title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 32

value: M

value: SIRS

value: OOHCA

value: Survived


title: 300BCG058_d0_PBMC

status: Public on Jan 08 2024

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
ATAC-seq reads were trimmed using Skewer and aligned to the GRCh38 assembly of the human genome using Bowtie 2 with the “-very-sensitive” parameter. Duplicate reads were removed using the sambamba “markdup” command, and only reads with mapping quality ≥ 30 and alignment to the genome were kept. Peak calling was performed with MACS2 using the “-nomodel” and “-extsize 147” parameters, and peaks overlapping blacklisted features as defined by the ENCODE project were discarded.
For quality control, the fraction of reads in peaks (FRiP) was calculated as the fraction of transposase cutting events overlapping identified peaks. Similarly, we quantified the fraction of transposase cutting events overlapping regions defined in the Ensembl Regulatory Build v20190329 and overlapping promoters. We defined the TSS enrichment statistic as the maximum value of the TSS enrichment plot, which is a histogram of transposase cutting events falling within ±1,000 bp from a reference set of TSSs normalized by the average tail value (calculated as the average coverage on the last 100 bp of both tails of the histogram). We then selected all samples with at least 5,000 called peaks and a TSS enrichment statistic of at least 4.5 for further analysis.
The chromatin accessibility peaks were combined into a single consensus region set by merging the peak summits, extended by 250 bp on both sides, across all samples that passed the quality control. This procedure yielded a consensus set.
Assembly: GRCh38
processed data files format and content: countData_ATAC_allsamples.csv : comma-separated count file of the ATAC-seq data
processed data files format and content: region_annotations.csv : comma-separated information on the genomic location and length of each region in the ATAC-seq data

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Briefly, at all three time points, 50,000 PBMCs were washed once in 50 μl cold PBS and lysed in a transposase reaction mix containing 10.25 μl nuclease free water, 12.50 μl 2 × Tagment DNA Buffer (Illumina), 2 μl Tagment DNA Enzyme (Illumina), and 0.25 μl 1% digitonin (Promega) for 30 minutes at 37 °C. Upon DNA purification with the MinElute kit (Qiagen), 1 μl of eluted DNA was used in a qPCR reaction in order to estimate the optimum number of amplification cycles. Next, the remaining 10 μl of each library was amplified for the number of cycles corresponding to the Cq value (the cycle number at which fluorescence has increased above background levels) from the qPCR.
Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments exceeding 1,200 bp in length. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers. Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50-bp single-end configuration.

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: vastus lateralis muscle,SLOW,YE,trained,1,male,PRE

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Basecalling performed using Illumina RTA v2.
bcl2fastq used to convert BCL files to fastq files
Quality control using FastQC v0.11.05
Quality control using Picard 2.7.1 RNASeqMetrics STRAND_SPECIFICITY=NONE
Reads were aligned using STAR v2.5.2b
Gene counts were quantified using featureCounts v1.5.0 with the following settings: -M --fraction -g gene_id
Assembly: hg38
Supplementary files format and content: space-delimited matrix of counts per transcript per sample (rows represent transcripts, columns represent samples).  First six columns are transcript information (geneid, chromosome, start, end, strand, length).

molecule: total RNA

source_name: vastus lateralis muscle

extract_protocol:
TriZol extraction (TRI Reagent, Molecular Research Center, Cincinnati, OH)
The SMARTer¬Æ Ultra¬Æ Low Input RNA kit (Takara, Mountain View, CA) was used to generate cDNA from 9 ng of total RNA. Using the ThruPLEX¬Æ DNA-seq kit (Takara), 1-2 ng of double-stranded cDNA was end-repaired and A-tailed to prepare for adaptor ligation. Indexed adaptors were ligated to sample DNA, and the adaptor-ligated DNA library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs. Sequencing was performed on the NextSeq 500 unit (Illumina, San Diego, CA)

tag: tissue

value: vastus lateralis muscle

tag: fiber-type

value: SLOW

value: YE

value: trained

tag: Sex

value: male

value: PRE


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 32

type: RNA

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

description: Gene expression in Peripheral Blood, Day: 2 OOHCA SIRS

hyb_protocol: mRNA purified from PBLs was labelled with Cy3 using the Agilent QuickAmp one colour labelling kit and then hybridised to Human SurePrint G3 Human Gene Expression v3 8x60K Microarrays according to the manufacturer’s instructions

scan_protocol: Slides were scanned using an Agilent Surescan Dx G5761AA Microarray Scanner using default settings.

data_processing: Raw numeric values were exported and uploaded into GeneSpring 14.0 software for further processing and analysis. Data were normalized to the 75th percentile and baseline transformed using the global median.

source_name: Peripheral Blood, Day: 2

label_protocol: Due to the small volumes of blood used in the study and consequently low yield of total RNA recovered, an enrichment step was then performed using the Genisphere SenseAmp RNA amplification kit according to manufactures instructions (http://genisphere.com/). The resulting amplified mRNA was purified using RNeasy Min-Elute Cleanup kit (Qiagen), again according to the manufacturers’ protocol. The mRNA concentration and purity (A260/A280 ratio ≥ 1.8) was then assessed by spectrophotometry using a NanoDrop ND-1000 spectrophotometer.

extract_protocol: RNA was prepared from patient PBLs using a semi-automated process using the Maxwell® 16 platform and the Maxwell® 16 LEV simplyRNA Blood Kit. Concentration and purity (A280/260 ratio ≥ 1.8) were assessed by spectrophotometry using a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: On collection, 5ml of whole heparinised blood was mixed with Erythrocyte Lysis (EL) Buffer (QIAGEN) followed by incubation for 10-15 minutes on ice. Peripheral blood leukocytes (PBLs) were recovered from erythrocyte lysed blood by centrifugation at 400 x g for 10 minutes at 4˚C and resuspended in a further 2ml of EL buffer. PBLs were recovered again by centrifugation at 400 x g for 10 minutes at 4˚C and stored at -80oC prior to ongoing analysis

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.4 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome GRCh38 The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 (Small-sample estimation of negative binomial dispersion, with applications to SAGE data) and incorporated in the EdgeR Bioconductor package (Robinson et al., 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data). Genome_build: Human genome GRCh38 Supplementary_files_format_and_content: tab-delimited text files include normalized CPM values for each sample
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized CPM values for each sample

source_name: bronchial

growth_protocol:
As described in the paper. Briefly, the bro-ALI and bro-ALI-CB models were developed using PBEC harvested from macroscopically normal bronchial tissue obtained from one donor in connection with lobectomy following written and informed consent as described in previous studies. The protocol was approved by the Swedish Ethical Review Authority (Institutional ethic committee reference number: 99-357; approved on 10th January 2000). All methods were performed in accordance with the relevant guidelines and regulations. The bro-ALI and bro-ALI-CB models were developed according to the procedure described previously [PMID: 28107509; PMID: 31462114]. Interleukin 13 (IL13;1 ng/ml) was added to the basal medium of each insert from the 1st day of PBEC in ALI condition to develop the bro-ALI-CB models. The detailed protocol and cellular differentiation (club cells, goblet cells, basal cells, ciliated cells, etc.) of the PBEC-ALI and PBEC-ALI-CB model development have been described in detail previously (PMID: 28107509). The models have been used in several other studies.
The alv-ALI model was developed using NCI-H441 (ATCC HTB-174; derived from the pericardial fluid of a patient with papillary adenocarcinoma of the lung) cell line. The detailed protocol and model characteristics have been described in detail previously and used in several recent studies [PMID: 33235237, PMID: 34960806, PMID: 36180488]. The NCI-H441 cells, representative of human type II pneumocytes, express constitutively the mRNA and protein of the major surfactant apo-protein. NCI-H441 cells were co-cultured with HULEC-5a (ATCC CRL-3244) representative of human lung microvascular endothelial cells for this purpose. The alv-ALI model characterization included light microscopy, confocal microscopy, transmission electron microscopy, and transepithelial electrical resistance measurement. Morphological characterization of the alv-ALI model demonstrated the presence of tight junction protein 1, lamellar bodies, surfactant protein C, microvilli, lipid bodies, desmosome, and tight junctions.

extract_protocol:
RNeasy Micro (QIAGEN)
UPX 3’ RNA sequencing technology using Qiagen Genomic Services, Germany

treatment_protocol:
As described in the paper. Briefly, the wood smoke was diluted in the ratio 1:20 with clean filtered room air. The exposure duration of 10 minutes (min) was decided based on the findings of a pilot dose response experiment (5,10, and 15 min exposure duration) assessing cytotoxicity (lactate dehydrogenase assay in basal media) and transcript expression of tumor necrosis factor (TNF; proinflammatory marker) and superoxide dismutase 3, extracellular (SOD3; oxidative stress marker).  The medium exposure dose was then chosen accordingly. None of the doses were cytotoxic.
The bro-ALI, bro-ALI-CB, and alv-ALI models were developed in transwell inserts in 12-well plates as previously described. After change of cell medium, the plates were placed in a 3L desiccator glass jar maintained at 37°C and 60% humidity and allowed to equilibrate for 5 min. The volume of the desiccator represents the functional residual capacity of a healthy adult human lung35. As the temperature of the electric smoker reached 80°C, the pump was switched on to suck wood smoke at a flow rate of 60 ml per min along with filtered air at a flow rate of 1.2 L per minute into the desiccator to obtain the 1:20 dilution.
The lung models were exposed to wood smoke or filtered clean air (Sham) for 10 min, where after they were transferred to a cell incubator (37°C, 60% humidity and 5% CO2) for 3 hours (h) until next exposure session on the same day. Two exposure sessions were performed on days 1 and 2; and one exposure on day 3 (5 exposures in total. Following completion of repeated exposures each day, the lung models were incubated for 24h (since start of exposure on previous day).  Cell culture medium was collected (and stored at -80°C) and replaced with fresh ALI medium 24 h after the first exposure each day and prior to the start of the exposure on the following day. Cell inserts were collected at the completion of 72 h since start of first exposure on day 1. The exposure regime did not induce cytotoxicity in any of bro-ALI, bro-ALI-CB, or alv-ALI models and therefore further molecular analysis was carried out. Cytotoxicity was assessed by lactate dehydrogenase (LDH; cat# 88953; Thermo Fisher scientific) for the pilot studies and propidium iodide staining (cat#556463; BD bioscience) for the repeated exposure studies.  Sham (clean air) exposed samples under identical conditions served as control.

