title: liver IDD_HID scRNAseq replicate 1

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

description: 10x Genomics (Chromium Next GEM Single Cell 3' GEM Kit v3.1)

data_processing:
Count matrices produced with kb-python (version 0.24.4, Python 3.7.4, reference genome GRCm38) were analyzed individually using Seurat V4.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Anaesthetized mice were perfused as previously described4 with a few modifications5. Calcium-free Hank’s Balanced Salt Solution (HBSS) buffer containing 0.2 mg/ml EDTA was used to perfuse the liver followed by sequential perfusion with calcium-containing HBSS and 0.5 mg/ml Collagenase D (Roche) for 7 minutes. The liver was excised and minced in 5 ml warm perfusion buffer before addition of 0.5 mg/ml pronase (Sigma; P5147) and 0.1 mg/ml DNase I (Roche) in a total volume of 50 ml. Ex vivo digestion was performed at 37oC for 20 min before filtering through a 70 μM filter. Cells were pelleted and collected by spinning at 580 g/10 min/4℃ and resuspended in 25 ml DMEM. A series of 4 spins at 50 g/2 min/4℃ were performed to pellet hepatocytes and collect non-parenchymal cells (NPCs) in supernatant. NPCs were then pelleted at 580 g/10 min/4℃ and treated with RBC lysis buffer (eBioscience™) according to the manufacturer’s instructions before resuspension in 5 ml sequencing buffer (phosphate-buffered saline containing 0.04% bovine serum albumin). Hepatocyte viability selection was performed as described6 on the hepatocyte pellet and cells were resuspended in sequencing buffer. A final mixture of cells was made by mixing 5% of the hepatocyte suspension with 95% of the NPC suspension before adjusting the cell concentration to 4000 cells/μl.
Single-cell suspensions were processed on the 10X scRNA-Seq platform (Chromium Next GEM Single Cell 3' GEM Kit v3.1)

treatment_protocol: The mice were fed a standard diet (Teklad Global 18% protein 2918, containing 200 ppm iron) or, when indicated, an iron-deficient diet (TD.80396, containing 2-6 ppm iron), or a high-iron diet (TD.09521, containing 2% carbonyl iron; or TD.09521, containing 0.25% carbonyl iron). Where indicated, the mice were injected intravenously (tail vein) with 10 mg apo- or holo-Tf. At the endpoints, the animals were sacrificed by CO2 inhalation. Experimental procedures were approved by the Animal Care Committee of McGill University (protocol 4966).

value: Liver

value: WT

value: iron-deficient diet + high iron diet


title: 17RA,W0

status: Public on Dec 21 2022

type: RNA

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_06.RCC

hyb_protocol: Hybrdization reactions were performed in final voulme of 15µl according to the manufacturer's instructions (MAN-10040-06). All hybridization reactions were incubated at 67°C for a minimum of 18 h

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

label: Fluorescently labeled target sequences

molecule: total RNA

organism: Bos taurus

source_name: Leukocytes

label_protocol: 1.1 µg of purified RNA in 7µl was added to tubes containing 8 µl of PlexSet master mix (Probe A & B as well as Reporter probes with flouresenct tags and Capture  probes) according to the manufacturer's instructions (MAN-10040-06).

extract_protocol: Total RNA was isolated from the samples using RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 3 mL of blood was transferred into a 50 mL falcon tube and 13.5 mL of chilled water was added (4.5 mL/ml of blood) to lyse the red blood cells. The tubes were quickly mix for 15 sec and 1.5 mL of 10X DPBS (500 µL/mL of blood) (Thermo Fisher Scientific, New Zealand) was added to equilibrate the sample. Subsequently, the cells were centrifuged at 250 μg for 10 min at 4°C, washed with PBS (10 mM, pH-7.3) and the cells were re-suspended in 0.5 mL of RPMI-1640 containing 10% fetal bovine serum (Thermo Fisher Scientific, New Zealand). Cell number and viability was measured by trypan blue exclusion method using TC20 cell counter (BioRad). A total of 2x106 cells were added to each well in a U-bottom 96-well tissue culture plate (Nunc(TM)) and stimulated with either media alone (un-stimulated), PPDA (24 μg/mL) or RA (10 µg/mL) at 37°C for 24 h. After incubation, plates were centrifuged in a swing out rotor at 350 μg for 10 min at room temperature. The supernatant was removed and 150 µL of a commercial lysis buffer for RNA preparation was added (RLT buffer, Qiagen, Hilden, Germany) to the samples and the plates were stored at –80°C until RNA isolation.

tag: nanostring plexset set in rcc files

tag: time

value: Week 0

tag: antigen

value: Recombinant antigen

tag: vaccine

value: Recombinant MAP fusion protein

tag: cell type

value: Leukocytes


title: chronic case 2

type: SRA

city: Berlin

first: Anja

middle: Erika

last: Hauser

address: Charitéplatz 1

department: Rheumatology and Clinical Immunology

country: Germany

institute: Charité - Universitätsmedizin and DRFZ

library_source: transcriptomic

data_processing:
Frames around the capture area on each Visium slide were aligned manually and spots covering the tissue were manually selected based on the immunofluorescence staining, using Loupe Browser 5.1.0 software (10x Genomics)
Sequencing data was mapped to GRCH38-2020-A reference transcriptome using the Space Ranger software (version 1.3.0, 10x genomics) to derive a feature spot-barcode expression matrix.
Space Ranger outputs (feature spot-barcode matrices and image data) from 31.801 barcoded spatial spots from twelve 10x Visium capture areas were filtered ( > 250 genes & < 13% mitochondrial) and integrated in R (version 4.1.0) with Seurat (version 4.0.4). For that, SCTransform normalization was performed, with nfeatures = 3000 and PC = 50
The spots were clustered on PCA space using the Shared Nearest Neighbor (SNN) algorithm implemented as FindNeighbors and FindClusters with parameters k =30 and res = 0.3. The method returned 12 spot clusters that represented lung microanatomical areas with distinct transcriptional signatures and that were then visualized on the UMAP space.
Genome_build: GRCH38-2020-A
Supplementary_files_format_and_content: Matrix table with filtered gene counts for every gene in every barcoded tissue spot, with its spatial coordinates

organism: Homo sapiens

source_name: lung

extract_protocol:
Lung tissue sections placed into the designated caputre areas of the Visium slides were permeabilised for 10 minutes, the RNA was captured in the spatially barcoded oligos in eah spot and then transcribed.
Spatially tagged cDNA libraries were constructed using the 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit. cDNA libraries were sequenced on an Illumina NextSeq 500/550 using 150 cycle high output kits  with sequencing depth of ~5000 reads per spot.

tag: tissue

value: lung

tag: disease group

value: chronic COVID-19

tag: tissue preservation

value: fresh frozen tissue sample


title: Liver, control, day1, rep2

city: Aberdeen Proving Ground

first: Jennifer

last: Sekowski

state: MD

address: 5183 Blackhawk Rd.

department: BioSciences Division

country: USA

institute: US Army DEVCOM Chemical Biological Center

data_processing:
Reads were trimmed for adapter sequences using Trimmomatic and filtered for quality using FASTQC. The reads were then aligned to the human genome using HISAT2. Next, to assemble transcripts and estimate their abundances, we processed the date through CuffLinks. The resulting Fragments Per Kilobase of transcript per million mapped reads (FPKM) data was later analyzed with Qlucore Omics Explorer 3.7 software.
Supplementary files format and content: CSV file containing FPKM values for each sample

source_name: liver

growth_protocol: Hepatocyte Seeding- Emulate chips were equilibrated to room temperature and washed 3X with 200 µL of Complete Hepatocyte Seeding Media. The final wash was left in the top and bottom channels of the chips. Human hepatocytes were removed from liquid nitrogen storage and the cryovial was quick thawed in a 37 ֯C water bath. The thawed cell solution was quickly added to 3 mL of warm Complete Hepatocyte Seeding Medium in a 50 mL conical tube. The vial was rinsed with 1 mL of medium, which was then transferred to the 50 mL conical tube.  Complete Hepatocyte Seeding Medium was slowly added to the 50 mL conical tube until the volume was brought to 35 mL. Then, 15 mL of 90% Percoll solution (Sigma Aldrich) in 1X DPBS was slowly layered on top of the 35 mL of cell solution. The cells were centrifuged at 96 x g for 6 minutes at room temperature. The supernatant was carefully aspirated leaving 3 to 5 mL and the pellet undisturbed. The cell pellet was gently resuspended by tilting and rotating the 50 mL conical tube. Complete Hepatocyte Seeding Medium was added to the 50 mL conical tube until the total volume was 50 mL, and the cell solution was centrifuged at 72 x g for 4 minutes at room temperature. The supernatant was carefully removed until the volume was down to 1-2 mL; the pellet was then carefully resuspended as described above. The human hepatocytes were counted in trypan blue solution using a hemocytometer and resuspended to a final cell density of 3.5 x 106 cells/mL in Complete Hepatocyte Seeding Medium. The hepatocyte suspension (50 µL) was then carefully added to the top channel of each chip. After adding the cells, the chips were incubated at 37 ֯C with 5% CO2 for 3 hours (or until the hepatocytes have fully attached). Once the hepatocytes have successfully attached to the channel, a gravity wash was performed on each chip by gently dropping 200 µL of Complete Hepatocyte Seeding Medium on top of both inlet ports of the top and bottom channels. The chips were then incubated overnight at 37 ֯C with 5% CO2.

