: 15-2103-Month-6

tag: treatment

tag: timepoint

tag: patient

value: N


title: Biopsy_690_2H


title: 15-2103-Month-3

tag: escape

tag: intrinsic subtype


title: Muscle_ALS4

value: M


title: Biopsy_829_CIT

source_name: Biopsy, time point: CIT


title: Muscle_ALS2


title: 11-Parenchyma-PBS.CS (X114)

description: RNAseq (11 week PBS.CS parenchyma)

tag: age

tag: exposure


title: 11-Airway-PBS.CS.DEX (X115)

description: RNAseq (11 week PBS.CS.DEX airway)

value: Airway


title: 11-Parenchyma-HDM.AIR.DEX (X112)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: Biopsy_690_CIT


title: 15-2103-Baseline


title: 11-Airway-PBS.CS (X113)

description: RNAseq (11 week PBS.CS airway)


title: 14-1956-Month-6


title: Muscle_ALS1


title: Muscle_CTR5

value: Healthy


title: 11-Airway-HDM.AIR.DEX (X111)

description: RNAseq (11 week HDM.AIR.DEX airway)


title: 14-1956-Month-3

value: Skin


title: Muscle_CTR4


title: Biopsy_681_CIT


title: Biopsy_728_2H


title: 11-Parenchyma-HDM.AIR (X110)

description: RNAseq (11 week HDM.AIR parenchyma)


title: 14-1953-Baseline

value: Abatacept

value: Inflammatory


title: 14-1956-Baseline

value: Placebo

value: Baseline


title: Muscle_ALS3

value: muscle

value: F


title: Biopsy_667_2H

value: lung


title: 11-1515-Month-6


title: Muscle_CTR2


title: 11-Parenchyma-PBS.AIR.DEX (X108)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: Biopsy_681_1H

value: Non-EVLP


title: Biopsy_667_CIT


title: Muscle_CTR1


title: 11-1515-Month-3


title: 11-Airway-PBS.AIR (X105)

description: RNAseq (11 week PBS.AIR airway)


title: 11-Airway-PBS.AIR.DEX (X107)

description: RNAseq (11 week PBS.AIR.DEX airway)


title: Biopsy_639_CIT


title: Biopsy_639_2H


title: 11-1509-Month-6

value: Proliferative


title: 11-1515-Baseline


title: 3-Parenchyma-HDM (X104)

description: RNAseq (3 week HDM parenchyma)

value: Parenchyma

value: Balb/C

value: HDM


title: Biopsy_728_CIT


title: Thymic tissue section, biol rep 6

city: Oslo

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: University Of Oslo

data_processing:
SpaceRanger v.1.2.2 pipeline
Assembly: GRCh38-2020-A (10x Genomics), based on Homo Sapiens GRCh38 (Gencode v32)
Supplementary files format and content: SpaceRanger (10x Genomics) raw barcode matrix and spatial output files a: Tab-separated values files, matrix files, image files in jpg and png format, javascript object notation files, comma-separated value files
Library strategy: Spatial transcriptomics

source_name: Thymus

extract_protocol:
Thymic tissue samples were collected in RPMI-1640 w/ 10% FBS and transportated on ice. Tissue was OCT embedded and snap frozen < 1hr after surgical removal. Storage at -80 degrees celcius until sectioning. Tissue was punched out at 6 mm diameter with 10um thickness, and stored at -80 degrees celcius until performing 10x visium protocol.
Libraries were prepared by use of the 10x Genomic Visium spatial gene expression kit, protocols CG000160, rev B and CG000239, rev.D. Incubation time for tissue permeabilization was 12 min. For the cDNA synthesis,  15-17 cycles were run on the Veriti Thermal Cycler, and the final index PCR was run for 10-13 cycles.

value: Thymus

value: 5 months

value: Male


title: Thymic tissue section, biol rep 8

value: 12 months

value: Female


title: Thymic tissue section, biol rep 7

value: 5.5 months


title: Muscle_CTR3

value: M

value: Healthy


title: Thymic tissue section, biol rep 5


title: Biopsy_630_CIT


title: 11-1509-Baseline

value: Skin

value: Placebo

value: Baseline

value: N


title: 3-Airway-HDM (X103)

description: RNAseq (3 week HDM airway)

value: Airway

value: 18-20 weeks


title: Biopsy_853_2H

value: lung

value: Non-EVLP


title: 11-1506-Baseline

value: Abatacept

value: Inflammatory


title: 3-Parenchyma-PBS (X102)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

value: Balb/C

value: PBS


title: 11-Parenchyma-PBS.AIR (X106)

description: RNAseq (11 week PBS.AIR parenchyma)

value: Female


title: 11-Airway-HDM.AIR (X109)

description: RNAseq (11 week HDM.AIR airway)


title: Biopsy_853_CIT


title: 11-Parenchyma-HDM.CS.DEX (X100)

description: RNAseq (11 week HDM.CS.DEX parenchyma)


title: Biopsy_614_2H


title: 11-1509-Month-3

value: Proliferative


title: Biopsy_614_CIT


title: Biopsy_630_1H


title: 11-Parenchyma-HDM.CS (X98)

description: RNAseq (11 week HDM.CS parenchyma)


title: 11-Airway-HDM.CS.DEX (X99)

description: RNAseq (11 week HDM.CS.DEX airway)


title: 11-1503-Month-3


title: 18-2553-Baseline

value: Y; 12mo- still can use!


title: 11-1503-Baseline


title: 11-Airway-HDM.CS (X97)

description: RNAseq (11 week HDM.CS airway)


title: 10-1353-Month-6


title: Biopsy_635_CIT


title: Biopsy_635_2H


title: 11-Parenchyma-PBS.CS.DEX (X96)

description: RNAseq (11 week PBS.CS.DEX parenchyma)


title: Thymic tissue section, biol rep 4

value: Thymus

value: 9 months


title: 10-1353-Month-3

value: Skin

value: Placebo


title: PBMC, biol rep 5, CITE-seq

description: CITE-Seq

data_processing:
CellRanger v.3.1.1. pipeline
Assembly: GRCh38-2020-A (10x Genomics), based on Homo sapiens GRCh38 (Gencode v32)
Supplementary files format and content: CellRanger (10x Genomics) raw barcode matrix output files: Tab-separated values files, matrix files
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Thymic tissue samples were collected in RPMI-1640 w/ 10% FBS and transportated on ice. Dissociation was initiated < 1 hr after surgival removal, by enzymatic and mechanical digestion. Dissociated cells were then subjected to indicated enrichement. Blood samples were collected in EDTA tubes, and PBMC isolation was performed <1hr after collection.
10x Genomics 5' immune profiling kit v1, according to protocol CCG000186 rev D. For the cDNA synthesis step, 13 PCR cycles were run for the PBMC and unenriched samples, while 15 cycles were run for antigen-presenting cell enriched and CD45 depleted samples. For the final gene expression index PCR, 14 cycles were run for all samples. For feature barcoding, the default 9 cycles were run for the PBMC and  CD45 depleted samples, while 6 cycles were run for the antigen-presenting cell  enriched and unenriched samples.

