title: Fibroblasts from Sotos patient_7

description:
Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.
US_257236337127_SoS1_3

value: Sotos patient


title: Embry.63.d Le 320_(SNOWBALLs520824F)

status: Public on Aug 03 2022

type: RNA

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description:
Gene expression data from liver of 63 dpc of F2 population basedbreed Pi and DL.
liver samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. liver samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: liver tissue from 63 dpc pig

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: tissue

value: liver

tag: genotype

value: F2 based DLXPi

tag: age

value: 63 dpc


title: EARLI 11111_No-Sepsis

type: SRA

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

country: USA

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Alignment against human genome- star
Fitering to retain samples with 50,000 gene counts
Differential expression with R package DESeq2
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

organism: Homo sapiens

source_name: Plasma

growth_protocol: Clinical plasma specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

tag: disease state

value: No-Sepsis

value: Plasma

tag: gender

value: Female

tag: race

value: Caucasian

tag: ethnicity


title: Taf7l konckin RS (KIRS1)rep1

city: Nanjing

first: Li

last: Fangfang

address: 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu Province,

country: China

institute: Nanjing Medical University

data_processing:
Illumina HiSeqTM 4000 system used for basecalling.
Clean data were obtained by filtering low-quality data and trimming adaptors ,and subsequently mapped to the mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: Differential expression profile for mutant knockin group and wildtype group

organism: Mus musculus

source_name: round spermatids

extract_protocol:
Pachytene spermatocytes and round spermatids from Taf7l wide-type and knock-in adult testes have been isolated by STA-PUT, and RNA was harvested using Trizol reagent.TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: testis

value: konckin


title: Relapsed, replicate 2, scRNAseq

city: Memphis

first: Jun

last: Yang

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were run on Cell Ranger version 3.1.0 to generate feature barcode matrices and information for clustering and gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Peripheral blood leukocytes were collected as aforementioned and cryopreserved using CryoStor® CS10 (STEMCELL, 07930), and stored in liquid nitrogen. 10% of the cells from each mouse were stained with CD4, CD8, and CD3 antibodies and used for cell population analysis by flow cytometry.  After 100 days of the experiment, six mice remained in remission, and six mice relapsed. Cells were thawed from liquid nitrogen, and live cells were collected by BD Biosciences Aria cell sorters.  We mixed the peripheral blood leukocyte from three mice as one scRNA-seq sample. Thus, we have two cured and two relapsed samples in total.
Libraries were prepared following the Chromium Next GEM 148 Single Cell 5’ Library and Gel Bead Kit v1.1 protocol and sequenced on Illumina NovaSeq 6000 149 system  (Illumina).

value: Peripheral blood

tag: cell line

value: Peripheral blood leukocytes

tag: cell type

value: 10 weeks old


title: Fibroblasts from Sotos patient_2

city: Genova

first: Giuseppina

last: Conteduca

state: GE

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale San Martino

description:
Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.
6US09453725_SoS1_3

hyb_protocol: Cyanine-3-CTP-labeled cRNA was hybridized onto the SurePrint G3 microarray chips  (Design ID: G4851C), which contained 50,599 probes for 32,776 human mRNA and 17,438 human lncRNAs, which are derived from authoritative databases, including RefSeq, Ensemble, GenBank, and the Broad Institute. After hybridization and washing, processed slides were scanned with the Agilent microarray scanner (Agilent Technologies).

scan_protocol: Raw data were extracted using Feature Extraction (version 12.0.1.1; Agilent Technologies).

data_processing: Data pre-processing including normalization and filters, were carried out by Genespring software (version 14.3; Agilent Technologies). Raw data was normalized by a 75 percentile shift, log2-transformed and shifted to the median of all samples.

source_name: Fibroblasts from Sotos patient

label_protocol: The microarray hybridization was performed using Agilent One Color  microarray gene expression kit and SurePrint G3, 8x60K Human Gene Expression V3 array (Agilent Technologies, Santa Clara, California, USA) following established protocols.

extract_protocol: Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, MA, USA). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by Agilent 2100 Bioanalyser.

value: skin sample

value: fibroblasts

tag: subject status


title: Embry.63.d Le 376_(SNOWBALLs520824F)


title: Embry.63.d Le377_(SNOWBALLs520824F)


title: EARLI 11097_Sepsisperiph

value: Sepsisperiph

value: Male

value: LatinX


title: Taf7l wildtype RS (WTRS2) rep2

value: wild type


title: EARLI 11062_SepsisBSI

value: SepsisBSI

value: African American


title: Cured, replicate1, scRNAseq

description: 10x Genomics


title: Taf7l wildtype RS (WTRS3) rep3


title: Taf7l konckin RS (KIRS3)rep3


title: Fibroblasts from Sotos patient_1

description:
Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.
4US09453725_SoS1_1

value: Sotos patient


title: 3MC-C3 Empty Vector rep3 [C33EV]

city: Madrid

first: Luis

last: del Peso

state: Madrid

address: Arzobispo Morcillo

department: Biochemistry

country: Spain

institute: Universidad Autonoma de Madrid

data_processing:
bcl2fastq v2.20.0.422 software was used for base calling
Pseudocounts for each gene were obtained from sequencing reads with Salmon software 34 using RefSeq 35 mRNA sequences for mouse genome assembly GRCm38/mm10 as reference
Assembly: GRCm38/mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: sarcoma cell line

extract_protocol:
Total RNA from cell and mice tumor samples (after tissue homogenization with a Polytron), were performed as previously described
cDNA libraries were generated from 600 ng of RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina). Libraries were sequenced on an Ilumina HiSeq2000 apparatus according to the manufacturer’s protocols

value: muscle

value: sarcoma


title: 3MC-C3 shRNA Erk5 rep2 [C32SH]

value: Erk5 Knock-down


title: 3MC-C3 shRNA Erk5 rep3 [C33SH]


title: EARLI 11086_Sepsissuspected

value: Sepsissuspected

value: Plasma

value: Asian


title: EARLI 11052_Sepsisperiph

value: Female


title: EARLI 11046_Indeterm

value: Indeterm

value: Caucasian


title: Relapsed, replicate 1, scRNAseq

description: 10x Genomics

value: Peripheral blood

value: Peripheral blood leukocytes

value: 10 weeks old


title: EARLI 11035_No-Sepsis

value: No-Sepsis


title: 3MC-C3 shRNA Erk5 rep1 [C31SH]


title: Taf7l konckin PS (KIPS3)rep3

source_name: pachytene spermatocytes

value: testis

value: konckin


title: 3MC-C3 Empty Vector rep2 [C32EV]

value: wild type


title: Taf7l wildtype PS (WTPS3) rep3


title: EARLI 11028_No-Sepsis


title: 3MC-C3 Empty Vector rep1 [C31EV]


title: Embry.63.d Le 340_(SNOWBALLs520824F)

value: liver

value: F2 based DLXPi

value: 63 dpc


title: Taf7l konckin PS (KIPS1)rep1


title: EARLI 11022_No-Sepsis

value: African American


title: Taf7l wildtype PS (WTPS2) rep2


title: Taf7l wildtype RS (WTRS1) rep1


title: 3MC-C1 shRNA Erk5 rep2 [C12SH]

value: muscle

value: Erk5 Knock-down

value: sarcoma


title: EARLI 11017_No-Sepsis

value: Plasma

value: Male

value: Asian


title: EARLI 10993_SepsisBSI

value: SepsisBSI

value: Female


title: Taf7l wildtype PS (WTPS1) rep1


title: 3MC-C1 Empty Vector rep2 [C12EV]


title: 3MC-C1 shRNA Erk5 rep1 [C11SH]


title: RNA-Seq neural D10 GLI1 OE rep3

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description: polyA mRNA-seq

data_processing: Differentialy expressed genes due to Gli1 overexpression at Day 5 and Day 10

source_name: immature neurons

growth_protocol: mESCs were maintained and differentiation was performed as previously described (Sasai et al., 2014; Ying and Smith, 2003).

extract_protocol:
RNA was harvested samples with a Nucleospin RNA extraction kit (Machery-Nagel 740955.250).
TruSeq RNA Sample prep kit v2 (Illumina RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were quantitated on an Agilent Bio-Analyzer and pooled in equimolar amounts. Pooled libraries were sequenced on the HiSeq4000 in Rapid Run Mode following the manufacturer's protocols to generate stranded single-end reads of 50bp.

treatment_protocol: GLI1 OE samples were treated with 500ng/ml doxycycline for 48 hours from D3 to D5. Cells were then washed and the differentiation was continued until the day of harvest.

value: mESC-derived neurons

tag: treatment

value: 500ng/ml doxycycline from D3-5

tag: day of harvest


title: Taf7l konckin PS (KIPS2)rep2

value: testis


title: EARLI 10983_No-Sepsis

value: No-Sepsis

value: Caucasian


title: RNA-Seq neural D10 GLI1 OE rep2

description: polyA mRNA-seq


title: 3MC-C1 Empty Vector rep1 [C11EV]

value: wild type


title: RNA-Seq neural D10 GLI1 OE rep1

description: polyA mRNA-seq


title: EARLI 10958_Sepsisperiph

value: Sepsisperiph


title: RNA-Seq neural D10 control rep3

description: polyA mRNA-seq

value: untreated


title: mouse E12.5 submandibular glands_rep2

city: Beijing

first: Siqi

last: Zhang

address: 22# Zhongguancun South Avenue, Haidian District

department: Department of Oral and Maxillofacial Surgery School and Hospital of Stomatology