value: bronchial

tag: disease state

value: chronic bronchitis-like

tag: treatment

value: Wood smoke


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 6

description: Gene expression in Peripheral Blood, Day: 1 OOHCA SIRS

source_name: Peripheral Blood, Day: 1

value: Died


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 102

description: Gene expression in Peripheral Blood, Day: 5 OOHCA SIRS

source_name: Peripheral Blood, Day: 5

value: M


title: vastus lateralis muscle,FAST,LLE,trained,9,male,POST

value: FAST

value: LLE

value: POST


title: vastus lateralis muscle,SLOW,YE,trained,1,male,POST


title: 300BCG057_d90_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol

tag: flowcell


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 6

tag: tissue


title: vastus lateralis muscle,FAST,LLE,trained,9,male,PRE

tag: fiber-type


title: 300BCG057_d0_PBMC

value: ATAC

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: vastus lateralis muscle,SLOW,LLE,trained,9,male,POST

value: vastus lateralis muscle

tag: Sex


title: 300BCG057_d14_PBMC


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 5


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 4


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 3


title: 300BCG056_d90_PBMC


title: vastus lateralis muscle,SLOW,LLE,trained,9,male,PRE

value: SLOW


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 2

tag: sample type

tag: patient id

tag: gender

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 6


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 51

description: Gene expression in Peripheral Blood, Day: Discharge from ICU OOHCA SIRS

value: Survived


title: vastus lateralis muscle,FAST,LLE,trained,8,male,POST

value: trained

value: male


title: 300BCG056_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 2

tag: tissue

value: bronchial

tag: disease state

tag: treatment


title: vastus lateralis muscle,FAST,LLE,trained,8,male,PRE

tag: fiber-type

value: PRE


title: Wood smoke, bronchial, chronic bronchitis-like, replicate 1

value: chronic bronchitis-like

value: Wood smoke


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 51

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M


title: vastus lateralis muscle,SLOW,LLE,trained,8,male,POST

value: LLE


title: 300BCG056_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: 300BCG055_d90_PBMC

tag: frip


title: Wood smoke, bronchial, replicate 6

value: healthy


title: 300BCG055_d14_PBMC

value: PBMC


title: vastus lateralis muscle,SLOW,LLE,trained,8,male,PRE

tag: Sex


title: Wood smoke, bronchial, replicate 5


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 51

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG055_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

value: ATAC


title: Wood smoke, bronchial, replicate 4

tag: tissue

tag: disease state

tag: treatment


title: vastus lateralis muscle,FAST,LLE,trained,7,male,POST

value: vastus lateralis muscle

tag: fiber-type

value: FAST

value: POST


title: 300BCG054_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Wood smoke, bronchial, replicate 3


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 50

description: Gene expression in Peripheral Blood, Day: 2 Pulmonary Sepsis

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Sepsis

value: Pulmonary


title: 300BCG054_d14_PBMC

tag: cell type

tag: genotype

tag: frip


title: Wood smoke, bronchial, replicate 2

tag: tissue


title: vastus lateralis muscle,FAST,LLE,trained,7,male,PRE

value: trained

tag: Sex


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 49

value: F

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived

value: Survived


title: Wood smoke, bronchial, replicate 1

value: bronchial

tag: disease state

tag: treatment

value: Wood smoke


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 50

description: Gene expression in Peripheral Blood, Day: 5 Pulmonary Sepsis

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M


title: vastus lateralis muscle,FAST,LLE,trained,5,male,POST

tag: fiber-type

value: LLE

value: male


title: 300BCG054_d0_PBMC

value: PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: vastus lateralis muscle,SLOW,LLE,trained,7,male,PRE

value: vastus lateralis muscle

value: SLOW

value: PRE


title: 300BCG053_d90_PBMC

tag: filtered peaks

tag: tss enrichment


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 50

description: Gene expression in Peripheral Blood, Day: 1 Pulmonary Sepsis

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Sepsis

value: Pulmonary


title: Wood smoke, alveolar, replicate 7

source_name: alveolar

tag: tissue

value: alveolar

value: healthy


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 49

value: F

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived


title: 300BCG053_d14_PBMC

tag: cell type

tag: genotype

tag: frip


title: vastus lateralis muscle,FAST,LLE,trained,5,male,PRE

tag: fiber-type

value: FAST

value: trained

tag: Sex


title: Wood smoke, alveolar, replicate 6

tag: disease state

tag: treatment

value: Wood smoke


title: Wood smoke, alveolar, replicate 5


title: vastus lateralis muscle,SLOW,LLE,trained,5,male,POST

value: LLE

value: POST


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 48

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M

value: Died


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 20


title: Wood smoke, alveolar, replicate 4


title: 300BCG052_d90_PBMC

value: PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: 300BCG053_d0_PBMC

tag: filtered peaks

tag: tss enrichment


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 46

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

value: Survived


title: vastus lateralis muscle,FAST,LLE,trained,4,male,POST

tag: tissue

value: vastus lateralis muscle

tag: fiber-type

value: male


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 49

tag: died/survived


title: Wood smoke, alveolar, replicate 3

value: alveolar

tag: disease state

value: healthy

tag: treatment


title: vastus lateralis muscle,FAST,LLE,trained,4,male,PRE

tag: Sex

value: PRE


title: 300BCG052_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 46

tag: sample type

value: F

value: SIRS

value: OOHCA


title: vastus lateralis muscle,SLOW,LLE,trained,5,male,PRE

value: SLOW

value: trained


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 43

tag: patient id


title: 300BCG052_d0_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: 300BCG051_d14_PBMC


title: 300BCG051_d90_PBMC


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 46

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Wood smoke, alveolar, replicate 1

tag: tissue

tag: disease state

tag: treatment

value: Wood smoke


title: vastus lateralis muscle,SLOW,LLE,trained,4,male,PRE

tag: fiber-type

value: LLE

tag: Sex


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 51

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M


title: donor 4 SEP1 infected hair follicles

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

institute: Monasterium Laboratory GmbH

data_processing:
Sequencing was performed on a NovaSeq 6000 using 2x100 bp read length with an output of appr. 30 M clusters (6 Gb) per sample.
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) and Trimmed raw reads were aligned  using STAR (version 2.7.10a).
Normalized counts have been calculated with DESeq2 (version 1.30.1) in R (version 3.6.1).
Assembly: GRCh38.105
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: hair follicles

growth_protocol: Microdissected hair follicles were directly snapfrozen or cultured in supplemented William's E medium without antibiotics for 24h

extract_protocol:
After 30h infection hair follicles were snapfrozen and total RNA was extracted
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After 24h anagen hair follicles were treated with supplemented William's E media and SM buffer (vehicle) or 1x10^8 PFU/mL of SEP1 phages for 30h

value: SEP1 phage solution

tag: donor

value: Male

tag: age


title: 300BCG051_d0_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: frip


title: donor 4 vehicle control hair follicles

value: SM buffer (vehicle control)


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 25

description: Gene expression in Peripheral Blood, Day: Discharge from ICU Pulmonary Sepsis

tag: sample type

tag: patient id

tag: gender

value: Sepsis

value: Pulmonary

value: Survived


title: vastus lateralis muscle,FAST,LLE,trained,3,male,POST

value: vastus lateralis muscle

value: FAST

value: male

value: POST


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 25

value: F

tag: disease

tag: disease 2

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 34

value: SIRS

value: OOHCA


title: donor 4 untreated control hair follicles

tag: treatment

value: untreated


title: Wood smoke, alveolar, replicate 2

tag: tissue

value: alveolar

tag: disease state

value: healthy

value: Wood smoke


title: 300BCG050_d14_PBMC

value: PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: 300BCG050_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

value: ATAC


title: vastus lateralis muscle,SLOW,LLE,trained,4,male,POST

tag: fiber-type

value: SLOW

value: LLE

value: trained

tag: Sex


title: vastus lateralis muscle,FAST,LLE,trained,3,male,PRE

value: PRE


title: vastus lateralis muscle,SLOW,LLE,trained,3,male,POST

value: vastus lateralis muscle


title: donor 3 SEP1 infected hair follicles

value: SEP1 phage solution

tag: donor

value: Male

tag: age


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 34

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

value: M

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 29

value: SIRS

value: OOHCA


title: donor 3 vehicle control hair follicles

tag: treatment

value: SM buffer (vehicle control)