value: Blood

value: PBMC, biol rep 5

tag: cell type enrichement

value: Peripheral blood mononuclear cell isolation by LympphoPrep (Abbott)

value: 13.5 months

value: Male

tag: antibodies/tags

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559)


title: CD45 depleted thymic cells, biol rep 5, CITE-seq

description: CITE-Seq

value: CD45 depleted thymic cells

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells, then magnetic depletion (STEMcell technolgies) of CD45-expressing cells

value: anti-CD3 (BioLegend 300479), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Unenriched thymic cells, biol rep 5, CITE-seq

description: CITE-Seq

value: Unenriched thymic cells

value: Unenriched

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125),  anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Thymic tissue section, biol rep 3

value: 4 months


title: Thymic tissue section, biol rep 1

value: Thymus

value: 5 months


title: Biopsy_607_2H

value: lung

value: Non-EVLP


title: Thymic tissue section, biol rep 2

value: 10 days


title: 10-1353-Baseline

value: Skin

value: Placebo

value: Baseline

value: N

value: Inflammatory


title: 11-1503-Month-6

value: Abatacept


title: Antigen-presenting cell enriched thymic cells, biol rep 5, CITE-seq

description: CITE-Seq

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells

value: 13.5 months

value: Male

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Biopsy_607_CIT


title: 11-Parenchyma-PBS.CS (X94)

description: RNAseq (11 week PBS.CS parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks

value: Female


title: 09-1206-Month-6

value: Proliferative


title: Biopsy_864_2H

value: lung

value: Non-EVLP


title: PBMC, biol rep 4, CITE-seq

description: CITE-Seq

value: Blood

value: PBMC, biol rep 4

value: Peripheral blood mononuclear cell isolation by LympphoPrep (Abbott)

value: 1.6 months

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559)


title: 09-1206-Month-3

value: Skin

value: Abatacept

value: N


title: 11-Airway-PBS.CS (X93)

description: RNAseq (11 week PBS.CS airway)

value: Airway


title: Biopsy_864_CIT


title: Unenriched thymic cells, biol rep 4, CITE-seq

description: CITE-Seq

value: Thymus

value: Unenriched thymic cells

value: Unenriched

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: 09-1206-Baseline

value: Baseline


title: 11-Parenchyma-HDM.AIR.DEX (X92)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks

value: Female


title: CD45 depleted thymic cells, biol rep 4, CITE-seq

description: CITE-Seq

value: CD45 depleted thymic cells

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells, then magnetic depletion (STEMcell technolgies) of CD45-expressing cells

value: anti-CD3 (BioLegend 300479), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Biopsy_571_CIT

value: lung

value: Non-EVLP


title: 09-1203-Month-6

value: Skin

value: Placebo

value: Proliferative


title: Biopsy_566_1H


title: 09-1203-Month-3

value: N


title: 11-Airway-HDM.AIR.DEX (X91)

description: RNAseq (11 week HDM.AIR.DEX airway)

value: Airway


title: 11-Parenchyma-HDM.AIR (X90)

description: RNAseq (11 week HDM.AIR parenchyma)


title: 11-Airway-PBS.CS.DEX (X95)

description: RNAseq (11 week PBS.CS.DEX airway)


title: 08-1071-Month-6


title: Biopsy_566_CIT


title: PBMC, biol rep 3, CITE-seq

description: CITE-Seq

value: Blood

value: PBMC, biol rep 3

value: Peripheral blood mononuclear cell isolation by LympphoPrep (Abbott)

value: 9 months

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559)


title: 11-Airway-HDM.AIR (X89)

description: RNAseq (11 week HDM.AIR airway)

value: Balb/C

value: 18-20 weeks


title: 09-1203-Baseline

value: Baseline


title: Biopsy_605_R


title: Antigen-presenting cell enriched thymic cells, biol rep 4, CITE-seq

description: CITE-Seq

value: Thymus

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells

value: 1.6 months

value: Female

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: CD45 depleted thymic cells, biol rep 3, CITE-seq

description: CITE-Seq

value: CD45 depleted thymic cells

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells, then magnetic depletion (STEMcell technolgies) of CD45-expressing cells

value: anti-CD3 (BioLegend 300479), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: 11-Parenchyma-PBS.AIR.DEX (X88)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)

value: Parenchyma


title: 08-1071-Month-3

value: Skin

value: Placebo

value: N


title: 11-Airway-PBS.AIR.DEX (X87)

description: RNAseq (11 week PBS.AIR.DEX airway)

value: Airway


title: Biopsy_587_CIT

value: lung

value: Non-EVLP


title: 08-1071-Baseline


title: Biopsy_605_CIT


title: 08-1068-Month-6

value: Abatacept


title: 11-Parenchyma-PBS.AIR (X86)

description: RNAseq (11 week PBS.AIR parenchyma)

value: Balb/C

value: 18-20 weeks


title: Biopsy_833_2H


title: 3-Parenchyma-HDM (X84)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: Unenriched thymic cells, biol rep 2, CITE-seq

description: CITE-Seq

value: Thymus

value: Unenriched thymic cells

value: Unenriched

value: 2.5 months

value: Male


title: PBMC, biol rep 2, CITE-seq

description: CITE-Seq

value: Blood

value: PBMC, biol rep 2

value: Peripheral blood mononuclear cell isolation by LympphoPrep (Abbott)

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559)


title: Unenriched thymic cells, biol rep 3, CITE-seq

description: CITE-Seq

value: 9 months

value: Female

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125),  anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: CD45 depleted thymic cells, biol rep 2, CITE-seq

description: CITE-Seq

value: CD45 depleted thymic cells

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells, then magnetic depletion (STEMcell technolgies) of CD45-expressing cells

value: anti-CD3 (BioLegend 300479), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Biopsy_587_1H

value: lung

value: Non-EVLP


title: Biopsy_833_CIT


title: 08-1068-Month-3

value: Skin

value: Abatacept

value: N


title: 08-1068-Baseline

value: Baseline


title: 3-Airway-HDM (X83)

description: RNAseq (3 week HDM airway)

value: Airway

value: Balb/C

value: 18-20 weeks

value: HDM


title: Biopsy_589_2H


title: Antigen-presenting cell enriched thymic cells, biol rep 2, CITE-seq

description: CITE-Seq

value: Thymus

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells

value: 2.5 months

value: Male

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: PBMC, biol rep 1, CITE-seq

description: CITE-Seq

value: Blood

value: PBMC, biol rep 1

value: Peripheral blood mononuclear cell isolation by LympphoPrep (Abbott)

value: 7 days

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559)


title: 08-1065-Month-6

value: Skin

value: Abatacept

value: Inflammatory


title: 3-Parenchyma-PBS (X82)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

value: Female

value: PBS


title: Biopsy_627_2H

value: lung

value: Non-EVLP


title: 3-Airway-PBS (X81)

description: RNAseq (3 week PBS airway)

value: Airway

value: Balb/C

value: 18-20 weeks


title: Antigen-presenting cell enriched thymic cells, biol rep 3, CITE-seq

description: CITE-Seq

value: Thymus

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells

value: 9 months

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: Unenriched thymic cells, biol rep 1, CITE-seq

description: CITE-Seq

value: Unenriched thymic cells

value: Unenriched

value: 7 days

value: Male

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: 08-1065-Month-3

value: Skin

value: Abatacept

value: N

value: Inflammatory


title: 08-1065-Baseline

value: Baseline


title: CD45 depleted thymic cells, biol rep 1, CITE-seq

description: CITE-Seq

value: CD45 depleted thymic cells

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells, then magnetic depletion (STEMcell technolgies) of CD45-expressing cells