extract_protocol:
Cell lysates were prepared on ice, using on-chip lysis using lysis buffer (QIAGEN Buffer RLT with 1% Betamercaptoethanol). Briefly, 175 µL of the lysis buffer was added to each of upper and lower channels and allowed to incubate on ice for 1 min. Lysates were then quickly removed from the two channels, combined in RNAse-free cryotubes, and frozen at -80 °C until further processing. RNA was extracted from these samples using the Rneasy® Mini Kit (QIAGEN; Frederick, MD), according to manufacturer’s instructions with minor modifications. Briefly, centrifugation was carried out at 10,000 x g and spun for 30s. On-column extraction was performed by incubating 30 µL RNase-free water directly on the spin column membrane for 2 min, followed by elution at 10,000 x g for 1 min. The eluate was run through the column again using the above centrifugation parameters and then stored at -80 °C for later analysis. The extracted samples were then quantified on a Qubit™ 4 Fluorometer using the Qubit™ RNA High Sensitivity (HS) Assay Kit following the recommended protocol in the Qubit Assay Kit User Guide. Further quantification and qualification was performed on a 2100 Agilent Bioanalyzer according to the Agilent RNA 6000 Nano Kit Guide. All samples with a RNA Integrity Number (RIN) higher than 8 were used in further analysis.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit was used for library generation. The protocol and corresponding calculations were carried out following the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Reference Guide with minor modifications. Centrifugation steps were at 280 x g for 1 min as opposed to the recommended 10 s due to plate centrifuge limitations. Library samples were then quantified using the Qubit 1X dsDNA High-Sensitivity (HS) Assay Kit and measured on a Qubit™ 4 Fluorometer, using manufacturer’s recommended parameters. To assess the quality and quantity during the preparation steps, library samples were measured on a 2100 Agilent Bioanalyzer according to the Agilent High Sensitivity DNA Kit Guide.

treatment_protocol: VX was synthesized and purified (99.1 %) by U.S. Army DEVCOM CBC in accordance with international regulations. Neat VX was then diluted into a working stock of 1 mg/mL in DMSO. Experimental VX dilutions were prepared from working stocks by diluting agent in NPC Maintenance Medium without FBS to final concentrations of 6.25 µM, 12.5 µM, and 25 µM. A vehicle control was also prepared by diluting cell culture grade DMSO in NPC Maintenance Medium to a final concentration of 0.6 %. The bottom channel inlet reservoir medium was aspirated and replaced with 3 mL of medium containing either VX or vehicle control (DMSO), so that the experimental compound would be introduced on the endothelial channel (similar to a potential in vivo exposure). The Pods were returned to the Zoë and the VX exposure was initiated by increasing the flow rate of the Zoë to 600 µL/h for 5 minutes. The flow rate was then returned to 30 µL/h. After 24 hours, the cells from 12 of the chips were trypsinized, pelleted, and flash frozen in liquid N2. Cell pellets were stored at -80 °C before protein, metabolite, and RNA extractions were performed.

value: liver

tag: gender

value: male

tag: day

tag: treatment

value: control


title: V01

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Probes were hybridized to microarray slide and incubated at 55°C for 20 hours.

scan_protocol: Microarrays were washed and scanned using the Agilent Microarray Scanner G2505C with Surescan High Resolution Technology.

data_processing:
Feature Extraction v10.7.3.1 software was utilized for feature extraction.
Bioconductor AgiMicroRna R package was applied to retrieve log2-transformed normalized expression for miRNAs annotated on miRBase 19.0

label_protocol: 100 ng of total RNA from each sample were labeled according to the manufacturer’s protocol.

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: group

tag: patient diagnosis

value: diffuse intrinsic pontine glioma

value: serum

value: M

tag: age


title: 17A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_05.RCC

value: PPBDA


title: acute case 3

value: acute COVID-19


title: 17N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_04.RCC

value: PBS


title: liver IDD_HTF scRNAseq replicate 1

country: Canada

library_source: transcriptomic single cell

organism: Mus musculus

value: Liver

tag: genotype

value: WT

value: iron-deficient diet + holo-Tf


title: 4A

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: 16S V3-V4 sequencing

library_source: genomic

data_processing: MiSeq Reporter Metagenomics Workflow

molecule: genomic DNA

organism: sulfo-oxidizing enrichment culture

growth_protocol: Suspended biomass growth in chemostatic conditions at 30 °C and pH of 7.6

extract_protocol:
Norgen, Biofilm-kit
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
OTHER: paired-end amplicon sequencing

treatment_protocol: Concentration of the suspended biomass through centrifugation and supernatant removal.

tag: sample type

value: microbial community


title: T01


title: 16RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_03.RCC

value: Week 0

value: Recombinant antigen

value: Silirum®

value: Leukocytes


title: 3CP

description: 16S V3-V4 sequencing


title: control case 3

value: lung

value: non-COVID-19-related pneumonia

value: fresh frozen tissue sample


title: Mouse Mammospheres, Shc1p66KO, 12 months old mice, rep2

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

data_processing:
Base calling is performed in real time during the Novaseq runs by Real-Time Analysis (RTA, Illumina) software and the BCL Convert App generates demultiplexed FASTQ files from a run as input.
Reads were aligned to the mus musculs  genome build mm10 using tophat (v2.1.0), which uses Bowtie (2.2.4) and Samtools (v0.1.18) using default parameters and --transcriptome Mus Musculus index, UCSC mm10 gtf.
Raw read counts were summarised using HTSeq (v0.6.1p1).
Assembly: mm10
Supplementary files format and content: The tab-delimited text files include TMM normalized expression value expressed as CPM (copy per milion) for each gene for each sample

source_name: mammospheres

extract_protocol:
RNAs were extracted with PicoPure™ RNA isolation kit (Cat#KIT0204, Applied Biosystems™). 200ng of RNA were used to prepare libraries.
RNAseq libraries were prepared with the Illumina TruSeq Stranded total RNA kit following the manufacturer’s protocol

value: mammospheres

value: Shc1p66 knock-out

value: 12 months


title: 2CP

description: 16S V3-V4 sequencing


title: prolonged case  3

value: prolonged COVID-19


title: 16A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_02.RCC

value: PPBDA


title: 16N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_01.RCC

value: PBS


title: prolonged case 4


title: Mouse Mammospheres, Shc1p66KO, 12 months old mice, rep1


title: chronic case 5

value: chronic COVID-19


title: 1CP

description: 16S V3-V4 sequencing


title: Mouse Mammospheres, Shc1p66KO, 2 months old mice, rep3

value: 2 months


title: T02

value: diffuse intrinsic pontine glioma

value: serum

value: M


title: 24N,W3_rep9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_12.RCC
Calibration Sample

value: Week 6

value: Recombinant MAP fusion protein


title: single cell RNA sequencing of breast cancer bone metastasis 8

city: Pittsburgh

first: Kai

last: Ding

state: PA

address: 204 Craft Ave

institute: University of Pittsburgh

description:
BoM8
single cell RNA

data_processing:
CellRanger for reads mapping, Seurat for cell filteration and data normalization.
Assembly: GRCh38
Supplementary files format and content: *.txt: text file of normalized counts, with row as gene column as cell.

molecule: polyA RNA

source_name: breast cancer bone metastases

extract_protocol:
10X genomic cell isolation protocol.
10X genomic single cell RNA protocol V3 3' end.

