title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 158

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Sepsis

tag: disease 2

tag: died/survived

value: Survived


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 202

status: Public on Jan 08 2024

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: 1 Abdominal Sepsis

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.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, Day: 1

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

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

value: F

value: Abdominal


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 77

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

value: M

value: SIRS

value: OOHCA

value: Died


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 159

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

value: Pulmonary


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 158

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

source_name: Peripheral Blood, Day: 2


title: Bacterial Infection, 20211215MCX006

type: SRA

city: Guangzhou

first: Bin

last: Yang

address: Guangzhou 510700

country: China

institute: Vision Medicals Co., Ltd.

library_source: transcriptomic

data_processing:
high-quality data were aligned to the human genome hg38 using HISAT2 with default parameters. Gene-level quantification was performed using FeatureCounts. The gene counts were aggregated using the featureCounts program from the Subread package release 2.0.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes raw per-gene counts for each sample.

source_name: BALF

extract_protocol:
1 mL BALF sample was centrifuged at 12,000 rpm for 10 min. Then, 200 μL of the precipitate was lysed in TRIzol LS (Thermo Fisher Scientific, Carlsbad, CA, USA), followed by RNA extraction using a Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions.
According to the manufacturer's instructions,  10 μL of purified RNA was used for cDNA generation and library preparation with an Ovation Trio RNA-Seq Library Preparation Kit (NuGEN, CA, USA).   A Qubit dsDNA HS Assay Kit was used to measure the library concentration.   The library quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a High Sensitivity DNA kit.   The library was sequenced using an Illumina NextSeq 550 sequencer with a 75-cycle single-end sequencing strategy.

tag: tissue

value: BALF

tag: disease state

value: Bacterial Infection


title: Bacterial Infection, 20210610MCX001


title: control_1H4_rep3

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

description:
RNAseI digested RNA
control-1H4_reps-merged.plus.CPM.bw
control-1H4_reps-merged.minus.CPM.bw

data_processing:
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)
bigWig generation using bamCoverage 3.3.1
Assembly: hg38
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands
Library strategy: FLASH-seq

source_name: Flp-In T-Rex HEK293

extract_protocol:
Cells were crosslnked with 0.199 mj/cm2 UV-C light,  after nuclei isolation lysed with 1xNLB buffer, 1H4 or a rabbit polyclonal Ab against DHX9 was used to IP targets proteins, 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.
FLASH-seq (Ilik et al., 2020)

tag: cell line

value: Flp-In T-Rex HEK293

tag: agent

tag: sirna

value: control


title: Bacterial Infection, 20210316MCX006


title: 300BCG149_d14_PBMC

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

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

value: HVCTNBBXX

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: control_DHX9_rep3

description:
RNAseI digested RNA
control-DHX9_reps-merged.plus.CPM.bw
control-DHX9_reps-merged.minus.CPM.bw

value: rabbit polyclonal Ab against DHX9


title: control_1H4_rep2


title: 300BCG150_d14_PBMC


title: Bacterial Infection, 20220319MCX007


title: control_1H4_rep1


title: EARLI_50681_Hypo

city: San Francisco

first: Lucile

middle: P A

last: Neyton

state: CA

address: 505 Parnassus Ave

country: USA

institute: UCSF

data_processing:
Alignment against human genome with kallisto v0.46.1
Gene-level aggregation using tximport v1.14
Genes with less than 16 counts in more than 10% of the samples were filtered
Assembly: ENSEMBL v99
Supplementary files format and content: CSV files with gene counts

source_name: whole blood

growth_protocol: PAXgene tubes

extract_protocol:
rRNA depletion with FastSelect from QIAGEN
NEBnext Ultra II RNAseq from New England Biolabs

value: whole blood

tag: lca

value: Hypo

tag: gender

value: Male

tag: age


title: 300BCG147_d14_PBMC


title: Bacterial Infection, 20210723MCX013

tag: tissue

tag: disease state


title: EARLI_50660_Hypo

value: Female


title: 300BCG146_d14_PBMC


title: Bacterial Infection, 20220210MCX018


title: 300BCG145_d14_PBMC


title: Bacterial Infection, 20220119MCX020


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 149

tag: sample type

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

tag: patient id

value: F

tag: disease

value: Sepsis

tag: disease 2

tag: died/survived

value: Survived


title: EARLI_50650_Hypo


title: Bacterial Infection, 20211223MCX008


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 152

value: M

value: Pulmonary


title: Bacterial Infection, 20211216MCX009

value: BALF

value: Bacterial Infection


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 152

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

source_name: Peripheral Blood, Day: 5


title: 300BCG144_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol


title: 300BCG148_d14_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_50647_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: 300BCG144_d0_PBMC

tag: frip


title: 300BCG143_d90_PBMC

value: HVCMYBBXX


title: EARLI_50642_Hypo


title: EARLI_50661_Hypo


title: Bacterial Infection, 20211026MCX022

tag: disease state


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 149

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 149


title: Bacterial Infection, 20211022MCX007


title: 300BCG143_d0_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol


title: EARLI_50635_Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 152


title: Bacterial Infection, 20211019MCX022


title: 300BCG142_d90_PBMC

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_50634_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 148

tag: sample type

tag: patient id

tag: disease

value: Abdominal


title: Bacterial Infection, 20210825MCX010

tag: disease state


title: EARLI_50631_Hypo


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 141

tag: disease 2

tag: died/survived

value: Died


title: Bacterial Infection, 20210821MCX012


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 78

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

value: SIRS

value: OOHCA


title: EARLI_50626_Hypo

value: whole blood

value: Hypo


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 78

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


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 77


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 110


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 77

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


title: EARLI_50624_Hypo

value: Male


title: Bacterial Infection, 20210817MCX018


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 74

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

value: F


title: 300BCG141_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 192

value: Survived


title: 300BCG140_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: Bacterial Infection, 20210811MCX009

tag: tissue


title: EARLI_50618_Hyper

tag: lca

value: Hyper

tag: gender

tag: age


title: EARLI_50600_Hypo


title: 300BCG140_d0_PBMC

tag: tss enrichment


title: Bacterial Infection, 20210806MCX011

tag: disease state


title: EARLI_50594_Hypo


title: Bacterial Infection, 20210805MCX008


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 73

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

tag: sample type

tag: patient id

tag: disease

value: Sepsis

tag: disease 2

tag: died/survived


title: 300BCG141_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 74


title: EARLI_50593_Hyper

value: Female


title: 300BCG139_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: Bacterial Infection, 20210728MCX008

tag: tissue

value: BALF

value: Bacterial Infection


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 74

tag: gender


title: EARLI_50586_Hyper

tag: lca

tag: age


title: Bacterial Infection, 20210618MCX006

tag: disease state


title: EARLI_50575_Hypo


title: 300BCG138_d90_PBMC

value: PBMC

value: HVCMYBBXX

tag: tss enrichment


title: Bacterial Infection, 20210607MCX008


title: 300BCG138_d14_PBMC

value: ATAC


title: Bacterial Infection, 20210517MCX008


title: 300BCG142_d0_PBMC


title: EARLI_50552_Hypo


title: 300BCG139_d90_PBMC


title: EARLI_50540_Hyper


title: Bacterial Infection, 20210429MCX007


title: 300BCG137_d90_PBMC


title: EARLI_50537_Hypo


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 73

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

tag: sample type

tag: patient id

tag: disease

tag: disease 2

value: Abdominal

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 73


title: Bacterial Infection, 20210429MCX006


title: Bacterial Infection, 220623MCX00022


title: EARLI_50515_Hypo


title: 300BCG135_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 153

value: Pulmonary

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 73

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


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 153


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 151


title: EARLI_50511_Hyper

value: whole blood


title: Bacterial Infection, 20220319MCX015


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 147

value: M


title: 300BCG135_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG138_d0_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 151