value: anti-CD3 (BioLegend 300479), anti-CD38 (BioLegend 303543), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: 11-Parenchyma-HDM.CS.DEX (X80)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks

value: Female


title: 11-Airway-HDM.CS.DEX (X79)

description: RNAseq (11 week HDM.CS.DEX airway)

value: Airway


title: 11-Airway-PBS.AIR (X85)

description: RNAseq (11 week PBS.AIR airway)


title: Biopsy_627_CIT

value: lung

value: Non-EVLP


title: Biopsy_578_2H


title: 08-1056-Month-3


title: 08-1056-Baseline


title: Biopsy_578_CIT


title: 08-1053-Month-6

value: Placebo


title: Biopsy_659_2H


title: 11-Parenchyma-PBS.CS.DEX (X76)

description: RNAseq (11 week PBS.CS.DEX parenchyma)


title: 08-1053-Month-3


title: Biopsy_589_CIT


title: 11-Airway-HDM.CS (X77)

description: RNAseq (11 week HDM.CS airway)


title: shoot, TORIN1 Rep. 2

city: Heidelberg

first: Denis

last: Janocha

address: INF 230

department: Stem cell research

country: Germany

institute: Center for Organismal Studies, Heidelberg University

data_processing:
RNAstar (v2.6) alignment
StringTie (v1.3.3), used to generate raw gene counts
DESeq2 (v.1.18.1), used to generate DEG and Normalized Counts
Genome_build: TAIR10
Supplementary_files_format_and_content: raw gene counts, Normalized Counts, DEG

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Shoot tissue

growth_protocol: Col-0 seedlings grown vertically under continuous light on 1/2 MS, 0.8% phyto-agar plates for 4 days after germination.

extract_protocol:
Whole RNA was extracted using plant RNA purification reagent (Invitrogen). Samples were digested with TURBO DNAse (Ambion) and purified with RNeasy Mini Kit (Quiagen). RNA integrity was checked on a bioanalyzer.
RNA was poly-(A) selected and prepared with standard Illumina protocols

treatment_protocol: Seedlings 4DAG were transferred to fresh plates containing 2µM AZD8055, 10 µM TORIN1 or 20 µM KU63749 or equal amounts of DMSO for 8h. Approximately 30mg of shoot tissue was harvested.

tag: ecotype

value: shoot


title: Biopsy_564_1H


title: 08-1053-Baseline

value: Skin


title: Biopsy_659_CIT


title: shoot, TORIN1 Rep. 1


title: shoot, KU63794 Rep. 3


title: 11-Airway-PBS.CS.DEX (X75)

description: RNAseq (11 week PBS.CS.DEX airway)

tag: strain


title: 11-Parenchyma-PBS.CS (X74)

description: RNAseq (11 week PBS.CS parenchyma)

source_name: Parenchyma

tag: tissue


title: Antigen-presenting cell enriched thymic cells, biol rep 1, CITE-seq

description: CITE-Seq

value: Thymus

tag: cell type

value: Optiprep gradient enrichement (Sigma Aldrich) for antigen-presenting cells

value: 7 days

value: Male

value: anti-CD3 (BioLegend 300479), anti-CD4 (BioLegend 344651), anti-CD8a (BioLegend 301071), anti-CD45RA (BioLegend 304163), anti-CD45RO (BioLegend 304259), anti-CD197 (BioLegend 353251), anti-CD123 (BioLegend 306045), anti-CD141 (BioLegend 344125), anti-CD11b (BioLegend 301359), anti-CD11c (BioLegend 371521), anti-CD14 (BioLegend 367137), anti-CD16 (BioLegend 302065), anti-CD19 (BioLegend 302265), anti-CD38 (BioLegend 303543), anti-CD56 (BioLegend 362559), anti-EPCAM (abcam AB252530, self-conjugated, barcode TAGTTGACATGCCAT), anti-CD249 (BD Bioscience BDB564532, self-conjugated, barcode GGCTGCGCACCGCCT), anti-CDR2 (Cortical dendritic reticulum antigen 2, donated by Kyewski lab, self-conjugated, barcode AAGGCAGACGGTGCA)


title: 06-0756-Month-6

value: Abatacept

value: N


title: shoot, KU63794 Rep. 1


title: 11-Parenchyma-HDM.AIR.DEX (X72)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)

value: Parenchyma


title: Biopsy_575_C


title: shoot, KU63794 Rep. 2


title: shoot, AZD8055 Rep. 3


title: Biopsy_857_2H


title: shoot, TORIN1 Rep. 3


title: 11-Airway-HDM.AIR.DEX (X71)

description: RNAseq (11 week HDM.AIR.DEX airway)

value: Balb/C


title: 05-0603-Month-6

value: Inflammatory


title: 06-0756-Month-3


title: 06-0756-Baseline

value: Baseline


title: shoot, AZD8055 Rep. 2


title: 05-0603-Baseline


title: 05-0603-Month-3


title: Biopsy_573_1H


title: shoot, AZD8055 Rep. 1


title: 11-Airway-HDM.AIR (X69)

description: RNAseq (11 week HDM.AIR airway)

value: Airway

value: 18-20 weeks

value: Female


title: 11-Parenchyma-HDM.AIR (X70)

description: RNAseq (11 week HDM.AIR parenchyma)


title: Biopsy_575_R

value: lung

value: Non-EVLP


title: Biopsy_645_2H


title: 11-Airway-PBS.CS (X73)

description: RNAseq (11 week PBS.CS airway)


title: shoot, Mock Rep.3

value: DMSO

value: shoot


title: shoot, Mock Rep.2


title: 04-0462-Month-3

value: Skin

value: Placebo


title: 11-Airway-PBS.AIR.DEX (X67)

description: RNAseq (11 week PBS.AIR.DEX airway)


title: 11-Parenchyma-PBS.AIR.DEX (X68)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: Biopsy_645_CIT


title: 04-0462-Baseline


title: shoot, Mock Rep.1


title: Biopsy_571_2H


title: Biopsy_857_CIT


title: 04-0459-Month-6


title: 11-Airway-PBS.AIR (X65)

description: RNAseq (11 week PBS.AIR airway)


title: Biopsy_564_CIT


title: PLC-PRF-5, 25OHD 500nM, 48 h

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

country: China

institute: Nankai University

library_source: genomic

data_processing:
We applied Circle-Map software (v2.0) to detect ecDNA from sequencing data. Firstly, sequencing reads were aligned to the human reference genome (hg38 genome download from UCSC) using BWA-MEM. Then, to detect the coordinates of each ecDNA, two BAM files which were sorted according to read names and coordinates for the extraction of circular reads were used.  Several filtering steps were conducted to improve the accuracy of ecDNA detection. The specific settings were as follows: (1) split reads ≥ 2, (2) circle score ≥ 20, (3) coverage increase in the start coordinate ≥ .33, (4) coverage increase in the end coordinate ≥ .33, (5) coverage continuity ≤ .1 and (6) The SD of coverage smaller than the mean coverage over the whole ecDNA region
Assembly: hg38
Supplementary files format and content: FastQC, identified ecDNA sequences
Library strategy: Circle-Seq

molecule: genomic DNA

extract_protocol:
MagAttract HMW DNA Kit (Qiagen, Hilden, Germany, 67563) was applied for genomic DNA extraction. To eliminate linear chromosomal DNA and purify circular DNA, the genomic DNA was treated with Plasmid-Safe ATP-dependent DNase (Lucigen) at 37°C, after 6 days of digestion, heat inactivate the exonuclease by incubating at 70°C for 30 minutes. To eliminate mitochondrial DNA, DNAs were eluted and digested with PacI (NEB) for 10 hours, and then extracted with Phenol/chloroform/isoamyl alcohol (PCI) solution (25:24:1).
Amplify the remaining circular DNA in the reaction by MDA using φ29 DNA polymerase and random hexamer primers (REPLI-g Mini Kit (Qiagen, Hilden, Germany, 150025)), followed by sample clean up (Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA, A63880)).

