title: CHD4_ChIP_ESCs+Pramel7DNterm

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

description: ChIPseq

data_processing:
Fastaq files were aligned to the mm10 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
for ChIP seq data,read counts were computed and normalized using “bamCoverage” from deepTools (version 3.2.1) using a bin size of 50bp.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells were cultured in either DMEM-Glutamax supplemented with 1× penicillin/streptomycin (Life Technologies), 15% Fetal Calf Serum (Gibco),  1x Non-essential aminoacids (Gibco), 50 μM β-mercaptoethanol (Life Technologies) and recombinant leukemia inhibitory factor, LIF (Polygene, 1,000 U/ml). ESCs were seeded at a density of 50,000 cells/cm2 in culture dishes (Corning® CellBIND® surface) coated with 0.1% gelatin without feeder layer. Propagation of cells was carried out every 2 days using enzymatic cell dissociation.

extract_protocol:
1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed with lysis buffer (50mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X protease inhibitor cOmplete EDTA-free cocktail, Roche). Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris–HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and incubated overnight with the ChIP-grade antibodies against H3K9me2 and H3K9me3. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K digestion (50°C for 3 h) and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified by qPCR.
The NEB Next Ultra II DNA Library prep Kit fro Illumina (NEB) was used in the following steps. ChIP samples (10 ng) was end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the TapeStation (Agilent Technologies). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina Novaseq 6000 single end 100 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

treatment_protocol: 9 x 105 ESC were plated in gelatin-coated 10cm culture dish and grown for 72h.

tag: cell line

value: E14 overexpressing Pramel7 with an Nterminal deletion of 50aa

tag: antibody


title: Pulmonary Tuberculosis, 20220225MCX010

status: Public on Jan 08 2024

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.

molecule: total RNA

organism: Homo sapiens

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: Pulmonary Tuberculosis


title: 300BCG215_d90_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

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Pulmonary Tuberculosis, 20220105MCX010


title: CHD4_ChIP_ESCs+Pramel7WT

description: ChIPseq

organism: Mus musculus

value: E14 overexpressing Pramel7WT

tag: treatment


title: Pulmonary Tuberculosis, 20210924MCX010


title: CHD4_ChIP_ESCs+Serum_WT

description: ChIPseq

value: E14 wild-type


title: wt_abm_hsc1

city: Lund

first: Mohamed

last: Eldeeb

address: DMH, BMC B12

country: Sweden

institute: Lund University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one sample greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-delimited file includes normalized counts (CPM)

source_name: Hematopoietic

extract_protocol:
Cells were harvested, lysed, and RNA extraction was performed using the Norgen single cell RNA purification kit (51800, Norgen Biotech).
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (634418, TaKaRa). Library concentration was measured using QuantIT 1X dsDNA HS Assay Kit (Q33232, Thermo Fisher), and quality was assessed on 5200 Fragment Analyzer™ 12-capillary (M3510AA, Agilent) using DNF-930 dsDNA Reagent Kit, 75 bp – 20,000 bp (K0500, Agilent).
The library pool was diluted to a final concentration of 1.25 nM and sequenced on a NovaSeq 6000 System (20012850, Illumina) using NovaSeq 6000 S2 Reagent Kit (2x100 paired end cycles) (20012861, Illumina).

value: Hematopoietic

value: WT

value: Dox


title: Run2-MA026_L

city: Ottawa

first: Lauren

middle: E

last: Carter

state: Ontario

address: 251 SIR FREDERICK BANTING

department: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

data_processing:
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0)
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from flash frozen tissue samples using Qiagen miRNeasy kits.  20mg of frozen liver was placed in pre-filled tube containing Qiazol reagent and Zirconium beads, then homogenized 2 x for 20 seconds.  Subsequent steps were followed as per manufacture's instructions.
3-methylfuran cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol. Furan cDNA libraries were prepared with the Illumina Stranded mRNA prep kit (updated release).

value: Liver

value: Diet A - 0.03 mg/kg bw/day furan


title: Run2-MA029_L


title: Input_ESCs+Pramel7DNterm

description: ChIPseq


title: Pulmonary Tuberculosis, 220625MCX00023


title: 300BCG216_d90_PBMC


title: 300BCG215_d0_PBMC


title: Run2-MA025_L


title: 300BCG214_d90_PBMC


title: Input_ESCs+Pramel7WT

description: ChIPseq


title: Pulmonary Tuberculosis, 20220310MCX026


title: Run2-MA023_L


title: 300BCG214_d0_PBMC


title: Run2-MA022_L


title: Input_ESCs+Serum_WT

description: ChIPseq


title: Pulmonary Tuberculosis, 20211216MCX010


title: 300BCG213_d90_PBMC


title: Pulmonary Tuberculosis, 20211207MCX007


title: cKO3 testis

city: Beijing

first: Jiali

last: Liu

address: 2 West Yuanmingyuan Road

institute: China Agricultural University

description: cKO

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: testis

growth_protocol: All mice were bred and housed under specific pathogen-free conditions with controlled temperature (22 ± 1℃) and exposed to a constant 12-hour light-dark cycle in the animal facilities of China Agricultural University. All experiments were conducted following the guidelines and with the approval of the Institutional Animal Care and Use Committee of China Agricultural University

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v3-cBot-HS was used with 0.4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conditional knockout

value: testis

value: cKO - Srsf1


title: Run2-MA021_L


title: 300BCG215_d14_PBMC


title: Run2-MA027_L


title: cKO2 testis

description: cKO


title: Pulmonary Tuberculosis, 20211119MCX011


title: Run1-ME092_L

value: Diet E - 2.0 mg/kg bw/day furan


title: 300BCG213_d14_PBMC


title: 300BCG213_d0_PBMC


title: Run1-ME089_L


title: cKO1 testis

description: cKO


title: Control3 testis

description: Ctrl

value: Ctrl


title: Run1-ME086_L


title: Control2 testis

description: Ctrl


title: Pulmonary Tuberculosis, 20211103MCX002


title: 300BCG212_d0_PBMC


title: Control1 testis

description: Ctrl


title: Run1-ME085_L


title: 300BCG214_d14_PBMC


title: Pulmonary Tuberculosis, 20210923MCX021


title: Run1-ME083_L


title: CLIP2

data_processing:
For the analyses of CLIP-seq data, the adaptor sequences were first removed from the reads by Trimmomatic (version 0.36)
Subsequently, Bowtie 2 (version 2.1.0) was applied for mapping of clean reads to the mm10 reference genome with the parameters "-p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end."
CLIP-seq peaks were identified by Piranha (version 1.2.1) with the following parameters: "-s -b 20 -d Zero Truncated Negative Binomial -p 0.05."
Homer (version 4.9.1) was used for peak annotation based on the mm10 genome assembly and for analyses of SRSF1-binding motifs
Assembly: mm10
Supplementary files format and content: bigWig (track)

extract_protocol:
Total cells were isolated from adult WT C57BL/6N mouse testes, and then the cells were cross-linked by ultraviolet light (254 nm) to maintain the covalent binding of RBPs to their cognate RNA. Subsequently, SRSF1 and cross-linked RNAs were immunoprecipitated with an anti-SRSF1 antibody and digested with micrococcal nuclease (EN0181, Thermo Fisher Scientific). An IR800-biotin adapter was ligated to the 3′ ends of the RNA fragments. Then, the SRSF1/RNA complexes were separated by SDS‒PAGE and transferred to a nitrocellulose membrane (HATF00010, Millipore). These RNA and protein complexes from approximately 47 to 62 kDa were extracted from the nitrocellulose membrane, after which proteinase K (9034, Takara) digestion was performed. RNA was isolated with saturated phenol (AM9712, Ambion),
RNA ligated with adaptors, and converted to cDNA with a SuperScript III First-Strand Kit (18080-051, Invitrogen). The cDNA was amplified by PCR to prepare the corresponding libraries and then sequenced on illumina NovaSeq 6000.