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was generated by quality control and then mapped to the reference genome (GRCh38_release95) using Hisat2.
Quantification of gene expression levels were measured by fragments per kilobase of transcript per million fragments mapped (FPKM) from Florea L,. F1000Res. 2013. In the equation, cDNA Fragments represents the number of PE reads mapped to the specific transcript; Mapped Fragments (Millions) is the number of all mapped reads, which is counted as 10^6; Transcript Length(kb) is the length of transcript in unit of 10^3 b.
Assembly: GRCm38
Supplementary files format and content: tab-delimited list files include FPKM values for each Sample

source_name: mouse E12.5 submandibular glands

growth_protocol: mESCs were seeded in 96-well U-bottom ultra-low attachment plates at a density of 3,000 cells per well ( day 0). On day 1, half of the medium was changed and after which the medium must contain 2% growth factor reduced Matrigel. 2ng/ml BMP4 was added to the cultures to stimulate the differentiation of OE at day 3. On day 4, the aggregates were treated with 25ng/ml bFGF and 1μM RA to induce the early salivary gland epithelium. On day 6, healthy aggregates were collected and transferred to 24-well ultra-low attachment plates with fresh medium containing 200ng/ml FGF10.

extract_protocol:
Total RNA was extracted from mES derived iE-SGs at day 10 using RNeasy mini kit (Qiagen) following the manufacturer’s instructions. RNA concentration and quality were measured by NanoDrop 2000 and the Agilent Bioanalyzer 2100 system.
Sequencing libraries were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: All samples were untreated.

value: mouse embryonic salivary glands


title: mouse E12.5 submandibular glands_rep1


title: EARLI 10957_Sepsisperiph


title: mES-derived induced embryonic salivary glands _rep2


title: RNA-Seq neural D10 control rep2

description: polyA mRNA-seq


title: EARLI 10929_SepsisBSI

value: African American


title: RNA-Seq neural D10 control rep1

description: polyA mRNA-seq


title: EARLI 10846_Sepsissuspected

value: Sepsissuspected


title: RNA-Seq neural D5 GLI1 OE rep4

description: polyA mRNA-seq

source_name: neural progenitor cells

value: mESC-derived neural progenitor cells


title: EARLI 10778_No-Sepsis

value: Plasma


title: EARLI 10755_Sepsisperiph


title: Fetal-Liver [7_1]

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the Mouse mm10 genome using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts with HTSeq.
Variance stabilization performed using log2 scaling.
Genome_build: mm10 mouse
Supplementary_files_format_and_content: tab-delimited text file include log2 counts values for each sample

source_name: Fetal-Liver

growth_protocol: Induced endothelial cells (iEC) and induced hepatic stem cells (iHepSC) were generated by direct conversion through delivering ETV2 or Hnf4alpha and Oct4 to the fibroblast. Generated iHepSCs were used to form liver organoids, and liver assembloids (iHEA) were generated by integrating iECs in the liver organoids (iHLO).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iHEA were transplanted in the kidney subcapsular area of 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC)-induced cholestatic liver fibrosis mouse model to analyze therapeutic potential of iHEA.


title: Fetal-Liver [7_2]

description: replicate 1


title: RNA-Seq neural D5 GLI1 OE rep3

description: polyA mRNA-seq


title: EARLI 10456_Sepsisperiph

value: Male


title: Adult-Liver [6_1]

description: replicate 1

source_name: Adult-Liver


title: RNA-Seq neural D5 GLI1 OE rep2

description: polyA mRNA-seq


title: RNA-Seq neural D5 GLI1 OE rep1

description: polyA mRNA-seq


title: EARLI_50749_Sepsisperiph


title: EARLI_50723_SepsisBSI


title: EARLI_50722_Sepsisperiph

value: Asian


title: RNA-Seq neural D5 control rep3

description: polyA mRNA-seq


title: 3D-iHEA [5_2]

description: replicate 1

value: 3 Dimensional Hepatic Endothelial Assembloids (3D-iHEAs)


title: Fibroblasts from Sotos patient_4

description:
Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.
10US09453725_SoS2_3

value: skin sample

value: fibroblasts

value: Sotos patient


title: RNA-Seq neural D5 control rep2

description: polyA mRNA-seq


title: RNA-Seq neural D5 control rep4

description: polyA mRNA-seq


title: 3D-iHEA [5_1]

description: replicate 1


title: 3D-iHA [4_2]

description: replicate 1

value: 3 Dimensional Hepatic Assembloids (3D-iHAs)


title: mES-derived induced embryonic salivary glands _rep1


title: RNA-Seq neural D5 control rep1

description: polyA mRNA-seq


title: 3D-iHA [4_1]

description: replicate 1


title: EARLI_50685_No-Sepsis

value: No-Sepsis

value: Other

value: LatinX


title: RNA-Seq D12 GLI1 OE rep2

description: polyA mRNA-seq

data_processing: none provided by the submitter

molecule: polyA RNA

source_name: immature cardiomyocytes

growth_protocol: mESCs were maintained and differentiated into CMs as previously described (Kattman et al., 2011).

treatment_protocol: GLI1 OE samples were treated with 500ng/ml doxycycline for 24 hours from D5 to D6. Cells were then washed and the differentiation was continued until the day of harvest.

value: mESC-derived cardiomyocytes

value: 500ng/ml doxycycline from D5-6


title: EARLI_50692_Sepsisperiph

value: Sepsisperiph


title: 2D-iHepSCiEC [3_2]

description: replicate 1

value: 2 Dimensional induced Hepatic Stem Cells integrating induced endothelial cells (2D-iHepSCECs)


title: EARLI_50695_SepsisBSI

value: SepsisBSI

value: Caucasian


title: EARLI 10741_Sepsisperiph

value: Plasma

value: Female


title: EARLI_50681_No-Sepsis

value: Male

value: African American


title: 2D-iHepSCiEC [3_1]

description: replicate 1


title: 2D-iHepSC [2_2]

description: replicate 1

value: 2 Dimensional induced Hepatic Stem Cells (2D-iHepSCs)


title: Adult-Liver [6_2]

description: replicate 1


title: EARLI_50660_Sepsisperiph


title: RNA-Seq D12 GLI1 OE rep1

description: polyA mRNA-seq


title: 2D-iHepSC [2_1]

description: replicate 1


title: RNA-Seq D12 control rep2

description: polyA mRNA-seq

value: untreated


title: EARLI_50661_Sepsisperiph

value: Asian


title: RNA-Seq D8 GLI1 OE rep2

description: polyA mRNA-seq


title: Fib [1_2]

description: replicate 1

source_name: Fib

value: Fibroblast


title: EARLI_50647_No-Sepsis

value: No-Sepsis


title: heart, Dst-b mutant_3

city: Niigata

first: Nozomu

last: Yoshioka

address: 1－757, Asahimachi-dori, Chuo-ku

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata university

data_processing:
alignment with OLego
to have BAM and Bed file
transcript level and alternative splicing events with Quantas
Genome_build: mm10
Supplementary_files_format_and_content: .txt gene_id gene_symbol, Tag_Number, RPKM

source_name: heart

growth_protocol: Dst-b mutant homozygotes were generated by crossing Dst-b mutant heterozygotes

extract_protocol:
Total RNA was obtained from independent three replicates of mouse hearts from control and Dst-b mutants. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using standard Illumina protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep Kit (E7760)

value: heart

value: Dst-b mutant


title: Fib [1_1]

description: replicate 1


title: RNA-Seq D8 GLI1 OE rep1

description: polyA mRNA-seq

value: mESC-derived cardiomyocytes


title: heart, Dst-b mutant_2


title: heart, Dst-b mutant_1


title: EARLI_50642_Sepsisperiph


title: EARLI_50634_No-Sepsis


title: RNA-Seq D6 GLI1 OE rep3

description: polyA mRNA-seq

source_name: cardiac progenitor cells

value: mESC-derived cardiac progenitor cells

value: 500ng/ml doxycycline from D5-6


title: RNA-Seq D8 control rep2

description: polyA mRNA-seq


title: RNA-Seq D6 GLI1 OE rep1

description: polyA mRNA-seq


title: EARLI_50640_Sepsisperiph

value: Sepsisperiph

value: Other

value: LatinX


title: heart, WT_4

value: WT


title: RNA-Seq D6 GLI1 OE rep2

description: polyA mRNA-seq


title: RNA-Seq D8 control rep1

description: polyA mRNA-seq


title: RNA-Seq D6 control rep2

description: polyA mRNA-seq


title: EARLI_50626_Sepsisperiph

value: Plasma

value: Female


title: EARLI_50624_Sepsisperiph

value: Male

value: Caucasian


title: heart, WT_1


title: RNA-Seq D12 control rep1

description: polyA mRNA-seq

value: untreated


title: MZ_TLR9WT.rep4

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: Marginal zone B cells_3-way BM chimera_sorted cells

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takata Cat# 634894).