tag: cell line

value: Hepatocellular carcinoma cells


title: 04-0459-Month-3


title: 3-Parenchyma-HDM (X64)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: 04-0459-Baseline


title: Biopsy_785_CIT


title: 3-Airway-HDM (X63)

description: RNAseq (3 week HDM airway)


title: PLC-PRF-5, DMSO, 48 h

value: Hepatocellular  carcinoma cells

value: DMSO, 48 h


title: PLC-PRF-5, 25OHD 100nM, 48 h


title: 3-Parenchyma-PBS (X62)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

value: PBS


title: Biopsy_785_2H


title: input mouse liver rep3

city: Beijing

first: Fangming

address: No.5 Dongdan 3 Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
ChIP-Seq was performed on Illumina HiSeq3000
For the bioinformatic analysis of ChIP-Seq data, Bowtie2 was used for alignment.
Enriched peaks were identified using MACS2 with FDR < 0.01.
ChIPseeker was used for peaks annotation.
Peaks enrichment distribution was analyzed by Deeptools
Genome_build: mm9
Supplementary_files_format_and_content: peaks.narrowPeak.annotation.xlsx

source_name: mouse liver tissues

extract_protocol:
Livers were sonicated using a M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). Chromatin was immunoprecipitated with 4μg antibodies against [beta]-catenin (Carboxy-terminal Antigen, #9587S) overnight at 4°C.
ChIP-Seq libraries were prepared using Kapa LTP Library Preparation Kit (Kapa Biosystems, Sigma-Aldrich).

value: mouse liver tissues

tag: genotype

tag: chip-antibody


title: Biopsy_573_CIT

tag: evlp type


title: 04-0462-Month-6

source_name: Skin

tag: treatment

value: N


title: 04-0453-Baseline

tag: timepoint

value: Baseline

value: Inflammatory


title: 3-Airway-PBS (X61)

description: RNAseq (3 week PBS airway)

source_name: Airway

value: Airway

value: Balb/C

value: 18-20 weeks

tag: Sex

value: Female


title: 11-Parenchyma-PBS.AIR (X66)

description: RNAseq (11 week PBS.AIR parenchyma)


title: Biopsy_856_CIT

value: lung

value: Non-EVLP


title: 03-0327-Month-6

value: Skin

value: Placebo

tag: patient

tag: escape


title: 03-0327-Month-3

tag: intrinsic subtype


title: 11-Parenchyma-HDM.CS.DEX (X60)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

tag: age

tag: exposure


title: Biopsy_856_1H


title: ChIP mouse liver rep2

value: [beta]-catenin (Carboxy-terminal Antigen, #9587S, CST)


title: Biopsy_832_2H


title: ChIP mouse liver rep3


title: 03-0327-Baseline


title: input mouse liver rep2


title: 11-Airway-HDM.CS.DEX (X59)

description: RNAseq (11 week HDM.CS.DEX airway)


title: Biopsy_832_CIT


title: input mouse liver rep1


title: 03-0321-Month-6

value: Proliferative


title: Biopsy_786_2H


title: Biopsy_786_CIT


title: ChIP mouse liver rep1


title: 11-Airway-HDM.CS (X57)

description: RNAseq (11 week HDM.CS airway)


title: Biopsy_704_2H


title: 11-Parenchyma-PBS.CS.DEX (X56)

description: RNAseq (11 week PBS.CS.DEX parenchyma)


title: 11-Airway-PBS.CS.DEX (X55)

description: RNAseq (11 week PBS.CS.DEX airway)


title: 03-0318-Month-6

value: Abatacept


title: 03-0318-Baseline


title: Biopsy_688_1H


title: Biopsy_688_CIT


title: 11-Parenchyma-PBS.CS (X54)

description: RNAseq (11 week PBS.CS parenchyma)

value: Parenchyma


title: 03-0315-Baseline


title: 11-Airway-PBS.CS (X53)

description: RNAseq (11 week PBS.CS airway)


title: Biopsy_602_2H


title: Biopsy_602_CIT


title: 11-Parenchyma-HDM.CS (X58)

description: RNAseq (11 week HDM.CS parenchyma)


title: 03-0321-Month-3


title: 11-Airway-HDM.AIR.DEX (X51)

description: RNAseq (11 week HDM.AIR.DEX airway)


title: 03-0312-Baseline


title: 03-0321-Baseline


title: 11-Parenchyma-HDM.AIR.DEX (X52)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: Biopsy_692_2H


title: 03-0309-Baseline


title: Biopsy_692_CIT


title: 11-Parenchyma-HDM.AIR (X50)

description: RNAseq (11 week HDM.AIR parenchyma)


title: 11-Airway-HDM.AIR (X49)

description: RNAseq (11 week HDM.AIR airway)


title: 11-Parenchyma-HDM.CS (X78)

description: RNAseq (11 week HDM.CS parenchyma)


title: Biopsy_704_CIT


title: 11-Parenchyma-PBS.AIR.DEX (X48)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: 03-0306-Month-6


title: cell3_JTC801_rep2

city: Guangzhou

first: jiao

last: liu

state: Guangdong

address: No. 63, Duobao Road, Liwan District

institute: Third Affiliated Hospital of Guangzhou Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: PDAC cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human PDAC cell lines were grown in Dulbecco's modified eagle's medium (DMEM) medium containing 10% fetal bovine serum and 1% streptomycin/penicillin , and maintained at 37 ℃, 95% humidity, and 5% CO2. All cell lines were mycoplasma-negative and characterized by short tandem repeat profiling.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Cells were treated with JTC801（3 µM） for 24 hours and total RNA was extracted

value: PDAC cells


title: cell3_JTC801_rep3


title: 03-0312-Month-6


title: Biopsy_834_2H


title: cell3_JTC801_rep1


title: 03-0306-Baseline


title: Biopsy_834_CIT


title: 11-Airway-PBS.AIR.DEX (X47)

description: RNAseq (11 week PBS.AIR.DEX airway)


title: 03-0303-Month-6

value: Y; 9mo


title: cell3_control_rep3

value: control


title: cell3_control_rep2


title: 11-Parenchyma-PBS.AIR (X46)

description: RNAseq (11 week PBS.AIR parenchyma)


title: cell3_control_rep1


title: 11-Airway-PBS.AIR (X45)

description: RNAseq (11 week PBS.AIR airway)


title: cell2_JTC801_rep3


title: cell2_JTC801_rep2


title: 03-0303-Month-3


title: Biopsy_744_CIT


title: 03-0306-Month-3

value: N


title: 03-0303-Baseline

value: Baseline


title: 02-0156-Month-6

value: Y; 6mo

value: Inflammatory


title: Biopsy_796_2H


title: cell2_JTC801_rep1


title: Biopsy_796_CIT


title: 3-Airway-HDM (X43)