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

tag: gender


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 134


title: EARLI_50498_Hypo

tag: tissue

tag: lca

value: Hypo

value: Male

tag: age


title: EARLI_50471_Hypo


title: Bacterial Infection, 20210906MCX013

tag: disease state


title: 300BCG134_d14_PBMC

tag: tss enrichment


title: 300BCG137_d0_PBMC


title: Bacterial Infection, 20210813MCX011


title: 300BCG134_d0_PBMC


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 140

tag: sample type

tag: patient id

value: F

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 153

value: Sepsis


title: Bacterial Infection, 20210622MCX005


title: 300BCG133_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: EARLI_50445_Hypo


title: 300BCG133_d14_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_50447_Hypo

tag: tissue

tag: lca

tag: gender

value: Female

tag: age


title: Bacterial Infection, 20210507MCX013

value: BALF

tag: disease state


title: Bacterial Infection, 20210318MCX014

value: Bacterial Infection


title: 300BCG134_d90_PBMC

value: PBMC

tag: tss enrichment


title: EARLI_50437_Hyper

value: Hyper


title: 300BCG133_d0_PBMC

value: ATAC


title: Bacterial Infection, 20210313MCX003


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 109

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Bacterial Infection, 20210227MCX003


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 148

value: Abdominal


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 148


title: EARLI_50428_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 147

value: Pulmonary


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 147


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 141

value: Died


title: EARLI_50435_Hyper

value: whole blood


title: EARLI_50452_Hyper


title: Bacterial Infection, 220406MCX00012


title: 300BCG132_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: Bacterial Infection, 220610MCX00019


title: 300BCG132_d0_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_50418_Hyper

tag: tissue

tag: lca

tag: gender

tag: age


title: Bacterial Infection, 20220112MCX018

tag: disease state


title: 300BCG131_d90_PBMC

tag: tss enrichment


title: EARLI_50417_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 63

tag: sample type

tag: patient id

value: M

tag: disease

tag: disease 2

tag: died/survived


title: Bacterial Infection, 20220111MCX017


title: EARLI_50413_Hypo


title: 300BCG131_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: 300BCG132_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_50400_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: Bacterial Infection, 20211230MCX012

tag: disease state


title: 300BCG130_d90_PBMC

tag: tss enrichment


title: EARLI_50398_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 57

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Bacterial Infection, 20211229MCX017


title: Bacterial Infection, 20211224MCX012


title: EARLI_50390_Hypo

value: Hypo


title: 300BCG130_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: Bacterial Infection, 20211218MCX005


title: EARLI_50383_Hypo

value: Male


title: 300BCG129_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG128_d90_PBMC


title: EARLI_50377_Hyper

tag: tissue

tag: lca

tag: gender

tag: age


title: Bacterial Infection, 20211125MCX009

tag: disease state


title: 300BCG126_d90_PBMC

tag: tss enrichment


title: Bacterial Infection, 20211117MCX015


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 59

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: EARLI_50375_Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 57

value: F


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 55

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 55

value: Sepsis


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 56

value: SIRS

value: OOHCA


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 55


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 54


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 57


title: 300BCG130_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: Bacterial Infection, 20211101MCX015

value: BALF

value: Bacterial Infection


title: 300BCG125_d0_PBMC

value: PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_50367_Hypo

tag: tissue

tag: lca

tag: gender

value: Female

tag: age


title: 300BCG124_d90_PBMC

value: ATAC

tag: tss enrichment


title: Bacterial Infection, 20211022MCX013

tag: disease state


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 43

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG123_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: EARLI_50366_Hyper

value: Hyper


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 53

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 39

value: Abdominal


title: Bacterial Infection, 20211012MCX016


title: 300BCG123_d14_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_50356_Hyper

tag: tissue

value: whole blood

tag: lca

tag: gender

tag: age


title: Bacterial Infection, 20210915MCX009

tag: disease state


title: 300BCG123_d0_PBMC

tag: tss enrichment


title: Bacterial Infection, 20210820MCX015


title: EARLI_50371_Hypo


title: EARLI_50316_Hyper


title: 300BCG122_d90_PBMC


title: Bacterial Infection, 20210804MCX006


title: Bacterial Infection, 20210726MCX012


title: EARLI_50302_Hyper


title: 300BCG122_d14_PBMC


title: Bacterial Infection, 20210705MCX013


title: 300BCG122_d0_PBMC


title: EARLI_50297_Hypo


title: EARLI_50292_Hypo


title: Bacterial Infection, 20210703MCX010


title: EARLI_50291_Hypo


title: Bacterial Infection, 20210609MCX005


title: 300BCG121_d90_PBMC


title: 300BCG121_d14_PBMC


title: EARLI_50288_Hypo


title: EARLI_50348_Hypo


title: 300BCG121_d0_PBMC


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 34

tag: sample type

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

tag: patient id

value: M

tag: disease

tag: disease 2

tag: died/survived


title: EARLI_50228_Hypo

value: Hypo


title: Bacterial Infection, 20210821MCX014


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 59


title: 300BCG120_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 90

value: F

value: Pulmonary


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 59

value: Sepsis

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 90


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 59


title: Bacterial Infection, 20211028MCX025


title: EARLI_50222_Hypo

value: Male


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 53

value: SIRS

value: OOHCA


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 91


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 84 (1 in 4)


title: 300BCG120_d0_PBMC

value: PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG120_d14_PBMC


title: EARLI_50216_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 58

tag: sample type

tag: patient id

tag: disease


title: Bacterial Infection, 20210903MCX010

value: BALF

tag: disease state

value: Bacterial Infection


title: EARLI_50185_Hypo


title: Bacterial Infection, 20210727MCX015


title: Bacterial Infection, 20211204MCX005


title: 300BCG119_d14_PBMC

tag: cell type

tag: genotype

value: ATAC

tag: tss enrichment


title: EARLI_50184_Hyper

value: Hyper


title: Bacterial Infection, 20210427MCX009


title: 300BCG119_d0_PBMC

tag: individual

tag: time point

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 83

tag: disease 2

tag: died/survived

value: Died


title: EARLI_50182_Hypo

value: whole blood

value: Female


title: 300BCG118_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG117_d90_PBMC


title: EARLI_50178_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: EARLI_50172_Hyper


title: Bacterial Infection, 20220112MCX014

tag: disease state


title: 300BCG116_d14_PBMC

tag: cell type

tag: genotype


title: 300BCG116_d0_PBMC

tag: individual

tag: tss enrichment


title: Bacterial Infection, 20210421MCX013


title: 300BCG115_d90_PBMC

tag: time point

tag: frip


title: EARLI_12113_Hyper


title: Bacterial Infection, 20211004MCX024


title: X3_106

city: Stockholm

first: Indranil

last: Sinha

address: The Wenner-Gren Institute

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

description:
bulk RNA-seq
3_106Aligned.sortedByCoord.out.bam
subreadCounts.txt

data_processing:
Indexed cDNA libraries were normalized, combined and the pools sequenced on the Illumina Nextseq 550 for a 75-cycle v2.5 sequencing generating 75bp single-end reads.
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program. STAR v2.5.2b was used to index the human reference genome (hg38/GRCh38) and align the resulting fastq files.
Mapped reads were then counted in annotated exons using featureCounts v1.5.1.
The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR package and its general linear models pipeline.
For the gene expression analysis genes that had 1 count per million in 3 or more samples were used and normalized using TMM normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: subreadCounts.txt: Count Matrix

source_name: intestinal stromal cells

growth_protocol: No growth.

extract_protocol:
FACS sorting from intestinal biopsy cell suspensions, freshly isolated.
Bulk seq.