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 29


title: vastus lateralis muscle,SLOW,LLE,trained,3,male,PRE

tag: tissue

value: male


title: 300BCG050_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: vastus lateralis muscle,FAST,LLE,trained,2,male,POST

tag: fiber-type

value: FAST

tag: Sex

value: POST


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 2

tag: sample type

value: Died


title: 300BCG049_d90_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

value: ATAC


title: donor 3 untreated control hair follicles

value: untreated

tag: donor

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 28

description: Gene expression in Peripheral Blood, Day: 1 Abdominal Sepsis

tag: patient id

tag: gender

tag: disease

value: Sepsis

tag: disease 2

value: Abdominal

tag: died/survived


title: 300BCG049_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: vastus lateralis muscle,SLOW,LLE,trained,7,male,POST

tag: tissue

value: vastus lateralis muscle

tag: fiber-type

value: SLOW

value: LLE

value: trained

tag: Sex


title: donor 2 SEP1 infected hair follicles

tag: treatment

value: SEP1 phage solution

value: Male


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 29

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M

value: SIRS

value: OOHCA

value: Survived


title: donor 2 vehicle control hair follicles

value: SM buffer (vehicle control)

tag: donor


title: vastus lateralis muscle,SLOW,LLE,trained,2,male,POST

value: male

value: POST


title: vastus lateralis muscle,SLOW,LLE,trained,2,male,PRE

value: PRE


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 27


title: 300BCG047_d90_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

value: ATAC

tag: tss enrichment

tag: frip


title: 300BCG047_d14_PBMC

tag: protocol


title: 300BCG047_d0_PBMC

tag: flowcell


title: vastus lateralis muscle,FAST,LLE,trained,1,male,POST

value: vastus lateralis muscle

value: FAST


title: donor 2 untreated control hair follicles

value: untreated

tag: age


title: donor 1 SEP1 infected hair follicles

value: Female


title: 300BCG046_d90_PBMC

tag: batch id

tag: pcr cq


title: vastus lateralis muscle,FAST,LLE,trained,1,male,PRE

tag: tissue

value: LLE

value: trained


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 27

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: vastus lateralis muscle,FAST,LLE,trained,2,male,PRE

tag: fiber-type

tag: Sex


title: donor 1 vehicle control hair follicles

tag: treatment

tag: donor


title: 300BCG046_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: filtered peaks

tag: tss enrichment


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 25

tag: sample type

value: F

value: Sepsis

value: Pulmonary


title: donor 1 untreated control hair follicles

tag: age


title: vastus lateralis muscle,SLOW,LLE,trained,1,male,PRE

tag: tissue

value: SLOW


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 25

tag: patient id

tag: gender

value: Survived


title: HeLa cells, triple KD, rep3

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 29 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

molecule: polyA RNA

source_name: HeLa

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo). Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

tag: cell line

value: HeLa

value: triple KD


title: 300BCG045_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: frip


title: Monocytes_CV0_M78

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

data_processing:
Purity-filtered reads were pre-processed using fastp (v. 0.19.11).
Reads were aligned against Homo sapiens GRCh38.p13 genome using STAR (v. 2.7.3a).
The number of read counts per gene locus was summarized with featureCounts from subread (v. 1.6.4) using Homo sapiens GRCh38.p13 Gencode release 32 gene annotation.
Assembly: Homo sapiens GRCh38.p13
Supplementary files format and content: Monocytes_rawCounts.txt: Tab-separated .txt file with gene-level read counts.

source_name: blood

extract_protocol:
20mL of whole blood of 92 male participants with T2D was drawn and PBMCs were isolated using Ficoll Paque+. CD14+ circulating monocytes were immunoselected using anti-human CD14 Milteny beads. A minimum of 2 million cells were lysed with RLT plus buffer and 3% β-mercaptoethanol for subsequent RNA extraction using the RNeasy Plus extraction kit (Qiagen), following user manual instructions.
Sequencing libraries were prepared from bulk RNA using the Tru-seq mRNA protocol (batch2018) or the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (batches 2020 and 2021).
Single-end (batch 2018) and paired-end (2x75) strand specific (batches 2020 and 2021) sequencing was performed on Nextseq500 sequencer (Illumina).

value: blood

tag: cell type

value: CD14+ monocytes

tag: diagnosis

value: type 2 diabetes

tag: cv group

tag: batch

tag: Sex

value: male


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 22

value: M

tag: disease

tag: disease 2

tag: died/survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 22

tag: sample type


title: Monocytes_CV0_M77

tag: tissue

tag: age


title: HeLa cells, triple KD, rep2

tag: cell line

tag: genotype


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 63

tag: patient id

tag: gender

value: Died


title: Monocytes_CV0_M76


title: 300BCG045_d0_PBMC

value: PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: HeLa cells, control, rep3

value: control


title: vastus lateralis muscle,SLOW,LLE,trained,1,male,POST

value: vastus lateralis muscle

tag: fiber-type

value: LLE

value: trained

tag: Sex

value: POST


title: Monocytes_CV0_M75

tag: cell type

tag: diagnosis

tag: cv group

tag: batch


title: 300BCG044_d90_PBMC

tag: genotype

tag: frip


title: Monocytes_CV0_M74

tag: tissue

tag: age


title: HeLa cells, control, rep1

tag: cell line


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 37

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

tag: disease

value: Sepsis

tag: disease 2

value: Pulmonary

tag: died/survived


title: 300BCG046_d0_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 38

value: F

value: Abdominal

value: Survived


title: 300BCG044_d14_PBMC

tag: cell type

tag: genotype

tag: frip


title: 300BCG044_d0_PBMC


title: HEK293 cells, triple KD, rep3

tag: cell line

value: triple KD


title: Monocytes_CV0_M73

tag: tissue

value: blood

value: CD14+ monocytes

tag: diagnosis

value: type 2 diabetes

tag: cv group

tag: batch

tag: Sex

value: male

tag: age


title: 300BCG045_d14_PBMC

value: PBMC

tag: individual

tag: time point

value: ATAC


title: Monocytes_CV0_M71


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 63

tag: sample type

tag: patient id

tag: gender

value: M

tag: disease

tag: disease 2

tag: died/survived

value: Died


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 60


title: HeLa cells, triple KD, rep1

value: HeLa

tag: genotype


title: 300BCG043_d90_PBMC

tag: cell type

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 60


title: Monocytes_CV0_M72

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: HEK293 cells, triple KD, rep2

tag: cell line


title: 300BCG043_d14_PBMC

tag: individual

tag: time point


title: Monocytes_CV0_M70

tag: cell type


title: HEK293 cells, triple KD, rep1

tag: genotype


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 61

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 60


title: HeLa cells, control, rep2

value: control


title: HEK293 cells, SLTM KD, rep3

value: SLTM KD


title: Monocytes_CV0_M69

tag: tissue


title: Monocytes_CV0_M68

tag: diagnosis


title: 300BCG042_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG042_d14_PBMC

tag: cell type

tag: individual

tag: time point


title: HEK293 cells, SLTM KD, rep2

tag: cell line

tag: genotype


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 44

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

tag: disease

value: Sepsis


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 61

value: F

tag: disease 2

value: Pulmonary

tag: died/survived


title: Monocytes_CV0_M66

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: HEK293 cells, SAFB2 KD, rep3

value: SAFB2 KD


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 61


title: Monocytes_CV0_M67

tag: cell type


title: 300BCG041_d90_PBMC

tag: individual

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG042_d0_PBMC

tag: genotype

tag: time point


title: 300BCG043_d0_PBMC


title: HEK293 cells, SAFB2 KD, rep2

tag: cell line


title: Monocytes_CV0_M65

tag: tissue

tag: diagnosis


title: 300BCG041_d0_PBMC


title: HEK293 cells, SAFB2 KD, rep1


title: 300BCG041_d14_PBMC


title: 300BCG040_d90_PBMC


title: Monocytes_CV0_M63

tag: cv group

tag: batch


title: Monocytes_CV0_M62

tag: Sex

tag: age


title: HEK293 cells, SAFB1 KD, rep1

value: SAFB1 KD


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 43-2

tag: sample type

tag: patient id

tag: gender

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived

value: Survived


title: HEK293 cells, SLTM KD, rep1


title: 300BCG040_d14_PBMC

tag: cell type

tag: individual

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 39

description: Gene expression in Peripheral Blood, Day: 5 Abdominal Sepsis

value: Abdominal


title: 300BCG040_d0_PBMC

value: PBMC

tag: genotype

tag: time point

tag: frip


title: HEK293 cells, SAFB1 KD, rep3

tag: cell line


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 39

description: Gene expression in Peripheral Blood, Day: 2 Abdominal Sepsis

tag: sample type

tag: patient id


title: Monocytes_CV0_M61

tag: tissue

value: blood

value: CD14+ monocytes

tag: diagnosis

value: type 2 diabetes

tag: cv group

tag: batch

tag: Sex

value: male

tag: age


title: HEK293 cells, control, rep3

value: control


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 44

tag: gender

value: M

tag: disease

tag: disease 2

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 42

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)


title: Monocytes_CV0_M60

tag: cell type


title: Monocytes_CV0_M64


title: 300BCG039_d90_PBMC

tag: genotype

tag: individual

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: HEK293 cells, control, rep2

tag: cell line


title: Monocytes_CV0_M59

tag: tissue

tag: diagnosis

tag: cv group

tag: batch


title: Monocytes_CV0_M58

tag: Sex

tag: age


title: 300BCG039_d14_PBMC

tag: time point

tag: frip


title: HEK293 cells, control, rep1

tag: genotype


title: HEK293 cells, SAFB1 KD, rep2


title: 300BCG039_d0_PBMC

tag: cell type

tag: individual


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 30

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Died


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 43


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 42


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 30


title: wt293_rep2

data_processing:
library strategy: FLASH-seq (Ilik et al., 2020)
Illumina base calling, demultiplexing and FASTQ conversion
Merging with bbmerge v. 38.72
Demultiplexing with flexbar v. 3.5.0
UMI extraction with umi_tools extract v. 1.0.0
Alignment to human (hg38), mouse (mm10) or Drosophila genomes (dm6) with bowtie2 v. 2.3.5 and bbmap v. 38.72
bigWigs generation using bamCoverage 3.3.1
Assembly: hg38, mm10, dm6
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

source_name: Flp-In T-Rex HEK293

extract_protocol:
Cells were crosslnked with 0.199 mj/cm2 UV-C light,  lysed with 1xNLB buffer, protein-of-interest purified with streptavidin beads, co-purifying RNA isolated with proteinase K digestion and purified with Oligo clean and concentrator-5 columns (Zymo).
Custom library prep, described in Ilik et al., 2020. Isolated RNA is ligated to s-oligo on beads, reverse-transcribed, RNaseH digested, circularized with CircLigase and PCR amplified.