description: RNAseq (3 week HDM airway)

value: Airway

value: Balb/C

value: 18-20 weeks

value: HDM


title: 3-Parenchyma-HDM (X44)

description: RNAseq (3 week HDM parenchyma)

value: Female


title: cell2_control_rep3


title: 3-Parenchyma-PBS (X42)

description: RNAseq (3 week PBS parenchyma)

value: PBS


title: 02-0156-Month-3

value: Skin

value: Placebo


title: cell2_control_rep2


title: Biopsy_744_2H

value: lung

value: Non-EVLP


title: Biopsy_606_2H


title: cell1_JTC801_rep3

value: PDAC cells


title: cell2_control_rep1


title: 3-Airway-PBS (X41)

description: RNAseq (3 week PBS airway)


title: 11-Parenchyma-HDM.CS.DEX (X40)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

value: Parenchyma


title: 02-0156-Baseline


title: 02-0153-Month-6

value: Abatacept


title: Biopsy_828_2H


title: 02-0153-Month-3

value: N


title: 11-Airway-HDM.CS.DEX (X39)

description: RNAseq (11 week HDM.CS.DEX airway)


title: Biopsy_828_CIT


title: Biopsy_858_2H


title: cell1_JTC801_rep2


title: S. mutans/V.p dual biofilm +copper ions 250µM

city: Chengdu

first: Yun

address: Qingyang District first Ring Road west second section

institute: Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China

description: SAMPLES 3

data_processing:
Illumina Hiseq4000
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Hiseq4000 benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genome using Bowtie2 software
By using GO database, a gene or a group of genes were classified and annotated in terms of biological process, molecular function and cellular component according to their reference
Gene expression levels were calculated by the number of sequences (clean reads) that were mapped to genomic regions. According to the comparison results between all samples and reference genomes, the FPKM value of each gene/transcript in the sample was calculated, and this value was used as the gene/transcript expression quantity in the sample. Finally, the significance analysis of differences in the expression of all genes/transcripts in each group of samples was conducted to find out the relative differentially expressed genes/transcripts, and the visualization analysis was carried out
Supplementary files format and content: Excel files and mat files include RPKM values for each Sample

organism: Streptococcus mutans

source_name: S. mutans strain UA159/V. parvula PK1910

extract_protocol:
RNA was harvested using Invitrogen(Invitrogen). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit's protocols.

value: copper ions 250µM


title: S. mutans/V.p dual biofilm +copper ions 500µM

description: SAMPLES 4

value: S. mutans strain UA159/V. parvula PK1910

value: copper ions 500µM


title: 11-Parenchyma-HDM.CS (X38)

description: RNAseq (11 week HDM.CS parenchyma)


title: 01-0072-Month-6

data_processing:
First, we applied the cutadapt (version 1.15) to remove the adapter sequence (in our case it is “AGATCGGAAGAGC”) for the FASTQ files. Then, STAR (version 2.5.3a) was applied to align the reads to the hg19 human genome(17). Next, gene abundance was quantified using RSEM (version 3.3.9)(18). Lastly, normalized RPKM was calculated using TMM function (edgeR package)(19).
Supplementary files format and content: RNA-seq_20180810_normalizedRPKM_GeneSymbol_labelled_fixed.csv contains normalized RPKM values for all samples in the study.

value: Inflammatory


title: Biopsy_858_CIT


title: cell1_JTC801_rep1


title: cell1_control_rep2

value: control


title: 11-Airway-HDM.CS (X37)

description: RNAseq (11 week HDM.CS airway)

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0  and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs  real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using STAR (v2.5.1b), followed by gene quantitation with RSEM (v1.2.31) and Kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: raw gene counts comma separated

value: Airway

value: Balb/C

value: 18-20 weeks


title: cell1_control_rep3


title: Biopsy_606_CIT


title: 01-0072-Month-3


title: S. mutans/V.p dual biofilm

description: SAMPLES 2


title: 11-Parenchyma-PBS.CS.DEX (X36)

description: RNAseq (11 week PBS.CS.DEX parenchyma)

value: Female


title: S. mutans mono biofilm

description: SAMPLES 1

source_name: S. mutans strain UA159

value: S. mutans strain UA159


title: Biopsy_898_2H


title: 01-0072-Baseline

value: Skin

value: Baseline


title: Biopsy_898_CIT

value: lung

value: Non-EVLP


title: 11-Airway-PBS.CS.DEX (X35)

description: RNAseq (11 week PBS.CS.DEX airway)


title: 01-0069-Month-6


title: 11-Parenchyma-PBS.CS (X34)

description: RNAseq (11 week PBS.CS parenchyma)

value: Parenchyma


title: 51237

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

description:
Ribo-Zero
D3

data_processing:
Reads were mapped to the Caenorhabditis elegans
Differential gene expression was analyzed using the DESeq2
Genome_build: Ensembl 85
Supplementary_files_format_and_content: .csv

organism: Caenorhabditis elegans

source_name: L1 stage worms

growth_protocol: Syncronized L1 worms were grown on NGM plates and fed with E. coli bacteria for 3 hours prior to the UV irradiation.

extract_protocol:
UV-irradiated or mock-treated L1 worms were washed off plates after 6h, using M9 buffer. After three washes with M9, samples were suspended in TRIzol™ reagent (ThermoFisher) with 0.7mm zirconia/silica beads (Biospec Products), and homogenized with Precellys24 (Bertin).  After lysis, total RNA were purified using the RNeasy™ Mini kit (Qiagen) according to the manufacturers’ specification, except for the use of  1-bromo-3-chloropropane (Sigma) instead of chloroform for phase separation. RNA QC for four replicates per strain/condition was performed, of which 3 replicates were chosen (RINe of 9.4 or higher)
Illumina TruSeq stranded including ribo-zero rRNA depletion

treatment_protocol: UVB 60mJ/cm2 treatment or mock-treatment was applied on L1 worms.

tag: developmental strain

value: 6h post UV-treatment


title: Biopsy_817_1H


title: 51239

description:
Ribo-Zero
D4


title: 51235

description:
Ribo-Zero
D2


title: 01-0069-Month-3

value: Abatacept

value: N


title: 02-0153-Baseline


title: Biopsy_817_CIT


title: 01-0069-Baseline


title: 51233

description:
Ribo-Zero
C3


title: Biopsy_855_CIT


title: Biopsy_719_2H


title: 11-Parenchyma-HDM.AIR.DEX (X32)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: 01-0066-Month-3

value: Placebo

value: Proliferative


title: 51231

description:
Ribo-Zero
C2


title: 11-Parenchyma-HDM.AIR (X30)

description: RNAseq (11 week HDM.AIR parenchyma)


title: 51229

description:
Ribo-Zero
C1


title: Biopsy_719_CIT


title: 11-Airway-HDM.AIR (X29)

description: RNAseq (11 week HDM.AIR airway)


title: 51227

description:
Ribo-Zero
B4

value: 6h post mock-treatment


title: 01-0063-Month-6


title: Biopsy_745_1H


title: 11-Airway-PBS.CS (X33)

description: RNAseq (11 week PBS.CS airway)