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

value: MRL/lpr (MRL.Faslpr)

tag: genotype/variation

value: 3-way BM chimera_sorted cells

value: Marginal zone B cells


title: heart, WT_3

value: heart


title: RNA-Seq D6 control rep3

description: polyA mRNA-seq


title: MZ_TLR9WT.rep3


title: EARLI_50635_Sepsisperiph


title: RNA-Seq D5 control rep4

description: polyA mRNA-seq


title: EARLI_50623_Sepsisperiph

value: African American


title: MZ_TLR9WT.rep2


title: EARLI_50621_SepsisBSI

value: SepsisBSI

value: Asian


title: RNA-Seq D6 control rep1

description: polyA mRNA-seq

value: mESC-derived cardiac progenitor cells


title: EARLI_50618_SepsisBSI


title: RNA-Seq D5 control rep2

description: polyA mRNA-seq


title: EARLI_50611_Sepsisperiph

value: Sepsisperiph


title: EARLI_50625_No-Sepsis

value: No-Sepsis


title: EARLI_50604_Sepsisperiph


title: MZ_TLR9P915H.rep4


title: MZ_TLR9WT.rep1


title: RNA-Seq D5 control rep1

description: polyA mRNA-seq


title: RNA-Seq D5 control rep3

description: polyA mRNA-seq


title: MZ_TLR9P915H.rep2


title: mESC D15 Rep3

description: polyA mRNA-seq

data_processing:
Reads were aligned to mouse genome version mm10 with STAR using parameter --quantMode GeneCounts to retrieve read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol:
RNA was harvested from 5x10E5 cells per sample with a Nucleospin RNA extraction kit (Machery-Nagel 740955.250).
TruSeq RNA Sample prep kit v2 (Illumina RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were quantitated on an Agilent Bio-Analyzer and pooled in equimolar amounts. Pooled libraries were sequenced on the HiSeq4000 in Rapid Run Mode following the manufacturer's protocols to generate stranded single-end reads of 50bp.

value: mESC-derived cardiomyocytes


title: MZ_TLR9P915H.rep3


title: MZ_TLR9P915H.rep1


title: mESC D15 Rep1

description: polyA mRNA-seq


title: MZ_TLR9KO.rep4


title: EARLI_50593_SepsisBSI


title: mESC D15 Rep2

description: polyA mRNA-seq


title: MZ_TLR9KO.rep3


title: mESC D10 Rep2

description: polyA mRNA-seq


title: mESC D10 Rep3

description: polyA mRNA-seq


title: Embry.63.d Le 312_(SNOWBALLs520824F)

source_name: liver tissue from 63 dpc pig

value: liver

value: F2 based DLXPi

value: 63 dpc


title: MZ_TLR9KO.rep2


title: mESC D10 Rep1

description: polyA mRNA-seq


title: EARLI_50561_SepsisBSI

source_name: Plasma

value: Plasma

value: Female


title: EARLI_50562_No-Sepsis

value: Male


title: EARLI_50600_No-Sepsis

value: Caucasian


title: mESC D8 Rep3

description: polyA mRNA-seq

value: untreated


title: EARLI_50552_No-Sepsis


title: EARLI_50594_No-Sepsis

value: Other

value: LatinX


title: FO_TLR9WT.rep4

description: Follicular B cells_3-way BM chimera_sorted cells

value: MRL/lpr (MRL.Faslpr)

value: 3-way BM chimera_sorted cells

value: Follicular B cells


title: mESC D8 Rep2

description: polyA mRNA-seq


title: EARLI_50551_No-Sepsis


title: FO_TLR9WT.rep3


title: EARLI_50532_No-Sepsis


title: mESC D7 Rep3

description: polyA mRNA-seq

value: mESC-derived cardiac progenitor cells


title: mESC D8 Rep1

description: polyA mRNA-seq


title: EARLI_50537_Sepsisperiph

value: Sepsisperiph

value: African American


title: EARLI_50576_Sepsisperiph


title: FO_TLR9P915H.rep4


title: mESC D7 Rep1

description: polyA mRNA-seq


title: FO_TLR9P915H.rep3


title: EARLI_50525_No-Sepsis

value: No-Sepsis


title: EARLI_50515_Sepsisperiph

value: Asian


title: FO_TLR9P915H.rep2


title: mESC D6 Rep3

description: polyA mRNA-seq


title: mESC D6 Rep2

description: polyA mRNA-seq


title: EARLI_50514_Sepsisperiph


title: mESC D6 Rep1

description: polyA mRNA-seq


title: EARLI_50498_Sepsisperiph


title: EARLI_50542_No-Sepsis


title: FO_TLR9KO.rep4


title: FO_TLR9WT.rep2


title: mESC D5 Rep3

description: polyA mRNA-seq


title: FO_TLR9KO.rep3


title: EARLI_50481_No-Sepsis


title: mESC D5 Rep1

description: polyA mRNA-seq


title: mESC D5 Rep2

description: polyA mRNA-seq


title: EARLI_50478_No-Sepsis


title: FO_TLR9KO.rep1


title: RNA-Seq CD1 HT rep6

description: polyA mRNA-seq

data_processing:
Reads were aligned to moue genome version mm10 with STAR using parameter --quantMode GeneCounts to retrieve read counts.
DESeq2 was used for differential expression testing with default settings
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet with results from DESeq2

source_name: embryonic heart tube (HT)

extract_protocol:
pSHFs and HT were microdissected from the same embryo, flash frozen on dry ice, and RNA was harvested using a Nucleospin RNA extraction kit (Machery-Nagel 740955.250).
TruSeq RNA Sample prep kit v2 (Illumina RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were quantitated on an Agilent Bio-Analyzer and pooled in equimolar amounts. Pooled libraries were sequenced on the HiSeq4000 in Rapid Run Mode following the manufacturer's protocols to generate stranded single-end reads of 50bp.

value: heart tube (HT)

value: WT


title: FO_TLR9KO.rep2


title: FO_TLR9WT.rep1


title: EARLI_50471_Sepsisperiph

value: Plasma


title: EARLI_50447_Sepsisperiph

value: Female


title: mESC D7 Rep2

description: polyA mRNA-seq


title: RNA-Seq CD1 HT rep5

description: polyA mRNA-seq


title: EARLI_50511_SepsisBSI

value: SepsisBSI

value: Male


title: ABC_TLR9WT.rep2

description: Aged associated B cells_3-way BM chimera_sorted cells

value: Aged associated B cells


title: RNA-Seq CD1 HT rep3

description: polyA mRNA-seq


title: RNA-Seq CD1 HT rep4

description: polyA mRNA-seq


title: ABC_TLR9WT.rep1


title: ABC_TLR9WT.rep4


title: RNA-Seq CD1 HT rep2

description: polyA mRNA-seq


title: ABC_TLR9WT.rep3


title: EARLI_50435_SepsisBSI


title: RNA-Seq CD1 HT rep1

description: polyA mRNA-seq


title: EARLI_50430_No-Sepsis

value: Other


title: ABC_TLR9P915H.rep3


title: EARLI_50428_Sepsisperiph

value: Caucasian


title: EARLI_50445_SepsisBSI


title: RNA-Seq CD1 pSHF rep6

description: polyA mRNA-seq

source_name: embryonic posterior second heart field (pSHF)

value: posterior second heart field (pSHF)


title: ABC_TLR9P915H.rep4

value: MRL/lpr (MRL.Faslpr)

value: 3-way BM chimera_sorted cells


title: EARLI_50418_SepsisBSI


title: RNA-Seq CD1 pSHF rep4

description: polyA mRNA-seq


title: EARLI_50417_SepsisBSI

value: LatinX


title: EARLI_50413_Sepsisperiph

value: Sepsisperiph

tag: gender description

value: Transgender


title: ABC_TLR9KO.rep4


title: ABC_TLR9P915H.rep1


title: RNA-Seq CD1 pSHF rep3

description: polyA mRNA-seq


title: EARLI_50406_No-Sepsis

value: No-Sepsis


title: RNA-Seq CD1 pSHF rep2

description: polyA mRNA-seq


title: ABC_TLR9KO.rep3


title: EARLI_50398_SepsisBSI


title: ABC_TLR9KO.rep2


title: EARLI_50400_Sepsisperiph

value: Asian


title: RNA-Seq CD1 pSHF rep1

description: polyA mRNA-seq


title: FO_TLR9P915H.rep1

value: Follicular B cells


title: ABC_TLR9KO.rep1


title: CD1 Drop-seq rep2

description: droplet-based single cell RNA-seq (Drop-seq)