tag: cell line

value: Flp-In T-Rex HEK293

tag: molecule subtype

value: RNAseI digested RNA


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 38

description: Gene expression in Peripheral Blood, Day: Discharge from ICU Abdominal Sepsis

value: F

value: Sepsis


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 41

value: SIRS

value: OOHCA


title: Monocytes_CV0_M57

tag: tissue

tag: diagnosis

tag: cv group


title: wt293_rep1


title: Monocytes_CV0_M56

tag: batch

tag: Sex

tag: age


title: Monocytes_CV0_M55


title: 300BCG038_d90_PBMC

tag: genotype

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG038_d14_PBMC

tag: cell type

tag: individual


title: 300BCG038_d0_PBMC


title: hnRNPU_rep2

tag: cell line

tag: molecule subtype


title: 300BCG037_d90_PBMC


title: hnRNPU_rep1


title: Monocytes_CV0_M54

tag: tissue

tag: diagnosis

tag: cv group


title: Monocytes_CV0_M53

tag: batch

tag: Sex

tag: age


title: 300BCG037_d14_PBMC

tag: genotype

tag: time point

tag: protocol


title: hnRNPR_rep1


title: hnRNPR_rep2


title: Monocytes_CV0_M52


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 35

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

value: Abdominal

tag: died/survived

value: Survived


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 35


title: 300BCG037_d0_PBMC

tag: cell type

value: PBMC

tag: individual

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 17


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 32


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 41


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 17


title: Monocytes_CV0_M51

tag: tissue

value: blood

value: CD14+ monocytes

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: 300BCG036_d90_PBMC

tag: genotype

tag: time point

tag: protocol


title: hnRNPK_rep1

tag: cell line

tag: molecule subtype


title: hnRNPK_rep2


title: 300BCG036_d14_PBMC

tag: cell type

tag: individual

tag: flowcell


title: Monocytes_CV0_M50

value: type 2 diabetes

value: male


title: hnRNPF_rep1


title: 300BCG035_d14_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks


title: hnRNPF_rep2


title: 300BCG036_d0_PBMC

tag: tss enrichment

tag: frip


title: Monocytes_CV0_M47

tag: tissue

tag: diagnosis

tag: cv group


title: hnRNPC_rep2


title: 300BCG035_d90_PBMC


title: Monocytes_CV0_M46

tag: batch

tag: Sex

tag: age


title: hnRNPC_rep1

tag: genotype


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 14

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: U2AF2_rep2

tag: cell line

tag: molecule subtype


title: 300BCG035_d0_PBMC

tag: cell type

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Monocytes_CV0_M49

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 14

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Monocytes_CV0_M48

tag: cell type


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 16

value: Pulmonary


title: 300BCG034_d90_PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: frip


title: Monocytes_CV0_M45

tag: tissue

tag: diagnosis

tag: cv group

tag: batch


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 17

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

value: M


title: U2AF1_rep2

tag: cell line

tag: molecule subtype


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 5

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Monocytes_CV0_M44

tag: cell type

tag: Sex

tag: age


title: U2AF2_rep1

tag: genotype


title: 300BCG034_d14_PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Monocytes_CV0_M43

tag: tissue

tag: diagnosis

tag: cv group

tag: batch


title: 300BCG034_d0_PBMC

tag: cell type


title: U2AF1_rep1

tag: cell line

value: Flp-In T-Rex HEK293

tag: molecule subtype


title: 300BCG033_d90_PBMC

tag: genotype


title: Monocytes_CV0_M42

tag: Sex

tag: age


title: U1-70K_rep2

value: RNAseI digested RNA


title: Monocytes_CV0_M41


title: 300BCG033_d14_PBMC

tag: individual

tag: time point

tag: protocol


title: U1-70K_rep1


title: Monocytes_CV0_M40


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 41

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 8

value: Sepsis


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 5


title: 300BCG032_d90_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 40

value: SIRS


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 37


title: TRA2B_rep2

tag: cell line

tag: genotype

tag: molecule subtype


title: 300BCG033_d0_PBMC

tag: cell type

tag: individual

tag: time point


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 5

tag: sample type

tag: patient id


title: TRA2B_rep1


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 37

tag: gender

tag: disease


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 40

tag: disease 2

value: OOHCA

tag: died/survived


title: Monocytes_CV0_M39

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: Monocytes_CV0_M38


title: TRA2A_rep2

tag: cell line

tag: genotype


title: Monocytes_CV0_M37

tag: cell type


title: 300BCG032_d14_PBMC

tag: individual

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Monocytes_CV0_M36

tag: tissue


title: TRA2A_rep1

tag: molecule subtype


title: 300BCG031_d90_PBMC

tag: time point


title: 300BCG032_d0_PBMC


title: Monocytes_CV0_M35

tag: diagnosis

tag: cv group

tag: batch


title: TDP43_rep1

tag: cell line


title: Monocytes_CV0_M34

tag: Sex

tag: age


title: 300BCG031_d14_PBMC

tag: cell type

tag: genotype

tag: individual


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 31

tag: sample type

tag: patient id

tag: gender

value: F

tag: disease

tag: disease 2

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 35

value: Abdominal

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 37


title: TAF15_rep2

tag: molecule subtype


title: 300BCG031_d0_PBMC

value: PBMC

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 30


title: 300BCG030_d90_PBMC

tag: cell type

tag: genotype


title: Monocytes_CV0_M33

tag: tissue

value: blood

value: CD14+ monocytes

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: 300BCG030_d14_PBMC

tag: individual


title: Monocytes_CV0_M32

value: type 2 diabetes

value: male


title: TAF15_rep1

tag: cell line

tag: molecule subtype


title: 300BCG030_d0_PBMC

tag: time point

tag: protocol

tag: flowcell


title: TDP43_rep2


title: Monocytes_CV0_M31


title: SRSF9_rep2


title: SRSF9_rep1


title: Monocytes_CV0_M29


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 19

tag: sample type

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG029_d14_PBMC

tag: cell type

tag: genotype

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: SRSF8_rep2

tag: cell line

tag: molecule subtype


title: SRSF8_rep1


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 31

value: Pulmonary


title: 300BCG029_d90_PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC


title: Monocytes_CV0_M30

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: Monocytes_CV0_M28

tag: cell type


title: SRSF7_rep2

value: Flp-In T-Rex HEK293

tag: genotype


title: 300BCG029_d0_PBMC

tag: flowcell

tag: batch id

tag: pcr cq


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 19

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 4


title: 300BCG028_d90_PBMC

tag: individual

tag: time point

tag: protocol

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 17

value: M


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 19


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 33


title: SRSF7_rep1

tag: cell line

tag: molecule subtype

value: RNAseI digested RNA


title: 300BCG028_d14_PBMC

tag: cell type

tag: genotype

tag: flowcell


title: SRSF6_rep2


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 33

tag: sample type

value: Sepsis


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 4

tag: patient id

value: Died


title: Monocytes_CV0_M24

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: Monocytes_CV0_M23


title: Monocytes_CV0_M25


title: Monocytes_CV0_M27


title: 300BCG027_d14_PBMC

tag: individual

tag: time point

tag: protocol

tag: batch id

tag: pcr cq


title: SRSF5_rep1

tag: cell line

tag: molecule subtype


title: 300BCG027_d90_PBMC

tag: cell type

tag: genotype

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Monocytes_CV0_M26

tag: tissue

tag: diagnosis


title: Monocytes_CV0_M22

tag: cv group

tag: batch


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 33

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: SRSF4_rep2

tag: cell line


title: 300BCG027_d0_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq


title: 300BCG028_d0_PBMC

tag: cell type

tag: genotype

tag: filtered peaks

tag: tss enrichment

tag: frip


title: SRSF5_rep2

tag: molecule subtype


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 33

tag: sample type

tag: patient id

tag: gender


title: Monocytes_CV0_M21

tag: tissue

tag: diagnosis

tag: cv group

tag: batch

tag: Sex

tag: age


title: Monocytes_CV0_M20


title: SRSF4_rep1

tag: cell line


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 16

tag: disease

tag: disease 2

tag: died/survived


title: SRSF3_rep2

tag: genotype


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 16


title: HUVEC stretch 6%_Donor6

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Assembly: GRCm38.96

source_name: Human umbilical vein

growth_protocol: Cells were grown in dishes coated with 1.5% gelatin at 37◦C in a humidified atmosphere containing 5% CO2. Cells were cultured in Endothelial Cell Growth Medium (EGM)-2 medium (C-22111, PromoCell) and were used at passages 5–6.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA II (Macherey-Nagel) according to the manufacturers’ instructions. The Quality of the all samples per condition was verified using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit (Agilent Technologies).
cDNA libraries were constructed using the Illumina TruSeq RNA sample preparation kit according to the manufacturers’ protocol.
Libraries were sequenced using single- end (50 nt-long) on Illumina HiSeq2000. FastQ reads were mapped to the ENSEMBL reference genome (GRCh38.96) using STAR version 2.4.0j [30] with standard settings, except that any reads mapping to more than one location of the genome (ambiguous reads) were discarded (m=1).