tag: clip antibody

value: SRSF1 antibody (sc-33652, Santa Cruz Biotechnology)

tag: strain


title: 300BCG211_d14_PBMC


title: Pulmonary Tuberculosis, 20210922MCX010


title: CLIP1


title: Run1-ME081_L


title: 300BCG211_d0_PBMC


title: 300BCG210_d90_PBMC


title: Pulmonary Tuberculosis, 20210916MCX007


title: IgG2

value: normal mouse IgG (sc-3879, Santa Cruz Biotechnology)


title: Run1-MD072_L

value: Diet D - 0.5 mg/kg bw/day furan


title: IgG1


title: Pulmonary Tuberculosis, 20211118MCX015

value: BALF

value: Pulmonary Tuberculosis


title: Pulmonary Tuberculosis, 20211104MCX009


title: 300BCG210_d14_PBMC

value: PBMC

value: ATAC


title: Pulmonary Tuberculosis, 20210916MCX005


title: Run1-MD071_L


title: 300BCG212_d14_PBMC


title: LMD_DMH_shPpp1r17_4

city: St Louis

first: Kyohei

last: Tokizane

state: MO

address: 660 S Euclid Ave

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

data_processing:
Illumina’s bcl2fastq2
RNA-seq reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premises server running version 3.9.3-8 software.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
The TMM size factors and the matrix of counts were imported into the R/Bioconductor package Limma
Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
Assembly: Illumina DRAGEN Bio-IT
Supplementary files format and content: sf files include TPM values for each Sample

source_name: DMH

extract_protocol:
RNA was isolated from each DMH sample using the Arcturus PicoPureTM RNA isolation kit
RNA libraries for RNA-seq were prepared using Clontech SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: DMH

value: Ppp1r17 knockdown


title: Pulmonary Tuberculosis, 20210914MCX012


title: LMD_DMH_shPpp1r17_3


title: 300BCG211_d90_PBMC


title: Pulmonary Tuberculosis, 20210825MCX012


title: Run1-MD069_L


title: Run1-MD067_L


title: 300BCG209_d90_PBMC


title: 300BCG210_d0_PBMC


title: Pulmonary Tuberculosis, 20210811MCX011


title: Run1-ME082_L


title: LMD_DMH_shPpp1r17_2


title: 300BCG209_d0_PBMC


title: Pulmonary Tuberculosis, 20210923MCX015


title: Run1-MD064_L


title: LMD_DMH_shPpp1r17_1


title: Pulmonary Tuberculosis, 20210719MCX006


title: 300BCG208_d90_PBMC


title: LMD_DMH_shfLuc_4

value: fLuc knockdown


title: 300BCG208_d14_PBMC


title: Run1-MD063_L


title: Run1-MD062_L


title: LMD_DMH_shfLuc_3


title: Run1-MC012_L

value: Diet C - Control 0


title: Pulmonary Tuberculosis, 20210517MCX004


title: 300BCG208_d0_PBMC


title: Pulmonary Tuberculosis, 20211127MCX011


title: LMD_DMH_shfLuc_2


title: Run1-MC011_L

value: Liver


title: LMD_DMH_shfLuc_1


title: 300BCG207_d90_PBMC


title: Pulmonary Tuberculosis, 20211022MCX016


title: Run1-MC010_L


title: 3T3 cells, triple KD, rep2

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCm38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 19 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: mm10
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

molecule: polyA RNA

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: triple KD


title: 300BCG207_d14_PBMC


title: Pulmonary Tuberculosis, 20211209MCX017

tag: tissue


title: 300BCG207_d0_PBMC


title: Pulmonary Tuberculosis, 20211224MCX018

tag: disease state


title: Run1-MC009_L


title: 3T3 cells, triple KD, rep3


title: Run1-MC008_L


title: 300BCG206_d90_PBMC

tag: cell type


title: 3T3 cells, triple KD, rep1

tag: genotype


title: Pulmonary Tuberculosis, 20210629MCX009


title: Run1-MC007_L


title: 3T3 cells, control, rep3

value: control


title: Pulmonary Tuberculosis, 20211123MCX011


title: Pulmonary Tuberculosis, 20211120MCX005


title: 300BCG206_d0_PBMC

tag: individual


title: 3T3 cells, control, rep2


title: Pulmonary Tuberculosis, 20211103MCX005


title: 300BCG205_d90_PBMC

tag: time point


title: Run1-MC003_L


title: 300BCG205_d14_PBMC

tag: protocol


title: Run1-MB052_L

value: Diet B - 0.12 mg/kg bw/day furan


title: Pulmonary Tuberculosis, 20210828MCX008


title: Mus3T3_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: 300BCG205_d0_PBMC

tag: flowcell

tag: batch id


title: 3T3 cells, control, rep1


title: Pulmonary Tuberculosis, 20210629MCX010


title: Run1-MB050_L


title: Mus3T3_control_rep1


title: 300BCG206_d14_PBMC

tag: pcr cq

tag: filtered peaks


title: Pulmonary Tuberculosis, 20210626MCX006


title: Pulmonary Tuberculosis, 20210622MCX006


title: Mus3T3_Safb1_rep1


title: Run1-MB045_L


title: Run1-MB048_L


title: Run1-MC004_L


title: Mus3T3_Safb1_rep2


title: Run1-MB046_L


title: ESCs+Pramel7DNterm rep2

description: RNAseq

data_processing:
Fastaq files were aligned to the mm10 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
The bam files were analyzed using the damidseq pipeline script from the Brand group (http://owenjm.github.io/damidseq_pipeline) (Marshall and Brand, 2015). The pipeline bins the mapped reads into GATC-fragments according to GATC-sites indicated by a gff file for the GRCm38 mouse genome (already provided by the authors of the pipeline on the website above) and normalizes reads against the Dam control, in our case the H2B-Dam sample. The pipeline gives a bedgraph file with the log2 ratio of the m6A between H2B-Dam-NoLS and the H2B-Dam only.  The bedgraph files were processed with the find_peaks software associated with the pipeline (https://github.com/owenjm/find_peaks) adjusting the values of the FDR and the minimum quantile (FDR <0.01 and min_quant 0.70). Only the significative peaks common to both replicates were considered as NADs for further analysis. The intersection of identified NADs and previously published lamina associated domains (LADs, Peric-Hupkes et al., 2010) results in the classification of NADonly, NAD/LAD, and LAD.
for RNA SEQ, reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; 50) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount 51 with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10

growth_protocol: ESCs cultured in 15% serum medium +LIF

extract_protocol:
Total RNA from two independent mouse ESC dishes was purified with TRIzol reagent (Life Technologies). In order to remove DNA contaminants, the samples were treated with 1U DNaseI (Thermo Scientific) for 1h at 37°C and the RNA samples were re-purified using TRIzol. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the NovaSeq 6000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

value: E14 overexpressing Pramel7 with an Nterminal deletion of 50aa


title: Pulmonary Tuberculosis, 20210604MCX007


title: ESCs+Pramel7DNterm rep1

description: RNAseq


title: Pulmonary Tuberculosis, 20210515MCX006


title: 300BCG203_d14_PBMC

tag: tss enrichment

tag: frip


title: Pulmonary Tuberculosis, 20210902MCX009


title: Run1-MB042_L

tag: treatment


title: ESCs+Pramel7WT rep2

description: RNAseq

value: E14 overexpressing Pramel7WT


title: Run1-MB041_L


title: Pulmonary Tuberculosis, 20210410MCX006


title: 300BCG204_d90_PBMC


title: ESCs+Pramel7WT rep1

description: RNAseq


title: 300BCG202_d90_PBMC


title: 300BCG204_d14_PBMC


title: Pulmonary Tuberculosis, 20210309MCX010


title: ESCs+Serum_WT rep2

description: RNAseq

value: E14 wild-type


title: Run1-MA029_L

value: Diet A - 0.03 mg/kg bw/day furan


title: 300BCG202_d14_PBMC


title: ESCs+Serum_WT rep1

description: RNAseq


title: Run1-MB044_L


title: 300BCG204_d0_PBMC


title: Run1-MA027_L


title: Pulmonary Tuberculosis, 20210831MCX008

value: BALF


title: 300BCG203_d90_PBMC


title: 300BCG201_d90_PBMC


title: Pulmonary Tuberculosis, 20220106MCX009

value: Pulmonary Tuberculosis


title: Run1-MA026_L


title: 300BCG201_d14_PBMC

value: PBMC


title: 300BCG201_d0_PBMC

value: ATAC


title: Run1-MA025_L


title: 300BCG203_d0_PBMC


title: Run1-MA023_L


title: 300BCG200_d90_PBMC


title: Pulmonary Tuberculosis, 20210517MCX007


title: Pulmonary Tuberculosis, 20210531MCX004


title: Pulmonary Tuberculosis, 20210323MCX004


title: Pulmonary Tuberculosis, 20210525MCX011


title: Run1-MA030_L


title: Run1-MA022_L


title: 300BCG200_d14_PBMC


title: Run1-MA021_L


title: 300BCG200_d0_PBMC


title: Pulmonary Tuberculosis, 20211008MCX018


title: Pulmonary Tuberculosis, 20220127MCX026


title: mESCs_RNF12_input

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
The SNPs in the 129/Sv and Cast/Ei lines were downloaded from the Sanger institute (v.5 SNP142) (Keane et al., 2011). These were used as input for SNPsplit v0.3.4 (Felix Krueger & Andrews, 2016) to construct an N-masked reference genome based on mm10 in which all SNPs between 129/Sv and Cast/Ei are masked. The ChIP-seq reads were trimmed and aligned to the N-masked reference genome using Trim Galore v0.6.7 (F Krueger, 2015) and bowtie2 v2.5.0 (D. Kim, Langmead, & Salzberg, 2015), respectively. SNPsplit was then used to assign the reads to either the 129/Sv or Cast/Ei bam file based on the best alignment or to an unassigned bam file if mapping to a region without allele-specific SNPs. The allele-specific and unassigned bam files were merged into a composite bam file using samtools v1.10 (Li et al., 2009).
Peaks were called from the merged bam files using macs2 v2.2.7.1 (Feng, Liu, Qin, Zhang, & Liu, 2012) callpeak with --broad and default settings. For visualization, the tracks were normalized using macs2 bdgcmp with the Poisson P-value as normalization method.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for input samples)