title: 11-Parenchyma-PBS.AIR.DEX (X28)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: 01-0063-Month-3


title: 11-Airway-PBS.AIR.DEX (X27)

description: RNAseq (11 week PBS.AIR.DEX airway)


title: 51225

description:
Ribo-Zero
B3


title: Biopsy_745_CIT


title: cell1_control_rep1

value: PDAC cells

value: control


title: 11-Parenchyma-PBS.AIR (X26)

description: RNAseq (11 week PBS.AIR parenchyma)

value: Balb/C


title: 51223

description:
Ribo-Zero
B2


title: 51221

description:
Ribo-Zero
A4


title: Biopsy_705_2H


title: Biopsy_705_CIT


title: 01-0063-Baseline


title: 01-0066-Month-6


title: 11-Airway-HDM.AIR.DEX (X31)

description: RNAseq (11 week HDM.AIR.DEX airway)

value: Airway

value: 18-20 weeks


title: 11-Airway-PBS.AIR (X25)

description: RNAseq (11 week PBS.AIR airway)

value: Female


title: 3-Parenchyma-HDM (X24)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: Biopsy_824_2H


title: Biopsy_824_CIT


title: 01-0066-Baseline

value: Skin

value: Baseline


title: 3-Airway-HDM (X23)

description: RNAseq (3 week HDM airway)


title: 51217

description:
Ribo-Zero
A1


title: Biopsy_793_CIT

value: lung

value: Non-EVLP


title: 3-Parenchyma-PBS (X22)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

value: PBS


title: 01-0054-Month-6

value: Y; 6mo

value: Inflammatory


title: Biopsy_793_2H


title: 01-0054-Baseline

value: Placebo


title: 3-Airway-PBS (X21)

description: RNAseq (3 week PBS airway)


title: Pat2_3_O_NF_rep8

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

description:
tumor organoids
co-culture

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using RSEM tool v1.3.1
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include expected counts values for each sample
Supplementary files format and content: Matrix table with expected gene counts for every gene and every sample gathered by RSEM tool

source_name: tumor

growth_protocol: tumor organoids and fibroblasts were established from primary tumor or healthy colon tissues. Organoids were grown in matrigel covered by established organoid medium. Fibroblasts were extracted and grown flasks supplemented with EGM-M2 medium.

extract_protocol:
total RNA was extracted with a QIAGEN RNAeasy kit
Library preparation was executed with NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: organoids and fibroblasts were grown either in a co-culture or separately in mono-culture

value: epithelial

value: colon


title: Pat3_3_O_NF_rep9

description:
tumor organoids
co-culture


title: 01-0054-Month-3

extract_protocol:
Samples were stored in RNAlater and subsequently homogenized using a Qiagen Tissuelyser II.  RNA was purified using Qiagen’s RNeasy Fibrous Tissue minikit. Quality and concentration of RNA was assessed on a TapeStation 4400 (Agilent)
100ng of total RNA was used for library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were prepared manually or automated on an epMotion 5075t (Eppendorf, Hauppauge, NY). Libraries were assessed for size and concentration using the TapeStation 4400. Sequencing libraries were quantified on a Qubit fluorometer 3.0 (Thermo Fisher Scientific, Waltham, MA) prior to normalization for equimolar pooling.
Single-index paired-end sequencing was performed on Illumina’s NextSeq 500 to achieve >40 million reads per sample.


title: Biopsy_740_2H


title: Biopsy_740_CIT


title: Pat1_3_O_NF_rep7

description:
tumor organoids
co-culture


title: 11-Parenchyma-HDM.CS.DEX (X20)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

extract_protocol:
RNA was prepared using TRizol (Invitrogen) extraction method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 11-Airway-HDM.CS.DEX (X19)

description: RNAseq (11 week HDM.CS.DEX airway)


title: Pat3_3_O_CAF_rep9

description:
tumor organoids
co-culture


title: 01-0060-Baseline

value: N


title: 01-0051-Month-6

value: Proliferative


title: Biopsy_772_2H


title: 51219

description:
Ribo-Zero
A2

value: 6h post mock-treatment


title: Pat2_3_O_CAF_rep8

description:
tumor organoids
co-culture


title: 01-0060-Month-6


title: 01-0051-Month-3


title: 11-Parenchyma-HDM.CS (X18)

description: RNAseq (11 week HDM.CS parenchyma)

value: Balb/C

value: 18-20 weeks


title: Biopsy_772_CIT


title: Pat1_3_O_CAF_rep7

description:
tumor organoids
co-culture


title: 11-Airway-HDM.CS (X17)

description: RNAseq (11 week HDM.CS airway)

value: Airway

value: Female


title: 01-0060-Month-3

value: Skin


title: 01-0051-Baseline

value: Baseline


title: Biopsy_654_2H

value: lung

value: Non-EVLP


title: Pat3_3_NF_rep9

description:
normal fibroblast
mono-culture

source_name: healthy mucosa

value: fibroblast


title: 01-0048-Baseline

value: Abatacept

value: Y; 3mo


title: 11-Parenchyma-PBS.CS.DEX (X16)

description: RNAseq (11 week PBS.CS.DEX parenchyma)

value: Parenchyma


title: 01-0048-Month-6

value: Inflammatory


title: Biopsy_654_CIT


title: Pat1_3_NF_rep7

description:
normal fibroblast
mono-culture

value: colon


title: 11-Airway-PBS.CS.DEX (X15)

description: RNAseq (11 week PBS.CS.DEX airway)


title: Biopsy_763_2H


title: Pat2_3_NF_rep8

description:
normal fibroblast
mono-culture


title: Pat2_3_NF_O_rep9

description:
normal fibroblast
co-culture


title: 11-Airway-PBS.CS (X13)

description: RNAseq (11 week PBS.CS airway)


title: Biopsy_763_CIT


title: 01-0045-Month-3

value: N


title: 11-Parenchyma-PBS.CS (X14)

description: RNAseq (11 week PBS.CS parenchyma)


title: Biopsy_756_1H


title: 01-0045-Baseline


title: 11-Parenchyma-HDM.AIR.DEX (X12)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: 11-Airway-HDM.AIR.DEX (X11)

description: RNAseq (11 week HDM.AIR.DEX airway)


title: Pat1_3_NF_O_rep7

description:
normal fibroblast
co-culture


title: Pat2_3_NF_O_rep8

description:
normal fibroblast
co-culture


title: Biopsy_756_CIT


title: 01-0042-Month-3

value: Y; 6mo


title: Pat3_3_ENAS_rep9

description:
tumor organoids
mono-culture

value: epithelial


title: Biopsy_758_CIT


title: 11-Parenchyma-HDM.AIR (X10)

description: RNAseq (11 week HDM.AIR parenchyma)

value: Balb/C


title: Pat2_3_ENAS_rep8

description:
tumor organoids
mono-culture


title: 11-Airway-HDM.AIR (X9)

description: RNAseq (11 week HDM.AIR airway)

value: 18-20 weeks


title: Biopsy_626_2H


title: Pat1_3_ENAS_rep7

description:
tumor organoids
mono-culture


title: 01-0045-Month-6


title: Biopsy_626_CIT


title: 01-0039-Month-6-R

value: Placebo


title: Pat3_3_control_rep9

description:
tumor organoids
mono-culture


title: 01-0042-Baseline


title: 11-Parenchyma-PBS.AIR.DEX (X8)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)