treatment_protocol: No treatment.

value: intestinal stromal cells

tag: population


title: EARLI_12110_Hyper


title: 300BCG115_d14_PBMC

tag: protocol


title: X3_097

description:
bulk RNA-seq
3_097Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: Bacterial Infection, 20211215MCX012


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 15

tag: sample type

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

tag: patient id

value: M

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG115_d0_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_12087_Hyper

tag: tissue

tag: lca

tag: gender

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 62

value: Abdominal


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 64

value: F


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 14

value: Sepsis


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 64


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 22

value: Pulmonary

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 52


title: EARLI_50169_Hypo

value: Hypo

value: Male


title: Bacterial Infection, 20211004MCX022

value: BALF

tag: disease state


title: EARLI_12045_Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 52


title: 300BCG114_d90_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: tss enrichment

tag: frip


title: EARLI_12018_Hyper


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 66

tag: sample type

tag: patient id

tag: disease

tag: disease 2


title: 300BCG114_d14_PBMC

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: 300BCG114_d0_PBMC

tag: filtered peaks


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 52

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

tag: gender

tag: died/survived


title: X2_106

description:
bulk RNA-seq
2_106Aligned.sortedByCoord.out.bam
subreadCounts.txt

tag: cell type

tag: population


title: EARLI_12013_Hypo

tag: tissue

tag: lca

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 130


title: X2_097

description:
bulk RNA-seq
2_097Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 52


title: EARLI_12012_Hypo


title: X2_091

description:
bulk RNA-seq
2_091Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: X3_091

description:
bulk RNA-seq
3_091Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: 300BCG113_d0_PBMC

tag: genotype

tag: individual

tag: time point

tag: tss enrichment

tag: frip


title: X1_106

description:
bulk RNA-seq
1_106Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: 300BCG112_d90_PBMC

tag: protocol


title: X1_097

description:
bulk RNA-seq
1_097Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: 300BCG112_d14_PBMC

tag: flowcell


title: EARLI_12004_Hyper

value: Hyper


title: EARLI_12003_Hyper


title: X1_091

description:
bulk RNA-seq
1_091Aligned.sortedByCoord.out.bam
subreadCounts.txt


title: EARLI_11990_Hypo


title: 300BCG111_d90_PBMC

tag: batch id


title: 300BCG112_d0_PBMC

tag: pcr cq


title: PDX model of HCC tissue treated with drug  thalidomide (THA)

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

organism:
Homo sapiens
Mus musculus

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

tag: treatment

value: thalidomide (THA)


title: EARLI_11959_Hypo

value: whole blood

tag: gender

value: Female


title: EARLI_11970_Hypo


title: 300BCG111_d0_PBMC

tag: filtered peaks


title: EARLI_11956_Hyper


title: PDX model of HCC tissue treated with drug  TCC (Thalidomide + Carmofur + Cantharidin)

description: 10x Genomics


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 130

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

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG110_d90_PBMC

tag: cell type

tag: genotype


title: PDX model of HCC tissue treated with placebo DMSO

description: 10x Genomics

tag: tissue

value: placebo DMSO


title: EARLI_12005_Hyper

tag: lca

tag: age


title: PDX model of HCC tissue treated with drug  TC (Thalidomide + Carmofur)

description: 10x Genomics

value: TC (Thalidomide + Carmofur)


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 124

value: F

value: Abdominal

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 124

value: Sepsis


title: EARLI_11945_Hypo

value: Hypo


title: 300BCG110_d14_PBMC

tag: individual

tag: time point

tag: protocol

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 125

tag: gender

value: M

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 123

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

value: Pulmonary


title: PDX model of HCC tissue treated with drug  carmofur (CAR)

description: 10x Genomics

tag: treatment

value: drug  carmofur (CAR)


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 92

tag: sample type


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 123

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

tag: patient id


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 67

tag: disease


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 80

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

tag: disease 2


title: EARLI_11943_Hypo

value: Male


title: 300BCG110_d0_PBMC

value: PBMC

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG111_d14_PBMC

tag: cell type

tag: genotype


title: Th17noTGFb_replicate.1

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

data_processing:
*library strategy: Single molecule DNA methylation WGS
Raw read quality was determined with pycoQC
Raw fast5 files were converted into pod5 format and basecalled with ‘dorado’ (version 0.4.2, ONT), allowing the simultaneous delineation of 5mCpG and 5hmCpG using the high accuracy model (‘dna_r9.4.1_e8_hac@v3.3’, ONT) for the detection of modified bases. Dorado was also used for simultaneous alignment to the mm10 assembly and demultiplexing, followed by sorting and indexing with ‘samtools’ (version 1.13). ‘Modkit’ (version 0.2.2) was used for piling of methylation data into bed files.
Bed files containing 5mC and 5hmC information were directly used for comparison after loading in R.
Assembly: mm10
Supplementary files format and content: bed files with methylation pileup data for each demultiplexed sample

organism: Mus musculus

source_name: blood

growth_protocol: CD4+ T cells were isolated from male Foxp3-GFP reporter mice and naïve T cells were cell sorted and activated with anti-CD3/CD28 under different polarizing conditions: Th0 (neutral), Th1, Th2, Th17, Treg as well as Th17s differentiated without TGFb (Th17-noTGFβ) representing an intermediate cell phenotype. Briefly, murine CD4+ T cells were purified using the MACS CD4+ T cell negative selection kit (Miltenyi Biotec) and naïve CD4+ T cells from WT, Foxp3-GFP were then sorted on the basis of a CD4+CD8-CD62L+CD44−GFP−CD25- expression profile on a FACSAria flow cytometer (BD Biosciences). T cell activation was performed using plate-bound α-CD3 (clone 145-2C11, 1 μg/ml) and α-CD28 (clone PV-1, 1 μg/ml) monoclonal antibodies in RPMI 1640 medium (Life Technologies) supplemented with 10% FCS, 1% penicillin/streptomycin (Gibco-Life technologies) and b-mercaptoethanol (50 μM). Cells were split 3 days later with medium supplemented with rhIL-2 (100U/mL). Cells were maintained in a standard tissue culture incubator containing atmospheric O2 and 5% CO2. Data from Tregs included in this study was previously published.

extract_protocol:
DNA was extracted from 1x10^6 CD4 Th cells/ replicate using the Qiagen DNA mini kit according to manufacturer's instructions (Qiagen Hilden, Germany).
DNA was sheared using g-tubes (Covaris, USA) to ~10KB before library preparation with ligation sequencing kit (ONT Cat #SQK-LSK109) followed by whole genome sequencing on Nanopore MinION flow cells with pore 9.4.1 chemistry for 72h.
Libraries were enriched using Cas9-targeting approach for a panel of 10 genes.

tag: tissue

value: blood

tag: cell line

value: lymphocytes

value: WT FoxP3-GFP reporter

value: in vitro polarized


title: Th17noTGFb_replicate.2


title: 300BCG109_d14_PBMC

tag: individual

tag: time point

tag: protocol


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 54

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

tag: gender

tag: died/survived


title: EARLI_11930_Hypo

value: whole blood

tag: lca

tag: age


title: EARLI_11942_Hypo

value: Female


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 124

tag: sample type

tag: patient id

value: F

tag: disease

value: Abdominal

value: Died


title: Th2_replicate.3

tag: treatment


title: EARLI_11848_Hyper

value: Hyper


title: Th17_replicate.3


title: PDX model of HCC tissue treated with drug cantharidin (CAN)

description: 10x Genomics

value: HCC tissue

value: drug cantharidin (CAN)


title: Th0_replicate.3


title: 300BCG108_d90_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: tss enrichment

tag: frip


title: EARLI_11831_Hypo

tag: tissue

value: Hypo


title: 300BCG108_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: filtered peaks