source_name: mESCs

extract_protocol:
The ChIP-seq experiments were performed as described (Soler et al., 2011) with minor modifications. For the RNF12 ChIP-seq experiments, 1 × 108 undifferentiated female ESCs expressing V5-tagged RNF12, V5-tagged RNF12H569A,C572A and control wild-type ESCs were cultured without feeders until they reached 80% confluence . Cells were treated for 3 h with proteasome inhibitor (15 μM MG132). All buffers used contained protease inhibitor cocktail tablet (Roche) and 15 μM MG132. The medium was removed, and cells were washed three times with PBS. Then, cells were cross-linked by incubating with PBS containing 2 mM DSG (Thermo Fisher Scientific) for 45 mins at room temperature (RT) on a rotating platform. After the incubation, cells were washed three times with PBS. In the last wash, formaldehyde was added to 1% final concentration and incubated for 10 mins at RT, followed by the addition of glycine to a final concentration of 0.125 M, and cells were incubated for an additional 5 mins at RT to quench the reaction. Cells were washed twice with ice-cold PBS, then scraped and collected in cold PBS. The fixed cell pellets were resuspended in lysis buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.5 mM EGTA) and incubated 10 mins on ice. Samples were sonicated on ice using a Sanyo Soniprep 150 sonicator (amplitude 9, 37 cycles of 15 sec on and 30 sec off) to a DNA fragment size in the range of 300–800 nucleotides. The sonicated chromatin samples were centrifuged at 13,000 rpm for 5 mins at 4°C. Chromatin was then diluted to a final volume of 10 ml with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl pH 8, 167 mM NaCl), precleared and immunoprecipitated overnight at 4°C with 60 μl of pre-blocked V5 agarose beads (Sigma) for each ChIP-seq experiment. Beads were washed twice with low salt buffer (0.1% SDS, 1% Triton X100, 2 mM EDTA, 20 mM Tris–HCl pH 8, 150 mM NaCl), followed by 2 washes with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–HCl pH 8, 500 mM NaCl), 2 washes with LiCl buffer (0.25 M LiCl, 1% Np40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris–HCl pH 8), and 2 washes with TE buffer (10 mM Tris–HCl pH 8, 1 mM EDTA). Each wash step was performed for 10 mins at 4°C on a rotating platform. Chromatin was eluted with 500 µL of Elution Buffer (1% SDS; 0.1 M NaHCO3 in H2O). Chromatin was decrosslinked by adding 20µL of 5 M NaCl and incubating at 65°C for 4 h. Then, 10 µL of 0.5 M EDTA, 20 µL of 1 M Tris–HCl pH 6.5, 20 µg of proteinase K were added and incubated at 45°C for 1 h to degrade proteins. DNA was then Phenol–Chloroform extracted and resuspended in 20 µL of H2O. The concentration was then measured.
Purified ChIP-DNA was prepared for sequencing according to the Illumina protocol and sequenced on a HiSeq 2000 sequencer (Illumina) resulting inwith a 36 bp single reads.

value: mESCs

value: WT

tag: Sex

value: Female

tag: strain

tag: chip antibody


title: 300BCG199_d90_PBMC


title: Pulmonary Tuberculosis, 20210923MCX016

tag: tissue

tag: disease state


title: 300BCG199_d0_PBMC

tag: cell type

tag: genotype


title: mESCs_RNF12_mutant

value: Rlim+/- with FLAG-V5-RNF12(H569A,C572A)


title: Fungal Infection, 230621MCX00018

value: Fungal Infection


title: mESCs_RNF12

value: Rlim+/- with FLAG-V5-RNF12 WT


title: 300BCG198_d90_PBMC

tag: individual

tag: time point


title: Fungal Infection, 230616MCX00017


title: 300BCG198_d14_PBMC

tag: protocol


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 15

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 OOHCA SIRS

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

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

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

source_name: Peripheral Blood, Day: 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

tag: sample type

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

tag: patient id

tag: gender

value: M

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived

value: Survived


title: mESCs_REX1_input


title: mESCs_REX1

value: WT with FLAG-V5-REX1


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 210

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

value: F

value: Sepsis

value: Pulmonary


title: Fungal Infection, 230620MCX00025

value: BALF


title: Fungal Infection, 230614MCX00013


title: A8T010_Rectal_Biopsy_After_Last_Dose_Cycle1

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

description:
A8T010_RBX_D260-W37_S73
gene_count_matrix.csv

data_processing:
Sequencing data was demultiplexed and trimmed using Trimmomatic v0.36 to remove adapters and low-quality reads.
Trimmed reads were aligned to the Mmul10 reference genome and transcripts quantified using the Hisat2-StringTie pipeline.
Differential gene expression analysis using the quantified gene transcripts was performed with DESeq2 R package
Assembly: Mmul10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Macaca mulatta

source_name: Rectal Biopsy

extract_protocol:
RNA was extracted with the RNeasy kit with on column DNA digestion (Qiagen).
Library preparation was performed using TruSeq Stranded Total RNA with Ribo-Zero Globin

tag: sample id

value: Rectal Biopsy

tag: treatment

value: galunisertib

tag: time

value: After Last Dose Cycle1


title: 300BCG198_d0_PBMC

value: PBMC

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 198

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

source_name: Peripheral Blood, Day: 2

value: Abdominal

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 117

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

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


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 210

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


title: 300BCG197_d14_PBMC

tag: cell type

tag: genotype

tag: individual

tag: time point


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 117

tag: sample type

tag: patient id

tag: gender

value: M


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 199

tag: disease

tag: disease 2

tag: died/survived


title: Fungal Infection, 230613MCX00010

tag: tissue

tag: disease state

value: Fungal Infection


title: 300BCG197_d90_PBMC

tag: protocol

tag: flowcell

tag: batch id


title: A8T010_Rectal_Biopsy_Before_Cycle1

description:
A8T010_RBX_D245-W35_S66
gene_count_matrix.csv

tag: sample id

tag: treatment

tag: time

value: Before Cycle1


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 198


title: Fungal Infection, 230610MCX00018


title: 300BCG197_d0_PBMC

tag: cell type

tag: genotype

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: A8T010_PBMC_After_Last_Dose_Cycle1

description:
A8T010_PBMC_D260-W37_S59
gene_count_matrix.csv


title: Fungal Infection, 230610MCX00012


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 199

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Survived


title: A8T010_PBMC_After_First_Dose_Cycle1

description:
A8T010_PBMC_D246-W35_S52
gene_count_matrix.csv

tag: tissue

value: After First Dose Cycle1


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 197

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

source_name: Peripheral Blood, Day: 5

value: F

tag: disease 2

tag: died/survived


title: Fungal Infection, 230609MCX00025

tag: disease state


title: A8T010_PBMC_Before_Cycle1

description:
A8T010_PBMC_D245-W35_S45
gene_count_matrix.csv

tag: sample id


title: 300BCG196_d14_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 194

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

value: Sepsis


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 197


title: 300BCG196_d90_PBMC

tag: cell type

tag: genotype

tag: pcr cq

tag: filtered peaks


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 197

tag: sample type

tag: patient id


title: 300BCG195_d90_PBMC

tag: tss enrichment

tag: frip


title: 300BCG196_d0_PBMC


title: A8R095_Rectal_Biopsy_Before_Cycle1

description:
A8R095_RBX_D245-W35_S65
gene_count_matrix.csv

tag: tissue

tag: treatment

tag: time


title: A8R095_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
A8R095_RBX_D260-W37_S72
gene_count_matrix.csv

tag: sample id


title: Fungal Infection, 230603MCX00017

tag: disease state


title: Fungal Infection, 230524MCX00019


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 194

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG195_d14_PBMC

tag: cell type

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: batch id


title: Fungal Infection, 230524MCX00017


title: 300BCG195_d0_PBMC

tag: genotype

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: A8R095_PBMC_After_First_Dose_Cycle1

description:
A8R095_PBMC_D246-W35_S51
gene_count_matrix.csv

tag: tissue

tag: treatment

tag: time


title: A8R095_PBMC_After_Last_Dose_Cycle1

description:
A8R095_PBMC_D260-W37_S58
gene_count_matrix.csv

tag: sample id


title: Fungal Infection, 230523MCX00019

tag: disease state


title: Healthy Control_Peripheral Blood, Day: 1, Patient 236

description: Gene expression in Peripheral Blood, Day: 1 Healthy Control

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Control

tag: disease 2

value: Healthy


title: Healthy Control_Peripheral Blood, Day: 1, Patient 237

tag: died/survived


title: Healthy Control_Peripheral Blood, Day: 1, Patient 165


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 194


title: Healthy Control_Peripheral Blood, Day: 1, Patient 226


title: 300BCG194_d90_PBMC

tag: cell type

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: frip


title: Fungal Infection, 230516MCX00036

tag: tissue

value: BALF


title: 300BCG193_d14_PBMC

tag: genotype

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: A8R095_PBMC_Before_Cycle1

description:
A8R095_PBMC_D245-W35_S44
gene_count_matrix.csv

tag: sample id

tag: treatment

value: galunisertib

tag: time


title: A8L057_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
A8L057_RBX_D260-W37_S71
gene_count_matrix.csv