data_processing:
Sequencing reads were aligned to the mouse reference genome (mm10) (Kent et al., 2002), and transcripts counts were quantified for each cell and gene. The pipeline is available here: https://github.com/aselewa/dropseqRunner.
Data QC and analysis of the Drop-seq data was performed using the Scanpy toolkit (Wolf et al., 2018).
Cells from both biological replicates were combined after removing cells with less than 1,100 detected genes and genes that were detected in less than 5 cells. We also excluded cells with more than 7,000 genes to avoid counting cell doublets and cells with more than 3% of reads mapped to mitochondrial genes indicative of low quality. This resulted in a final set of 3,824 high quality cellular transcriptomes.
Read counts in each cell were normalized to a total of 10,000 reads and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values files containing count data

source_name: embryonic posterior second heart field (pSHF) and heart tube (HT)

extract_protocol:
pSHFs and HT were microdissected from ~80 embryos and pooled for each sample. Tissue was dissociated in TrypLE for 5 minutes at room temperature with shaking at 1000 RPM, before quenching with 10% FBS. Cells were centrifuged at 800 x g and washed with 0.01% BSA in PBS.
Two single cell RNA-seq libraries were generated using the standard Drop-seq protocol (Macosko et al., 2015) with minor modifications. Briefly, cells were filtered using a 40 µm mesh filter (Nalgene, USA) and suspended in 1x PBS and 0.01% BSA at a concentration 120,000/mL. Custom-synthesized Drop-seq barcode (BC) beads (Chemgenes, USA) at 100,000/mL were likewise filtered trough 100 µm mesh filter and suspended in Drop-seq Lysis Buffer. Using 3 mL syringes for each, the solutions were co-encapsulated in monodisperse droplets of 125 µm in an inert carrier oil (BioRad Evagreen) using microfluidic device fabricated in-house. The cells underwent lysis in the microfluidic droplets and the mRNA were captured onto the BC beads via polydT oligoes affixed to the BC beads. The droplets were then broken to retrieve the BC beads with mRNA hybridized onto them in high salt solution that stabilized the BC oligo+mRNA complexes. The beads are thoroughly washed and reverse transcription is performed to convert the BC+mRNA complex into barcoded cDNA. An Exonuclease I digestion is performed to digest any barcodes that are unbound to mRNA. PCR of 12-15 cycles is performed to amplify the barcoded single cell library, quantified and the quality of cDNA library is assessed. Sequencing libraries are prepared using Illumina Nextera kit with sample-specific indices added that allow de-multiplexing each sample from sequence data. The samples were sequenced on the Illumina NextSeq platform using a 75 cycle kit, with a custom Read1 primer (Macosko et al., 2015). The two biological replicates were processed on different days.
Drop-seq

value: WT


title: BS cell H3K4ac

first: tao

middle: shen

last: tong

address: Weigang street 1st

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequences using trim_galore
Clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters
Peaks were called using macs2.1.1 bigwig files were generated using deeptools bamCoverage with parameters --centerReads -bs 20 --smoothLength 60 --normalizeUsing RPKM and were transformed to wig files using bigWigtoWig software
Supplementary files format and content: B73 RefGen_v4

molecule: genomic DNA

organism: Zea mays

source_name: BS cell

growth_protocol: Seeds of maize (Zea mays “B73”) background were germinated at room temperature in greehouse for 10 days followed by collection

extract_protocol:
Commercial H3K36me3 for both cell types (ab9050, abcam) and H3K9ac (07-352, Millipore), H3K4ac (07-539, Millipore), H4K12ac (07-595, Millipore) were used to perform ChIP-seq experiments
ChIP libraries were prepared for sequencing using the standard Illumina protocols

value: BS cell

tag: chip anti-body

value: H3K4ac (07-539, Millipore)


title: EARLI_50394_No-Sepsis

value: Plasma


title: CD1 Drop-seq rep1

value: posterior second heart field (pSHF) and heart tube (HT)


title: EARLI_50382_No-Sepsis

value: Male


title: Taf7l konckin(TKI)rep3

data_processing:
Illumina HiSeqTM 4000 system used for basecalling.
Clean data were obtained by filtering low-quality data and trimming adaptors ,and subsequently mapped to the mouse genome (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression profile for mutant knockin group and wildtype group

source_name: Taf7l konckin(TKI)_testis

extract_protocol:
Testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: Taf7l konckin (TKI)


title: BS cell H3K9ac

value: H3K9ac (07-352, Millipore)


title: ABC_TLR9P915H.rep2

value: MRL/lpr (MRL.Faslpr)

value: Aged associated B cells


title: EARLI_50379_No-Sepsis

value: Female

value: Other

value: LatinX


title: RNA-Seq CD1 pSHF rep5

description: polyA mRNA-seq

value: posterior second heart field (pSHF)


title: Taf7l konckin(TKI)rep2


title: M cell H3K36me3

source_name: M cell

value: M cell

value: H3K36me3 (ab9050, abcam)


title: BS cell H4K12ac

value: H4K12ac (07-595, Millipore)


title: EARLI_50377_SepsisBSI

value: SepsisBSI


title: Taf7l konckin(TKI)rep1


title: EARLI_50367_SepsisBSI

value: Caucasian


title: EARLI_50372_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: African American


title: BS cell H3K36me3

value: BS cell


title: Taf7l wildtype(TWT)rep2

source_name: Taf7l wildtype(TWT)_testis

value: testis

value: wild type


title: EARLI_50366_SepsisBSI

value: Male


title: Hemocytes; Efae-Primed-d8; Biol rep 3

city: Boston

first: Kevin

last: Cabrera

state: Massachusetts

address: 610 Commonwealth Avenue

institute: Boston University

data_processing:
Sequenced libraries were quality checked using FastQC and aligned to Drosophila reference genome dm6 using Bowtie 2
Counts were generated using the subread function featureCounts.
Counts were then loaded into EdgeR,  libraries were TMM normalized, and genes with CPM < 1 were filtered out.
Assembly: dm6
Supplementary files format and content: tab-delimited file containing raw counts for each sample

organism: Drosophila melanogaster

source_name: hemocytes

extract_protocol:
RNA from either fat bodies or hemocytes was extracted using a Zymo Direct-zol RNA Extraction kit and eluted in 20uL water.
Libraries were prepared using a modified version of the Illumina Smart-seq 2 protocol as previously described (Ramirez-Corona 2021). Libraries were sequenced on an Illumina Next-seq platform using a NextSeq 500/550 504 High Output v2.5 kit to obtain 43bp paired-end libraries.

value: hemocytes

value: Oregon-R

value: Efae-Primed

tag: time


title: Hemocytes; Mock-Primed-d8; Biol rep 2

tag: tissue

value: Mock-Primed


title: EARLI_50361_SepsisBSI

data_processing:
Alignment against human genome- star
Fitering to retain samples with 50,000 gene counts
Differential expression with R package DESeq2
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

value: Other

value: LatinX


title: Hemocytes; Mock-Primed-d8; Biol rep 1

tag: genotype


title: EARLI_50360_No-Sepsis

value: No-Sepsis

tag: age


title: EARLI_50316_SepsisBSI

tag: disease state


title: EARLI_50356_SepsisBSI

tag: gender

value: Asian


title: Co_SK36_3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Assembly: Streptococcus gordonii: NC_009785.1
Assembly: Streptococcus sanguinis: NC_009009.1
Assembly: Streptococcus oralis: CP079724.1
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame

organism:
Streptococcus sanguinis
Streptococcus mutans

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: grown in coculture (TYG) to OD600 nm = 0.5


title: Hemocytes; Efae High Dose-d1; Biol rep 3

value: Efae High Dose


title: EARLI_50302_SepsisBSI

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

value: SepsisBSI

tag: race


title: Quad_1

description: repeat 1 of 3

organism:
Streptococcus gordonii
Streptococcus oralis
Streptococcus sanguinis
Streptococcus mutans

value: grown in quadculture (TYG) to OD600 nm = 0.5


title: Taf7l wildtype(TWT)rep3


title: EARLI_50299_No-Sepsis

value: Plasma

value: Female

tag: ethnicity


title: Hemocytes; Efae High Dose-d1; Biol rep 2


title: Hemocytes; Efae High Dose-d1; Biol rep 1


title: EARLI_50297_SepsisBSI

value: African American


title: Hemocytes; Efae-Primed-d8; Biol rep 2


title: Co_SK36_2

description: repeat 2 of 3

tag: strain


title: Hemocytes; Efae Low Dose-d7; Biol rep 3

value: Efae Low Dose


title: pTEX-DEVH1 L. infantum promastigotes vs. pTEX L. infantum promastigotes (3 replicates)

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

description: Note: this is a dual channel experiment, but the independent raw data files (*.gpr) are provided. This is the file containing raw intensity data from the biological replicate 1 of stable pTEX-DEVH1 L. infantum promastigote knock-in transfectants.

hyb_protocol: Dual channel hybridization. Cy5-cDNA was from sand fly promastigotes and Cy3-cDNA from cultured ones. The protocol was performed as described (Alcolea et al., 2009. Genomics 93, 551-564).

scan_protocol: Scanning was performed with a GenePix 4100 instrument following the manufacturers' instructions.