value: Female


title: 01-0039-Baseline-R

value: Skin


title: 11-Airway-PBS.AIR.DEX (X7)

description: RNAseq (11 week PBS.AIR.DEX airway)

value: Airway


title: Biopsy_747_2H

value: lung


title: Pat2_3_control_rep8

description:
tumor organoids
mono-culture


title: 01-0039-Month-6


title: Biopsy_747_CIT

value: Non-EVLP


title: 01-0042-Month-6


title: Biopsy_758_2H


title: Pat1_3_control_rep7

description:
tumor organoids
mono-culture


title: 11-Parenchyma-PBS.AIR (X6)

description: RNAseq (11 week PBS.AIR parenchyma)


title: Biopsy_855_2H


title: 3-Parenchyma-HDM (X4)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: 01-0036-Month-3

value: Abatacept

value: Proliferative


title: 01-0036-Month-6


title: 3-Airway-HDM (X3)

description: RNAseq (3 week HDM airway)


title: Biopsy_823_1H


title: Pat1_3_CAF_rep7

description:
cancer associated fibroblasts
mono-culture

value: fibroblast


title: Pat2_3_CAF_rep8


title: 3-Parenchyma-PBS (X2)

description: RNAseq (3 week PBS parenchyma)

value: Parenchyma

value: PBS


title: 01-0036-Baseline

value: Baseline

value: N


title: Pat3_3_CAF_O_rep9

description:
cancer associated fibroblasts
co-culture

value: colon


title: 3-Airway-PBS (X1)

description: RNAseq (3 week PBS airway)

value: Balb/C


title: 01-0030-Month-6

value: Y; 6mo

value: Inflammatory


title: Biopsy_686_CIT


title: Biopsy_684_2H


title: 19075X6 GalTKO3

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
Mouse GRCm38 genome and gene annotation files were downloaded from Ensembl release 102
Reference database was created using STAR version 2.7.6a with splice junctions optimized for 150 base pair reads
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Genome_build: GRCm38; Ensembl release 102
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited matrix

source_name: ovary

extract_protocol:
ovaries removed and flash frozen on dry ice; Total RNA samples were hybridized with Ribo-Zero Gold
Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, Inc., 20020598) with TruSeq RNA UD Indexes (Illumina, Inc., cat# 20022371)

treatment_protocol: animals fed 2.5% galactose diet

value: GalT-/-

value: tx 2.5% galactose for 4 weeks

value: postnatal day 49


title: 01-0030-Month-3

value: Skin

value: Placebo


title: Pat2_3_CAF_O_rep8


title: 01-0039-Baseline


title: 01-0030-Baseline


title: 19075X5 GalTKO2


title: 11-Airway-PBS.AIR (X5)

description: RNAseq (11 week PBS.AIR airway)

value: Airway

value: 18-20 weeks

value: Female


title: 19075X4 GalTKO1


title: Pat3_3_CAF_rep9

value: fibroblast


title: Biopsy_684_CIT

value: lung

value: Non-EVLP


title: 01-0027-Month-6

value: Abatacept


title: Pat3_2_O_NF_rep6

description:
tumor organoids
co-culture

value: epithelial


title: Pat2_2_O_NF_rep5

description:
tumor organoids
co-culture

value: colon


title: 19075X3 wildtype3

value: wildtype


title: Pat1_2_O_NF_rep4

description:
tumor organoids
co-culture


title: 01-0024-Month-6

value: N


title: 19075X2 wildtype2


title: Biopsy_823_CIT


title: Biopsy_757_CIT


title: 01-0027-Baseline

value: Baseline

value: Y; 6mo

value: Inflammatory


title: Biopsy_686_2H


title: 19075X1 wildtype1

value: tx 2.5% galactose for 4 weeks

value: postnatal day 49


title: Pat1_3_CAF_O_rep7


title: 01-0024-Month-3

value: Skin

value: Placebo


title: 01-0024-Baseline


title: Biopsy_618_2H


title: Biopsy_679_CIT


title: Pat1_2_O_CAF_rep4

description:
tumor organoids
co-culture


title: Pat3_2_NF_rep6

description:
normal fibroblast
mono-culture


title: 01-0021-Month-6


title: Biopsy_618_CIT


title: vcAlkbh5_3

city: West Haven

first: Matthew

last: Simon

state: Connecticut

address: 300 Heffernan Dr, 300 Hefferna Dr

institute: Yale University

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the mm10 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Supplementary_files_format_and_content: Bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos)
Supplementary_files_format_and_content: Comma-separated values for raw read counts by gene

source_name: lineage-depleted bone marrow

growth_protocol: Mouse bone marrow cells were lineage depleted and grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) 1x L-glutamine, 50 ng/ml mSCF, 50 ng/mL mTPO, 50 ng/mL mFlt3L, 10 ng/mL mIL3. Cell cultures were maintained at 37℃.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq (TL-seq) genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018.
TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: Lineage-depleted bone marrow cells were treated with 100 µM s4U for 2 hours.

value: Vav-iCre+; Alkbh5fl/fl

tag: agent

value: s4U feed


title: Biopsy_757_2H

source_name: Biopsy, time point: H


title: vcAlkbh5_2

tag: strain


title: Biopsy_699_2H

tag: tissue


title: 01-0021-Month-3

city: Lebanon

first: Timothy

address: 1 Medical Center Dr.

institute: Dartmouth College


title: Pat2_2_O_CAF_rep5

description:
tumor organoids
co-culture

tag: cell type


title: 01-0018-Month-6


title: Pat2_2_NF_rep5

description:
normal fibroblast
mono-culture

value: fibroblast


title: vcAlkbh5_1


title: Biopsy_679_2H

value: lung


title: 01-0021-Baseline


title: Biopsy_780_2H

value: Non-EVLP


title: Pat1_2_NF_rep4

description:
normal fibroblast
mono-culture


title: Biopsy_699_CIT

source_name: Biopsy, time point: CIT


title: Pat2_2_NF_O_rep6

description:
normal fibroblast
co-culture


title: vcAlkbh5_unlab


title: WT_3

value: WT


title: Pat3_2_O_CAF_rep6

description:
tumor organoids
co-culture

value: epithelial


title: 01-0018-Month-3


title: WT_2


title: Biopsy_780_CIT


title: Pat2_2_NF_O_rep5

description:
normal fibroblast
co-culture

value: colon


title: 01-0018-Baseline


title: Pat1_2_NF_O_rep4

description:
normal fibroblast
co-culture


title: WT_1


title: Biopsy_717_CIT


title: IRF8-overexpression (xenograft)

city: Nanjing

first: Hongxi

last: Wu

state: Jiangsu

address: No. 639, LongMian Road, Jiangning District, Nanjing

institute: China Pharmaceutical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocellular carcinoma cells Hepa1-6 with IRF8-overexpression derived tumour

growth_protocol: Hepa1-6 cells stably transfected with IRF8 overexpression or vector control lentivirus were cultured in DMEM (Biological Industries, Israel) supplemented with 10% heat-inactivated fetal bovine serum (Biological Industries, Israel), 0.1mM nonessential amino acids (Gibico) and 1% Penicillin-Streptomycin (Gibico) at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent. RNA purity was checked using the NanoPhotomete spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Hepa1-6 cells stably transfected with IRF8 overexpression or vector control cells were co-injectedinto each side of the same mouse. Tumor tissues of the co-injected mice were harvested for RNA extract.