value: Rectal Biopsy

value: After Last Dose Cycle1


title: Fungal Infection, 230421MCX00028

tag: disease state


title: Fungal Infection, 230527MCX00019


title: 300BCG194_d14_PBMC

value: PBMC

value: ATAC


title: A8L057_PBMC_After_First_Dose_Cycle1

description:
A8L057_PBMC_D246-W35_S50
gene_count_matrix.csv


title: A8L057_PBMC_After_Last_Dose_Cycle1

description:
A8L057_PBMC_D260-W37_S57
gene_count_matrix.csv


title: 300BCG193_d90_PBMC


title: Fungal Infection, 230421MCX00020


title: A8L057_PBMC_Before_Cycle1

description:
A8L057_PBMC_D245-W35_S43
gene_count_matrix.csv


title: Fungal Infection, 230419MCX00028


title: 300BCG193_d0_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 216

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

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

value: Pulmonary

tag: died/survived


title: 300BCG194_d0_PBMC

tag: cell type

tag: individual

tag: time point

tag: protocol

tag: flowcell

tag: frip


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 188

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

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

value: SIRS

value: OOHCA

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 79

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

value: M

value: Abdominal


title: A8L057_Rectal_Biopsy_Before_Cycle1

description:
A8L057_RBX_D245-W35_S64
gene_count_matrix.csv

tag: tissue

value: Before Cycle1


title: Healthy Control_Peripheral Blood, Day: 1, Patient 234

value: F

value: Survived


title: Healthy Control_Peripheral Blood, Day: 1, Patient 238

value: Control

value: Healthy


title: Healthy Control_Peripheral Blood, Day: 1, Patient 235


title: 300BCG192_d90_PBMC

tag: genotype

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 79

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

tag: sample type

tag: patient id

value: Sepsis


title: Fungal Infection, 230414MCX00014

value: BALF

tag: disease state

value: Fungal Infection


title: Fungal Infection, 230516MCX00019


title: A8L014_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
A8L014_RBX_D260-W37_S70
gene_count_matrix.csv

tag: sample id

value: Rectal Biopsy

tag: treatment

value: galunisertib

tag: time

value: After Last Dose Cycle1


title: Fungal Infection, 230406MCX00012


title: 300BCG192_d14_PBMC

tag: cell type

value: PBMC

tag: individual

value: ATAC


title: 300BCG192_d0_PBMC

tag: time point

tag: protocol


title: A8L014_PBMC_After_Last_Dose_Cycle1

description:
A8L014_PBMC_D260-W37_S56
gene_count_matrix.csv


title: Fungal Infection, 230401MCX00022


title: 300BCG191_d90_PBMC

tag: flowcell

tag: frip


title: A8L014_PBMC_After_First_Dose_Cycle1

description:
A8L014_PBMC_D246-W35_S49
gene_count_matrix.csv

tag: tissue

value: After First Dose Cycle1


title: A8L014_Rectal_Biopsy_Before_Cycle1

description:
A8L014_RBX_D245-W35_S63
gene_count_matrix.csv


title: Healthy Control_Peripheral Blood, Day: 1, Patient 233

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

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Fungal Infection, 20210713MCX012


title: Fungal Infection, 20220218MCX014


title: Fungal Infection, 20211115MCX003


title: Healthy Control_Peripheral Blood, Day: 1, Patient 231

tag: sample type


title: Fungal Infection, 20210419MCX006


title: A6X003_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
A6X003_RBX_D260-W37_S75
gene_count_matrix.csv


title: 300BCG191_d0_PBMC

tag: genotype

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Healthy Control_Peripheral Blood, Day: 1, Patient 232

tag: patient id

value: M


title: A6X003_Rectal_Biopsy_Before_Cycle1

description:
A6X003_RBX_D245-W35_S68
gene_count_matrix.csv

tag: sample id

tag: treatment

tag: time


title: 300BCG190_d14_PBMC

tag: cell type

tag: individual

tag: time point

tag: protocol

tag: flowcell


title: 300BCG190_d0_PBMC

tag: frip


title: Fungal Infection, 20210409MCX016

tag: tissue

tag: disease state


title: Healthy Control_Peripheral Blood, Day: 1, Patient 229

description: Gene expression in Peripheral Blood, Day: 1 Healthy Control

tag: sample type

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: A6X003_PBMC_After_First_Dose_Cycle1

description:
A6X003_PBMC_D246-W35_S54
gene_count_matrix.csv


title: A6X003_PBMC_After_Last_Dose_Cycle1

description:
A6X003_PBMC_D260-W37_S61
gene_count_matrix.csv


title: Fungal Infection, 20211208MCX015


title: Fungal Infection, 20211112MCX014


title: 300BCG189_d14_PBMC

tag: genotype

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: 300BCG191_d14_PBMC

tag: cell type

tag: individual


title: 300BCG189_d0_PBMC

tag: time point

tag: protocol


title: A6X003_PBMC_Before_Cycle1

description:
A6X003_PBMC_D245-W35_S47
gene_count_matrix.csv

tag: sample id

tag: treatment

tag: time


title: 08M156_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
08M156_RBX_D260-W37_S74
gene_count_matrix.csv

tag: tissue


title: Healthy Control_Peripheral Blood, Day: 1, Patient 230

tag: sample type

tag: patient id

tag: gender


title: Fungal Infection, 20220104MCX011

tag: disease state


title: 08M156_Rectal_Biopsy_Before_Cycle1

description:
08M156_RBX_D245-W35_S67
gene_count_matrix.csv


title: Fungal Infection, 20210731MCX011


title: 300BCG188_d90_PBMC

tag: genotype

tag: flowcell

tag: frip


title: 300BCG188_d14_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 08M156_PBMC_After_Last_Dose_Cycle1

description:
08M156_PBMC_D260-W37_S60
gene_count_matrix.csv


title: Fungal Infection, 20210810MCX013


title: 300BCG189_d90_PBMC

tag: cell type

tag: individual

tag: tss enrichment


title: Fungal Infection, 20210706MCX012


title: A8L014_PBMC_Before_Cycle1

description:
A8L014_PBMC_D245-W35_S42
gene_count_matrix.csv

tag: sample id


title: 08M156_PBMC_After_First_Dose_Cycle1

description:
08M156_PBMC_D246-W35_S53
gene_count_matrix.csv

tag: treatment


title: 300BCG188_d0_PBMC

tag: time point

tag: protocol


title: 08M156_PBMC_Before_Cycle1

description:
08M156_PBMC_D245-W35_S46
gene_count_matrix.csv

tag: tissue

tag: time


title: Fungal Infection, 20220115MCX010


title: 300BCG187_d14_PBMC


title: Healthy Control_Peripheral Blood, Day: 1, Patient 177

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: Healthy Control_Peripheral Blood, Day: 1, Patient 227


title: 300BCG187_d90_PBMC

tag: genotype

tag: flowcell

tag: batch id

tag: pcr cq

tag: frip


title: 08M134_Rectal_Biopsy_After_Last_Dose_Cycle1

description:
08M134_RBX_D260-W37_S69
gene_count_matrix.csv

tag: sample id


title: Healthy Control_Peripheral Blood, Day: 1, Patient 228


title: Healthy Control_Peripheral Blood, Day: 1, Patient 178


title: Fungal Infection, 20210410MCX005

tag: disease state


title: 300BCG187_d0_PBMC

tag: cell type

tag: individual

tag: time point

tag: filtered peaks

tag: tss enrichment


title: Healthy Control_Peripheral Blood, Day: 1, Patient 163

tag: sample type

tag: patient id


title: Healthy Control_Peripheral Blood, Day: 1, Patient 179

tag: gender

tag: disease


title: Healthy Control_Peripheral Blood, Day: 1, Patient 162

tag: disease 2

tag: died/survived


title: 08M134_Rectal_Biopsy_Before_Cycle1

description:
08M134_RBX_D245-W35_S62
gene_count_matrix.csv

tag: tissue

tag: treatment

tag: time


title: Healthy Control_Peripheral Blood, Day: 1, Patient 160


title: Healthy Control_Peripheral Blood, Day: 1, Patient 161


title: Fungal Infection, 20210604MCX018


title: Fungal Infection, 20210428MCX012


title: Fungal Infection, 20211221MCX010


title: Fungal Infection, 20210413MCX011


title: 08M134_PBMC_After_First_Dose_Cycle1

description:
08M134_PBMC_D246-W35_S48
gene_count_matrix.csv


title: 08M134_PBMC_Before_Cycle1

description:
08M134_PBMC_D245-W35_S41
gene_count_matrix.csv


title: 300BCG186_d90_PBMC

tag: genotype

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq

tag: frip


title: 300BCG186_d0_PBMC

tag: cell type

tag: individual

tag: time point

tag: filtered peaks


title: Fungal Infection, 20210420MCX005

tag: disease state


title: Fungal Infection, 20210625MCX010


title: 08M134_PBMC_After_Last_Dose_Cycle1

description:
08M134_PBMC_D260-W37_S55
gene_count_matrix.csv

tag: sample id


title: 300BCG185_d14_PBMC

tag: tss enrichment


title: Healthy Control_Peripheral Blood, Day: 1, Patient 224

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG185_d0_PBMC

tag: genotype

tag: protocol

tag: flowcell


title: Fungal Infection, 20210924MCX011

tag: tissue


title: Fungal Infection, 20210709MCX011


title: IDR2.3_minusmet_rep2

city: University Park

first: James

last: Lee

state: PA

address: 406 South Frear Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
20 million of 50 bp paired-end reads were aligned to S. cerevisiae genome (sacCer3), FPKM was counted by featureCounts (version 2.0.3).
Assembly: sacCer3
Supplementary files format and content: fasta, deseq2, featureCounts