value: breast cancer bone metastases

value: breast cancer and stromal cells


title: liver IDD scRNAseq replicate 1

value: Liver

value: WT

value: iron-deficient diet


title: Mouse Mammospheres, Shc1p66KO, 2 months old mice, rep2

value: mammospheres

value: Shc1p66 knock-out


title: control case 2

value: lung

value: non-COVID-19-related pneumonia

value: fresh frozen tissue sample


title: 14RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_11.RCC

value: Recombinant antigen

value: Silirum®

value: Leukocytes


title: Mouse Mammospheres, Shc1p66KO, 12 months old mice, rep3

value: 12 months


title: Mouse Mammospheres, Shc1p66KO, 2 months old mice, rep1

value: 2 months


title: prolonged case 5

value: prolonged COVID-19


title: 14A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Week 6

value: PPBDA


title: Mouse Mammospheres, WT, 12 months old mice, rep3


title: Mouse Mammospheres, WT, 12 months old mice, rep2


title: chronic case 1

value: chronic COVID-19


title: acute case 2

value: acute COVID-19


title: Human postmortem brain MTG region AD 1, biol rep 1

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

description: 10x Genomics Visium platform

data_processing:
Raw sequencing data of six human MTG samples were obtained from Visium (BCL files) and processed with the SpaceRanger (v.1.2.2) software to generate FASTQ files via the SpaceRanger “mkfastq” function. FASTQ files were then aligned to and quantified to the expression matrix by using GRCh38 Reference-2020-A and the SpaceRanger “count” function. The two functions SpaceRanger “mkfastq” and “count” were used for demultiplexing sample and transcriptome alignment using default parameters.
Assembly: hg38
Supplementary files format and content: csv and png for spatial images, count matrix, and metadata

source_name: Human postmortem brain

extract_protocol:
Human postmortem brain tissue from MTG region was cryosectioned at 10 µm using the Cryostat
Spatially resoved transcriptomics (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following established 10x protocal (CG000239 Rev A)

value: Human postmortem brain


title: Mouse Mammospheres, WT, 12 months old mice, rep1

value: WT


title: acute case 1


title: 14N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_09.RCC

value: PBS


title: Human postmortem brain MTG region AD 2, biol rep 2

description: 10x Genomics Visium platform


title: Human postmortem brain MTG region AD 3, biol rep 3

description: 10x Genomics Visium platform


title: Human postmortem brain MTG region control 3, biol rep 3

description: 10x Genomics Visium platform


title: 13RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_08.RCC


title: GTML2 6hr DMSO 3

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.16.1).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent Proton sequencer  (Torrent suite ver.5.16.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file include gene symbol and raw counts.

source_name: Cell line

extract_protocol:
RNA from cell lines were extracted according to QUIAGEN RNEasy extraction protocol
Library was prepared according to Thermo Fisher Scientific protocol for AmpliSeq next generation sequencing application

tag: model


title: Mouse Mammospheres, WT, 2 months old mice, rep3

value: mammospheres


title: control case 1

value: lung


title: Human postmortem brain MTG region control 2, biol rep 2

description: 10x Genomics Visium platform


title: single cell RNA sequencing of breast cancer bone metastasis 7

description:
BoM7
single cell RNA

value: breast cancer bone metastases

value: breast cancer and stromal cells


title: 13A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_07.RCC

tag: nanostring plexset set in rcc files


title: GTML2 6hr DMSO 2


title: Human postmortem brain MTG region, control 1, biol rep 1

description: 10x Genomics Visium platform


title: Mouse Mammospheres, WT, 2 months old mice, rep2


title: 12RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_05.RCC

tag: time

value: Recombinant antigen


title: Mouse Mammospheres, WT, 2 months old mice, rep1


title: 13N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_06.RCC

tag: antigen

value: Silirum®


title: 12A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_04.RCC

tag: vaccine

value: Leukocytes


title: AB329

city: Worcester

first: Zeynep

last: Itah

address: 373 Plantation St. Suite 309

department: Program in Molecular Medicine

institute: UMass Medical School

description: JNK knockout primary mammary tumor cell line.

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt.
Clean reads were then mapped to mm10 genome using RSEM.
TPM and Counts were calculated using RSEM.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-separated files include read count values for each Sample.
Supplementary files format and content: Tab-separated files include TPM values for each Sample.

source_name: mammary gland tumor

growth_protocol: Cells were isloated from tumor tissues and cultured within DMEM/F12 supplemented with 2% fetal bovine serum and 1% penicillin/streptomycin on collagen I (Thermo Fisher Scientific # A1048301) coated plates. After two passages, the cells were plated on standard tissue culture dishes and maintained in DMEM/F12 supplemented with 10% fetal bovine serum, 20 ng/ml EGF, 10 μg/ml insulin and 1% penicillin/streptomycin).

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN#74004) with DNase treatment (QIAGEN #79254).
Libraries were prepared for sequencing by Novagene Inc. and were pair end sequenced for 150bp on NovaSeq6000 platform.

tag: cell type

value: primary mammary tumor cell line

value: JNK knockout

tag: strain

value: FVBN/J


title: 12N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_03.RCC

value: Week 6


title: GTML2 6hr Ona 3


title: GTML2 6hr Ona 2


title: Microglia, G795A, in vivo, rep 3

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description: Processed Data Column:G795A_3

data_processing:
BBDuk was used to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, and to quality trim any base pairs below a PHRED score of 10.
Reads were pseudoaligned to the human GRCh38 transcriptome (Ensembl release 99) using Kallisto version 0.46.0
Transcript counts were summarized to the gene level via tximport version 1.14.2
After removing genes with summed counts < 10, DESeq2 version 1.26.0 was used to generate the data object using the design equation ~Genotype
Data were then normalized and converted to a log2 scale using DESeq2′s varianceStabilizingTransformation with blind=TRUE.
Assembly: Ensembl GRCh38 release 99 cDNA All
Supplementary files format and content: *RawSeqCounts.tsv: Tab delimited file containing gene-level counts imported to DESeq2 from Kallisto using TxImport
Supplementary files format and content: *VSTSeqCounts.tsv: Tab delimited file containing gene-level counts normalized using the DESeq2 variance stabilizing transformation (VST)

source_name: UCI ADRC76

extract_protocol:
RNA was isolated via a modified Trizol/Chloroform procedure
RNA libraries were prepared using the SMART-Seq Ultra Low Input V4 kit following manufacturers guidelines

tag: cell line

value: UCI ADRC76

value: Xenotransplanted iPSC-Microglia


title: Microglia, G795A, in vivo, rep 2

description: Processed Data Column:G795A_2


title: Microglia, G795A, in vivo, rep 1

description: Processed Data Column:G795A_1


title: AB327


title: GTML2 6hr Ona 1


title: 11RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_02.RCC


title: GMYC1 6hr DMSO 3


title: AB165


title: AB209


title: Microglia, wildtype, in vivo, rep 2

description: Processed Data Column:WT_2


title: Microglia, wildtype, in vivo, rep 3

description: Processed Data Column:WT_3


title: 11A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_12.RCC

value: PPBDA


title: Microglia, wildtype, in vivo, rep 1

description: Processed Data Column:WT_1


title: 11N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_11.RCC


title: AB164


title: AB145


title: GTML2 6hr DMSO 1


title: GMYC1 6hr DMSO 1


title: 10RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_10.RCC


title: AB144


title: GMYC1 6hr Ona 3


title: 10A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_09.RCC


title: N301

description: Wild type primary mammary tumor cell line.

value: Wild type


title: 24N,W3_rep8

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_01.RCC
Calibration Sample

value: Recombinant MAP fusion protein


title: GMYC1 6hr Ona 1


title: Microglia, G795C, PLX5622, in vitro, rep 2

description: Processed Data Column: G795C_PLX_2

data_processing:
BBDuk was used to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, and to quality trim any base pairs below a PHRED score of 10.
Lane 1 (L1) and Lane 2 (L2) FASTQ files were then concatenated into a single FASTQ file for each sample
Reads were pseudoaligned to the human GRCh38 transcriptome (Ensembl release 99) using Kallisto version 0.46.0
Transcript counts were summarized to the gene level via tximport version 1.14.2
After removing genes with summed counts < 10, DESeq2 version 1.26.0 was used to generate the data object using the design equation ~Genotype+Treatment+Genotype:Treatment
Data were then normalized and converted to a log2 scale using DESeq2′s varianceStabilizingTransformation with blind=TRUE.
Assembly: Ensembl GRCh38 release 99 cDNA All
Supplementary files format and content: *RawSeqCounts.tsv: Tab delimited file containing gene-level counts imported to DESeq2 from Kallisto using TxImport
Supplementary files format and content: *VSTSeqCounts.tsv: Tab delimited file containing gene-level counts normalized using the DESeq2 variance stabilizing transformation (VST)

extract_protocol:
RNA was isolated via a modified Trizol/Chloroform procedure
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA kit following manufacturers guidelines

value: iPSC-Microglia


title: Microglia, G795C, PLX5622, in vitro, rep 4

description: Processed Data Column: G795C_PLX_4


title: Microglia, G795C, PLX5622, in vitro, rep 3

description: Processed Data Column: G795C_PLX_3


title: GMYC1 6hr Ona 2


title: 10N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_08.RCC

value: PBS


title: Microglia, G795C, PLX5622, in vitro, rep 1

description: Processed Data Column: G795C_PLX_1


title: N300R2


title: GTML/ARFKO 55162

value: GTML/ARFKO


title: GMYC1 6hr DMSO 2


title: Microglia, G795C, DMSO, in vitro, rep 4

description: Processed Data Column: G795C_DMSO_4

value: 0.1% DMSO


title: 9RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_07.RCC


title: 9A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_06.RCC


title: 9N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_05.RCC


title: N75


title: GTML/ARFKO 50076


title: Microglia, G795C, DMSO, in vitro, rep 3

description: Processed Data Column: G795C_DMSO_3


title: N47


title: GTML/ARFKO 50074


title: N20


title: 8RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_04.RCC


title: GTML/ARFKO 53106


title: 8A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_03.RCC


title: N300L3


title: Spleen_OX40plus_Mouse3_rep2

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
FASTQ files were processed using kallisto (PMID: 27043002) followed by a tximport (PMID: 26925227) transcript-to-gene level transformation. Transcript indices for kallisto were created using FASTA files from Ensembl release 95 for mm10 for all annotated cDNA and ncRNA transcripts. Gene-level read counts were then processed using the limma suite of tools (PMID: 25605792) first with a voom transformation, followed by linear model fitting to determine differentialy expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include read counts at gene level for each samples