value: Human umbilical vein

tag: treatment

value: Cells were submitted to cyclic stretch of 6% for 48H


title: Monocytes_CV0_M19

tag: cell type


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 13

value: SIRS

value: OOHCA


title: SRSF3_rep1

tag: molecule subtype


title: HUVEC STATIC_Donor5

value: Cells were kept under static condition for 48H


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 16

tag: sample type

value: F

value: Survived


title: Monocytes_CV0_M17

value: blood

value: CD14+ monocytes

value: type 2 diabetes


title: SRSF2_rep2


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 13

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

tag: patient id


title: HUVEC stretch 6%_Donor5


title: Monocytes_CV0_M18

value: male


title: Monocytes_CV0_M16


title: SRSF2_rep1

value: Flp-In T-Rex HEK293


title: HUVEC stretch 6%_Donor4


title: SRSF1_rep2


title: Monocytes_CV0_M15


title: HUVEC STATIC_Donor4


title: HUVEC STATIC_Donor6


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 13

tag: gender

value: M


title: SRSF1_rep1

value: RNAseI digested RNA


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 12


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 12


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 7

value: Sepsis

value: Pulmonary


title: HUVEC stretch 6%_Donor3

tag: tissue

value: Human umbilical vein


title: Monocytes_CV0_M14

tag: diagnosis


title: Monocytes_CV0_M11

tag: cv group


title: Monocytes_CV0_M13

tag: batch


title: SRSF12_rep2


title: HUVEC STATIC_Donor2


title: HUVEC STATIC_Donor1


title: SRSF10_rep2


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 7


title: HUVEC stretch 6%_Donor2

value: Cells were submitted to cyclic stretch of 6% for 48H


title: SRSF11_rep2


title: HUVEC stretch 6%_Donor1


title: m 4 1 [IL-13-30-28]

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

data_processing:
GeneTiles (Veneman et al., 2015; Immunogenetics 67, 135-147)
Bowtie2 was used to align the reads to the reference genome (Danio rerio GRCz11).
Samtools was used to convert SAM to BAM and to sort reads.
Aligned reads were counted using Htseq and pysam.
DESeq was used to perform statistical analysis of differentially expressed genes.
Assembly: GRCz11
Supplementary files format and content: Microsoft Office Excel file (.xlsx) with the following columns: chromosome; gene;  Ensembl gene-id; Entrez gene-id; baseMean; GO accessions; Human homologs; library name "raw" and "scaled" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or -CTRL/MEAS (scaled); p-value; adjusted p-value; best exon p-value

organism: Danio rerio

source_name: whole embryo/larva

growth_protocol: AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy mini kit.
RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.

treatment_protocol: 16-128-cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.

tag: strain

value: AB/TL

value: wild type

value: Mtb in PVP

tag: time

value: 4 dpf

value: whole embryo/larva


title: Monocytes_CV0_M09

value: blood

tag: Sex

tag: age


title: m 4 2 [IL-13-30-29]


title: p 6 s [IL-13-30-31]

value: PVP alone

value: 6 dpf


title: SRSF11_rep1

tag: cell line


title: Monocytes_CV0_M12

value: CD14+ monocytes

value: type 2 diabetes


title: m 6 s - 2 [IL-13-30-32]


title: m 4 s [IL-13-30-30]


title: SRSF12_rep1

value: Flp-In T-Rex HEK293


title: SRSF10_rep1


title: Monocytes_CV0_M10

value: male


title: 16S sequences

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Purified products were sequenced using the Illumina MiSeq platform . FASTQ data was processed and analyzed using Quantitative Insights into Microbial Ecology 2 (QIIME2) version 2019.4 32. Single-end sequences were demultiplexed, and reads were denoised and clustered using Divisive Amplicon Denoising Algorithm (DADA2) 31. Primers were trimmed off and single end reads were truncated to ‚â•150 base pairs. A phylogenetic tree was constructed and features were assigned taxonomy using Greengenes reference database with 99% confidence 31.
Analysis was performed on a rarefied feature table of 7340 reads per sample after filtration of mitochondria and chloroplast sequences.
Assembly: Greengenes reference database
Supplementary files format and content: Supplementary files format and content: Xlsx file includes OTUs, taxonomy and reads per sample.
Library strategy: 16S DNA-seq

organism: Bacteria

source_name: Feces

growth_protocol: Mice grown under SPF conditions

extract_protocol:
DNA was extracted from fecal samples using the Invitrogen Purelink‚Ñ¢ Microbiome DNA Purification Kit according to the manufacturer‚Äôs instructions, following two minutes of bead beating (Bio Spec). Following DNA extraction, the V4 variable region of the bacterial 16S rRNA gene was amplified by polymerase chain reaction (PCR) using the 515F and 806R primers, and each sample received a unique 515F barcoded primer. Primer sequences used were: 515F- (barcode) 5‚Ä≤-AATGATACGGCGACCACCGAGATCTACACGCTAGCCTTCGTCGCTATGGTAATTGTG TGYCAGCMGCCGCGGTAA-3‚Ä≤ and 806‚ÄâR 5‚Ä≤- CAAGCAGAAGACGGCATACGAGATAGTCAGTCAGCCGGACTACHVGGGTWTCTAAT -3‚Ä≤ 31.
PCR reactions were carried out with the Primestar taq polymerase (Takara) for 30 cycles of denaturation (95‚Äâ¬∞C), annealing (55‚Äâ¬∞C) and extension (72‚Äâ¬∞C), and a final elongation at 72‚Äâ¬∞C. Amplicons were purified using AMPure magnetic beads (Beckman Coulter), and subsequently quantified using Picogreen dsDNA quantitation kit (Invitrogen). Samples were pooled at equal concentrations (50‚Äâng/¬µl), loaded on 2% E-Gel (Thermo Fisher), and purified using NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).

treatment_protocol: WT and IL-1b-/- C57BL/6 mice were orally infected with 10^7 CFU of Salmonella typhimurium SL1334. Feces were collected 4 days post-infection and DNA was extracted.

value: Feces


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 12

value: Heparinised whole  blood - purified peripheral blood leukocytes (PBLs)

value: M

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived

value: Survived


title: HUVEC STATIC_Donor3

value: Human umbilical vein

tag: treatment

value: Cells were kept under static condition for 48H


title: p 4 s [IL-13-30-27]

value: AB/TL

tag: genotype

value: wild type

value: 4 dpf


title: SLTM_rep2

tag: molecule subtype

value: RNAseI digested RNA


title: Monocytes_CV0_M06

value: blood

tag: cell type


title: p 4 2  [IL-13-30-26]

value: PVP alone

value: whole embryo/larva


title: 120h_3

city: Beijing

first: hao

last: ding

state: Beijing

address: BeiChen Road

country: China

institute: institute of microbiology

data_processing:
FastQC v0.11.5
trimmomatic v0.39
Hisat2 v2.1.0
Stringtie v1.3.3
DEseq2 v1.16.1
Assembly: Cryptococcus neoformans var. grubii H99
Supplementary files format and content: tpm TPM of all strains

organism: Cryptococcus neoformans H99

extract_protocol:
The level and integrity of RNA in each sample were evaluated using a Qubit RNA Assay Kit on a Qubit 2.0 Flurometer (Life Technologies, CA, USA) and RNA Nano 6000 Assay Kit with the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. RNA purity was assessed using a Nano Photometer spectrophotometer (IMPLEN, CA, USA).
The transcriptome libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) according to the manufacturer’s instructions.

value: WT

value: YPD liquid medium, 120h


title: Monocytes_CV0_M05

value: CD14+ monocytes

value: type 2 diabetes

value: male


title: p 4 1 [IL-13-30-25]


title: SAFB2_rep2

value: Flp-In T-Rex HEK293


title: Monocytes_CV0_M04


title: SAFB2_rep1


title: SAFB1_rep2


title: 96h_2

value: YPD liquid medium, 96h


title: Monocytes_CV0_M03


title: m 3 s [IL-13-30-23]

value: Mtb in PVP

value: 3 dpf


title: p 3 s [IL-13-30-21]


title: p 5 s [IL-13-30-22]

value: 5 dpf


title: 120h_1


title: 96h_3


title: SAFB1_rep1


title: Monocytes_CV0_M02


title: 96h_1


title: Monocytes_CV0_M08


title: RBM25_rep2


title: CAF9/MSCmono

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: MSCmono

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: To induce the CAF-like cells, 3 × 105 MSCs were seeded into 100 mm dish, and 2 × 105 TE-9 cells were seeded in the same dish after 3 hours. Direct co-culture was performed for 4 days in DMEM high-glucose (Wako) with 10% FBS and 1% antibiotic-antimycotic. MSCs and TE cells were seeded and cultured similarly without co-culture as controls.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: MSCmono


title: Monocytes_CV0_M01


title: m 8 s [IL-13-30-20]

value: AB/TL

value: wild type

value: 8 dpf


title: Monocytes_CV0_M07

value: blood


title: SLTM_rep1

value: RNAseI digested RNA


title: 120h_2


title: m 5 s [IL-13-30-24]

value: whole embryo/larva


title: 72h_3

value: WT

value: YPD liquid medium, 72h


title: 72h_2


title: LUC7L_rep2


title: M 8 1 [IL-13-30-19]