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in 5 ml of SCD +10x met overnight. 5 ml of fresh SCD +10x was innoculated with 5 µl of saturated culture until OD660 ~0.2. The culture is collected by centrifugation and washed 3x with sterile H2O. The collected culture is then grown in SCD -met media for 2 hrs to reach OD660 ~0.4 and centrifuged at 300g for 4 mins at RT.

extract_protocol:
Standard trizol/chloroform RNA extraction protocol was followed. The extracted RNA was analyzed with Tapestation to check their integrity. RNA with RIN (>7.5) was used for downstream analysis.
Messenger RNA was captured using RNA purification beads (NEB). The eluted mRNA was fragmented and denatured for first and second strand synthesis for conversion into cDNA. The sequencing libraries were constructed using conventional protocols (NEB).

treatment_protocol: The pellet was washed twice with sterile H2O and resuspended in 250 µl of RNA lysis buffer (10mM Tris-HCl pH8.5, 5mM EDTA, 2% SDS, 2% stock 2-mercaptoethanol) and placed on a heat block at 85ºC for 20 mins mixing every 2 mins. The mixture was centrifuged at 12,000g for 5 mins and the supernatant was transferred to a new tube. The supernatant was then mixed with 1 ml of trizol and heated at 65ºC for 20 mins with mixing in between.

tag: cell line

tag: treatment

value: SCD-met


title: IDR2.3_minusmet_rep1


title: full_length_minusmet_rep1


title: Healthy Control_Peripheral Blood, Day: 1, Patient 172


title: Healthy Control_Peripheral Blood, Day: 1, Patient 225


title: Healthy Control_Peripheral Blood, Day: 1, Patient 173


title: Healthy Control_Peripheral Blood, Day: 1, Patient 170


title: Healthy Control_Peripheral Blood, Day: 1, Patient 174


title: full_length_minusmet_rep2


title: Fungal Infection, 20210902MCX005


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 188

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

value: SIRS

value: OOHCA

value: Died


title: 300BCG184_d0_PBMC

tag: cell type

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: frip


title: 300BCG185_d90_PBMC

tag: filtered peaks

tag: tss enrichment


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 187

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

tag: sample type

tag: patient id

tag: gender

tag: disease

value: Pulmonary

value: Survived


title: 300BCG186_d14_PBMC

tag: genotype

tag: protocol


title: full_length_plusmet_rep2

value: SCD+10x met


title: 300BCG183_d90_PBMC

tag: flowcell


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 187

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

value: Sepsis

tag: disease 2

tag: died/survived


title: Fungal Infection, 20220308MCX017

tag: tissue

value: BALF

tag: disease state

value: Fungal Infection


title: Healthy Control_Peripheral Blood, Day: 1, Patient 171

description: Gene expression in Peripheral Blood, Day: 1 Healthy Control

value: F

value: Control

value: Healthy


title: 300BCG184_d14_PBMC

tag: cell type

value: PBMC

tag: individual

tag: time point

value: ATAC


title: full_length_plusmet_rep1

tag: cell line

tag: treatment


title: 300BCG183_d14_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 187

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

tag: sample type

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

tag: patient id

tag: gender

tag: disease


title: 300BCG183_d0_PBMC

tag: genotype

tag: protocol

tag: flowcell


title: Fungal Infection, 20220125MCX016

tag: tissue

tag: disease state


title: Fungal Infection, 20220118MCX016


title: S.cere Met4_IDR2.3-TAP ChIP -met rep1

data_processing:
Paird-end reads of 50bp or 150bp were processed with fastp and aligned to S.cerevisiae genome (sacCer3) with BMW. Peaks were called from aligned bam files with MACS2. bigwig files were generated by deeptools bamCoverage for visualization.
Assembly: sacCer3
Supplementary files format and content: fasta, bigwig

extract_protocol:
genomic DNA
Illumina sequencing library

treatment_protocol: Yeast strains were grown to OD660 of 0.4 in 50 mL of SCD-met medium and crosslinked with 1.39 mL of 37% formaldehyde for 20 mins at room temperature. Crosslinking was quenched by adding 2.7 mL of 2.5 M glycine and incubation for 5 mins. Crosslinked cells were centrifuged at 1882 × g for 3 mins at 4°C, and then washed twice with cold 1x Tris-buffer saline (TBS). Cell pellet was then resuspended in 250 μL of fresh FSPP buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% protease inhibitor cocktail, and 1 mM phenylmethylsulfonyl fluoride (PMSF) and vortexed with ∼300 μL glass beads for 2 cycles of 20 mins with an intervening 10 mins in a 4°C cold room. Another 250 μL of fresh FSPP was added to each sample, and the cap and bottom of tubes were punched with a hot needle so that cell lysate could be collected by centrifuging at 836 × g for 5 mins at 4°C. FSPP (0.5 mL) was added to the cell lysate to resuspend the pellet. The cell lysate was then sonicated using a 30 s on 30 s off cycle at 4°C for 7 cycles. Sonicated cell lysate was transferred to 1.5 mL tube and centrifuged at 17,136 × g for 20 mins at 4°C. Two hundred microliters of supernatant was saved as input. Another 400 μL of supernatant was mixed with 600 μL of FSPP buffer and 20 μL of pre-blocked Magnetic IgG beads and TAP antibody (Thermo) or Rpb3 antibody (Biolegend) for 10–12 hrs at 4ºC. Chromatin was incubated with the beads overnight at 4°C, and then washed sequentially at 4°C with 1xFA-lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), 1xFA-lysis buffer containing 150 mM NaCl, 1xFA-lysis buffer containing 500 mM NaCl, LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8.0), and lastly TE buffer, pH 8.0. Chromatin was then eluted with 400 μL ChIP elution buffer (50 mM NaCl, 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS). Samples were mixed by rotation at 30°C for 30 mins. Beads were pelleted by centrifugation at 17,136 × g and discarded. Five microliters of 20 mg/mL Proteinase K was added to supernatant; 180 μL of 1xFA-lysis buffer, 20 μL of 10% SDS and 5 μL of 20 mg/mL Proteinase K were added into the input samples. ChIP and input samples were then incubated overnight at 65°C to reverse crosslinking. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation. Input samples were then treated with 200 μg RNase A and precipitated with ethanol after adding 20 μg glycogen. Enrichments of target TFs were quantified by quantitative PCR (qPCR). All ChIP experiments were done in biological duplicates.

value: TAP-Antibody (CAB1001)


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 218

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

value: M

tag: disease 2

tag: died/survived


title: S.cere Input rep2

tag: cell line

tag: treatment


title: Fungal Infection, 20210901MCX015


title: 300BCG182_d14_PBMC

tag: cell type

tag: individual

tag: time point

tag: batch id

tag: pcr cq


title: S.cere Input rep1


title: Fungal Infection, 20210923MCX014


title: 300BCG182_d0_PBMC

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 216

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

tag: sample type

tag: patient id

tag: gender

tag: disease


title: S.cere Cbf1-TAP ChIP -met rep2


title: Fungal Infection, 20210612MCX012

tag: tissue

tag: disease state


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 195

tag: disease 2

tag: died/survived


title: S.cere Cbf1-TAP ChIP -met rep1

tag: cell line

tag: treatment


title: 300BCG181_d90_PBMC

tag: cell type

tag: genotype

tag: individual

tag: protocol

tag: flowcell


title: Fungal Infection, 20210330MCX006


title: 300BCG181_d14_PBMC

tag: time point

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: S.cere Met4_IDR2.3-TAP ChIP -met rep2