source_name: spleen Treg

extract_protocol:
RNA was harvested using Qiagen Rneasy Micro kit. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: spleen

value: Treg

tag: ox40 status

value: plus


title: Microglia, G795C, DMSO, in vitro, rep 1

description: Processed Data Column: G795C_DMSO_1


title: GMYC/ARFKO 50673

value: GMYC/ARFKO


title: Microglia, G795A, PLX5622, in vitro, rep 4

description: Processed Data Column: G795A_PLX_4


title: GMYC/ARFKO 112628


title: Spleen_OX40plus_Mouse3_rep1


title: 8N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_02.RCC

value: Leukocytes


title: Microglia, G795A, PLX5622, in vitro, rep 2

description: Processed Data Column: G795A_PLX_2


title: Spleen_OX40minus_Mouse3_rep2

value: minus


title: 24N,W3_rep7


title: Microglia, G795A, PLX5622, in vitro, rep 3

description: Processed Data Column: G795A_PLX_3


title: Spleen_OX40plus_Mouse2_rep2


title: Microglia, G795A, DMSO, in vitro, rep 4

description: Processed Data Column: G795A_DMSO_4


title: Microglia, G795C, DMSO, in vitro, rep 2

description: Processed Data Column: G795C_DMSO_2


title: Microglia, G795A, PLX5622, in vitro, rep 1

description: Processed Data Column: G795A_PLX_1


title: 7RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_12.RCC

value: Recombinant antigen


title: Spleen_OX40minus_Mouse3_rep1


title: Spleen_OX40plus_Mouse2_rep1


title: 7A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_11.RCC

value: Week 6


title: 7N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_10.RCC


title: 6RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_09.RCC


title: Spleen_OX40minus_Mouse2_rep2


title: 6A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_08.RCC


title: SKF 38393 2

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

hyb_protocol: 5 μg Cy5-labeled aRNA

scan_protocol: Agilent 0.1 XDR Protocol

data_processing:
Histogram and Volcano Plot
Number of Differentially Expressed Genes
Array QA: Clustering and PCA Analysis
Pathway and Gene Ontology Analysis

source_name: U1 cells

label_protocol: Protocol for labeling is Phalanx proprietary, One Array.

growth_protocol: Cells obtained from the NIH HIV Reagents Program, Catalog number ARP-165, maintained with omplete RPMI.

extract_protocol: RNA extraction was performed with Qiagen kits.

treatment_protocol: Cells were plated at 10^6/ml and stimulated with dopamine or selective agonists for 24 hrs.

value: U1 cells

tag: agent


title: Microglia, G795A, DMSO, in vitro, rep 2

description: Processed Data Column: G795A_DMSO_2

value: UCI ADRC76

tag: treatment


title: PD 168077 2


title: SKF 38393 1


title: Spleen_OX40minus_Mouse2_rep1


title: Spleen_OX40plus_Mouse1_rep2


title: PD 168077 1


title: Microglia, WT, PLX5622, in vitro, rep 4

description: Processed Data Column: WT_PLX_4


title: 6N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_07.RCC


title: 5RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_06.RCC


title: V03

tag: group

value: diffuse intrinsic pontine glioma

value: serum

tag: gender

value: F


title: Microglia, WT, PLX5622, in vitro, rep 3

description: Processed Data Column: WT_PLX_3

value: iPSC-Microglia


title: Spleen_OX40plus_Mouse1_rep1


title: DC 2

city: Gent

first: Dmitri

last: Krysko

address: C. Heymanslaan 10, 4B3

department: Department of Human Structure and Repair

country: Belgium

institute: Ghent University

data_processing:
Read quality was checked for each sample using FastQC v0.11.5.
Then the paired-end reads were mapped to the Ensembl Mus musculus GRCm39 genome using the BWA-MEM v.0.7.17.
Gene quantification was calculated by using featureCounts v2.0.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: BMDCs

growth_protocol: Murine glioma GL261 cells were cultured at 37°C under 5% CO2 in DMEM containing 4.5 g/L glucose and supplemented with 2 mM glutamine, 100 µM sodium pyruvate, 100 units/ml penicillin, 100 µg/L streptomycin and 10% fetal bovine serum, all purchased from Thermo Fisher Scientific.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN).
The TruSeq Stranded mRNA kit (Illumina) was used to prepare a RNA-seq library according to the manufacturer’s protocol, followed by PE100 cycles sequencing on one lane of a NovaSeq 6000 S1 run (Illumina).

treatment_protocol: Cell death was induced by photosens (PS)-based PDT or mitoxantrone (MTX, Sigma Aldrich). For PS-PDT, GL261 cells were first incubated with 1.4 µM PS in serum-free DMEM for 4 h and then irradiated with a light dose of 20 J/cm2 in photosensitizer-free media. After PDT, the cells were cultured in complete DMEM for 24 h. For MTX induction, the cells were cultured in full medium with 2.0 µM MTX for 24 h. Cells loaded with PS or MTX were handled in the dark or in subdued light. DCs isolated from four C57BL/6J mice were used for each experimental group. DCs were cocultured for 6 h with dying/dead glioma GL261 cells in a ratio of 1:5. There were three experimental groups: DCs alone (negative control), DCs cocultured with glioma GL261 cells pulsed with PS-PDT (PS at a dose of 1.4 µM, 24 h) or MTX (positive control, 2 µM, 24 h).

value: BMDCs

value: wild type

value: untreated


title: Microglia, G795A, DMSO, in vitro, rep 3

description: Processed Data Column: G795A_DMSO_3

value: 0.1% DMSO


title: Spleen_OX40minus_Mouse1_rep2

value: spleen

value: Treg


title: Dopamine 2

value: Dopamine


title: Dopamine 1


title: Control 2

value: Control


title: Microglia, WT, PLX5622, in vitro, rep 2

description: Processed Data Column: WT_PLX_2


title: 5N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_04.RCC

value: PBS

value: Leukocytes


title: Spleen_OX40minus_Mouse1_rep1

value: minus


title: Microglia, G795A, DMSO, in vitro, rep 1

description: Processed Data Column: G795A_DMSO_1


title: Microglia, WT, PLX5622, in vitro, rep 1

description: Processed Data Column: WT_PLX_1


title: Brain endothelial cell_KO

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
Using Perl scripts to process the Raw Data to ensure the quality of the data for further analysis.The filtering standards are as follows:1) Delete reads contaminated by the adapter. (Reads containing more than 5 adapter-polluted bases were considered as adapter contamination readings and would be filtered out;2) Eliminate low-quality reading. Low-quality Reads (phred quality value less than 19) accounted for more than 15% of the total base number.3) Remove reads with more than 5% of the number of N bases.
The genome index was built with Bowtie2 v2.2.3 and the Clean Data was mapped to the reference genome using TopHat v2.0.12.
Using the Integrative Genomics Viewer (IGV) to view mapping results through a Heatmap, histogram, scatter plot, or other stytles.
The Reads Count of each gene in each sample were calculated by HTSeq v0.6.0, and then FPKM (Fragments per Kilobase per Million Mapped Fragments) was calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Brain endothelial cell

extract_protocol:
Total RNA was collected with the RNA microextraction kit. A sequencing library was constructed with 2ug total RNA.
RNA libraries sequencing  were performed with standard Illumina protocols.

tag: developmental stage


title: Brain endothelial cell_WT

tag: genotype


title: 4A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_02.RCC

value: Week 6

value: PPBDA


title: Microglia, WT, DMSO, in vitro, rep 4

description: Processed Data Column: WT_DMSO_4

value: UCI ADRC76


title: Microglia, WT, DMSO, in vitro, rep 3

description: Processed Data Column: WT_DMSO_3


title: Tumor_OX40minus_Mouse4_rep1

source_name: tumor Treg

value: tumor


title: 5A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_05.RCC


title: Control 1

value: U1 cells


title: 4RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_03.RCC

value: Recombinant antigen


title: 24N,W3_rep6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_01.RCC
Calibration Sample

value: Recombinant MAP fusion protein


title: Tumor_OX40plus_Mouse4_rep2

value: plus


title: Tumor_OX40minus_Mouse4_rep2


title: Microglia, WT, DMSO, in vitro, rep 2

description: Processed Data Column: WT_DMSO_2

value: iPSC-Microglia


title: Donor_17-day2-OKT3_aCD28

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

data_processing:
STAR2 was used for genome alignment
Htseq-count was used for read-gene frequency calculation
DESeq2 was used for DE normalization.
Assembly: hg19
Supplementary files format and content: tab-delimited matrix of normalized gene digital expression

growth_protocol: CD4+ cells were culcured with 50 ng of anti-CD3, 200 ng biotnylated costimulatory ligand in 2% Pen/Strep and 10% FBSat 37 degree plus 5% CO2.