title: p 8 s [IL-13-30-18]

value: PVP alone


title: LUC7L2_rep2


title: LUC7L_rep1


title: p 8 1 [IL-13-30-17]


title: m 6 s [IL-13-30-16]

value: 6 dpf


title: 48h_2

value: YPD liquid medium, 48h


title: LUC7L2_rep1

value: Flp-In T-Rex HEK293


title: m 6 1 [IL-13-30-15]


title: 48h_3


title: GFP-N_rep1


title: GFP-N_rep2


title: RBM25_rep1


title: 36h_3

value: YPD liquid medium, 36h


title: p 6 2 [IL-13-30-14]


title: p 6 1 [IL-13-30-13]


title: GFP-N-NLS_rep2


title: 3T3L1 preadipocytes berberine_2

city: Hong Kong

first: Jiawen

last: SHOU

address: Shatin

country: Hong Kong

institute: the Chinese University of Hong Kong

description: Gene expression after MDI-induced differentiation and berberine (13.47 uM) treatment for 48 hours

hyb_protocol: Phalanx OneArray Plus Protocol  1. Hybridized to a mouse Oligo Microarray (Phalanx Mouse OneArray v2, Phalanx Biotech) according to the manufacturer's protocol.  2. Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: identify differentially expressed genes are established at log2 |fold change| ≧ 1 and P-value < 0.05  Each single sample was at least performed twice in terms of technical or biological replicates under the reproducibility more than 0.975. The signal intensity was loaded into Rosetta Resolver System® (Rosetta Biosoftware, USA) to do data preprocessing and apply to median centering normalization. The errors of the sample were estimated by using the error-weighted approach at the same time. Both of fold change and p-value for pair-wise sample comparison were calculated for evaluating differentially expressed genes. The criteria with fold change ≥ 2 or ≤ -2 and p-value < 0.05 are strongly recommended for further analysis.

organism: Mus musculus

source_name: 3T3L1 preadipocytes with MDI and berberine (13.47 uM) treatment for 48 hours

label_protocol: 5 μg Cy5-labeled aRNA

growth_protocol: DMEM+10% FBS+1% PS

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen, Cat No./ID: 74104)

treatment_protocol: 3T3L1 preadipocytes with MDI ( 0.5mM Isobutylmethylxanthine, 1 uM dexamethasone and 1ug/ml insulin) and berberine (13.47 uM) treatment for 48 hours

tag: differentiated  cell type

value: preadipocytes


title: HepG2 cell Berberine_2

source_name: HepG2 cells withberberine (26.95 uM) treatment for 24 hours

treatment_protocol: HepG2 cells with/without berberine (26.95 uM) treatment for 24 hours

value: hepatocellular carcinoma


title: 72h_1


title: m 5 2 [IL-13-30-12]

value: Mtb in PVP

value: 5 dpf

tag: tissue


title: 3T3L1 preadipocytes control_2

description: Gene expression after MDI-induced differentiation for 48 hours

source_name: 3T3L1 preadipocytes with MDI treatment for 48 hours


title: 36h_2


title: 36h_1


title: 3T3L1 preadipocytes control_1


title: m 5 1 [IL-13-30-11]

value: AB/TL


title: HepG2 cell Berberine_1


title: 24h_3

value: YPD liquid medium, 24h


title: 3T3L1 preadipocytes berberine_1


title: 48h_1


title: p 5 2 [IL-13-30-10]

value: wild type


title: GFP-C_rep1


title: HepG2 cell control_1

source_name: HepG2 cells without berberine treatment


title: 24h_2


title: FUS_rep2


title: 24h_1


title: p 5 1 [IL-13-30-9]


title: m 3 2 [IL-13-30-8]

value: 3 dpf


title: GFP-N-NLS_rep1

value: RNAseI digested RNA


title: FUS_rep1


title: HepG2 cell control_2


title: AAPH damaged-C17.2 neural stem cells berberine_1

description: Gene expression after 7.38 mM AAPH and 1.69 uM berberine treatment for 12 hours

source_name: C17.2 cells with 7.38 mM AAPH and 1.69 uM berberine treatment for 12 hours

growth_protocol: DMEM+10% FBS+ 5% HS+1% PS

treatment_protocol: C17.2: AAPH 7.38 mM without/with berberine 1.69 uM for 12-h treatment

value: Mouse multipotent neural progenitor cells


title: DHX9-endoBIO_rep2


title: m3 1 [IL-13-30-7]

value: whole embryo/larva


title: DHX9-endoBIO_rep1


title: 18h_2

value: WT

value: YPD liquid medium, 18h


title: AAPH damaged-C17.2 neural stem cells control_2

description: Gene expression after 7.38 mM AAPH treatment for 12 hours

source_name: C17.2 cell with 7.38 mM AAPH treatment for 12 hours


title: p 3 2 [IL-13-30-6]

value: PVP alone


title: AAPH damaged-C17.2 neural stem cells control_1


title: 18h_1


title: m 0 s [IL-13-30-4]

value: 0 dpf


title: 12h_3

value: YPD liquid medium, 12h


title: p 3 1 [IL-13-30-5]


title: AAPH damaged-C17.2 neural stem cells berberine_2


title: CPSF6_rep1

value: Flp-In T-Rex HEK293


title: m 0 1 [IL-13-30-3]


title: LMD_DMH3

city: St Louis

first: Kyohei

last: Tokizane

state: MO

address: 660 S Euclid Ave

department: Developmental Biology

institute: Washington University School of Medicine

description: Gene expression in pooled Nkx2-1-positive neurons (marked by ZsGreen) in the DMH

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent Mouse_v1 8x60K microarrays (Design ID-028005). Hybridization was carried out at 65C for 20 hours. Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: Dorsomedial hypothalamus, replicate 3

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol. cDNAs were quantitated on a Nanodrop spectrophotometer.

extract_protocol: RNA was isolated using the proteinase K/acid phenol method as described previously (Khodosevich et al., 2007). The quality of total RNA was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Nkx2-1-CreERT2 x Rosa-ZsGreen

value: Dorsomedial hypothalamus

tag: gender

value: female

value: 2 months


title: LMD_VMH2

description: Gene expression in pooled Nkx2-1-positive neurons (marked by ZsGreen) in the VMH

source_name: Ventromedial hypothalamus, replicate 2

value: Ventromedial hypothalamus


title: HCC tissue with gene SAMD4B high expression 4

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
We used the Seurat R package (v4.1.3) to perform unsupervised clustering of the single cells using the reads count matrix as input. First, the read counts for each cell were divided by the total counts for that cell and multiplied by the scale factor (10,000), and then natural-log transformed. We performed principal component analysis (PCA) on the normalized expression matrix using highly variable genes identified by ‘‘SCTransform’’ function
harmony R package “RunHarmony“ was used to remove the batch effect between samples. Following the results of Harmony, the appropriate principal components (Harmonys) were selected for clustering with the specific resolution parameters. Finally, to detect cluster-specific expressed genes, the clusters were compared pairwise using the Seurat ‘‘FindAllMarkers’’ function to test genes with > 0.25-fold difference (log-scale) on average between the two groups of cells.
For the clustering of all cells, the top 25 Harmonys were selected with a resolution parameter equal to 0.6. For the clustering of T lymphocytes,the top 20 PCs were selected with a resolution parameter equal to 1.
Marker genes for each cluster were identified with the Wilcoxon rank-sum test with default parameters via the FindAllMarkers function in Seurat。differential expression analysis was carried out using ‘‘FindMarkers’’ function, implemented in the Seurat package, with log-scaled fold change >=0.25 and P value <= 0.05 (Wilcoxon Rank Sum test) CD8 cell developmental trajectory.
Assembly: hg38, mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: HCC tissue

extract_protocol:
Fresh tumor and adjacent normal tissue samples were surgically removed from patients and immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks (no necrotic foci / no hemorrhagic foci /less fibrous connective tissue) were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, MiltenyiBiotec). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Cat# 130-093-235, MiltenyiBiotec) following these steps: milled; incubated at 37C for 30 min on a shaker; milled; incubated at 37C for 30 min; milled; filtered through a 70 mm filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃.
This process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not conThis process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not contain cells, and most of the remaining GEM contained one cell

value: HCC tissue


title: GFP-C_rep2


title: 18h_3


title: p 0 2 [IL-13-30-2]

value: AB/TL

value: wild type


title: 6h_3

value: YPD liquid medium, 6h


title: HCC tissue with gene SAMD4B high expression 3

description: 10x Genomics


title: CPSF6_rep2

value: RNAseI digested RNA


title: 6h_2


title: HCC tissue with gene SAMD4B high expression 2

description: 10x Genomics


title: 6h_1


title: HCC tissue with gene SAMD4B high expression 1

description: 10x Genomics


title: ROR+ 20(OH)7DHC

status: Public on Jan 07 2024

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

data_processing:
BGI used SOAPnuke to create the FASTQ files by filtering reads by removing reads with adaptors, removing reads in which unknown bases (N) are more than 10%, and remove low quality reads (percentage of base which quality is lesser than 15 is greater than 50% in a read).
FASTQ files were aligned to genome using STAR version 2.5.4b with parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All --outFilterIntonMotifs RemoveNoncanonicalUnannotated
Transcript abundances were calculated with Cufflinks version 2.2.1 with parameters -G; -L; --library-type fr-firststrand
Cuffmerge with default settings was used to merge the data
Cuffdiff with default settings was used to calculate differentially expressed genes
Assembly: Gencode GRCm38 p4 Release M11
Supplementary files format and content: Tab delimited Excel file containing FPKM values for each gene

source_name: Fibroblasts

growth_protocol: Skin tissue from newborn mice, RoRγ wild type (RORγ+/+), heterozygotes (RORγ-/+) or knock out (RORγ-/-) was collected. Fibroblasts were isolated from the skin of 1-2 day old mice. The dermis was separated from the epidermis and a suspension of single fibroblasts cells was prepared from dermis. Cells were grown in complete DMEM media containing 10% serum, mouse FGF and 1% antibiotic.Cells in their early passage were used for experiments and were treated with compounds diluted in DMEM and 10% charcoal-stripped fetal bovine serum. In addition, cells isolated from different mice were pooled together to provide more representative samples.