title: S.cere Cbf1-TAP ChIP +met rep2


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 216

tag: sample type

tag: patient id

tag: gender

tag: disease


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 154

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

tag: disease 2

value: Abdominal

tag: died/survived


title: 300BCG181_d0_PBMC

tag: frip


title: Fungal Infection, 20210915MCX007

tag: tissue

tag: disease state


title: 300BCG182_d90_PBMC

tag: cell type

tag: genotype

tag: individual


title: S.cere Met28-TAP ChIP -met rep2

tag: cell line

tag: treatment


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 113


title: 300BCG180_d90_PBMC

tag: time point

tag: protocol

tag: flowcell

tag: batch id

tag: pcr cq


title: Fungal Infection, 20220114MCX015


title: S.cere Cbf1-TAP ChIP +met rep1


title: Fungal Infection, 20210619MCX013


title: S.cere Met28-TAP ChIP -met rep1


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 211

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

tag: sample type

tag: patient id

tag: gender


title: Fungal Infection, 20210707MCX011


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 193

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG180_d0_PBMC

tag: filtered peaks

tag: tss enrichment

tag: frip


title: S.cere Met28-TAP ChIP +met rep2


title: 300BCG180_d14_PBMC

tag: cell type

tag: genotype

tag: individual


title: Fungal Infection, 20210401MCX008

tag: tissue

tag: disease state


title: 300BCG179_d90_PBMC

tag: time point

tag: protocol

tag: flowcell


title: S.cere Met32-TAP ChIP -met rep2

tag: cell line

tag: treatment


title: S.cere Met28-TAP ChIP +met rep1


title: Fungal Infection, 20210617MCX008


title: Fungal Infection, 20220226MCX022


title: 300BCG179_d14_PBMC

tag: batch id

tag: pcr cq


title: S.cere Met32-TAP ChIP -met rep1


title: Fungal Infection, 20220215MCX021


title: 300BCG179_d0_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 183

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 114

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

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 215


title: Pulmonary Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 113


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 113


title: S.cere Met32-TAP ChIP +met rep1


title: S.cere Met4-TAP ChIP -met rep2


title: Fungal Infection, 20211217MCX014


title: Fungal Infection, 20211130MCX014


title: 300BCG177_d14_PBMC

tag: cell type

tag: genotype

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 112


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 113


title: Fungal Infection, 20220215MCX018

tag: tissue

tag: disease state


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 112


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 112


title: Fungal Infection, 20211119MCX007


title: 300BCG178_d90_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell


title: Fungal Infection, 20220112MCX017


title: S.cere Met32-TAP ChIP +met rep2

tag: cell line

tag: treatment


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 209

tag: sample type

tag: patient id

tag: gender


title: 300BCG176_d14_PBMC

tag: batch id

tag: pcr cq


title: Fungal Infection, 20210907MCX019


title: 300BCG178_d14_PBMC

tag: cell type

tag: genotype


title: Fungal Infection, 20211217MCX015


title: 300BCG177_d0_PBMC

tag: filtered peaks

tag: tss enrichment


title: S.cere Met4-TAP ChIP -met rep1


title: Fungal Infection, 20210904MCX008

tag: tissue


title: 300BCG176_d0_PBMC

tag: frip


title: S.cere Met4-TAP ChIP +met rep2


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 201

tag: disease

tag: disease 2

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 209


title: 300BCG178_d0_PBMC

tag: individual

tag: time point

tag: protocol

tag: flowcell


title: S.cere Met4-TAP ChIP +met rep1

tag: cell line

tag: treatment


title: 300BCG177_d90_PBMC

tag: batch id


title: Carcinoma-associated fibroblasts Replicate 3

city: Chengdu

first: Jin

state: Sichuan

address: West China Hospital of Stomatology, Chengdu

institute: sichuan university

description: lncRNAs or mRNAs expression in the third passage of primary cells

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Carcinoma-associated fibroblasts

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from the third passage of primary cells using Trizol reagent (Tianmo Biotech, Beijing, China) and quantified by measuring the optical density 260/280 and optical density 260/230. For RNA Sequence, RNA integrity was assessed by standard denaturing agarose gel electrophoresis. We performed the RNA sequence with the help of KangChen Bio-tech (Shanghai, China). RNA labeling and array hybridization were performed according to the manufacturer’s protocol.

value: oral squamous cell carcinoma

value: fibroblasts

tag: gender

value: Male


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 200

tag: sample type

tag: patient id

value: Pulmonary

value: Survived


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 215

value: Sepsis


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 201


title: Fungal Infection, 20210810MCX012

value: BALF

tag: disease state


title: 300BCG174_d90_PBMC

tag: cell type

tag: genotype

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: Normal fibroblasts Replicate 2

source_name: Normal fibroblasts

tag: tissue

value: normal oral mucosal tissues


title: 300BCG175_d90_PBMC

tag: individual

tag: frip


title: Carcinoma-associated fibroblasts Replicate 2


title: Fungal Infection, 20210719MCX005

value: Fungal Infection


title: Fungal Infection, 20210601MCX009


title: 300BCG175_d14_PBMC

tag: time point

tag: protocol


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 191

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG174_d0_PBMC

tag: flowcell

tag: batch id


title: Fungal Infection, 20210514MCX011


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 200

tag: sample type

tag: patient id

tag: gender


title: Carcinoma-associated fibroblasts Replicate 1

tag: cell type


title: Normal fibroblasts Replicate 3


title: 300BCG174_d14_PBMC

tag: genotype

tag: pcr cq


title: 1_Lcr35 + Candida SC5314

city: Clermont-ferrand

first: sylvie

last: miquel

address: 28 place henri Dunant

country: France

institute: UCA

data_processing:
Base-calling bcl2fastq v2.20
Quality check - FastQC (v.0.11.9)/MultiQC (v.1.11)
Short reads were mapped against the genome of L. rhamnosus Lcr35 (using BWA software (v0.7.15-r1140). Counting was performed with the software feature Counts (v2.0.3) using a gff file from Nexbiome Therapeutics. DESeq2 (v1.32.0) in R (v4.1.1) has been used to perform normalization of the read counts.
Assembly: Lcr35 (Nexbiome Therapeutics)
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene (gene id|gene symbol) and every sample
Supplementary files format and content: tab-delimited text file include normalized gene counts for every gene (gene id|gene symbol) and every sample

organism: Lacticaseibacillus rhamnosus

growth_protocol: The C. albicans ATCC MYA-2876 strain was grown in Sabouraud dextrose broth medium, and L. rhamnosus Lcr35 in MRS medium containing or not 1 g/L STS for 48 hours. A coculture was prepared by mixing equal volumes of Lcr35 -/+ STS subculture and C. albicans ATCC MYA-2876 subculture. The controls included Lcr35 culture in MRS with and without STS and C. albicans ATCC MYA-2876 culture. The co-cultures were incubated for 6 hours at 37 ⁰C after which they were centrifuged.

extract_protocol:
Total RNA was extracted by the TRIzol method. Harvested cells were immediately submerged in TRIzol reagent (Ambion) on ice (1 mL of TRIzol per 50 cm2 of culture dish surface area). The cells were disrupted using a Fastprep apparatus twice for 45 sec at speed 6. The samples were subsequently centrifuged for 10 min at 14,000 rpm and purified in TRIzol/chloroform (5:1) and chloroform. For RNA precipitation, the samples were incubated in isopropanol at −20°C overnight and centrifuged for 30 min at 10,000 g. RNA samples were washed in ethanol and resuspended in 30 μL of DEPC water (Ambion). Residual DNA in the RNA samples was removed by DNase I treatment (Ambion). The concentration of the RNA samples was determined by Invitrogen Qubit Fluorometer (Thermo Fisher Scientific), and RNA qualities were determined by Agilent RNA pico chip (Agilent Technologies, Santa Clara, California, USA).
Sequencing and analysis of the RNA data were performed by the MGX Genomics platform (Montpellier France). Ribosomal RNA was removed from each total RNA sample and libraries were produced using the Stranded mRNA Prep Ligation Kit, and sequenced using NovaSeq flow cell SP in single-read 100 pb (Illumina, San Diego, California, USA).

tag: strain

tag: environmental condition

value: with Candida albicans


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 200


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 191


title: Fungal Infection, 20210312MCX003

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.

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

tag: disease state


title: 3_Lcr35 + STS

value: with sodium thiosulfate (STS)


title: Fungal Infection, 20220304MCX013


title: Fungal Infection, 20210716MCX019


title: 300BCG173_d0_PBMC

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

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.

value: PBMC

tag: individual

tag: time point

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG172_d90_PBMC

tag: protocol

value: ATAC

tag: flowcell


title: 1_Lcr35 + STS


title: 300BCG175_d0_PBMC

tag: batch id


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 154

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Fungal Infection, 20210601MCX013


title: 300BCG172_d14_PBMC

tag: cell type

tag: genotype

tag: pcr cq


title: Fungal Infection, 20220212MCX010

tag: tissue

tag: disease state


title: 3_Lcr35 + Candida SC5314

tag: strain

tag: environmental condition


title: Fungal Infection, 20211117MCX012


title: 2_Lcr35 + Candida SC5314


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 195

tag: gender

value: F

value: Died


title: Normal fibroblasts Replicate 1


title: Bacterial Infection, 20210412MCX007

value: Bacterial Infection


title: 300BCG171_d14_PBMC

tag: individual

tag: time point

value: HWVYMBBXX

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Fungal Infection, 20210710MCX007