extract_protocol:
Qiagen AllPrep DNA/RNA 96-well system
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, USA) was used for cDNA synthesis with an input of 150 pg total RNA.

treatment_protocol: Five treatment reagents: anti-CD3 Ab, anti-CD28 Ab, MadCAM, cV2, RA.

value: WT


title: Tumor_OX40plus_Mouse4_rep1


title: Donor_17-day2-OKT3_gp120


title: Donor_17-day2-OKT3_aCD28_RA


title: 15RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_12.RCC

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

extract_protocol: Total RNA was isolated from the samples using RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

value: Week 0

value: Silirum®


title: Donor_17-day2-OKT3_gp120_RA


title: Tumor_OX40minus_Mouse3_rep2

value: Treg


title: Microglia, WT, DMSO, in vitro, rep 1

description: Processed Data Column: WT_DMSO_1

value: 0.1% DMSO


title: 4N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_11.RCC

value: PBS


title: Donor_17-day2-OKT3_MadCAM_RA


title: 3RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Leukocytes


title: Donor_17-day2-OKT3_MadCAM


title: Tumor_OX40minus_Mouse3_rep1

value: minus


title: 3A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_09.RCC

value: Week 6


title: KO-BRPF1-2#-RNA-2

city: Guangzhou

first: Cong

last: Zhang

state: Guangdong Province

address: No. 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Assembly: GRCh38/hg38
Supplementary files format and content: count

source_name: blastocyst

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

value: blastocyst

value: hESCs

value: BRPF1 knockout


title: KO-BRPF1-2#-RNA-1


title: Donor_17-day2-OKT3_RA


title: KO-BRPF1-1#-RNA-2


title: 3N,W3

city: Lincoln

first: Paul

last: Maclean

institute: AgResearch NZ LTD

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_08.RCC


title: Tumor_OX40plus_Mouse3_rep2

value: tumor


title: KO-BRPF1-1#-RNA-1


title: 2RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_07.RCC

value: Recombinant antigen


title: Donor_16-day2-OKT3_aCD28_RA


title: Tumor_OX40plus_Mouse3_rep1


title: Tumor_OX40minus_Mouse2_rep1


title: Tumor_OX40plus_Mouse2_rep2


title: Donor_16-day2-OKT3_gp120


title: 2A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_06.RCC

value: PPBDA


title: H1-RNA-1


title: KO-BRPF1-H3K4me3-ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of specific antibodies enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig

extract_protocol:
For  ChIP-seq, 1×10^7 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with specific antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody


title: 2N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_05.RCC


title: Tumor_OX40plus_Mouse2_rep1

value: plus


title: Donor_16-day2-OKT3_gp120_RA


title: H1-RNA-2


title: 1RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_04.RCC


title: 1A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_03.RCC


title: KO-BRPF1-INPUT-ChIP-seq


title: Tumor_OX40minus_Mouse1_rep2


title: Donor_16-day2-OKT3_MadCAM_RA


title: KI-BRPF1-input-ChIP-seq

value: 3xFLAG knock in


title: 1N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_02.RCC


title: Donor_16-day2-OKT3_MadCAM

value: WT


title: Donor_17-day2-OKT3


title: KI-BRPF1-H3K23ac-ChIP-seq


title: Tumor_OX40plus_Mouse1_rep2


title: 24N,W3_rep5

value: Recombinant MAP fusion protein


title: Tumor_OX40minus_Mouse2_rep2


title: Donor_16-day2-OKT3_RA


title: Tumor_OX40plus_Mouse1_rep1


title: Tumor_OX40minus_Mouse1_rep1


title: KI-BRPF1-FLAG-ChIP-seq

value: FLAG


title: 15N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_11.RCC

value: Week 0

value: Silirum®


title: alcohol-FMT 31

city: Chongqing

first: li

last: hui

address: Xinqiao Street, Shapingba District

institute: Xinqiao Hospital of Army Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

extract_protocol:
Total RNA was extracted from the testicular tissues of animals in the alcohol-FMT and control-FMT groups, with three replicates in each group. RNA integrity was assessed using an RNA Nano 6000 Assay Kit and a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). The cDNA libraries were prepared using an Illumina TruSeq RNA sample prep kit. The average size of the library cDNAs was 150 bp (excluding adapters). The integrity and quality of cDNA libraries were assessed using an Agilent 2100 Bioanalyzer and an ABI StepOne Plus real-time PCR system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: alcohol


title: Donor_14-day2-OKT3_aCD28


title: 14RA,W0

address: Cnr Springs Road and Gerald Street

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Leukocytes


title: KI-BRPF1-H3K4me3-ChIP-seq


title: alcohol-FMT 18


title: Donor_14-day2-OKT3_gp120


title: 14A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_09.RCC


title: 15A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_12.RCC


title: control-FMT 21

value: control


title: alcohol-FMT 24


title: KO-BRPF1-D12-ATAC-seq-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig

extract_protocol:
In brief, 5×10^4 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: blastocyst

value: Day 12


title: Donor_14-day2-OKT3_gp120_RA


title: Donor_16-day2-OKT3


title: 14N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_08.RCC

value: PBS


title: KO-BRPF1-D12-ATAC-seq-1

value: hESCs

value: BRPF1 knockout


title: 13RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_07.RCC

value: Recombinant antigen


title: Donor_14-day2-OKT3_MadCAM_RA


title: 13A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_06.RCC

value: PPBDA


title: H1-ATAC-seq-2


title: control-FMT 16


title: Donor_14-day2-OKT3_MadCAM


title: H1-ATAC-seq-1


title: 13N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_05.RCC


title: KO-BRPF1-D30-ATAC-seq-1

value: Day 30


title: KO-BRPF1-D30-ATAC-seq-2


title: 12RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_04.RCC


title: Donor_14-day2-OKT3_RA

value: WT


title: LTKO4

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

data_processing:
Fastq files were aligned to the mouse genome using HISAT2 (v2.1.0). Read counts were generated using featureCounts and statistical analysis was carried out using edgeR (v3.28.1) with TMM normalisation and applying a significance threshold of FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: LT-WT-KO-counts.csv contains a matrix of gene counts for each biological sample

source_name: CD4+ T cells

extract_protocol:
Mouse knees were subjected to enzymatic digestion and CD4+ T cells were sorted from the resulting single suspension. Cells were lysed with RLT buffer and RNA was extracted using the Qiagen RNeasy microkit including on-column DNase digestion step, eluted in water and frozen at -80oC.
RNA libraries were prepared for sequencing using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina. Sequencing was carried out on the Illumina NovaSeq6000 platform using NovaSeq 6000 S2/S4 reagent kit (v1.0), 300 cycles.

tag: disease state

value: antigen induced arthritis

value: Slc7a5 knockout

tag: Sex

value: Male

tag: age

value: 16 weeks

value: CD4+ T cells sorted from knee joint


title: Donor_16-day2-OKT3_aCD28

tag: time


title: Donor_14-day2-OKT3


title: JLE33

first: Katherine

middle: E

last: Miller

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
FASTQs were generated using cellranger (v6.0.0) mkfastq with default parameters.
Raw counts were generated by aligning FASTQs to a combined custom reference using cellranger (v6.0.0) count with default parameters.
Assembly: made using cellranger mkref with default parameters using GRCh38
Supplementary files format and content: Raw counts are provided in sparse matrices and were generated by aligning FASTQs using cellranger (v6.0.0) count with default parameters.