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 91

tag: gender

value: M

value: Sepsis

tag: disease 2

tag: died/survived

value: Survived


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 84

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

tag: sample type


title: Th1_replicate.3

value: blood

tag: cell line


title: 300BCG109_d90_PBMC

value: PBMC

tag: time point

tag: protocol

value: ATAC


title: 300BCG108_d0_PBMC

tag: flowcell


title: EARLI_11807_Hyper

tag: lca

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 92

tag: patient id

tag: disease


title: 300BCG109_d0_PBMC

tag: batch id

tag: pcr cq

tag: tss enrichment

tag: frip


title: 300BCG107_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: filtered peaks


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 66

tag: sample type

tag: gender

tag: disease 2

tag: died/survived


title: Th2_replicate.2

tag: tissue

tag: cell line

value: lymphocytes

value: WT FoxP3-GFP reporter

tag: treatment

value: in vitro polarized


title: EARLI_11814_Hyper

value: whole blood

tag: lca

value: Male

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 140

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

tag: patient id

value: F

tag: disease

value: Abdominal


title: EARLI_11841_Hypo


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 66

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


title: 300BCG107_d14_PBMC

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: tss enrichment


title: Th17_replicate.2

tag: cell type

tag: genotype


title: 300BCG107_d0_PBMC

tag: individual

tag: filtered peaks

tag: frip


title: EARLI_11796_Hypo

tag: tissue

tag: gender

value: Female


title: Th1_replicate.2

tag: cell line

tag: treatment


title: EARLI_11827_Hyper

tag: lca

value: Hyper

tag: age


title: Th0_replicate.2


title: EARLI_11795_Hyper


title: 300BCG106_d90_PBMC

tag: time point


title: EARLI_11781_Hyper


title: Th17_replicate.1


title: 300BCG106_d14_PBMC

tag: protocol


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 140

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Th2_replicate.1

tag: cell type

tag: genotype


title: 300BCG106_d0_PBMC

tag: individual

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11780_Hypo

tag: tissue

tag: lca

value: Hypo

tag: gender


title: EARLI_11774_Hypo

tag: age


title: 300BCG105_d90_PBMC

tag: time point

tag: protocol

tag: frip


title: 300BCG105_d14_PBMC


title: EARLI_11773_Hypo


title: EARLI_11766_Hypo


title: 300BCG105_d0_PBMC


title: S2 cells, safb KD, rep3

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the D.melanogaster genome (dm6 assembly) using STAR 2.7.4a
Reads counted on Ensembl release 94 gene models using featureCounts (Subread 2.0.0)
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: dm6
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Unstranded raw RNA-seq coverage tracks in bigwig format

molecule: polyA RNA

organism: Drosophila melanogaster

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: safb KD


title: 300BCG104_d90_PBMC


title: S2 cells, safb KD, rep2


title: 300BCG104_d14_PBMC


title: EARLI_11752_Hypo


title: S2 cells, control, rep3

value: control


title: 300BCG104_d0_PBMC


title: EARLI_11742_Hyper


title: Th0_replicate.1

tag: treatment


title: Th1_replicate.1

tag: cell type


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 136

tag: sample type

tag: patient id

value: M

tag: disease

value: Sepsis

tag: disease 2

value: Pulmonary

tag: died/survived

value: Died


title: S2 cells, control, rep2

tag: genotype


title: EARLI_11737_Hyper


title: 300BCG103_d90_PBMC

value: PBMC

tag: individual

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11764_Hyper

tag: tissue

tag: lca

tag: gender

tag: age


title: S2 cells, control, rep1

tag: cell line


title: EARLI_11734_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 136

tag: sample type


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 136

tag: patient id


title: 300BCG103_d14_PBMC

tag: cell type

tag: time point

tag: protocol

tag: frip


title: S2 cells, safb KD, rep1

tag: genotype


title: Dmel_control_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

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: molecule subtype

value: RNAseI digested RNA


title: EARLI_11727_Hypo

value: whole blood


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 157

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: 300BCG103_d0_PBMC

tag: individual

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11724_Hypo

tag: tissue

tag: lca

tag: gender

value: Male

tag: age


title: Dmel_control_rep1

tag: cell line


title: 300BCG102_d90_PBMC

tag: cell type

tag: time point

tag: protocol

tag: frip


title: 300BCG102_d14_PBMC

tag: genotype


title: EARLI_11707_Hyper


title: EARLI_11704_Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 93

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Dmel_SafB_rep1

tag: molecule subtype


title: EARLI_11690_Hypo


title: 300BCG102_d0_PBMC

tag: individual

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 133

tag: gender

value: F


title: 300BCG101_d90_PBMC

tag: cell type

tag: time point


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 127


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 133


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 157


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 135

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

value: SIRS

value: OOHCA


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 135

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


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 134


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 133


title: 300BCG101_d14_PBMC

tag: protocol

tag: frip


title: Dmel_SafB_rep2

tag: cell line

tag: genotype


title: Plant, M_oryze B, 3 day

city: Kurashiki

first: Yoji

last: Kawano

state: Okayama

department: Institute of Plant Science and Resources

country: Japan

institute: Okayama University

description: rice (Oryza sativa L. subsp. japonica cv. Nipponbare)

data_processing:
Check the quality of sequencing data with FastQC. Filter the low-quality base pairs (Q < 17) in the raw sequencing data with DynamicTrim, a program in SolexaQA
Remove the reads less than 25 bp with LengthSort in SolexaQA.
Remove adapter sequences with Cutadapt
Map clean reads to the rice genome (MSU7) using hisat2 with default parameters and the following adjustments: -p 28, which means using 28 threads to improve computational speed
Assembly: Map clean reads to the rice genome (MSU7) using hisat2
Supplementary files format and content: Include rawcounts for each sample

organism: Oryza sativa Japonica Group

source_name: Leaf

growth_protocol: Grow rice plants in a growth chamber under long-day conditions (16 h : 8 h, light : dark, 28°C: 22°C) for 4 weeks.

extract_protocol:
RNA is extracted with a TRIzol reagent according to the manufacturer’s instructions.
Quantify RNAs with a Qubit RNA HS Assay Kit, and examine their integrity using a Bioanalyzer 2100. Use RNA samples with RIN > 7 for library preparation with the TruSeq Stranded mRNA LT Sample Prep Kit following the manufacturer's protocol. Libraries were sequenced to generate paired-end 150-bp reads on a Hiseq2500 platform.

treatment_protocol: Calculate the spore concentration with platelet counter and microscope, and adjust the conidial suspension to 105 conidia/mL. Spray the M. oryzae solution on rice plants with a sprayer, ensure that all plants are sprayed, and collect leaf samples after 0, 1, 2, and 3 d.