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 115

tag: sample type

tag: patient id

value: M


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 116

tag: disease

tag: disease 2

value: Abdominal


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 191

value: Pulmonary

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 114

value: Survived


title: 300BCG173_d90_PBMC

tag: cell type

tag: genotype

tag: protocol

tag: flowcell

tag: batch id


title: in3127_4_calu3_sars_48hrs

city: Berkeley

first: Diana

last: Bautista

state: California

address: University Avenue

institute: University of California, Berkeley

description:
SARS_calu3_rawcounts.csv
viral_transcipts_calu3_tpm.csv

data_processing:
Mouse trigeminal ganglia gene expression sequences are aligned to grcm39 using defaut settings of STAR
Calu-3 cells gene expression sequences are aligned to grch38 using defaut settings of STAR
SARS-CoV-2 transcripts are aligned to ASM985889v3 using Kallisto
Assembly: grcm39, grch38, ASM985889v3
Supplementary files format and content: Two comma-separated values file (csv) includes raw counts for each sample. One for the mouse TG, another for the Calu-3.
Supplementary files format and content: Two comma-separated values file (csv) includes TPM of Viral Transcripts for each sample. One for the mouse TG, another for the Calu-3.

growth_protocol: Mouse trigeminal ganglia were dissected and incubated in warmed Collagenase P (Roche) in Hanks calcium-free balanced salt solution followed by incubation in 0.25% trypsin with gentle agitation. Cells were washed, triturated, and plated in MEM Eagle's with Earle's BSS medium, supplemented with 10% horse serum (vol/vol), MEM vitamins, penicillin/streptomycin and L-glutamine. Cells were plated on poly-D-Lysine and laminin-coated 96-well plates for infection. Human airway epithelial cell and primary mouse neuron infection: Human adenocarcinoma lung epithelial (Calu-3) cells (ATCC, HTB-55) were maintained with RPMI (Fisher Scientific) supplemented with fetal bovine serum (FBS), L-glutamine, penicillin/streptomycin.

extract_protocol:
RNA are harvest using DNA/RNA Shield (Zymo Research).
lncRNA library with rRNA removal are prepared by Novogene

treatment_protocol: Approximately 500,000 Calu-3 cells were incubated with SARS-CoV-2 (WA1) in medium (10% heat-inactivated FBS, sodium pyruvate, HEPES, L-glutamine, penicillin/streptomycin) diluted in phenol-red free RPMI to an MOI of 1 for 24 or 48 hours. Mouse trigeminal ganglia cells were cultured as described above and plated in a 96-well plate. Eight trigeminal ganglia from 4 animals were combined and plated into 8 wells. TG cultures were infected with 500,000 SARS-CoV-2 virions or medium (mock infection) for 48 hours.

tag: cell line

value: Human Airway Epithelial Cells

value: WT

tag: treatment


title: 300BCG173_d14_PBMC

tag: individual

tag: pcr cq


title: 1_Lcr35

tag: strain

tag: environmental condition

value: neutral


title: 2_Lcr35 + STS


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 211

tag: gender

value: Sepsis


title: Bacterial Infection, 20211123MCX010

tag: tissue

value: BALF

tag: disease state


title: Fungal Infection, 20210909MCX011

value: Fungal Infection


title: 3_Lcr35


title: 300BCG172_d0_PBMC

value: PBMC

tag: time point

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG170_d0_PBMC

tag: cell type

tag: genotype

value: ATAC


title: Fungal Infection, 20210603MCX009


title: Bacterial Infection, 20210807MCX009


title: 300BCG169_d90_PBMC

tag: protocol

tag: flowcell


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 116

tag: sample type

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

tag: patient id

tag: disease

tag: disease 2

tag: died/survived


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 219


title: in3127_5_calu3_sars_48hrs

tag: cell line

tag: treatment


title: Bacterial Infection, 20220322MCX015

tag: tissue


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 212

tag: gender

value: F


title: in3126_4_calu3_sars_24hrs


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 203


title: 2_Lcr35

tag: strain

tag: environmental condition


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 114


title: Bacterial Infection, 20210811MCX014

tag: disease state


title: 300BCG171_d0_PBMC

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: 300BCG171_d90_PBMC

tag: cell type

tag: genotype

tag: protocol

tag: flowcell


title: 300BCG167_d14_PBMC


title: Bacterial Infection, 20220305MCX010


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 190

tag: sample type

tag: patient id

tag: disease

value: SIRS

tag: disease 2

value: OOHCA

tag: died/survived


title: in3127_3_calu3_sars_48hrs

tag: cell line

tag: treatment


title: Abdominal Sepsis_Peripheral Blood, Day: Discharge from ICU, Patient 219

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

tag: gender


title: 300BCG170_d90_PBMC

tag: individual

tag: time point

value: HWVYMBBXX

tag: batch id


title: 300BCG170_d14_PBMC

tag: pcr cq

tag: filtered peaks

tag: tss enrichment


title: in3126_2_calu3_mock_24hrs

tag: cell type

tag: genotype


title: Bacterial Infection, 20210402MCX009

tag: tissue

tag: disease state

value: Bacterial Infection


title: 300BCG167_d0_PBMC

tag: protocol

tag: flowcell

tag: frip


title: in3127_1_calu3_mock_48hrs


title: in3127_2_calu3_mock_48hrs


title: in3126_25_calu3_mock_48hrs


title: in3126_6_calu3_sars_24hrs


title: Bacterial Infection, 20210827MCX011


title: 300BCG169_d14_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 193

tag: sample type

tag: patient id

value: M

tag: disease

tag: disease 2

tag: died/survived


title: 300BCG166_d90_PBMC

tag: individual

tag: time point


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 218

tag: gender

value: Died


title: Bacterial Infection, 20220308MCX015


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 219

value: Abdominal

value: Survived


title: Bacterial Infection, 20220127MCX022


title: 300BCG166_d14_PBMC

tag: batch id

tag: pcr cq

tag: filtered peaks


title: ventral FeBO_maturation_6months

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

institute: Hubrecht Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina output demultiplexed (bcl files) converted to fastq files using mkfastq (CellRanger v5.0.1)
Alignment, filtering, barcode and UMI counting done using CellRanger count (CellRanger v5.0.1)
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: Per sample matrix.mtx, features.tsv, and barcodes.tsv files

source_name: human fetal ventral forebrain organoids

extract_protocol:
FeBOs were cut into small pieces, and dissociated using the Neural Dissociation kit (P) (Miltenyi). Cells were washed 3 times with HBSS. To enhance viability, the Dead Cell Removal kit (Miltenyi) was used with MS columns after dissociation. Live cells were manually counted using Trypan blue and resuspended in 1X PBS containing 0.04% BSA at an optimal concentration of 700-1200 cells/ul.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.0/v3.1

value: human fetal ventral forebrain organoids

tag: genotype

value: wild type

tag: treatment

value: maturation


title: Bacterial Infection, 20210707MCX007

tag: tissue

value: BALF

tag: disease state


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 212

value: Sepsis


title: in3126_5_calu3_sars_24hrs

tag: cell line

tag: cell type

value: Human Airway Epithelial Cells

value: WT


title: 300BCG169_d0_PBMC

value: PBMC

tag: protocol

value: ATAC

tag: flowcell

tag: tss enrichment

tag: frip


title: Bacterial Infection, 20220127MCX014


title: 300BCG167_d90_PBMC


title: 300BCG165_d90_PBMC


title: 300BCG165_d0_PBMC


title: Bacterial Infection, 20220318MCX013


title: in3126_3_calu3_mock_24hrs


title: dorsal FeBO_expansion_3months

description: 10x Genomics

source_name: human fetal dorsal forebrain organoids

value: human fetal dorsal forebrain organoids

value: expansion


title: Bacterial Infection, 20220311MCX014


title: Bacterial Infection, 20211028MCX021


title: in3126_1_calu3_mock_24hrs


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 138

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: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 193