source_name: seizure-affected brain tissue

extract_protocol:
Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3’ reagent kits.
10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol.
paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1)

tag: diagnosis

value: Focal cortical dysplasia type I


title: LTKO3

tag: cell type


title: LTKO2


title: 12A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_03.RCC

source_name: Leukocytes

tag: nanostring plexset set in rcc files

value: Week 0

tag: antigen

tag: vaccine

value: Silirum®

value: Leukocytes


title: Donor_13-day2-OKT3_aCD28


title: LTKO1


title: NB4327

source_name: autopsy control brain tissue


title: control-FMT 19

tag: strain

tag: tissue

value: testis

value: control


title: NB1499


title: 12N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_02.RCC

value: PBS


title: Donor_13-day2-OKT3_gp120_RA

tag: treatment


title: 24N,W3_rep4

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_01.RCC
Calibration Sample

value: Week 6

value: Recombinant MAP fusion protein


title: 11RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_12.RCC

value: Recombinant antigen


title: JLE23

value: Rasmussen Encephalitis


title: LTWT3

value: Wild type


title: Donor_13-day2-OKT3_gp120

value: WT


title: 11A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_11.RCC

value: PPBDA


title: Donor_13-day2-OKT3_MadCAM_RA


title: LTWT2

value: antigen induced arthritis

value: Male


title: LTWT1

value: 16 weeks

value: CD4+ T cells sorted from knee joint


title: 11N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Week 0


title: Hela_KO_4

city: Copenhagen

first: Salvatore

last: Rizza

email: salvatoreri@gmail.com, rizza@cancer.dk

address: Strandboulevarden 49

department: Redox Biology

country: Denmark

institute: Danish Cancer Institute

description: Cells were gene-edited by CRISPr-Cas9 technique

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build GRCh38 using STAR
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. ≥ 1.5 and  ≤ 1.5 Fold change and pAdj 0.05
Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, (https://rdrr.io/bioc/topGO/) was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction.
Assembly: Homo sapiens genome build GRCh38
Supplementary files format and content: tab-delimited text files include log2FoldChange, pvalue and padj for each experimental group

source_name: HeLa cells

growth_protocol: 4x105 Cells/well were plated in DMEM in 6-well cell culture plates and placed in a 5% CO2 37 °C incubator for 24 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library

treatment_protocol: HeLa cells were unstimulated

value: HeLa cells

value: untreated


title: Donor_13-day2-OKT3_MadCAM


title: JLE20


title: Donor_13-day2-OKT3_aCD28_RA


title: JLE18

value: Focal cortical dysplasia type I


title: Hela_KO_3


title: 10RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_09.RCC

value: Silirum®

value: Leukocytes


title: Donor_13-day2-OKT3_RA


title: Sample564_TVB

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Patient-derived explant_TVB

growth_protocol: Fresh tumor samples were dissected into 1mm^3 specimens, and placed on hydrated gelatin sponges in explant media containing 5% CCS FBS at 37℃.

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: After 24hours  of culturing, the media was replaced with fresh media containing 1% CCS FBS wontainign either the vehicle or 200 nM of TVB for 72 hours.

value: breast tumor explant 564

value: 200 nM TVB inhibitor

tag: harvest time

value: After 72 hours of treatment


title: 10A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_08.RCC


title: Hela_KO_2


title: 9RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_06.RCC

value: Recombinant antigen


title: LTWT4

value: Wild type


title: Donor_12-day2-OKT3_aCD28_RA

value: WT


title: Donor_13-day2-OKT3


title: Sample518_Control

source_name: Patient-derived explant_control

value: breast tumor explant 518

value: Untreated control


title: Hela_KO_1


title: Sample518_TVB


title: Donor_12-day2-OKT3_aCD28


title: Donor_12-day2-OKT3_gp120


title: Hela_wt_1

value: wild-type


title: Donor_12-day2-OKT3_MadCAM_RA


title: Donor_12-day2-OKT3_gp120_RA


title: 9A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_05.RCC

value: PPBDA


title: Hela_wt_2


title: H1819 S. typhimurium GFP Theta rep 3

first: Dhruba

last: Deb

address: 550 W 120th Street

institute: Columbia University

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment was performed to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: mm5
Supplementary files format and content: tab deliminated txt files comparing TPM values of 3 biological replicates under each of the 2 treatment conditions for each cell line were normalized

source_name: Metastatic, lymph node

growth_protocol: H460 and H1819 spheroids were maintained in RPMI-1640 with phenol red and 5% FBS and S. typhimurium was grown in LB agar with appropriate antibiotic selection, to form bacteria-spheroid co-culture

extract_protocol:
RNA was extracted using RNA easy mini kit (Qiagen), quantified by NanoDrop Onec 368, and, the quality was assayed by Agilent bioanalyzer
Poly-A pull-down was used to enrich mRNAs from total RNA samples, then library construction was done using Illumina TruSeq chemistry

treatment_protocol: Toxin production was induced by adding 10 nM N-(β-Ketocaproyl)-L-homoserine lactone (AHL) in the growth media

value: Metastatic, lymph node

tag: cell line

value: Metastatic

value: S. typhimurium Theta toxin secretion co-culture


title: 9N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_04.RCC

value: Week 0

value: PBS


title: Sample564_Control


title: 8RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_03.RCC


title: Donor_12-day2-OKT3_MadCAM


title: 8A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_02.RCC


title: 10N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_07.RCC

value: Silirum®


title: 24N,W3_rep3

value: Week 6

value: Recombinant MAP fusion protein

value: Leukocytes


title: Donor_12-day2-OKT3_RA


title: H1819 S. typhimurium GFP Theta rep 1


title: H1819 S. typhimurium GFP Theta rep 2


title: Hela_wt_3

value: HeLa cells

value: untreated


title: Hela_wt_4


title: H1819 S. typhimurium GFP control rep 3

value: S. typhimurium co-culture


title: Donor_12-day2-OKT3

value: WT


title: Donor_10-day2-OKT3_aCD28_RA


title: IH45

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent miRNA hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were processed and normalised using the Bioconductor  AgiMicroRna implementation in R

source_name: FFPE

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Agilent MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

tag: grading

tag: Stage

value: IC

tag: histotype

value: endometroid

value: early stage ovarian cancer


title: II88

value: IIA

tag: disease state


title: IH46

value: IA


title: H1819 S. typhimurium GFP control rep 2

value: Metastatic, lymph node

value: Metastatic

tag: genotype


title: II87

tag: age

value: serous


title: IH10

value: IIB


title: Donor_14-day2-OKT3_aCD28_RA

tag: time


title: 7A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Week 0

value: PPBDA

value: PBS


title: 7N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_09.RCC

value: Leukocytes


title: IJ34


title: 8N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_12.RCC


title: 6RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_08.RCC

value: Recombinant antigen


title: H460 S. typhimurium GFP Theta rep 3

source_name: Lung, pleural effusion

value: Lung, pleural effusion

value: Epithelial

value: S. typhimurium Theta toxin secretion co-culture


title: IJ15

value: clear cells


title: 7RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_11.RCC


title: H460 S. typhimurium GFP Theta rep 2

value: WT


title: IH44

value: mucinous

value: early stage ovarian cancer


title: 6A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_07.RCC


title: 6N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_06.RCC


title: Donor_10-day2-OKT3_MadCAM_RA


title: Donor_10-day2-OKT3_aCD28


title: H460 S. typhimurium GFP Theta rep 1


title: IJ14

value: IA


title: IH09


title: IH08

value: endometroid


title: H1819 S. typhimurium GFP control rep 1

value: Metastatic, lymph node

value: Metastatic

value: S. typhimurium co-culture


title: H460 S. typhimurium GFP control rep 3


title: Donor_10-day2-OKT3_MadCAM


title: 5RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_05.RCC

value: Week 0


title: Donor_10-day2-OKT3_RA


title: 5A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_04.RCC

value: PPBDA


title: Donor_10-day2-OKT3


title: IH43

value: IC


title: IH07


title: H460 S. typhimurium GFP control rep 2


title: Donor_10-day2-OKT3_gp120_RA


title: Donor_10-day2-OKT3_gp120


title: II86

value: IIA


title: H460 S. typhimurium GFP control rep 1


title: Donor_17-day1-OKT3_aCD28_RA


title: 24N,W3_rep2

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_01.RCC
Calibration Sample

value: Week 6

value: PBS

value: Recombinant MAP fusion protein

value: Leukocytes


title: PAX5-WT-WT, H3K27Ac, CST

city: Memphis

first: Jun

middle: J

state: Tennessee

address: 262 Danny Tomas Pl, MS 313

institute: St Jude Children's Research Hospital

data_processing:
Quality trimmed reads are mapped to the selected reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943). biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads.
Uniquely mapped reads were extracted by samtools(v1.2, PMID: 19505943) and extended to the estimated fragment size from Cross-Correlation Analysis by bedtools(v2.24.0, PMID: 20110278), then converted to bigwig track file by UCSC tools(v4, PMID: 22908213). To review the tracks, download IGV Genomics Browser
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: A total of 2 × 10^6 cells were fixed with Complete Cell Fixation Solution for 15 minutes and then stopped by Stop Solution for 5 minutes, followed by sonication. Both buffers were provided by ChIP-IT High Sensitivity kit (active motif).