extract_protocol:
After 24 h of incubation, cells were harvested for RNA isolation (RNAeasy Micro kit, Qiagen) following the manufacturers’ protocol. At least 200 ng of RNA for each sample was used for RNASeq processing and analysis done by BGI Americas Corporation Service (Cambridge, MA). Sample quality and concentration were determined using Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine fibroblasts were treated with the following sterols: 20(OH)cholesterol (from Sigma) or 20(OH)Lumiserol3 synthesized chemically, or 20(OH)7dehydrocholestrerol synthesized chemically , diluted in ethanol in DMEM medium containing charcoal-treated serum. Final concentration of the sterol hydroxyderivatives was 100 nM, with the final ethanol concentration being 0.1% which was also used as a vehicle control.

value: fibrobroblast cells from skin

value: skin

tag: mice genotype

value: wild type (RORgamma+/+)


title: ROR- 20(OH)Cholesterol

value: knock out (RORgamma-/-)


title: ROR+ 20(OH)Cholesterol


title: Lymph node, 8 macaques, Before and After Galunisertib

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

description: Parse-Nucore

library_source: transcriptomic single cell

data_processing:
Alignment, Gene counting and aggregation were made using the Parse pipeline.
The Partek software was used for scRNAseq analysis.
Assembly: Mmul10/SIVmic239
Supplementary files format and content: all_genes.csv. CSV file containing gene ids and gene names.
Supplementary files format and content: cell_metadata.csv. CSV file containing barcodes and the associated metadata
Supplementary files format and content: DGE.mtx. MatrixMarket file containing the count matrix.
Supplementary files format and content: barcode_data.csv CSV file containing sequences for three rounds of barcoding in plate wells

organism: Macaca mulatta

source_name: Lymph node

extract_protocol:
Cells isolated from lymph nodes before (BC1) and after (AC1) galuniertib were fixed with the Parse fixation kit.
Barcoded and sequenced at the NUseq Core.

tag: sample id

value: Lymph node

value: mixed sample (representing  Before Galunisertib and After Galunisertib)

tag: infection

value: SIVmac239M2 IV

tag: time after infection

value: mixed sample (representing  W35 and W37)


title: LMD_VMH3

source_name: Ventromedial hypothalamus, replicate 3

tag: strain

value: Nkx2-1-CreERT2 x Rosa-ZsGreen


title: LMD_Arc1

description: Gene expression in pooled Nkx2-1-positive neurons (marked by ZsGreen) in the arcuate nucleus

source_name: Arcuate nucleus, replicate 1

value: Arcuate nucleus

value: female

tag: age


title: 12h_2

value: WT

value: YPD liquid medium, 12h


title: ROR- 20(OH)L3


title: LMD_DMH1

source_name: Dorsomedial hypothalamus, replicate 1

value: Dorsomedial hypothalamus

value: 2 months


title: 12h_1


title: LMD_DMH2

source_name: Dorsomedial hypothalamus, replicate 2


title: ROR+ 20(OH)L3


title: LMD_VMH1

source_name: Ventromedial hypothalamus, replicate 1

value: Ventromedial hypothalamus


title: Week4.CD80SP.NPFic.1.ATAC

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: Balb/c transfer system. Week 4.

data_processing:
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
ATAC-seq reads were aligned to thereference genome assembly mm10 using Bowtie2 v2.3.3.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function. PCR duplicates were removed using Picard (v 2.18.12)
Peaks and peaks summit were called using MACS2  (with parameter -q 0.05 -B --nomodel --shift -75 --extsize 150) after merging filtered reads from replicate 1 and replaictes 2  from all sampels into two files.  These mereged replicates peak file was accessed using IDR and significnat peaks (Soft IDR threshold  < 0.1) was kept as true peaks.
Raw counts overlapping each peaks were quantified using bwtool summary (v.1.0.0) and normalised using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

extract_protocol:
The protocol was adapted from Corces, et al. Resuspension buffer (RSB) was made at a final concentration of 10 mM Tris-HCl pH 7.5 (Thermo Fisher #15567027), 3 mM MgCl2 (Thermo Fisher #AM9530G), and 2 mM NaCl (Thermo Fisher #AM9760G) in molecular grade H20. 20,000-50,000 viable cells were pelleted in low-bind 1.5 ml microcentrifuge tubes (Eppendorf # 022431021), and washed once with PBS supplemented with 1% fetalplex and protease inhibitor (Sigma #P8340, stock at 100x). Supernatant was vacuum aspirated, and 50 µl of cold lysis buffer containing 0.1% IGEPAL CA-360 (Sigma #I8896, 0.01% Digitonin (Promega #G9441) , and 0.1% Tween-20 (Sigma #11332465001) in RSB was added to each sample by gently pipetting. Samples were incubated on ice for 3 minutes to isolate nuclei, then washed with 950 ul of 0.1% Tween-20 in RSB and pelleted at 500 x g for 10 minutes at 4⁰ C. Supernatant was aspirated using p1000 and p200 pipets, followed by addition of 50 ul transposition mix containing 25 ul TD buffer, 2.5 ul TDE1 Tagment DNA Eznyme (Illumina #20034197), 16.5 µl PBS, 0.01% Digitonin, 1% Tween-20, brought to 50 µl with molecular grade H20. Samples were incubated at 37⁰ C for 30 minutes, with mixing every 10 minutes by flicking the tube. Transposed DNA was then purified using the Qiagen MinElute PCR purification kit (Qiagen #28004).
To generate libraries, adapters (IDT for Illumina Nextera DNA Unique Dual Indexes, Illumina, #20027215) were added during amplification using 2X Phusion High Fidelity Mastermix with HF Buffer (ThermoFisher #F531L). Libraries were cleaned up with Zymo DNA Clean & Concentrator-5 columns (Zymo Research #D4004) and assessed with a Qubit Flex Fluorometer (ThermoFisher $Q33327) and a TapeStation 4200 (Agilent #G2991BA).

treatment_protocol: Cells were surfaced stained using antibodies for flow cytometry and sorted on BD FacsAria

value: Balb/c

value: spleen

value: CD80SP NP-Ficoll MBC


title: Week4.CD80SP.NPFic.2.ATAC

description: Balb/c transfer system. Week 4.


title: Week4.CD80SP.FGK.1.ATAC

description: Balb/c transfer system. Week 4.

value: CD80SP FGK MBC


title: LMD_Arc2

source_name: Arcuate nucleus, replicate 2


title: Week4.CD80SP.FGK.2.ATAC

description: Balb/c transfer system. Week 4.


title: p 0 1 [IL-13-30-1]

source_name: whole embryo/larva

value: AB/TL

value: wild type

value: PVP alone

tag: time

value: 0 dpf

value: whole embryo/larva


title: Week10.DPGC.NPCGG.2.ATAC

description: Balb/c transfer system. Week 10.

value: DPGC MBC (Ly6Dlo PlexinB2hi)


title: Week10.DPGC.NPCGG.1.ATAC

description: Balb/c transfer system. Week 10.


title: Week10.DPEX.NPCGG.2.ATAC

description: Balb/c transfer system. Week 10.

value: DPEX MBC (Ly6Dhi PlexinB2hi/lo)


title: Week10.DPEX.NPCGG.1.ATAC

description: Balb/c transfer system. Week 10.


title: Week10.CD80SP.NPCGG.2.ATAC

description: Balb/c transfer system. Week 10.

value: CD80SP MBC


title: ROR- 20(OH)7DHC

value: fibrobroblast cells from skin

value: skin

value: knock out (RORgamma-/-)


title: Week10.CD80SP.NPCGG.1.ATAC

description: Balb/c transfer system. Week 10.


title: Tc1-scTCR sequence

city: Houston

first: Liuling

last: Xiao

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description:
Tc1_TCR
10x Genomics

data_processing:
Sample demultiplexing, barcode processing, read alignment, filtering, UMI counting and TCR clonotype calling were performed using Cell Ranger software v7.0.0. The paired single-cell gene expression library and single-cell VDJ library from each sample were processed together using Cell Ranger multi pipeline. The RNA library was aligned to mm10-2020-A reference genome, and the VDJ library was aligned to GRCm38-alts-ensembl-7.0.0 provided by 10x Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: Comma-separated filtered_contig_annotations.csv files.
Library strategy: scTCR-seq

source_name: tumor tissue

extract_protocol:
Fresh tumors were collected and cut into small pieces in RPMI-1640 medium and enzymatically digested with gentleMACS (Miltenyi) for 42 min on a rotor at 37 °C. Dissociated cells were subsequently passed through a 70-μm SmartStrainer and centrifuged at 500g for 5 min. Tumor-infiltrating CD4+ T cells were then enriched by Percoll density gradient centrifugation and sorted with a BD FACSAria Fusion.
The single cell capture and library construction were performed by following the Chromium Next GEM Single cell 5ʹ Reagent Kits v2 protocol (CG000331). Briefly, cells were resuspended in PBS with 0.04% BSA at a concentration of 700-1200 cells/µl and more than 85% viability. The single cells were loaded onto Chromium Next GEM Chip K with partitioning oil and barcoded singe cell gel beads. The barcoded and full-length cDNA is produced after incubation of the gel beads-in-emulsion (GEMs) and amplified via PCR for library construction. The library preparation is performed by following the protocol of Chromium Next GEM Single Cell 5ʹ GEM, Library & Gel Bead Kit v2 (PN-1000267). The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The qualified libraries were sent for the paired-end sequencing on an Illumina Novaseq System (Illumina, Inc., USA).