tag: gender

value: M


title: ventral FeBO_expansion_6months

description: 10x Genomics


title: 300BCG166_d0_PBMC

tag: individual

tag: time point

value: HWVYMBBXX

tag: batch id

tag: pcr cq

tag: filtered peaks


title: 300BCG163_d90_PBMC

tag: genotype


title: Bacterial Infection, 20220105MCX008

tag: tissue

tag: disease state

value: Bacterial Infection


title: dorsal FeBO_maturation_6months

description: 10x Genomics

tag: treatment


title: Bacterial Infection, 20211124MCX016


title: dorsal FeBO_expansion_6months

description: 10x Genomics


title: 300BCG165_d14_PBMC

tag: cell type

tag: protocol

tag: flowcell

tag: tss enrichment


title: Bacterial Infection, 20211120MCX006


title: dorsal FeBO_maturation_3months

description: 10x Genomics


title: Bacterial Infection, 20210916MCX006


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 183

tag: sample type

tag: patient id

tag: disease

value: Survived


title: 300BCG162_d90_PBMC

value: HVCTNBBXX

tag: frip


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 208

tag: gender

tag: disease 2

tag: died/survived

value: Died


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 137

value: F

value: Abdominal


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 181

value: Sepsis


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 181


title: 300BCG164_d0_PBMC

tag: individual

tag: time point

tag: batch id

tag: pcr cq


title: HEK293 cells, whole cell extract, triple KD, rep3

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

tag: cell line

tag: sirna

value: triple KD

tag: fraction

value: WCE


title: Bacterial Infection, 20211116MCX012

tag: tissue

value: BALF

tag: disease state


title: 300BCG162_d14_PBMC

tag: cell type

value: PBMC

tag: genotype

tag: protocol

value: ATAC

tag: flowcell

tag: filtered peaks

tag: tss enrichment


title: HEK293 cells, whole cell extract, control, rep1

value: control


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 183

tag: sample type

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

tag: patient id

tag: gender

tag: disease

tag: disease 2


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 205

tag: died/survived


title: 300BCG164_d14_PBMC

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: frip


title: HEK293 cells, whole cell extract, control, rep2

tag: cell line

tag: sirna

tag: fraction


title: Bacterial Infection, 20211021MCX010

tag: tissue

tag: disease state


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 138

value: Pulmonary


title: Bacterial Infection, 20210729MCX010


title: HEK293 cells, cytoplasmic fraction, triple KD, rep3

value: cytoplasmic


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 206

value: M


title: HEK293 cells, whole cell extract, triple KD, rep2


title: Bacterial Infection, 20211015MCX011

value: Bacterial Infection


title: 300BCG163_d14_PBMC

tag: cell type

tag: genotype

tag: protocol

tag: flowcell

value: HWVYMBBXX

tag: filtered peaks

tag: tss enrichment


title: Bacterial Infection, 20210716MCX016


title: HEK293 cells, whole cell extract, triple KD, rep1


title: Bacterial Infection, 20210924MCX012


title: HEK293 cells, whole cell extract, control, rep3


title: Bacterial Infection, 20210612MCX010


title: 300BCG163_d0_PBMC


title: 300BCG161_d14_PBMC

value: HVCTNBBXX


title: HEK293 cells, cytoplasmic fraction, triple KD, rep1


title: Bacterial Infection, 20211103MCX004


title: 300BCG161_d0_PBMC


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 138

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: Bacterial Infection, 20210820MCX014


title: Bacterial Infection, 20210427MCX011


title: 300BCG160_d14_PBMC

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: frip


title: 300BCG162_d0_PBMC

tag: cell type


title: HEK293 cells, cytoplasmic fraction, control, rep2

tag: cell line

tag: sirna

tag: fraction


title: Bacterial Infection, 20210707MCX008

tag: tissue

tag: disease state


title: HEK293 cells, cytoplasmic fraction, triple KD, rep2


title: 300BCG161_d90_PBMC

tag: genotype

tag: protocol

tag: flowcell

tag: filtered peaks

tag: tss enrichment


title: Bacterial Infection, 20211106MCX005


title: 300BCG159_d90_PBMC


title: HEK293 cells, nuclear fraction, triple KD, rep3

value: nuclear


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 204

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived


title: OOHCA SIRS_Peripheral Blood, Day: Discharge from ICU, Patient 190

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

value: SIRS

value: OOHCA


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 204

value: Sepsis


title: Bacterial Infection, 20210820MCX013


title: HEK293 cells, cytoplasmic fraction, control, rep3


title: HEK293 cells, nuclear fraction, triple KD, rep1

value: triple KD


title: 300BCG158_d14_PBMC

tag: cell type

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: frip


title: Bacterial Infection, 20210419MCX007

tag: tissue

value: BALF

tag: disease state


title: OOHCA SIRS_Peripheral Blood, Day: 2, Patient 190


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 203


title: HEK293 cells, cytoplasmic fraction, control, rep1

tag: cell line

tag: sirna

tag: fraction


title: HEK293 cells, nuclear fraction, triple KD, rep2


title: OOHCA SIRS_Peripheral Blood, Day: 5, Patient 190

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

tag: sample type


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 203

tag: patient id


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 184

tag: gender

value: Abdominal


title: Healthy Control_Peripheral Blood, Day: 1, Patient 175

value: F

tag: disease

value: Control

value: Healthy


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 184

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

tag: disease 2


title: 300BCG159_d0_PBMC

value: PBMC

tag: genotype

tag: protocol

value: ATAC

tag: flowcell

tag: filtered peaks

tag: tss enrichment


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 184

value: M

tag: died/survived


title: HEK293 cells, nuclear fraction, control, rep3

value: control


title: Bacterial Infection, 20210720MCX011

value: Bacterial Infection


title: Bacterial Infection, 20210807MCX013


title: 300BCG159_d14_PBMC

tag: cell type

tag: individual

tag: time point

value: HVCTNBBXX

tag: batch id

tag: pcr cq

tag: frip


title: 300BCG160_d0_PBMC


title: Bacterial Infection, 20210907MCX021

tag: tissue

tag: disease state


title: HEK293 cells, nuclear fraction, control, rep2

tag: cell line

tag: sirna

tag: fraction

value: nuclear


title: 300BCG157_d0_PBMC

tag: genotype


title: HEK293 cells, nuclear fraction, control, rep1


title: Bacterial Infection, 20220224MCX007


title: HCT116 cells, SAFB1+SLTM KD, rep2

value: SAFB1+SLTM KD


title: 300BCG157_d14_PBMC

tag: protocol


title: Bacterial Infection, 20210626MCX008


title: 300BCG156_d90_PBMC

tag: flowcell


title: Bacterial Infection, 20210604MCX008


title: 300BCG158_d0_PBMC

tag: filtered peaks


title: 300BCG156_d14_PBMC

tag: tss enrichment


title: HCT116 cells, SAFB1+SLTM KD, rep1


title: Bacterial Infection, 20210629MCX008


title: 300BCG155_d14_PBMC


title: HCT116 cells, SAFB1+SLTM KD, rep3


title: 300BCG155_d0_PBMC


title: Bacterial Infection, 20210625MCX009


title: Abdominal Sepsis_Peripheral Blood, Day: 2, Patient 111

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Survived


title: tripleKD_DHX9_rep3

description:
RNAseI digested RNA
triple-DHX9_reps-merged.plus.CPM.bw
triple-DHX9_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)

value: Flp-In T-Rex HEK293

tag: agent

value: rabbit polyclonal Ab against DHX9

value: siRNAs against SAFB1, SAFB2 and SLTM


title: Bacterial Infection, 20211012MCX008

tag: tissue

value: BALF


title: Abdominal Sepsis_Peripheral Blood, Day: 1, Patient 111

value: Sepsis

value: Abdominal


title: Abdominal Sepsis_Peripheral Blood, Day: 5, Patient 111


title: 300BCG154_d90_PBMC

tag: cell type

tag: individual

tag: time point

tag: batch id

tag: pcr cq

tag: frip


title: Bacterial Infection, 20220301MCX019

tag: disease state


title: tripleKD_DHX9_rep2

tag: cell line

tag: sirna


title: 300BCG154_d14_PBMC

tag: genotype

tag: protocol

tag: flowcell

tag: filtered peaks

tag: tss enrichment


title: 300BCG156_d0_PBMC


title: tripleKD_DHX9_rep1


title: Bacterial Infection, 20211223MCX009


title: Pulmonary Sepsis_Peripheral Blood, Day: 1, Patient 158

tag: sample type

tag: patient id

tag: gender

value: F

tag: disease

tag: disease 2

value: Pulmonary

tag: died/survived


title: Healthy Control_Peripheral Blood, Day: 1, Patient 176

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

value: Control

value: Healthy


title: 300BCG154_d0_PBMC

tag: cell type

value: PBMC

tag: individual

tag: time point

value: ATAC

tag: batch id


title: Bacterial Infection, 20211117MCX016

tag: tissue

tag: disease state

value: Bacterial Infection


title: tripleKD_1H4_rep3

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

tag: cell line

tag: agent

tag: sirna


title: Bacterial Infection, 20220122MCX010


title: tripleKD_1H4_rep2


title: 300BCG153_d14_PBMC

tag: genotype

tag: protocol

tag: flowcell

value: HVCTNBBXX

tag: pcr cq

tag: filtered peaks

tag: frip


title: 300BCG153_d0_PBMC

tag: tss enrichment


title: Bacterial Infection, 20210929MCX011


title: tripleKD_1H4_rep1


title: Bacterial Infection, 20210904MCX014


title: 300BCG152_d14_PBMC


title: Bacterial Infection, 20210603MCX015


title: Pulmonary Sepsis_Peripheral Blood, Day: 5, Patient 159

tag: sample type

tag: patient id

tag: gender

tag: disease

tag: disease 2

tag: died/survived

value: Died


title: 300BCG151_d14_PBMC

tag: cell type

tag: individual

tag: time point

tag: batch id


title: OOHCA SIRS_Peripheral Blood, Day: 1, Patient 156

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

value: SIRS

value: OOHCA


title: Pulmonary Sepsis_Peripheral Blood, Day: 2, Patient 159


title: Bacterial Infection, 20210420MCX006

tag: tissue

tag: disease state


title: control_DHX9_rep2

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

tag: cell line

value: Flp-In T-Rex HEK293

tag: agent

value: rabbit polyclonal Ab against DHX9

tag: sirna

value: control


title: 300BCG153_d90_PBMC

tag: genotype

tag: protocol

tag: flowcell

tag: pcr cq

tag: filtered peaks

tag: frip


title: control_DHX9_rep1


title: 300BCG151_d0_PBMC

tag: tss enrichment