value: B-ALL

tag: chip antibody

value: H3K27Ac, CST


title: 5N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_03.RCC

tag: cell type


title: PAX5-WT-WT, PAX5, Abcam

value: PAX5, Abcam


title: PAX5-WT-WT, H3K4me3, CST

value: H3K4me3, CST


title: Donor_17-day1-OKT3_gp120

value: WT


title: 4RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_02.RCC

tag: nanostring plexset set in rcc files

value: Recombinant antigen


title: IH42

value: IA

value: endometroid

value: early stage ovarian cancer


title: PAX5-WT-WT, Total


title: Donor_17-day1-OKT3_MadCAM_RA


title: Donor_17-day1-OKT3_gp120_RA


title: II79

value: clear cells


title: II78


title: Donor_17-day1-OKT3_aCD28


title: PAX5-WT-Indel, H3K4me3, CST


title: IH35

value: serous


title: 3RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_10.RCC

value: Week 0

tag: antigen


title: PAX5-WT-Indel, H3K27Ac, CST


title: Donor_17-day1-OKT3_RA


title: 4N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_11.RCC

tag: vaccine


title: 4A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_12.RCC

value: PPBDA


title: 3A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_09.RCC


title: 3N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_08.RCC


title: PAX5-WT-Indel, PAX5, Abcam


title: IH06


title: Donor_17-day1-OKT3


title: 2RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_07.RCC


title: Donor_16-day1-OKT3_aCD28_RA


title: PAX5-WT-Indel, Total


title: Parental, H3K4me3, CST


title: IH34


title: Donor_17-day1-OKT3_MadCAM


title: 2N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_05.RCC


title: IH33

value: IC


title: Donor_16-day1-OKT3_aCD28


title: IJ13


title: Donor_16-day1-OKT3_gp120_RA


title: Parental, H3K27Ac, CST


title: 1RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200718_cJD immune Run-1 S1_01_04.RCC

value: PBS


title: Parental, PAX5,Abcam


title: Parental, Total


title: IH32


title: II77


title: IG99

value: IIB


title: Donor_16-day1-OKT3_MadCAM


title: 1A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_03.RCC

value: Leukocytes


title: 24N,W3_rep1

value: Week 6

value: Recombinant MAP fusion protein


title: Donor_16-day1-OKT3_gp120


title: Donor_16-day1-OKT3_MadCAM_RA


title: II76


title: Donor_16-day1-OKT3_RA


title: IJ11

value: mucinous


title: PAX5-P80R-Indel, H3K4me3, CST

value: B-ALL

value: H3K4me3, CST


title: 1N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200718_cJD immune Run-1 S1_01_02.RCC


title: 2A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200718_cJD immune Run-1 S1_01_06.RCC


title: Donor_16-day1-OKT3

value: WT


title: IJ12

value: IIA


title: II75

value: endometroid


title: PAX5-P80R-Indel, H3K27Ac, CST

value: H3K27Ac, CST


title: PAX5-P80R-Indel, PAX5, Abcam

value: PAX5, Abcam


title: RNA-seq_OEB_C7_3

city: Hangzhou

first: Fu

last: Guo

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina HCS 2.2.68 software used for basecalling.
The adapters and low-quality reads were removed by Trimmomatic v0.36.
The clean reads were mapped to the rice reference genome Oryza_sativa. IRGSP-1.0.45 using Hisat2 program v2.1.0. The transcripts were assembly and merged using StringTie v1.3.4d.
Genome_build: Oryza_sativa. IRGSP-1.0.45
Supplementary_files_format_and_content: The excel file includes FPKM values and raw counts for every gene and every sample.

organism: Oryza sativa

source_name: RNA-seq datasets of OEMIR393b mature embryos on CIM medium for 7 days

growth_protocol: The plants were grown in greenhouse at 16 h light, 28 ℃/8 h dark, 24 ℃ cycle.

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

tag: background ecotype

value: Nipponbare

value: mature embryo

tag: time for treatment

value: 7 days


title: PAX5-P80R-Indel, Total


title: RNA-seq_OEB_C7_2

tag: tissue


title: RNA-seq_OEB_C7_1


title: Donor_14-day1-OKT3_aCD28_RA

tag: treatment


title: Tcell, Nalm6CD58KO, blina, rep 2

data_processing:
Quality trimmed reads are mapped to the selected reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and convert to bam file (a binary version of sam file) by samtools (v1.2, PMID: 19505943). biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) were used to mark duplicated reads.
Properly paired mapped reads were extracted by samtools (v1.2, PMID: 19505943) and center 80bp of nucleosome free fragment were extracted by bedtools (v2.24.0, PMID: 20110278). Then converted to bigwig track file by UCSC tools (v4, PMID: 22908213). To review the tracks, download IGV Genomics Browser
Assembly: hg38
Supplementary files format and content: bigwig

source_name: pan T cell

extract_protocol:
ATAC-seq was performed following the Fast-ATAC protocol
Libraries were made using NEB ultra II DNA library protocol

treatment_protocol: Blinatumomab (1ng/mL) or control

tag: cell line

value: pan T cell

value: T cell

value: incubated with parental CD58 knockout Nalm6 B-ALL cell line

tag: agent

value: Blinatumomab (1ng/mL), 48 hours


title: RNA-seq_OEB_C5_3

source_name: RNA-seq datasets of OEMIR393b mature embryos on CIM medium for 5 days

value: 5 days


title: IJ10

tag: grading

tag: Stage

value: serous

value: early stage ovarian cancer


title: IG98

value: IA

tag: histotype

tag: disease state


title: Donor_14-day1-OKT3_aCD28

tag: genotype


title: IG97

tag: age

value: mucinous


title: Donor_14-day1-OKT3_gp120_RA

value: WT

tag: time


title: RNA-seq_OEB_C5_1


title: Donor_14-day1-OKT3_RA

tag: cell type


title: Donor_14-day1-OKT3_MadCAM_RA


title: Donor_14-day1-OKT3_MadCAM


title: RNA-seq_OEB_C2_3

source_name: RNA-seq datasets of OEMIR393b mature embryos on CIM medium for 2 days

value: 2 days


title: RNA-seq_OEB_C2_2


title: RNA-seq_OEB_C5_2


title: 697, WT-WT

value: B-ALL


title: 697, WT-Indel


title: Tcell, Nalm6CD58KO, blina, rep 1


title: RNA-seq_OEB_C2_1


title: Tcell, Nalm6parental, blina, rep 2

value: incubated with parental Nalm6 B-ALL cell line


title: RNA-seq_OEB_N2_3

source_name: RNA-seq datasets of OEMIR393b mature embryos on N6 medium for 2 days


title: Donor_14-day1-OKT3


title: IJ27

value: IIB

value: clear cells


title: II74


title: IH30


title: Donor_14-day1-OKT3_gp120


title: 697, P80R-Indel


title: RNA-seq_OEB_N2_2

value: Nipponbare

value: mature embryo


title: IH31

value: endometroid


title: Tcell, Nalm6parental, blina, rep 1

value: pan T cell

value: T cell


title: Donor_13-day1-OKT3_aCD28_RA


title: IJ26


title: 697, Parental


title: Tcell, Nalm6CD19KO, control, day2, rep 2

description: RNA-seq is performed for T cells incubated with parental CD19 knockout Nalm6 B-ALL cell line

data_processing:
the bigwig files are generated by a program “wigToBigWig” using wig files created by the STAR mapping program
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: RPMI1640 contain 10% FBS

extract_protocol: Qiagen Rneasy Mini Kit

value: control


title: RNA-seq_OEB_N2_1


title: Donor_13-day1-OKT3_aCD28


title: IJ25

value: IIA


title: Donor_13-day1-OKT3_gp120_RA


title: RNA-seq_NIP_C7_3

source_name: RNA-seq datasets of NIP mature embryos on CIM medium for 7 days

value: 7 days

value: NIP


title: Tcell, Nalm6CD19KO, control, day2, rep 1

value: incubated with parental CD19 knockout Nalm6 B-ALL cell line


title: Tcell, Nalm6CD58KO, control, day2, rep 2

description: RNA-seq is performed for T cells incubated with parental CD58 knockout Nalm6 B-ALL cell line


title: IG96

value: serous

value: early stage ovarian cancer


title: Donor_13-day1-OKT3_MadCAM_RA

value: WT


title: RNA-seq_NIP_C7_1


title: RNA-seq_NIP_C7_2


title: Tcell, Nalm6parental, control, day2, rep 2

description: RNA-seq is performed for T cells incubated with parental Nalm6 B-ALL cell line


title: Donor_13-day1-OKT3_MadCAM


title: Tcell, Nalm6parental, control, day2, rep 1


title: Donor_13-day1-OKT3_RA


title: IH23

value: IC


title: II66


title: II67

value: IA

value: mucinous


title: Donor_13-day1-OKT3


title: Tcell, Nalm6CD19KO, blina, day2, rep 1

value: blinatumomab (1 ng/mL)