tag: tissue

value: Leaf

value: WT

tag: treatment

value: Magnaporthe oryzae


title: Plant, M_oryze A, 3 day


title: Plant, M_oryze C, 3 day


title: EARLI_11636_Hyper

tag: lca

value: Hyper

tag: age


title: EARLI_11599_Hypo

value: Hypo


title: Plant, Contol C, 3 day

value: Mock


title: 300BCG100_d90_PBMC

tag: individual


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 131

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

tag: sample type

tag: patient id

value: M

tag: disease

value: Sepsis

tag: disease 2

value: Pulmonary

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 132

tag: gender


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 131


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 132


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 132

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


title: EARLI_11586_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 131


title: Plant, Contol B, 3 day


title: EARLI_11642_Hypo

value: Female


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 131


title: Plant, Contol A, 3 day


title: 300BCG100_d14_PBMC

tag: cell type

value: PBMC

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11568_Hypo

tag: tissue

value: whole blood

value: Male


title: Plant, M_oryze C, 2 day

tag: genotype

tag: treatment


title: 300BCG099_d90_PBMC

tag: time point

tag: protocol

tag: frip


title: EARLI_11556_Hypo

tag: lca

tag: age


title: 300BCG101_d0_PBMC

tag: individual


title: Plant, M_oryze B, 2 day


title: 300BCG099_d14_PBMC


title: Plant, M_oryze A, 2 day


title: EARLI_11550_Hyper


title: 300BCG099_d0_PBMC


title: EARLI_11544_Hyper


title: 300BCG098_d90_PBMC


title: 300BCG100_d0_PBMC


title: Plant, Contol B, 2 day


title: Plant, Contol C, 2 day


title: 300BCG098_d14_PBMC


title: Plant, Contol A, 2 day


title: EARLI_11539_Hyper


title: EARLI_11530_Hypo


title: 300BCG097_d14_PBMC


title: Plant, M_oryze C, 1 day


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 157

tag: sample type

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

tag: patient id

value: F

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: Plant, M_oryze B, 1 day

value: Leaf


title: EARLI_11526_Hypo

tag: gender


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 155


title: 300BCG097_d0_PBMC

tag: cell type

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 155


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 145

value: Died


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 155


title: Plant, M_oryze A, 1 day

tag: tissue

tag: genotype

value: WT

tag: treatment

value: Magnaporthe oryzae


title: EARLI_11521_Hypo

tag: lca

value: Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 144


title: 300BCG096_d14_PBMC

tag: time point

tag: protocol

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 157

tag: sample type

tag: patient id

tag: disease


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 144

tag: gender

tag: disease 2

tag: died/survived


title: EARLI_11533_Hyper

value: Hyper

tag: age


title: EARLI_11515_Hypo


title: 300BCG098_d0_PBMC

tag: cell type

tag: individual

tag: flowcell

tag: batch id

tag: pcr cq


title: 300BCG096_d0_PBMC

tag: genotype

tag: filtered peaks


title: EARLI_11555_Hypo

tag: tissue

tag: lca


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 143

value: M

value: Abdominal


title: 300BCG095_d90_PBMC

tag: time point

tag: protocol

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 144

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Sepsis

value: Pulmonary


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 144

tag: disease 2

tag: died/survived


title: EARLI_11510_Hyper

value: Female

tag: age


title: Plant, Contol B, 1 day

tag: treatment

value: Mock


title: EARLI_11503_Hypo

value: whole blood


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 91


title: 300BCG094_d90_PBMC

tag: cell type

value: PBMC

tag: individual

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: Plant, Contol A, 1 day

tag: tissue

tag: genotype


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 143

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


title: 300BCG093_d90_PBMC

tag: time point

tag: protocol

tag: filtered peaks

tag: tss enrichment


title: EARLI_11498_Hyper

tag: lca

tag: gender


title: Plant, Contol C, 1 day


title: 300BCG092_d90_PBMC

tag: frip


title: Plant, Contol B, 0 day


title: EARLI_11489_Hypo


title: EARLI_11486_Hyper


title: 300BCG091_d90_PBMC


title: Plant, Contol A, 0 day


title: EARLI_11479_Hypo


title: 300BCG090_d90_PBMC


title: Cell, Chitin 3, 12 h

source_name: suspension cell

growth_protocol: Grow rice suspension cells in a flask on a shaker at 50 rpm at 30°C.

treatment_protocol: Add chitin at a final concentration of 2 µg/mL, and harvest the samples at 0, 1, 3, 6, and 12 h.

value: suspension cell

value: chitin


title: 300BCG089_d90_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 107

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: Cell, Chitin 2, 12 h

tag: cell type

value: WT

tag: treatment


title: EARLI_11463_Hyper

value: Male

tag: age


title: Cell, Chitin 1, 12 h


title: Plant, Contol C, 0 day

tag: tissue

value: Leaf


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 107


title: EARLI_11456_Hypo

value: Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 122

value: M


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 97

value: Abdominal


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 129

value: F

value: Sepsis

value: Died


title: Cell, Mock 3, 12 h

tag: genotype

value: Mock


title: EARLI_11445_Hypo

value: whole blood


title: 300BCG088_d90_PBMC

value: PBMC

tag: individual

tag: time point

tag: flowcell

tag: batch id

tag: pcr cq


title: EARLI_11430_Hypo

tag: lca

tag: gender

value: Female


title: Cell, Mock 2, 12 h


title: 300BCG087_d90_PBMC

tag: protocol

value: ATAC

tag: filtered peaks

tag: tss enrichment

tag: frip


title: EARLI_11428_Hypo


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 129

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

value: Pulmonary

tag: died/survived


title: Cell, Mock 1, 12 h

tag: cell type

value: suspension cell

tag: genotype

tag: treatment


title: 300BCG087_d14_PBMC

tag: individual

tag: time point

tag: flowcell


title: EARLI_11424_Hyper

tag: tissue

tag: lca

value: Hyper

tag: age


title: 300BCG089_d14_PBMC

tag: protocol

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG087_d0_PBMC

tag: tss enrichment

tag: frip


title: Cell, Chitin 2, 6 h

value: WT

value: chitin


title: EARLI_11422_Hyper

tag: gender

value: Male


title: 300BCG086_d90_PBMC


title: Cell, Chitin 1, 6 h


title: 300BCG086_d14_PBMC


title: EARLI_11417_Hyper


title: Cell, Mock 3, 6 h


title: EARLI_11412_Hyper


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 129

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG086_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 128

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 128


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 129


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 128


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 105-2

value: Abdominal


title: Cell, Mock 2, 6 h

tag: treatment


title: 300BCG085_d90_PBMC

tag: protocol

tag: flowcell


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 127

value: F


title: Cell, Mock 1, 6 h


title: Cell, Chitin 3, 6 h


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 127

value: Sepsis


title: 300BCG085_d14_PBMC

tag: batch id

tag: pcr cq


title: EARLI_11403_Hyper

tag: tissue

tag: lca

tag: age


title: Cell, Chitin 3, 3 h


title: 300BCG085_d0_PBMC

tag: filtered peaks

tag: tss enrichment

tag: frip


title: EARLI_11353_Hypo

value: Hypo

tag: gender


title: 300BCG084_d90_PBMC


title: Cell, Chitin 2, 3 h


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 126

tag: sample type

tag: patient id

value: M

tag: disease

tag: disease 2

tag: died/survived


title: EARLI_11411_Hypo

value: whole blood


title: Cell, Chitin 1, 3 h

tag: cell type

tag: genotype

tag: treatment


title: EARLI_11404_Hyper


title: EARLI_11344_Hypo


title: 300BCG084_d0_PBMC

value: PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id


title: EARLI_11343_Hyper

tag: tissue

tag: lca

value: Female

tag: age


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 127

tag: gender


title: Cell, Mock 3, 3 h

value: Mock


title: Cell, Mock 2, 3 h


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 126

tag: sample type

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


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 125

tag: patient id


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 126

tag: disease

value: Pulmonary


title: 300BCG083_d14_PBMC

value: ATAC

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 125

tag: disease 2

tag: died/survived


title: Cell, Mock 1, 3 h

tag: cell type

value: suspension cell

tag: genotype

tag: treatment


title: EARLI_11321_Hyper

value: Hyper


title: Cell, Chitin 3, 1 h

value: WT

value: chitin


title: 300BCG083_d0_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id


title: EARLI_11320_Hypo

tag: tissue

tag: lca

tag: gender

tag: age


title: Cell, Chitin 2, 1 h


title: EARLI_11317_Hypo


title: 300BCG084_d14_PBMC

tag: pcr cq

tag: filtered peaks


title: EARLI_11309_Hyper

value: Male


title: EARLI_11310_Hypo


title: EARLI_11329_Hypo


title: 300BCG082_d0_PBMC

tag: tss enrichment

tag: frip


title: Cell, Chitin 1, 1 h


title: 300BCG083_d90_PBMC


title: 300BCG081_d14_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 96

tag: sample type

tag: patient id

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: EARLI_11308_Hypo


title: Cell, Mock 3, 1 h

tag: cell type

tag: genotype

tag: treatment


title: Cell, Mock 2, 1 h


title: 300BCG081_d0_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

value: HWVYYBBXX

tag: batch id


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 93

tag: gender

value: Sepsis


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 103

value: F

value: Abdominal


title: Cell, Mock 1, 1 h


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 122

value: M


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 122


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 89


title: EARLI_11300_Hyper

tag: tissue

value: whole blood

tag: lca

tag: age


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 93

tag: sample type


title: 300BCG080_d90_PBMC

value: PBMC

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Cell, Mock 3, 0 h

tag: cell type

value: Mock


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 121

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

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG082_d90_PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol


title: EARLI_11299_Hyper

tag: tissue

tag: gender


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 120

value: Pulmonary


title: 300BCG080_d0_PBMC

value: ATAC

tag: flowcell

tag: batch id


title: EARLI_11290_Hyper

tag: lca

tag: age


title: EARLI_11221_Hypo

value: Hypo


title: 300BCG079_d90_PBMC

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 121

tag: sample type

tag: patient id


title: Cell, Mock 1, 0 h

tag: cell type

value: suspension cell

tag: treatment


title: EARLI_11203_Hyper

value: Hyper


title: 300BCG079_d14_PBMC

tag: genotype

tag: frip


title: EARLI_11182_Hyper

value: Female


title: 300BCG079_d0_PBMC

tag: individual

tag: time point


title: EARLI_11180_Hyper

tag: tissue

value: Male


title: 300BCG080_d14_PBMC

tag: protocol


title: 300BCG078_d90_PBMC

tag: flowcell


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 120

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 120


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 120


title: Huh7.5.1, uninfected and untreated, Gecko A

city: SAN FRANCISCO

first: Andreas

middle: S

last: Puschnik

address: 499 Illinois St, 4th floor

institute: Chan Zuckerberg Biohub

data_processing:
Demultiplexed FASTQ files were processed using MaGeCK (PMID: 25476604). First, FASTQ files were aligned to a reference table containing sgRNA sequences to determine the counts of each sgRNA in each control and selected cell population. Then, count tables for GeCKO sublibraries A and B were combined and gene enrichment was calculated from sgRNA count tables using the total norm-method.
Assembly: Human GeCKOv2 sgRNA sequences (Addgene #1000000049)
Supplementary files format and content: csv file with sgRNA counts for each sample and sublibrary
Supplementary files format and content: txt file with gene enrichment analyzed via MaGeCK

growth_protocol: Cells were cultured in DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS, Omega Scientific), penicillin/streptomycin (GIBCO), non-essential amino acids (GIBCO) and L-glutamine (GIBCO) at 37C and 5% CO2.

extract_protocol:
For SARS-CoV, surviving cells were harvested at 12 days post-infection in RLT buffer and genomic DNA was extracted with AllPrep DNA/RNA spin columns (Qiagen). Eluted DNA was irradiated for biosafety reasons. For MERS-CoV, surviving cells were harvested in DNA/RNA Shield (Zymo) at 8 days post-infection and genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo).
The sgRNA expression cassettes were amplified from genomic DNA in a two-step nested PCR using KAPA HiFi HotStart ReadyMixPCR Kit (Kapa Biosystems) and sequenced on an Illumina NextSeq 500 using a custom sequencing primer, as previously described (PMID: 33333024).
OTHER: Amplicon library of sgRNA expression cassettes from genomic DNA

treatment_protocol: All experiments were performed under required biosafety conditions. For the SARS-CoV screen, a genome-wide knockout gene library using the human GeCKOv2 library (Addgene, #1000000049, gift from Feng Zhang) (PMID: 25075903) was generated in clonal Huh7.5.1-Cas9 cells expressing ACE2-IRES-TMPRSS2 (PMID: 33333024). 144 million cells were infected with SARS-CoV at an MOI of 0.0001. Surviving cells were harvested at 12 days post-infection in RLT buffer and genomic DNA was extracted with AllPrep DNA/RNA spin columns (Qiagen). Eluted DNA was irradiated for biosafety reasons. Library cells at day 0 were extracted as baseline control. For the MERS-CoV screen, Huh7.5.1-Cas9 cells transduced with the human GeCKOv2 library were infected with MERS-CoV at an MOI of 0.0001. The furin inhibitor Decanoyl-RVKR-CMK was added to the media at 5 μM throughout the experiment to prevent excessive syncytia formation. Surviving cells were harvested in DNA/RNA Shield (Zymo) at 8 days post-infection and genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo). Uninfected, Decanoyl-RVKR-CMK-treated library cells were cultured in parallel and harvested for comparison. Library cells at day 0 were extracted as baseline control.

tag: cell line

value: genome-wide CRISPR KO library

value: uninfected and untreated, day 0


title: Huh7.5.1, uninfected and untreated, Gecko B


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 98

value: SIRS

value: OOHCA


title: Huh7.5.1, uninfected and CMK treated, Gecko B

value: uninfected and CMK treated, day 8


title: 300BCG078_d14_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11168_Hyper

value: whole blood

tag: lca

tag: age


title: Huh7.5.1, MERS-CoV infected and CMK treated, Gecko B

tag: genotype

tag: treatment

value: MERS-CoV infected and CMK treated, day 8


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 97

tag: sample type

tag: patient id

value: M

value: Sepsis

value: Abdominal


title: Cell, Mock 2, 0 h

tag: cell type

value: WT

value: Mock


title: 300BCG078_d0_PBMC

value: PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 97

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

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Huh7.5.1, MERS-CoV infected and CMK treated, Gecko A

tag: cell line


title: 300BCG077_d90_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: EARLI_11140_Hypo

tag: tissue

tag: lca

value: Hypo

value: Female

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 97

tag: sample type

tag: patient id

value: Survived


title: EARLI_11139_Hypo

value: Male


title: 300BCG077_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol


title: Huh7.5.1-ACE2-TMPRSS2, uninfected, Gecko B

value: genome-wide CRISPR KO library and lentiviral overexpression of ACE2-IRES-TMPRSS2

tag: treatment

value: uninfected, day 0


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 93

tag: gender

tag: disease

tag: disease 2

value: Pulmonary

tag: died/survived


title: EARLI_11137_Hyper

value: whole blood

value: Hyper


title: Huh7.5.1-ACE2-TMPRSS2, uninfected, Gecko A

tag: cell line


title: EARLI_11175_Hypo


title: 300BCG077_d0_PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG076_d90_PBMC

tag: cell type


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 94

tag: sample type

tag: patient id

value: M


title: Huh7.5.1, uninfected and CMK treated, Gecko A

tag: genotype

value: genome-wide CRISPR KO library

value: uninfected and CMK treated, day 8


title: Huh7.5.1-ACE2-TMPRSS2, SARS-CoV infected, Gecko A

value: SARS-CoV infected, day 12


title: EARLI_11122_Hyper

tag: tissue

tag: lca

tag: age


title: 300BCG076_d14_PBMC

tag: individual

tag: time point

tag: protocol


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 94

tag: gender

tag: disease

value: Sepsis

tag: disease 2

tag: died/survived


title: EARLI_11093_Hypo


title: 300BCG076_d0_PBMC

value: PBMC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: Huh7.5.1-ACE2-TMPRSS2, SARS-CoV infected, Gecko B

tag: cell line

tag: treatment


title: EARLI_11086_Hypo


title: BC393, PT, scRNA-seq

city: Duarte

first: Peter

middle: P

last: Lee

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

description: 10x genomics Single Cell 3' v5

library_source: transcriptomic single cell

data_processing:
CellRanger (v3.0) was used to align sequence reads to human genome (GRCh38) and count the aligned transcripts for each cell. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast

extract_protocol:
Fresh breast tumors tissues from 4 ER+ breast cancer patients were separated from fat tissues and minced into pieces up to 2 mm in diameter with scalpel blades. Single-cell suspensions were prepared by using the gentle MACS Dissociator (Miltenyl Biotec, Auburn, CA, USA) according to the standard protocol. Tissue homogenates were treated with 0.26 Wunsch U/ml Liberase and 10 U/ml DNase (Sigma-Aldrich, St. Louis, MO, USA) for up to 1 h as needed.
Single-cell RNA sequencing was performed using the Chromium Single-Cell v3 3′ Chemistry Library, Gel Bead, Multiplex and Chip Kits (10x Genomics) according to the manufacturer’s protocol.