data_processing: Normalization was performed by the LOWESS per pin method (AlmaZen software) and statistical inference by the Student´s t test with FDR adjustment. Please note that the AlmaZen software only provides the average of normalized data, the fold changes, the p-value (Student's t test), z-score, etc., but not the individual outcome of each array.

organism: Leishmania infantum

label_protocol: First strand cDNA synthesis was performed with 3 ug random hexamer primers and the SuperScript III reverse transcriptase (Invitrogen), incorporating 2/3 dTTP and 1/3 aminoallyl-dUTP. After purification, Cy5 and Cy3 dyes were coupled. So, the labelling protocol was indirect.

growth_protocol: RPMI plus 10% heat inactivated fetal bovine serum in the presence of 100 µg/mL ampicillin – 100 UI penicillin. Only during and after selection of stable transfectants, 40 µg/mL geneticin (G418) was added to the culture medium. Incubations were performed at 26 ºC for 7 days (stationary phase) for culture passages and for obtention of the samples from the stable transfectants directly used in the triplicate microarray experiment (biological replicates).

extract_protocol: Total RNA was obtained by the TRIzol method (Invitrogen) following the manufacturer instructions. Then, RNA from pTEX-DEVH1 knock-in and pTEX control promastigotes was amplified with Message AmpII aRNA Amplification Kit (Ambion).

treatment_protocol: L. infantum promastigotes from the JPCM5 isolate (zymodeme MON-1) were grown at 26 °C in complete medium containing RPMI 1640 supplemented with L-glutamine and 10% HIFBS. The cells were harvested at mid-logarithmic phase and resuspended at 108 cells/ml in pre-chilled transfection buffer (21 mM HEPES, 137 mM NaCl, 5 mM KCl, 0.7 mM NaH2PO4, 6 mM glucose, pH 7.4). Aliquots of 0.4 ml of the cell suspension were poured into 0.2 cm-gap electroporation cuvettes and incubated on ice for 10 min. 20 μg of pTEX or pTEX-DEVH1 plasmid at a starting concentration of 1 mg/mL were added to the cell suspension and an electric pulse was applied at 450V, 500 μF, and 25 W with Electro Cell Manipulator® ECM 630 Precision PulseTM (BTX®). The cuvettes were immediately chilled at 4°C for 10 min. Then, the cell suspension was transferred to 4 ml of complete medium and incubated at 26°C for 24h. Selection with 40 μg/ml G418 was applied using wild type parasites that also received the electrical pulse as a selection control. The stable pTEX or pTEX-DEVH1 transfectants were scaled up and centrifuged at stationary phase (day 7) at 2,000g for 10 min. Harvested promastigotes were at passage 16.

tag: isolate

tag: plasmid

tag: stable transfection

value: Yes

source_name: Leishmania infantum (Kinetoplastida: Trypanosomatidae) MHOM/CAN/ES/98/10448

value: pTEX


title: Taf7l wildtype(TWT)rep1

value: testis

value: wild type


title: EARLI_50292_Sepsisperiph

value: Sepsisperiph


title: Hemocytes; Efae-Primed-d8; Biol rep 1

value: hemocytes

value: Oregon-R

tag: treatment

value: Efae-Primed


title: Hemocytes; Efae Low Dose-d7; Biol rep 2


title: Hemocytes; Efae Low Dose-d7; Biol rep 1


title: Quad_3

description: repeat 3 of 3


title: S. aureus_P. aeruginosa_dual-species biofilm [2M24-N0793]

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description:
RNA-Seq reads alignment was performed using only S. aureus genome -or- only P. aeruginosa genome.
S. aureus_single vs dual-species

data_processing:
Bcl2fastq version 2 (Illumina) was used for base calling and to convert data to FASTQ files.
CLC Genomics Workbench version 21 (QIAGEN) was used for quality, ambiguity and length trimming, using default settings. In addition, CLC was used for alignment, normalization of the reads (to Transcripts Per Million – TPM) and for the analysis of differential gene expression in single- vs dual-species biofilms. In the case of dual-species biofilms, reads were aligned with either S. aureus or P. aeruginosa genomes. Fold-change was calculated using single-species biofilms as control. Baggerley's test was applied to identify statistically significant alterations.
In the case of genes whose sequences were not detected (TPM = 0), TPM was replaced with 1 in order to be able to determined the minimum expression value for that particular gene.
Genome_build: CP009361 (S. aureus)
Genome_build: NZ_CP034244 (P. aeruginosa)
Supplementary_files_format_and_content: Processed data files are tab-delimited text files that contain (i) the gene locus tag, (ii) expression values (TPM) for each sample (in duplicates), (iii) mean of expression values (TPM) for each sample and, finaly, (iv) expression fold-change (using single species biofilms as a control). The list of genes presented was defined considering fold-change values greater than 2 and p-values less than 0.05.

organism:
Pseudomonas aeruginosa
Staphylococcus aureus

growth_protocol: Single- and dual-species biofilms were grown as described in Magalhaes et al., 2021, Environmental Microbiology, 23(9), 5639-5649. In brief, overnight cultures of each species, grown in Tryptic Soy Broth (TSB) at 37ºC and 120 rpm in air conditions, were washed in sterile water and diluted in fresh TSB to obtain 1x10E7 CFU/mL. For dual-species cultures, a combination of 50% of the suspended inoculum of each species was used. Bacterial suspensions were further transferred to 24-well polystyrene plates (Orange Scientific, Braine- l’Alleud, Belgium) and incubated at 37ºC on a horizontal shaker (120 rpm) for 24h. This assay was performed six independent times.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) and as described in França et al., 2012, PLoS One 7 (5): e37480. In brief, cells were suspended in 600 µL of the lysis buffer provided by the kit, plus 500 µL of phenol and 12 µL of β-mercaptoethanol. This suspension was transferred to a safe lock tube (2 mL) with 0.4 g of acid-washed 150–212 mm glass beads (Sigma) and, using a BeadBugTM 6 (Benchmark Scientific) cells disruptor, the cells were lysed (4× 4500 rpm for 35 seconds, with 5 minutes intervals on ice between cycles). Finally, the tubes were centrifuged, and the suspension was transferred into a new tube. An equal volume of 70% of ethanol was added, the suspensions transferred into the RNeasy mini kit columns and the manufacturer's instructions were strictly followed. RNA quality was determined using Agilent TapeStation 4200 (Agilent) and RNA quality indicators were above 8 for all samples. Thereafter, total RNA obtained from three independent experiments were mixed and treated with TURBO DNase (Ambion) to degrade genomic DNA. Additionally, before the library construction, a NEBNext rRNA Depletion Kit (Bacteria) (NEB) was used to remove bacterial ribosomal RNA.
RNA libraries were prepared by strictly following the instructions of the kit KAPA HyperPrep (Roche). Libraries quality was determined using Agilent TapeStation 4200 and data were generated using Illumina NovaSeq 6000 (Illumina) from paired-end read (2 × 150 bp).

treatment_protocol: Biofilms cells (24h-old) were then collected and suspended in 1 mL of RNA protect bacteria reagent (Qiagen), diluted 2:1 in RNase-free water, as indicated by the manufacturer. After 5 minutes of incubation at room temperature, biofilm cells were harvested by centrifugation (3132 g, 20 minutes) and RNA isolation was performed.

value: ATCC 25923 + UCBPP-PA14

tag: cell type

value: Biofilm cells (24h)


title: Hemocytes; Efae Low Dose-d1; Biol rep 2


title: Hemocytes; Efae Low Dose-d1; Biol rep 3


title: S. aureus_P. aeruginosa_dual-species biofilm [1M24-N0792]


title: EARLI_50277_No-Sepsis

value: No-Sepsis

value: Male

value: Asian


title: Hemocytes; Efae Low Dose-d1; Biol rep 1


title: EARLI_50269_No-Sepsis

value: Plasma


title: Patient 85_mes100

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

hyb_protocol: RNA was hybridized to capture and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a flourescent barcode specific for each transcript.

scan_protocol: Scanning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (AMMECR1L, ERCC3, ZNF346). Raw values correspond to the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the twenty available in the panel based on the lowest coefficients of variation (CV= ratio between standard deviations and mean counts across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls.

label: Molecular barcode on reporter probe

source_name: Malignant Pleural Mesothelioma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tissues of MPM were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 70 genes by a NanoString Custom Panel called MPM_C9073 (NanoString Technologies).

treatment_protocol: Specimens from MPM affected patients were included in this study.