title: RNA-seq_NIP_C2_3

source_name: RNA-seq datasets of NIP mature embryos on CIM medium for 2 days

value: Nipponbare

value: 2 days


title: IG95


title: Tcell, Nalm6CD58KO, control, day2, rep 1

value: incubated with parental CD58 knockout Nalm6 B-ALL cell line


title: RNA-seq_NIP_C5_2

source_name: RNA-seq datasets of NIP mature embryos on CIM medium for 5 days

value: mature embryo

value: 5 days


title: Tcell, Nalm6CD19KO, blina, day2, rep 2

value: pan T cell


title: Donor_13-day1-OKT3_gp120


title: RNA-seq_NIP_C2_1


title: Donor_12-day1-OKT3_aCD28_RA


title: RNA-seq_NIP_C5_3


title: RNA-seq_NIP_C5_1


title: Donor_12-day1-OKT3_aCD28


title: Tcell, Nalm6CD58KO, blina, day2, rep 2


title: RNA-seq_NIP_C2_2


title: Tcell, Nalm6CD58KO, blina, day2, rep 1


title: Donor_12-day1-OKT3_gp120_RA


title: II65

value: IIA


title: IG94

value: endometroid


title: IJ24

value: IIB


title: RNA-seq_NIP_N2_3

source_name: RNA-seq datasets of NIP mature embryos on N6 medium for 2 days

value: NIP


title: Donor_12-day1-OKT3_gp120


title: Tcell, Nalm6parental, blina, day2, rep 2

value: incubated with parental Nalm6 B-ALL cell line


title: IG87

value: early stage ovarian cancer


title: IG86


title: II64

value: clear cells


title: RNA-seq_NIP_N2_2


title: Tcell, Nalm6parental, blina, day2, rep 1

value: WT


title: Differentiating cells D5 N1KO

city: Columbus

first: Cankun

last: Wang

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

data_processing:
12 samples were obtained using 10X Genomics Chromium Single Cell RNA v3 chemistry. Libraries were sequenced on an Illumina Novaseq instrument and counted with CellRanger v3.1.0 using hg38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV format, gene-cell raw count matrix and metadata for cells

source_name: Human iPSC N1KO

growth_protocol: Human induced pluripotent stem cells were cultured in Essential 8 medium (Thermo Fisher Scientific). Cardiac differentiation was performed by sequential modulation of WNT signaling by small molecules (CHIR99021 for 2 days and IWR-1 for 2 days) as we previously published (PMID: 33645570).

extract_protocol:
Single-cell suspension was processed and loaded into a Chromium Next GEM Chip G (10x Genomics) to generate single-cell gel bead in emulsions on a 10x Genomics Chromium Controller.
Single-cell RNA-seq libraries were constructed using a Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics).

treatment_protocol: Differentiating cells were collected at D0, D2, D5, D10, D14, and D30 during cardiac differentiation of WT and N1KO human iPSCs.

tag: cell type source

value: induced pluripotent stem cells

value: NOTCH1 knockout

tag: timepoint

value: Day 5


title: RNA-seq_NIP_N2_1

value: Nipponbare


title: II63


title: Donor_12-day1-OKT3_MadCAM

data_processing:
STAR2 was used for genome alignment
Htseq-count was used for read-gene frequency calculation
DESeq2 was used for DE normalization.
Assembly: hg19
Supplementary files format and content: tab-delimited matrix of normalized gene digital expression

extract_protocol:
Qiagen AllPrep DNA/RNA 96-well system
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, USA) was used for cDNA synthesis with an input of 150 pg total RNA.


title: IG85

value: IA


title: Differentiating cells D30 N1KO

value: Day 30


title: II62

value: serous


title: G088_O04_CyCMV_36959_D14_RNA_mRNAseq_run07_S9

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Read quality for each sample was first assessed with FASTQC
Residual adapters were removed with trim galore. Globin and rRNA reads were filtered out using bowtie2.
Remaining reads were alligned to the Macaca mulatta genome using STAR version 2.7.5
Gene counts were calculated with HTSeq-count version 0.12
Genes with counts less than 10 averaged across all samples were filtered out. The filtered count matrix then underwent TMM normalization followed by voom transformation.
Assembly: Mmul10, Ensembl v100
Supplementary files format and content: Normalized Count Matrix

organism: Macaca fascicularis

extract_protocol:
RNA was extracted using the RNAdvance Blood Kit from Beckman Coulter
mRNA-seq libraries were constructed using KAPA RNA HyperPrep kit with RIboErase (HMR) Globin in conjunction with the KAPA mRNA Capture kit by Roche.
Libraries were sequenced on an Illumina NextSeq500 sequencer using Illumina NextSeq 500/550 High Output v2 kits (150 cycles) following the manufacturer's protocol for sample handling and loading.

tag: age (years)

tag: group

value: Boost

tag: outcome

value: Unprotected

tag: time point

tag: Sex

value: M

value: Whole Blood


title: Donor_12-day1-OKT3_RA

tag: treatment


title: Donor_10-day1-OKT3_aCD28_RA


title: G086_O04_CyCMV_36957_D14_RNA_mRNAseq_run09_S4

value: Protected

tag: tissue


title: G087_O04_CyCMV_36958_D14_RNA_2_mRNAseq_run13_S25


title: Differentiating cells D2 N1KO

value: Day 2


title: Differentiating cells D14 N1KO

value: Day 14


title: Donor_12-day1-OKT3


title: IJ03

tag: grading

value: endometroid

value: early stage ovarian cancer


title: IH21

tag: Stage


title: Differentiating cells D10 N1KO

value: Day 10


title: G085_O04_CyCMV_36953_D14_RNA_mRNAseq_run13_S24


title: Donor_10-day1-OKT3_aCD28

value: WT


title: G084_O04_CyCMV_36959_BD7_RNA_mRNAseq_merged


title: Donor_10-day1-OKT3_gp120_RA


title: Donor_12-day1-OKT3_MadCAM_RA


title: Differentiating cells D0 N1KO

value: induced pluripotent stem cells

value: NOTCH1 knockout

value: Day 0


title: Differentiating cells D5 WT

source_name: Human iPSC WT

value: Wild type

value: Day 5


title: IH22

value: IA

tag: histotype


title: II55

value: mucinous

tag: disease state


title: G083_O04_CyCMV_36958_BD7_RNA_2_mRNAseq_run13_S26

value: Boost

value: Unprotected


title: Differentiating cells D30 WT

tag: genotype

value: Day 30


title: II54

tag: age

value: IC

value: serous


title: Donor_10-day1-OKT3_MadCAM_RA

tag: time


title: Donor_10-day1-OKT3_MadCAM

tag: cell type


title: G082_O04_CyCMV_36957_BD7_RNA_mRNAseq_run10_S1

value: Protected

value: M

value: Whole Blood


title: Differentiating cells D2 WT

tag: cell type source

value: Day 2


title: II53

value: endometroid

value: early stage ovarian cancer


title: G081_O04_CyCMV_36953_BD7_RNA_mRNAseq_run09_S9


title: Differentiating cells D14 WT

value: induced pluripotent stem cells

tag: timepoint

value: Day 14


title: II52

value: IIB


title: G080_O04_CyCMV_36959_BD3_RNA_mRNAseq_run13_S22

tag: age (years)


title: Donor_10-day1-OKT3

value: WT


title: G079_O04_CyCMV_36958_BD3_RNA_mRNAseq_run11_S6

tag: group


title: Donor_10-day1-OKT3_RA


title: G078_O04_CyCMV_36957_BD3_RNA_mRNAseq_run11_S7

tag: outcome


title: Donor_10-day1-OKT3_gp120


title: Differentiating cells D10 WT

value: Wild type

value: Day 10


title: Differentiating cells D0 WT

value: Day 0


title: G077_O04_CyCMV_36953_BD3_RNA_mRNAseq_merged

value: Boost

tag: time point


title: IG84

value: IB


title: JNKKO-BBTGF3 [RNA-seq]

city: Worcester

first: Zeynep

last: Itah

address: 373 Plantation St. Suite 309

institute: UMass Medical School

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
Clean reads were then mapped to hg38 genome using RSEM
TPM and Counts were calculated using RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab separated files include read count values for each Sample
Supplementary_files_format_and_content: tab separated files include TPM values for each Sample

source_name: Mammary epithelial cell line

growth_protocol: Cells (2-2.5x10^6) were routinely cultured in growth media containing DMEM:F12 with 5% horse serum, EGF, insulin, hydrocortizone, cholera toxin and penicillin and streptomycin. Cells were splitted within 2-3 days.

extract_protocol:
Acini structures  were removed from GFR- matrigel using cell recovery solution on ice and total RNA was harvested using miRNeasy kit with Dnase I treatment (QIAGEN# 217084).
mRNAs were enriched using oligo(dT) beads. After rRNA depletion using Ribo-Zero kit, mRNA was fragmented randomly, and cDNA was synthesized with random hexamer primers. After second strand synthesis, terminal repair, A ligation and adaptor ligation was performed. Following to size selection and PCR enrichment, cDNA libraries were pair end sequenced for 150bp on NovaSeq6000  platform.

treatment_protocol: For the experiment, cells were grown on growth factor reduced(GFR) matrigel within assay media ( DMEM/F12 supplemented with 2% donor horse serum and insulin,  cholera toxin, hydrocortisone,  penicillin and streptomycin). On day 7, EGF replaced with Ethanol (control) or B/B homodimerizer with or without TGF-β1 for 14 days.

tag: cell line background

value: JNK knockout

value: B/B homodimerizer+TGF-β1

value: 21 days= 7+14day with treatments


title: JNKKO-BBTGF2 [RNA-seq]

tag: treatment


title: II51

value: serous


title: IJ02

value: IA


title: G076_O04_CyCMV_36959_BD1_RNA_mRNAseq_run12_S26

value: Unprotected

tag: Sex

value: M

tag: tissue

value: Whole Blood