value: Breast

tag: Sex

tag: cancer subtype

value: ER+


title: BC397, PT, scRNA-seq

description: 10x genomics Single Cell 3' v6

tag: tissue


title: 300BCG075_d90_PBMC

tag: cell type

tag: genotype

value: ATAC

tag: tss enrichment

tag: frip


title: 300BCG075_d14_PBMC

tag: individual

tag: time point

tag: protocol


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 103

tag: sample type

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

tag: patient id

tag: gender

value: F

tag: disease

tag: disease 2

value: Abdominal

tag: died/survived


title: EARLI_11080_Hypo

tag: lca

value: Hypo

value: Female

tag: age


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 104

value: Pulmonary

value: Survived


title: BC392, PT, scRNA-seq

description: 10x genomics Single Cell 3' v4

tag: Sex

tag: cancer subtype


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 87


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 72


title: EARLI_11079_Hypo

tag: tissue

value: whole blood


title: 300BCG075_d0_PBMC

tag: cell type

tag: genotype

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks


title: EARLI_11097_Hypo

value: Male


title: EARLI_11062_Hypo


title: 300BCG074_d14_PBMC

tag: individual

tag: time point

tag: protocol

tag: tss enrichment

tag: frip


title: BC389, PT, scRNA-seq

description: 10x genomics Single Cell 3' v3


title: EARLI_11053_Hypo

tag: gender


title: EARLI_11052_Hypo

tag: lca


title: vastus lateralis muscle,SLOW,OH,untrained,9,male,POST

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

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).

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)

value: vastus lateralis muscle

tag: fiber-type

value: SLOW

value: OH

value: untrained

value: male

value: POST


title: vastus lateralis muscle,SLOW,OH,untrained,8,male,POST

tag: Sex


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 96

tag: sample type

tag: patient id

tag: disease

value: Sepsis

tag: disease 2

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 100

value: SIRS

value: OOHCA


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 98

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

value: M


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 100

value: F


title: vastus lateralis muscle,FAST,OH,untrained,7,male,POST

tag: tissue

value: FAST


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 100


title: vastus lateralis muscle,SLOW,OH,untrained,7,male,POST


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 108

value: Pulmonary


title: 300BCG073_d0_PBMC

tag: cell type

value: PBMC

tag: genotype

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: EARLI_11038_Hypo

value: whole blood

value: Hypo

value: Male

tag: age


title: vastus lateralis muscle,FAST,OH,untrained,9,male,POST

value: vastus lateralis muscle

value: OH


title: vastus lateralis muscle,FAST,OH,untrained,6,male,POST

value: untrained

value: male


title: EARLI_11035_Hyper

value: Hyper

value: Female


title: 300BCG072_d90_PBMC

tag: individual

tag: time point

tag: protocol

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG072_d14_PBMC


title: 300BCG074_d0_PBMC


title: vastus lateralis muscle,SLOW,OH,untrained,6,male,POST

tag: fiber-type

value: SLOW

tag: Sex

value: POST


title: 300BCG072_d0_PBMC


title: 300BCG073_d90_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 89

tag: sample type

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

tag: patient id

tag: gender

value: M

tag: disease

value: Sepsis

tag: disease 2

value: Survived


title: EARLI_11043_Hypo

tag: tissue

tag: lca


title: vastus lateralis muscle,FAST,OH,untrained,8,male,POST

value: FAST


title: EARLI_10993_Hyper


title: EARLI_11046_Hypo


title: 300BCG073_d14_PBMC

tag: cell type

value: PBMC

tag: genotype

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq


title: EARLI_10991_Hypo

value: whole blood

value: Hypo

tag: age


title: vastus lateralis muscle,FAST,OH,untrained,5,male,POST

value: vastus lateralis muscle


title: 300BCG071_d90_PBMC

tag: individual

tag: time point

tag: protocol

tag: filtered peaks

tag: tss enrichment


title: EARLI_10981_Hyper

value: Male


title: 300BCG071_d14_PBMC

tag: frip


title: vastus lateralis muscle,SLOW,OH,untrained,5,male,POST

tag: fiber-type

value: OH

value: untrained

tag: Sex


title: vastus lateralis muscle,FAST,OH,untrained,4,male,POST

value: male


title: EARLI_10971_Hyper

value: Hyper

tag: gender


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 88

tag: sample type

tag: patient id

value: F

tag: disease

tag: disease 2

value: Pulmonary

tag: died/survived


title: 300BCG071_d0_PBMC

tag: cell type

tag: genotype

tag: flowcell

tag: batch id


title: EARLI_10963_Hypo

tag: tissue

tag: lca

tag: age


title: 300BCG070_d14_PBMC

tag: individual

tag: time point

tag: protocol

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: vastus lateralis muscle,SLOW,OH,untrained,4,male,POST