value: F

tag: histology

value: epithelioid

tag: tnm

tag: status

value: alive

tag: survival (months)

tag: abestos exposure

value: no


title: Co_SK36_1

description: repeat 1 of 3

value: grown in coculture (TYG) to OD600 nm = 0.5

tag: genotype


title: Hemocytes; No Injection-d7; Biol rep 3

tag: tissue

value: No Injection

tag: time


title: Patient 86_mes101

tag: gender

value: M

tag: age

value: biphasic

value: professional


title: EARLI_50267_No-Sepsis

tag: disease state

tag: race

value: Caucasian

tag: ethnicity


title: Patient 83_mes98


title: Patient 84_mes99


title: EARLI_50265_No-Sepsis

value: African American


title: EARLI_50291_No-Sepsis

value: Female

value: Other

value: LatinX


title: EARLI_50184_SepsisBSI

value: SepsisBSI

value: Male


title: EARLI_50288_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Asian


title: EARLI_50172_Sepsisperiph


title: Hemocytes; No Injection-d0; Biol rep 4

value: hemocytes

value: Oregon-R


title: EARLI_12113_SepsisBSI


title: Hemocytes; No Injection-d0; Biol rep 3


title: Patient 81_mes96

value: alive


title: Patient 80_mes95


title: Hemocytes; No Injection-d0; Biol rep 2

value: No Injection


title: EARLI_12110_SepsisBSI


title: Hemocytes; No Injection-d0; Biol rep 1


title: Patient 79_mes94

value: M

value: epithelioid

value: dead


title: EARLI_12087_SepsisBSI


title: Patient 78_mes93

value: no


title: Fat body; Efae-Primed-d8; Biol rep 3

source_name: fat body

value: fat body

value: Efae-Primed


title: Patient 77_mes92

value: biphasic

value: professional


title: EARLI_12083_No-Sepsis

value: No-Sepsis


title: Hemocytes; No Injection-d7; Biol rep 2


title: Hemocytes; No Injection-d7; Biol rep 1


title: EARLI_12070_No-Sepsis

value: Male


title: Fat body; Efae-Primed-d8; Biol rep 1


title: Fat body; Efae-Primed-d8; Biol rep 2


title: Patient 82_mes97


title: EARLI_12045_Sepsisperiph

value: Sepsisperiph

value: Unknown


title: Patient 75_mes87

value: F


title: Patient 76_mes88


title: Fat body; Mock-Primed-d8; Biol rep 3

value: Mock-Primed


title: EARLI_12027_No-Sepsis

value: Plasma

value: Female

value: Asian


title: Patient 74_mes86

value: M

value: alive


title: EARLI_12012_Sepsisperiph

value: Caucasian


title: Fat body; Mock-Primed-d8; Biol rep 2

value: Oregon-R


title: Patient 73_mes85

value: dead

value: no


title: Fat body; Mock-Primed-d8; Biol rep 1

value: fat body


title: EARLI_12008_No-Sepsis


title: Patient 72_mes84

value: biphasic

value: familial


title: EARLI_12005_Sepsisperiph

value: Male


title: Fat body; Efae High Dose-d1; Biol rep 2

value: Efae High Dose


title: Fat body; Efae High Dose-d1; Biol rep 1


title: EARLI_12003_Sepsisperiph

value: Sepsisperiph


title: Patient 71_mes83

value: professional


title: Patient 70_mes82


title: Patient 69_mes81

value: F


title: Fat body; Efae Low Dose-d7; Biol rep 5

value: Efae Low Dose


title: Fat body; Efae Low Dose-d7; Biol rep 3


title: Fat body; Efae Low Dose-d7; Biol rep 4


title: Patient 66_mes78

value: sarcomatoid


title: Quad_2

description: repeat 2 of 3

tag: strain

value: grown in quadculture (TYG) to OD600 nm = 0.5


title: Patient 67_mes79

value: M


title: Patient 68_mes80


title: EARLI_11991_No-Sepsis

value: No-Sepsis

value: Plasma


title: EARLI_11983_Sepsisperiph

value: Asian


title: EARLI_50469_No-Sepsis

value: Other

value: LatinX


title: EARLI_11976_No-Sepsis


title: Fat body; Efae High Dose-d1; Biol rep 3

value: fat body

value: Oregon-R


title: Patient 65_mes77

value: epithelioid

value: dead


title: Fat body; Efae Low Dose-d7; Biol rep 2


title: EARLI_11970_Sepsisperiph

value: Female

value: Caucasian


title: Fat body; Efae Low Dose-d7; Biol rep 1


title: Patient 64_mes76

value: no


title: Y505

first: Gang

last: Wu

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

data_processing:
Standed mRNA sequencing data were processed by  the internal AutoMapper pipeline.
First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (GRCh37-lite) (STAR v2.7)
and then the gene level values were quantified (RSEM v1.31) based on GENCODE annotation (r19) .
Assembly: hg19
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Blood

extract_protocol:
Lymphoblasts were purified from bone marrow or peripheral blood specimens using the Ficoll-Paque centrifugation method and RNA was extracted using NucleoZol reagent (MACHEREY-NAGEL, Cat#740404)
Libraries were prepared from 1~1.5 ug total RNA using TruSeq Stranded mRNA preparation kit and mRNA was enriched using oligo-dT capture.
Stranded mRNA

value: Blood

value: T-cell Acute lymphoblastic leukemia


title: Y546


title: EARLI_12004_SepsisBSI

first: Charles

last: Langelier

address: HSE 401, 513 Parnassus Ave

institute: University of California San Francisco

value: SepsisBSI

value: Male


title: Fat body; Efae Low Dose-d1; Biol rep 3

value: Efae Low Dose


title: Leukemia-Y535


title: Patient 63_mes75

value: M

value: professional


title: EARLI_11997_No-Sepsis

value: No-Sepsis

value: Plasma

value: Asian


title: Fat body; Efae Low Dose-d1; Biol rep 2

value: fat body


title: MZ_TLR9KO.rep1

value: MRL/lpr (MRL.Faslpr)

tag: genotype/variation

value: 3-way BM chimera_sorted cells

value: Marginal zone B cells


title: EARLI_11956_SepsisBSI

value: Female

value: Other

value: LatinX


title: EARLI_11945_No-Sepsis


title: Leukemia-905

value: Blood


title: Patient 62_mes74

value: F

value: epithelioid

value: dead


title: EARLI_11942_Sepsisperiph

value: Sepsisperiph

value: Unknown


title: EARLI_11943_Sepsisperiph

value: Male


title: Fat body; Efae Low Dose-d1; Biol rep 1

value: Oregon-R

tag: treatment

value: Efae Low Dose


title: Fat body; No Injection-d7; Biol rep 3

value: No Injection


title: Leukemia-746

value: T-cell Acute lymphoblastic leukemia


title: Patient 61_mes73

value: M

value: professional


title: Leukemia-762


title: Patient 60_mes72

value: biphasic


title: Leukemia-744


title: Fat body; No Injection-d7; Biol rep 1

value: fat body


title: Patient 59_mes71


title: EARLI_11859_No-Sepsis

value: No-Sepsis

value: Plasma

value: Caucasian


title: Fat body; No Injection-d7; Biol rep 2


title: EARLI_11846_No-Sepsis

value: Female

value: African American


title: Leukemia-730

value: Blood


title: Fat body; No Injection-d0; Biol rep 3


title: EARLI_11841_SepsisBSI

value: SepsisBSI


title: Patient 58_mes70

value: epithelioid

value: alive


title: Patient 57_mes69

value: dead


title: Leukemia-722


title: EARLI_11827_SepsisBSI


title: Fat body; No Injection-d0; Biol rep 2

value: Oregon-R


title: Fat body; No Injection-d0; Biol rep 1

value: No Injection


title: EARLI_11814_Sepsisperiph

value: Sepsisperiph

value: Male

value: Unknown


title: Patient 56_mes68

value: m

value: biphasic

value: professional


title: Patient 54_mes64

value: F


title: Patient 55_mes66

value: M


title: EARLI_11807_SepsisBSI

value: Plasma

value: Female

value: Asian


title: OL NSC - w1118 control NanoDam Replicate 6

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

description:
OgreGal4_DichaeteGFP_vs_OgreGal4_w1118.bw
OgreGal4_EyelessGFP_vs_OgreGal4_w1118.bw
OgreGal4_DichaeteGFP_vs_OgreGal4_w1118.bedgraph
OgreGal4_EyelessGFP_vs_OgreGal4_w1118.bedgraph