value: tumor tissue

value: tumor-infiltrating CD4+ T cells

value: WT B6

value: adoptively transferred with Tc1 cells with adjuvant


title: Tc9-scRNA sequence

description:
Tc9_GEX
10x Genomics

data_processing:
Sample demultiplexing, barcode processing, read alignment, filtering, UMI counting and TCR clonotype calling were performed using Cell Ranger software v7.0.0. The paired single-cell gene expression library and single-cell VDJ library from each sample were processed together using Cell Ranger multi pipeline. The RNA library was aligned to mm10-2020-A reference genome, and the VDJ library was aligned to GRCm38-alts-ensembl-7.0.0 provided by 10x Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: Comma-separated filtered_contig_annotations.csv files.

value: adoptively transferred with Tc9 cells with adjuvant


title: Tc1-scRNA sequence

description:
Tc1_GEX
10x Genomics


title: CITE-seq pooled MBC subsets

data_processing:
The 10x raw data from each sample were demultiplexed and FASTQ files were generated using the “mkfastq” Cell Ranger pipeline (v5.0.0, 10X Genomics).
Cell Ranger “count” was used to align reads to the mm10 reference genome, and mRNA transcript, and HTO unique molecular identifier (UMI) quantification tables were generated.
The raw barcode matrix files generated from the Cell Ranger pipeline were further utilized for downstream analysis using the Seurat package (v3.0.2) in R (v3.4.3).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: Raw count output file from Cellranger.

source_name: MBC subsets defined by our lab (PDL2-CD80-, PDL2+CD80-, PDL2+CD80+)

extract_protocol:
10x Genomics Chromium System
Gene expression and antibody hashtag/feature barcode libraries were generated, their quality was assessed through the Agilent TapeStation High Sensitivity D5000 Screentape, and their amounts were quantified with the KAPA Library Quantification Kit for Illumina Platforms. We used the 3’ V2 library; the feature barcode library was generated according to the New York Genome Center protocol. For hash-tagging, we followed the “feature barcode” instructions from the manufacturer.

treatment_protocol: Splenic MBC subsets were sorted as described above. After sorting, cells were washed once in PBS with 0.04% BSA. TotalSeq anti-mouse Hashtag Antibodies (Biolegend) were added at a 1:50 dilution to each of the sorted samples (DN MBC: TotalSeq-A0310, PD-L2 SP MBC: TotalSeq-A0311, DP MBC: TotalSeq-A0312) . Cells were stained on ice in PBS with 0.04% BSA for 20 minutes and then washed once in PBS with 0.04% BSA.

value: Balb/c

value: Spleen


title: Week6.DP.YFP.pos.2.ATAC

data_processing:
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
ATAC-seq reads were aligned to thereference genome assembly mm10 using Bowtie2 v2.3.3.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function. PCR duplicates were removed using Picard (v 2.18.12)
Peaks and peaks summit were called using MACS2  (with parameter -q 0.05 -B --nomodel --shift -75 --extsize 150) after merging filtered reads from replicate 1 and replaictes 2  from all sampels into two files.  These mereged replicates peak file was accessed using IDR and significnat peaks (Soft IDR threshold  < 0.1) was kept as true peaks.
Raw counts overlapping each peaks were quantified using bwtool summary (v.1.0.0) and normalised using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10)
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: B6 direct NP-KLH immunization GCET-Cre mice Week 6

extract_protocol:
The protocol was adapted from Corces, et al. Resuspension buffer (RSB) was made at a final concentration of 10 mM Tris-HCl pH 7.5 (Thermo Fisher #15567027), 3 mM MgCl2 (Thermo Fisher #AM9530G), and 2 mM NaCl (Thermo Fisher #AM9760G) in molecular grade H20. 20,000-50,000 viable cells were pelleted in low-bind 1.5 ml microcentrifuge tubes (Eppendorf # 022431021), and washed once with PBS supplemented with 1% fetalplex and protease inhibitor (Sigma #P8340, stock at 100x). Supernatant was vacuum aspirated, and 50 µl of cold lysis buffer containing 0.1% IGEPAL CA-360 (Sigma #I8896, 0.01% Digitonin (Promega #G9441) , and 0.1% Tween-20 (Sigma #11332465001) in RSB was added to each sample by gently pipetting. Samples were incubated on ice for 3 minutes to isolate nuclei, then washed with 950 ul of 0.1% Tween-20 in RSB and pelleted at 500 x g for 10 minutes at 4⁰ C. Supernatant was aspirated using p1000 and p200 pipets, followed by addition of 50 ul transposition mix containing 25 ul TD buffer, 2.5 ul TDE1 Tagment DNA Eznyme (Illumina #20034197), 16.5 µl PBS, 0.01% Digitonin, 1% Tween-20, brought to 50 µl with molecular grade H20. Samples were incubated at 37⁰ C for 30 minutes, with mixing every 10 minutes by flicking the tube. Transposed DNA was then purified using the Qiagen MinElute PCR purification kit (Qiagen #28004).
To generate libraries, adapters (IDT for Illumina Nextera DNA Unique Dual Indexes, Illumina, #20027215) were added during amplification using 2X Phusion High Fidelity Mastermix with HF Buffer (ThermoFisher #F531L).  Libraries were cleaned up with Zymo DNA Clean & Concentrator-5 columns (Zymo Research #D4004) and assessed with a Qubit Flex Fluorometer (ThermoFisher $Q33327) and a TapeStation 4200 (Agilent #G2991BA).

value: spleen

value: YFP- DP MBC


title: Week6.DP.YFP.pos.1.ATAC

value: YFP+ DP MBC


title: Week6.DP.YFP.neg.1.ATAC


title: TW-3

city: Suita

first: Junjun

last: Li

address: 2-2 Yamadaoka

institute: Osaka University

data_processing:
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks ver. 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was harvested using TRIzol™ Reagent ((Invitrogen, USA)) according to the manufacturer’s protocol.
Library preparation was performed using the TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: cell line

value: Human iPSC-derived cardiomyocytes

value: WT

value: Traveling Wave


title: Week6.DP.YFP.neg.2.ATAC


title: TW-2


title: TW-1


title: Week4.Ctrl.DN.1.ATAC

source_name: Balb/c transfer system Week 4

value: PBS + NP-CGG derived DN MBC


title: Week4.Ctrl.DP.2.ATAC

value: PBS + NP-CGG derived DP MBC


title: Control-2


title: Control-3


title: Week4.DP.FGK.2.ATAC

value: FGK + GK1.5 treated DP MBC


title: HepG2 m6A 2

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
*library strategy: m6A-seq
Raw FASTQ files were trimmed by fastp 0.23.2
Reads were mapped to human genome version hg38 by HiSat2 version 2.2.1
MACS2 was used to call peaks
deeptools were used to create bw files
Assembly: hg38
Supplementary files format and content: bigwig, narrow peak

source_name: liver cancer

growth_protocol: HepG2 cell lines were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
total cellular RNA extracted from cells were fragmented by RNA fragmentation reagents (Thermo, AM8740). Fragmented RNA was incubated with an anti-m6A antibody (#202003, Synaptic Systems) or IgG IP Grade Rabbit polyclonal antibody at 4°C for 6 h in 500 μl of NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U ml–1 RNase inhibitor).
The purified RNA fragments were used to construct libraries with the SMARTer Stranded Total RNA-seq Kit v2 (Takara)

value: liver cancer

tag: rip antibody


title: Week4.DP.FGK.1.ATAC


title: Week4.DP.NPFic.1.ATAC

value: GK1.5 + NP-Ficoll derived DP MBC


title: Tc9-scTCR sequence

description:
Tc9_TCR
10x Genomics

value: tumor tissue

value: tumor-infiltrating CD4+ T cells


title: Week4.DP.aCD40L.2.ATAC

value: MR1 treated DP MBC


title: HepG2 m6A 1


title: MCF7 A-DCCs_3 [A_3]

city: Hangzhou

first: Yao-Shun

last: Yang

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: hg18
Supplementary_files_format_and_content: tab-delimited text files include gene_count for each Sample

source_name: MCF7 A-DCCs

extract_protocol:
Cells were freezed 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

value: A-DCCs


title: MCF7 A-DCCs_1 [A_1]


title: HepG2 m6A input 2


title: MCF7 DCCs_3 [Q_3]

source_name: MCF7 DCCs

value: dormant cancer cells (DCCs)


title: Week4.Ctrl.DP.1.ATAC

value: Balb/c


title: Week4.Ctrl.DN.2.ATAC

value: spleen


title: HepG2 m6A input 1


title: Week4.DN.NPFic.2.ATAC

value: GK1.5 + NP-Ficoll derived DN MBC


title: 769-P sihnRNPA2B1-3

description: hnRNPA2B1 count

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were assemblyed by stringtie
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: exprSet.csv, csv format, containing the raw counts.

source_name: clear cell Renal Carcinoma

growth_protocol: 769-P cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

value: clear cell Renal Carcinoma


title: MCF7 DCCs_2 [Q_2]


title: MCF7 DCCs_1 [Q_1]