tag: fiber-type

value: SLOW

tag: Sex

value: POST


title: vastus lateralis muscle,FAST,OH,untrained,3,male,POST


title: 300BCG070_d0_PBMC

tag: frip


title: EARLI_10957_Hyper

tag: gender


title: 300BCG069_d90_PBMC

tag: cell type


title: vastus lateralis muscle,SLOW,OH,untrained,3,male,POST


title: vastus lateralis muscle,FAST,OH,untrained,2,male,POST


title: EARLI_10956_Hypo


title: EARLI_10929_Hyper

value: Female


title: vastus lateralis muscle,SLOW,OH,untrained,2,male,POST


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 95

tag: sample type

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

tag: patient id

tag: disease

value: Sepsis

tag: disease 2

value: Abdominal

tag: died/survived

value: Survived


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 104

value: M


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 95


title: 300BCG068_d90_PBMC

value: PBMC

tag: genotype

value: ATAC

tag: flowcell

tag: batch id


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 87


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 103


title: 300BCG069_d0_PBMC

tag: individual

tag: time point

tag: protocol


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 95


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 88


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 94


title: vastus lateralis muscle,FAST,OH,untrained,1,male,POST

tag: tissue

value: vastus lateralis muscle

value: FAST


title: EARLI_10958_Hyper

value: whole blood

tag: lca

tag: age


title: vastus lateralis muscle,SLOW,OH,untrained,1,male,POST

tag: fiber-type

value: OH

value: untrained

tag: Sex

value: male


title: 300BCG068_d14_PBMC

tag: cell type

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: EARLI_10820_Hypo

value: Hypo

tag: gender

value: Male


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

value: YE

value: trained

value: POST


title: EARLI_10825_Hypo


title: 300BCG068_d0_PBMC

tag: genotype


title: 300BCG069_d14_PBMC

tag: flowcell


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

value: PRE


title: EARLI_10846_Hyper

value: Hyper


title: 300BCG067_d90_PBMC

tag: batch id


title: EARLI_10819_Hypo


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

value: SLOW


title: 300BCG067_d14_PBMC

tag: individual


title: EARLI_10755_Hyper

value: Female


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 85

tag: sample type

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

tag: patient id

value: F

tag: disease

value: Sepsis

tag: disease 2

value: Pulmonary

tag: died/survived

value: Survived


title: 300BCG067_d0_PBMC

value: PBMC

tag: time point

tag: protocol

value: ATAC


title: EARLI_10741_Hypo

tag: tissue

value: whole blood

tag: lca

tag: age


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 88


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

value: vastus lateralis muscle

tag: fiber-type

tag: Sex

value: male


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

value: FAST

value: YE


title: 300BCG066_d90_PBMC

tag: cell type

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


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

value: trained


title: 300BCG066_d14_PBMC

tag: genotype

tag: individual

tag: flowcell

tag: batch id


title: EARLI_10691_Hypo

value: Hypo

tag: gender


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

value: POST


title: EARLI_10740_Hypo

value: Male


title: 300BCG066_d0_PBMC

tag: time point


title: EARLI_10757_Hypo


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

value: SLOW

value: PRE


title: EARLI_10584_Hypo

value: Female


title: 300BCG065_d90_PBMC

tag: protocol


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 82

tag: sample type

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

tag: patient id

value: F

tag: disease

value: Sepsis

tag: disease 2

value: Abdominal

tag: died/survived

value: Died


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 85

value: Pulmonary

value: Survived


title: 300BCG065_d14_PBMC

tag: cell type

value: PBMC

value: ATAC


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 85


title: vastus lateralis muscle,FAST,YE,trained,6,male,POST

tag: tissue

value: vastus lateralis muscle

tag: fiber-type

value: FAST

value: YE

tag: Sex

value: male


title: EARLI_10456_Hypo

value: whole blood

tag: lca

value: Hypo

value: Male

tag: age


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 72


title: vastus lateralis muscle,FAST,YE,trained,6,male,PRE

value: trained

value: PRE


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 85

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

value: F


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 86

value: Sepsis

value: Abdominal


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 86


title: 300BCG065_d0_PBMC

tag: genotype

tag: individual

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 72

tag: sample type

tag: gender


title: EARLI_10447_Hyper

value: Hyper


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 82

tag: patient id

tag: disease

value: Died


title: 300BCG064_d90_PBMC

value: PBMC

tag: time point

tag: protocol

tag: flowcell

tag: batch id


title: vastus lateralis muscle,SLOW,YE,trained,6,male,PRE

tag: tissue

tag: fiber-type

value: SLOW

tag: Sex


title: Sham, bronchial, chronic bronchitis-like, replicate 7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

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: Sham


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 72

tag: disease 2

tag: died/survived

value: Survived


title: 300BCG064_d14_PBMC

tag: cell type

tag: genotype

tag: individual

value: ATAC

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 71

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Pulmonary


title: Sham, bronchial, chronic bronchitis-like, replicate 6

tag: tissue


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 71


title: Sham, bronchial, chronic bronchitis-like, replicate 5


title: 300BCG064_d0_PBMC

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 71

tag: disease 2

tag: died/survived


title: vastus lateralis muscle,SLOW,YE,trained,6,male,POST

value: vastus lateralis muscle

tag: fiber-type

value: YE

tag: Sex

value: male

value: POST


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

value: trained


title: 300BCG063_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: pcr cq


title: Sham, bronchial, chronic bronchitis-like, replicate 3

tag: disease state

tag: treatment


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

value: FAST

value: PRE


title: Sham, bronchial, chronic bronchitis-like, replicate 2


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 70

tag: sample type

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

tag: patient id

tag: gender

value: M

tag: disease

value: SIRS

value: OOHCA


title: 300BCG062_d90_PBMC

value: PBMC

tag: time point

tag: protocol

tag: flowcell

tag: filtered peaks

tag: tss enrichment


title: Sham, bronchial, chronic bronchitis-like, replicate 1

tag: tissue

value: bronchial

value: chronic bronchitis-like


title: 300BCG062_d14_PBMC

tag: batch id

tag: frip


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

tag: fiber-type

tag: Sex


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 45

tag: disease 2

tag: died/survived

value: Survived


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

value: SLOW


title: Sham, bronchial, replicate 6

tag: disease state

value: healthy

tag: treatment

value: Sham


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 45

tag: sample type

tag: patient id


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 45

tag: gender

tag: disease


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 142

value: F

value: Sepsis

value: Pulmonary


title: Sham, bronchial, replicate 5


title: 300BCG062_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: pcr cq


title: 300BCG063_d90_PBMC

tag: flowcell

tag: batch id

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG063_d14_PBMC


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

tag: tissue

value: vastus lateralis muscle

tag: fiber-type

value: FAST

value: YE

value: trained

tag: Sex

value: male

value: POST


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


title: Sham, bronchial, replicate 4

tag: disease state

tag: treatment


title: 300BCG061_d90_PBMC

value: PBMC


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 105

tag: sample type

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

tag: patient id

tag: gender

tag: disease

tag: disease 2

value: Abdominal

tag: died/survived


title: Sham, bronchial, chronic bronchitis-like, replicate 4

value: bronchial

value: chronic bronchitis-like


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

value: PRE


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 104

value: M

value: Survived


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


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 104

value: Sepsis


title: Sham, bronchial, replicate 3

value: healthy

value: Sham


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

value: vastus lateralis muscle

value: SLOW


title: Sham, bronchial, replicate 2


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

value: YE


title: 300BCG061_d0_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: pcr cq


title: Sham, bronchial, replicate 1

tag: tissue


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

tag: fiber-type

value: FAST

value: trained

value: male


title: 300BCG060_d14_PBMC

value: PBMC

tag: flowcell

tag: batch id

tag: filtered peaks

tag: tss enrichment

tag: frip


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

tag: Sex


title: Sham, alveolar, replicate 7

source_name: alveolar

value: alveolar

tag: disease state

tag: treatment


title: Sham, alveolar, replicate 6


title: 300BCG060_d0_PBMC


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 102

tag: sample type

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

tag: patient id

tag: gender

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived

value: Died


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

value: PRE


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

value: POST


title: 300BCG061_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point

tag: protocol

tag: pcr cq


title: Sham, alveolar, replicate 5

tag: tissue

value: healthy


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 70

value: M


title: 300BCG059_d90_PBMC

tag: flowcell

tag: batch id

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG059_d14_PBMC


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 105

tag: sample type

tag: patient id

value: F

value: Sepsis

value: Abdominal

value: Survived


title: Sham, alveolar, replicate 4

tag: disease state

tag: treatment

value: Sham


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 102

tag: gender

tag: disease

tag: disease 2

tag: died/survived


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

value: vastus lateralis muscle

tag: fiber-type

value: SLOW

value: YE

value: trained

tag: Sex


title: 300BCG060_d90_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: pcr cq


title: Sham, alveolar, replicate 3

tag: tissue

value: alveolar


title: 300BCG059_d0_PBMC

tag: flowcell

tag: batch id

tag: filtered peaks

tag: tss enrichment

tag: frip


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

value: FAST

value: male


title: 300BCG058_d90_PBMC


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

value: PRE


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 87

tag: sample type

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

tag: patient id

tag: gender

tag: disease

value: Pulmonary


title: Sham, alveolar, replicate 2

tag: disease state

value: healthy

tag: treatment


title: 300BCG058_d14_PBMC

tag: cell type

tag: genotype


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 82

value: F

value: Sepsis

tag: disease 2

tag: died/survived

value: Died


title: Sham, alveolar, replicate 1

value: Sham