data_processing:
Library strategy: DamID-seq
Quality control for all raw *.fastq.gz-files was performed with FastQC (v0.11.5).
Reads were mapped to the Drosophila dm6 genome assembly with bowtie2 (v2.3.4.1).
Read counts per 500 bp-bin were acquired by 'bamCoverage' based on *.bam-files of individual samples including a read extension to 150 bp (https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html).
Reads were assigned to GATC-fragment bins based on 'GATC fragment'-file generated with 'gatc.track.maker.pl' (https://github.com/AHBrand-Lab/DamID_scripts).
All pairwise 'NanoDam/TaDa-vs-DamOnly'-comparisons were quantile normalized to each other via 'quant_norm_bedgraph.pl' (https://github.com/AHBrand-Lab/DamID_scripts).
Quantile normalized files were averaged with 'average_tracks.pl' (https://github.com/AHBrand-Lab/DamID_scripts).
Bedgraph files were converted into the bigwig-format with 'bedGraphToBigwig' (https://www.encodeproject.org/software/bedgraphtobigwig/).
Peak calling was conducted using MACS2 ('--broad') based on *.bam files from pairs of each one NanoDam/TaDa- and one DamOnly-sample.
All steps were performed for all files in an automated manner via 'damMer.py', 'damMer_tracks.py' and 'damMer_peaks.py' based on the 'damidseq_pipeline_vR.1' and the slurm workload manager (v15.08.13; https://github.com/AHBrand-Lab/NanoDam_analysis).
All single cell RNA sequencing files were mapped and count matrices generated by Cell Ranger (v2.1.1.).
Genome_build: dm6
Supplementary_files_format_and_content: *.sort.bam.bin500.ext150.bgr'-files (bedgraph-format): Raw read counts per 500 bp-bin after extension to 150 bp.
Supplementary_files_format_and_content: *_vs_*.bedgraph'-files (bedgraph-format): Normalized, averaged scores across all pairwise comparisons (i.e., DichaeteGal4_*; OgreGal4_*) or scores for individual comparisons normalized across all comparisons (i.e., Cph_*).
Supplementary_files_format_and_content: *_vs_*.bw'-files (bigwig-format): Normalized, averaged scores across all pairwise comparisons (i.e., DichaeteGal4_*; OgreGal4_*) or scores for individual comparisons normalized across all comparisons (i.e., Cph_*).
Supplementary_files_format_and_content: *_vs_*.broadPeak'-files (bed-format): List of broad peaks as called by MACS2 on individual, pairwise comparisons.
Supplementary_files_format_and_content: *.mergePeak' (bed-format): Peakset merged across peaks of all individual, pairwise comparisons that satisfied a particular FDR threshold.
Supplementary_files_format_and_content: *.reproPeak' (bedgraph-format): '*.mergePeak' (bed-format): Reproducible peakset merged across peaks of all individual, pairwise comparisons that satisfied a particular FDR threshold and that occur in at least 50% of all comparisons.
Supplementary_files_format_and_content: *.tsv' (tsv-format): Lists of barcodes and gene identifiers accompanying single cell count matrices.
Supplementary_files_format_and_content: *.mtx' (mex-format): Single cell count matrices.

source_name: Optic lobe medulla Neural Stem Cells - 3rd instar larval brain

growth_protocol: Embryos collected at 25°C on yeasted apple juice plates, transferred to 18°C; Larvae reared at 18°C on yeasted food plates for 6 d, shifted to 25°C  for 14 h

extract_protocol:
Genomic DNA extracted from 50 dissected brains per replicate according to Marshall, O et al., 2016, Nat Protoc
For all DamID-samples, genomic DNA was extracted with the QiAmp DNA Micro kit, digested with DpnI, DamID-adaptors were ligated followed by DpnII-digestion and PCR-amplification (Marshall, O et al., 2016, Nat Protoc).
For all DamID-libraries, the amplified products were sonicated to average size of 300 bp, DamID-adaptors removed by AlwI-digestion, end-repaired, A-tailed, followed by ligation of Sequencing-adaptors and PCR-amplification (see Marshall, O et al., 2016, Nat Protoc).
Single cell RNAseq libraries were generated with the 10xGenomics 'SC3Pv2'-chemistry kit.

value: Wandering 3rd instar larval brain

tag: expression conditions

value: 14 h expression during 3rd instar larval stage

tag: cell type

value: Optic lobe medulla Neural Stem Cells

tag: dam complex

value: NanoDam


title: Leukemia-717

value: Blood

value: T-cell Acute lymphoblastic leukemia


title: Leukemia-715


title: EARLI_11805_No-Sepsis

value: No-Sepsis

value: Caucasian


title: OL NSC - w1118 control NanoDam Replicate 4


title: OL NSC - w1118 control NanoDam Replicate 5


title: EARLI_11801_No-Sepsis


title: Patient 53_mes63

tag: histology

value: sarcomatoid

tag: tnm

tag: status

value: dead


title: Patient 52_mes62

value: biphasic

tag: survival (months)

tag: abestos exposure


title: Leukemia-735

tag: tissue


title: Leukemia-702


title: Leukemia-693


title: EARLI_11796_Sepsisperiph

value: Sepsisperiph

tag: gender


title: OL NSC - w1118 control NanoDam Replicate 3


title: EARLI_11795_Sepsisperiph

value: Male

tag: age


title: Leukemia-568

tag: disease state


title: OL NSC - w1118 control NanoDam Replicate 2


title: Patient 50_mes60

value: F

value: epithelioid

value: no


title: Leukemia-721


title: Patient 51_mes61

value: M

value: professional


title: Patient 49_mes59


title: Leukemia-1087


title: 994


title: EARLI_11780_SepsisBSI

value: SepsisBSI

value: Plasma

tag: race

value: Asian


title: EARLI_11792_No-Sepsis

value: Female

value: African American

tag: ethnicity


title: OL NSC - Eyeless-GFP NanoDam Replicate 5

description:
OgreGal4_EyelessGFP_vs_OgreGal4_w1118.bw
OgreGal4_EyelessGFP_vs_OgreGal4_w1118.bedgraph

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage

value: Optic lobe medulla Neural Stem Cells

value: Eyeless-GFP, NanoDam


title: OL NSC - Eyeless-GFP NanoDam Replicate 6


title: Patient 47_mes57

value: dead


title: EARLI_11777_No-Sepsis

value: No-Sepsis


title: OL NSC - Eyeless-GFP NanoDam Replicate 4


title: 941

value: Blood

value: T-cell Acute lymphoblastic leukemia


title: 939


title: Patient 48_mes58

value: sarcomatoid


title: OL NSC - Eyeless-GFP NanoDam Replicate 2


title: 920


title: Patient 46_mes56

value: epithelioid


title: 915


title: OL NSC - w1118 control NanoDam Replicate 1

value: NanoDam


title: EARLI_11765_No-Sepsis


title: Patient 43_mes53

value: M

value: professional


title: EARLI_11774_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Male


title: Patient 45_mes55


title: EARLI_11773_Sepsisperiph

value: Asian


title: 935


title: EARLI_11766_Sepsisperiph

value: Female

value: Caucasian

value: LatinX


title: EARLI_11724_Sepsisperiph


title: 1091


title: Patient 44_mes54

value: F


title: EARLI_11764_SepsisBSI

value: SepsisBSI


title: OL NSC - Eyeless-GFP NanoDam Replicate 3

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage

value: Optic lobe medulla Neural Stem Cells

value: Eyeless-GFP, NanoDam


title: OL NSC - Eyeless-GFP NanoDam Replicate 1


title: OL NSC - Dichaete-GFP NanoDam Replicate 4

description:
OgreGal4_DichaeteGFP_vs_OgreGal4_w1118.bw
OgreGal4_DichaeteGFP_vs_OgreGal4_w1118.bedgraph

value: Dichaete-GFP, NanoDam


title: Patient 42_mes51

value: epithelioid

value: dead


title: EARLI_11713_No-Sepsis

value: No-Sepsis

value: Other


title: 1076

value: Blood

value: T-cell Acute lymphoblastic leukemia


title: EARLI_11712_No-Sepsis

value: Plasma

value: Male


title: OL NSC - Dichaete-GFP NanoDam Replicate 5


title: Patient 41_mes50

value: M

value: familial


title: Patient 39_mes48

value: biphasic

value: professional


title: OL NSC - Dichaete-GFP NanoDam Replicate 6

value: Wandering 3rd instar larval brain


title: OL NSC - Dichaete-GFP NanoDam Replicate 1

value: 14 h expression during 3rd instar larval stage


title: Patient 38_mes47


title: 1077


title: OL NSC - Dichaete-GFP NanoDam Replicate 3

value: Optic lobe medulla Neural Stem Cells


title: 1045


title: Patient 37_mes46

value: F


title: OL NSC - Dichaete-GFP NanoDam Replicate 2

value: Dichaete-GFP, NanoDam


title: 1057


title: EARLI_11708_SepsisBSI

value: SepsisBSI

value: Caucasian


title: 1050


title: EARLI_11707_SepsisBSI

value: Female

value: Asian


title: Patient 36_mes44

value: sarcomatoid

value: dead


title: Patient 40_mes49

value: epithelioid


title: 1036

value: Blood

value: T-cell Acute lymphoblastic leukemia


title: 1034


title: EARLI_11704_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Other

value: LatinX


title: EARLI_11666_No-Sepsis

value: No-Sepsis

value: Male


title: 1002


title: Patient 34_mes42

value: F

value: familial


title: INP - w1118 control NanoDam Replicate 7

description:
DichaeteGal4_DichaeteGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_EyelessGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_GrainyheadGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_DichaeteGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_EyelessGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_GrainyheadGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_DichaeteGFP_FDR25.reproPeak
DichaeteGal4_EyelessGFP_FDR25.reproPeak
DichaeteGal4_GrainyheadGFP_FDR25.reproPeak

source_name: Type 2 Neural Stem Cell-derived Intermediate Progenitors - 3rd instar larval brain