tag: sample type

value: Xenograft in C57bl/6 mice

tag: cell line

value: Hepa1-6 cells transfected with IRF8-overexpression-GFP-Puro lentivirus

tag: tumors

value: Hepa1-6 cells transplanted into C57bl/6 mice


title: Pat3_2_ENAS_rep6

description:
tumor organoids
mono-culture


title: 01-0015-Month-6-R

value: Abatacept

value: Y; 6mo


title: Biopsy_652_2H

tag: evlp type


title: 01-0015-Month-3-R

tag: treatment

value: Inflammatory


title: Vector (xenograft)

source_name: Hepatocellular carcinoma cells Hepa1-6 derived tumour

value: Hepa1-6 cells transfected with vector control-GFP-Puro lentivirus

tag: tumor


title: Pat2_2_ENAS_rep5

description:
tumor organoids
mono-culture


title: 01-0015-Month-6

value: Skin

tag: timepoint


title: IRF8-overexpression

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample
Genome_build: mm10
Supplementary_files_format_and_content: EXCEL-delimited files include raw gene counts for each Sample ...

source_name: Hepa1-6 hepatocellular carcinoma cell line

treatment_protocol: IRF8 overexpression（IRF8OE） or vector control(Vector) lentivirus lentiviruses were purchased from HanBio Technology Co.Ltd. (HanBio, Shanghai, China). Lentiviral supernatants incubated with Hepa1-6 cells for 24h, These infected cells were treated with 2 μg/ml of puromycin (Invitrogen) to generate stable transfectants.

value: C57bl/6 mice

value: Hepa1-6 cells

tag: lentivirus


title: Biopsy_652_CIT


title: Pat1_2_ENAS_rep4

description:
tumor organoids
mono-culture


title: Biopsy_791_CIT


title: 01-0015-Baseline-R

value: Baseline

tag: patient

tag: escape


title: 01-0015-Month-3

tag: intrinsic subtype


title: Pat3_2_control_rep6

description:
tumor organoids
mono-culture


title: 01-0015-Baseline


title: Biopsy_791_1H


title: Pat1_2_control_rep4

description:
tumor organoids
mono-culture


title: LZ-WT-noAb (non Antibody)

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Library strategy: CUT&Tag
R-loop CUT&Tag raw data was trimmed to filter low-quality bases using TrimGalore.
Trimmed reads were aligned to mm9 genome reference (UCSC) using Bowtie2 aligner
For unique alignments, duplicate reads were marked by “MarkDuplicates” function of Picard software.
The coverage of R-loop CUT&Tag data was calculated and normalized by RPKM using deepTools.
Uniquely mapped reads were used to carry out peak calling using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files to perform visualization

source_name: no antibody

growth_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

extract_protocol:
After removal of the tunica albuginea, the testes were incubated in 5mL of DPBS containing 120 U/mL of collagenase type I at 32 °C with gentle agitation for 8~10 min until seminiferous tubules were dispersed, The dispersed seminiferous tubules were further digested with 5 ml 0.25% trypsin, plus 0.1 ml 5mg/ml DNase I at 32°C for 8 min. The digestion was terminated by adding 0.5 mL FBS to inactivate trypsin. The cell suspension was filtered through a 70 μm cell strainer and then centrifuged at 500 g for 5 min at 4 °C. The cells’ pellet was resuspended at a concentration of 106 cells/ml in DMEM with Hoechst 33342 (5 μg/106 cells) and 5 μl DNase I, followed by cell suspension was rotated for 30min at 32 °C with gentle rotation. Centrifuged at 500 g for 5 min at 4 °C to remove supernatant. Immediately before sorting, the cells were stained with propidium iodide (1 μg/106 cells) at 25 °C and filtered with a 40 μm cell strainer.
5 × 10^4 spermatogonia were sorted and washed once in 0.5 ml wash buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, and 1× protease inhibitors], and were incubated with 10 μl pre-washed concanavalin A–coated magnetic beads in a 1.5 ml microtube at 25 °C for 10 min. Cells were resuspended in 80 μl ice-cold antibody incubation buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.025% digitonin, 0.01% NP-40, and 2 mM EDTA] with S9.6 antibody (MABE1095, Millipore) at 1:100 dilution, and then rotated end-over-end at 4 °C overnight. Subsequently, cells were resuspended in 100 μl dig-wash buffer [20 mM Hepes (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1 × protease inhibitors, and 0.025% digitonin] with rabbit anti-mouse IgG (Ab6709, Thermo Fisher) at 1:100 dilution and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer [20 mM Hepes (pH 7.5), 300 mM NaCl, 0.5 mM spermidine, 1 × protease inhibitors, and 0.01% digitonin] were added to samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, cells were resuspended in 300 μl tagmentation buffer [dig-300 buffer with 10 mM MgCl2] and incubates at 37 °C for 1 h. To stop tagmentation and solubilize DNA fragments, 10 μl 0.5M EDTA, 3 μl 10% SDS and 2.5 μl 20 mg/mL Proteinase K were added to each sample and incubated at 50 °C for 1 h. After extraction with phenol-chloroform and ethanol precipitation, libraries were amplified by PCR. The barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform to generate 150 bp paired-end reads.

treatment_protocol: Mice were kept under steady state, or subjected to different stress conditions such as aging, rosiglitazone diet feeding, sub-lethal irradiation, or mid-diaphyseal femur fracture.

value: Testis

value: Leptotene/zygotene

tag: genotype

value: Wild-type


title: Pat2_2_control_rep5

description:
tumor organoids
mono-culture


title: Biopsy_717_2H

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used Affymetrix Human Genome U133 Plus 2.0 Array annotation data (hgu133plus2.db package in R)

value: lung

value: Non-EVLP


title: Pat3_2_CAF_rep6

value: fibroblast

value: colon


title: LZ-cKO2 (S9.6 CUT&Tag)

source_name: S9.6 CUT&Tag

value: Rnaseh1 conditional knock-out


title: 01-0012-Month-6-R

last: Sullivan

source_name: Skin

value: N


title: 01-0012-Month-3-R

value: Abatacept


title: LZ-cKO1 (S9.6 CUT&Tag)


title: WT_unlab

value: WT


title: Pat2_2_CAF_rep5


title: MII-WT3 (S9.6 CUT&Tag)

value: Secondary spermatocytes


title: Vector

value: vector control-GFP-Puro


title: Pat1_2_CAF_rep4


title: 01-0012-Month-6

value: Skin


title: 01-0012-Month-3


title: MII-WT1 (S9.6 CUT&Tag)


title: MII-WT2 (S9.6 CUT&Tag)


title: Pat3_2_CAF_O_rep6


title: Pat2_2_CAF_O_rep5


title: PD-WT3 (S9.6 CUT&Tag)

value: Pachytene/diplotene


title: Pat1_2_CAF_O_rep4


title: 01-0012-Baseline


title: 01-0006-Month-6

value: Placebo


title: PD-WT1 (S9.6 CUT&Tag)


title: Pat3_1_O_NF_rep3

description:
tumor organoids
co-culture

value: epithelial


title: 01-0006-Month-3


title: 01-0012-Baseline-R

value: Baseline


title: Pat2_1_O_NF_rep2

description:
tumor organoids
co-culture