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage

value: NanoDam


title: Patient 35_mes43

value: M

value: biphasic


title: INP - w1118 control NanoDam Replicate 5

value: Type 2 Neural Stem Cell-derived Intermediate Progenitors


title: EARLI_11663_No-Sepsis

value: Female

value: Asian


title: EARLI_11649_No-Sepsis


title: Patient 33_mes41

value: epithelioid

value: dead

value: professional


title: Patient 32_mes40


title: Y461

value: Blood

value: B-cell acute lymphoblastic leukemia


title: EARLI_11642_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Caucasian


title: Y437


title: INP - w1118 control NanoDam Replicate 8


title: INP - w1118 control NanoDam Replicate 3


title: INP - w1118 control NanoDam Replicate 4


title: Patient 31_mes39


title: INP - w1118 control NanoDam Replicate 2


title: Y433


title: EARLI_11620_No-Sepsis

value: No-Sepsis

value: Male

value: Other


title: INP - w1118 control NanoDam Replicate 1

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage

value: NanoDam


title: Patient 30_mes38

value: M


title: EARLI_11599_SepsisBSI

value: SepsisBSI


title: INP - w1118 control NanoDam Replicate 6

value: Type 2 Neural Stem Cell-derived Intermediate Progenitors


title: Leukemia-Y555


title: EARLI_11597_No-Sepsis

value: Female


title: Leukemia-mRNA-lib-1027


title: EARLI_11658_No-Sepsis

value: Asian


title: Patient 29_mes37

value: epithelioid

value: dead

value: professional


title: EARLI_11586_SepsisBSI


title: INP - Grainyhead-GFP NanoDam Replicate 5

description:
DichaeteGal4_GrainyheadGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_GrainyheadGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_GrainyheadGFP_FDR25.reproPeak

value: Grainyhead-GFP, NanoDam


title: Y472

value: Blood

value: B-cell acute lymphoblastic leukemia


title: INP - Grainyhead-GFP NanoDam Replicate 4


title: INP - Grainyhead-GFP NanoDam Replicate 3


title: Leukemia-984


title: Patient 28_mes36

value: F


title: EARLI_11585_No-Sepsis

value: No-Sepsis

value: Plasma

value: Male

value: Caucasian


title: Patient 26_mes34

value: biphasic

value: familial


title: EARLI_11582_No-Sepsis


title: INP - Grainyhead-GFP NanoDam Replicate 2

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage


title: Leukemia-976


title: Leukemia-952


title: Patient 25_mes32

value: M


title: INP - Grainyhead-GFP NanoDam Replicate 1

value: Type 2 Neural Stem Cell-derived Intermediate Progenitors


title: EARLI_11550_SepsisBSI

value: SepsisBSI

value: Asian


title: Patient 23_mes30

value: epithelioid

value: dead

value: professional


title: Leukemia-925

value: Blood

value: B-cell acute lymphoblastic leukemia


title: EARLI_11556_SepsisBSI

value: Female

value: Other

value: LatinX


title: Patient 24_mes31


title: EARLI_11544_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Male

value: Caucasian


title: INP - Eyeless-GFP NanoDam Replicate 4

description:
DichaeteGal4_EyelessGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_EyelessGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_EyelessGFP_FDR25.reproPeak

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage

value: Eyeless-GFP, NanoDam


title: INP - Eyeless-GFP NanoDam Replicate 3

value: Type 2 Neural Stem Cell-derived Intermediate Progenitors


title: Leukemia-999


title: Leukemia-919


title: Patient 21_mes28

value: M


title: INP - Eyeless-GFP NanoDam Replicate 2


title: Patient 22_mes29

value: F

value: epithelioid


title: Leukemia-918


title: INP - Eyeless-GFP NanoDam Replicate 1


title: Patient 27_mes35

value: dead

value: professional


title: Patient 20_mes27


title: EARLI_11533_SepsisBSI

value: SepsisBSI


title: Leukemia-906

value: Blood

value: B-cell acute lymphoblastic leukemia


title: INP - Dichaete-GFP NanoDam Replicate 4

description:
DichaeteGal4_DichaeteGFP_vs_DichaeteGal4_w1118.bw
DichaeteGal4_DichaeteGFP_vs_DichaeteGal4_w1118.bedgraph
DichaeteGal4_DichaeteGFP_FDR25.reproPeak

value: Dichaete-GFP, NanoDam


title: Leukemia-898


title: EARLI_11526_SepsisBSI

value: Female


title: INP - Dichaete-GFP NanoDam Replicate 3


title: Patient 19_mes26


title: Patient 18_mes24

value: biphasic


title: Leukemia-893


title: Leukemia-890


title: EARLI_11521_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Male


title: INP - Dichaete-GFP NanoDam Replicate 2

value: Wandering 3rd instar larval brain

value: 14 h expression during 3rd instar larval stage


title: INP - Dichaete-GFP NanoDam Replicate 1

value: Type 2 Neural Stem Cell-derived Intermediate Progenitors


title: EARLI_11515_SepsisBSI

value: Asian


title: EARLI_11539_Sepsisperiph


title: Leukemia-872


title: Leukemia-889


title: EARLI_11503_Sepsisperiph

value: Caucasian


title: EARLI_11511_No-Sepsis

value: No-Sepsis


title: Patient 15_mes20

value: M

value: dead


title: Neural Stem Cell - TaDa DamOnly Replicate 1

description:
Cph_TaDa_1_vs_Dam_TaDa_1.bw
Cph_TaDa_2_vs_Dam_TaDa_1.bw
Dam_TaDa_2_vs_Dam_TaDa_1.bw
Cph_TaDa_1_vs_Dam_TaDa_1.bedgraph
Cph_TaDa_2_vs_Dam_TaDa_1.bedgraph
Dam_TaDa_2_vs_Dam_TaDa_1.bedgraph
Cph_TaDa_1_vs_Dam_TaDa_1.broadPeak
Cph_TaDa_2_vs_Dam_TaDa_1.broadPeak
Cph_TaDa_peaks_FDR5.mergePeak
Dam_TaDa_2_vs_Dam_TaDa_1.broadPeak

source_name: Embryonic Neural Stem Cells - stage 16

growth_protocol: Embryos collected at 25°C; 10-15 µl embryos harvested at stage 16

extract_protocol:
Genomic DNA extracted from 10-15 µl embryos per replicate according to Marshall, O et al., 2016, Nat Protoc
For all DamID-samples, genomic DNA was extracted with the QiAmp DNA Micro kit, digested with DpnI, DamID-adaptors were ligated followed by DpnII-digestion and PCR-amplification (Marshall, O et al., 2016, Nat Protoc).
For all DamID-libraries, the amplified products were sonicated to average size of 300 bp, DamID-adaptors removed by AlwI-digestion, end-repaired, A-tailed, followed by ligation of Sequencing-adaptors and PCR-amplification (see Marshall, O et al., 2016, Nat Protoc).
Single cell RNAseq libraries were generated with the 10xGenomics 'SC3Pv2'-chemistry kit.

value: Embryo

value: Embryonic stage 10-16

value: Embryonic Neural Stem Cells

value: Dam


title: Patient 16_mes22

value: professional


title: Neural Stem Cell - TaDa DamOnly Replicate 2

description:
Cph_Tada_1_vs_Dam_TaDa_2.bw
Cph_TaDa_2_vs_Dam_TaDa_2.bw
Dam_TaDa_2_vs_Dam_TaDa_1.bw
Cph_TaDa_1_vs_Dam_TaDa_2.bedgraph
Cph_TaDa_2_vs_Dam_TaDa_2.bedgraph
Dam_TaDa_2_vs_Dam_TaDa_1.bedgraph
Cph_Tada_1_vs_Dam_TaDa_2.broadPeak
Cph_TaDa_2_vs_Dam_TaDa_2.broadPeak
Cph_TaDa_peaks_FDR5.mergePeak
Dam_TaDa_2_vs_Dam_TaDa_1.broadPeak


title: Patient 14_mes19

value: biphasic


title: Leukemia-868

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Patient 13_mes17

value: sarcomatoid


title: Leukemia-864


title: Patient 12_mes16

value: familial


title: Neural Stem Cell - Chronophage-Dam TaDa Replicate 1

description:
Cph_TaDa_1_vs_Dam_TaDa_1.bw
Cph_Tada_1_vs_Dam_TaDa_2.bw
Cph_TaDa_1_vs_Dam_TaDa_1.bedgraph
Cph_TaDa_1_vs_Dam_TaDa_2.bedgraph
Cph_TaDa_1_vs_Dam_TaDa_1.broadPeak
Cph_Tada_1_vs_Dam_TaDa_2.broadPeak
Cph_TaDa_peaks_FDR5.mergePeak

value: Cph-Dam


title: EARLI_11494_No-Sepsis

source_name: Plasma

value: Plasma

value: Female

value: African American


title: Neural Stem Cell - Chronophage-Dam TaDa Replicate 2

description:
Cph_TaDa_2_vs_Dam_TaDa_1.bw
Cph_TaDa_2_vs_Dam_TaDa_2.bw
Cph_TaDa_2_vs_Dam_TaDa_1.bedgraph
Cph_TaDa_2_vs_Dam_TaDa_2.bedgraph
Cph_TaDa_2_vs_Dam_TaDa_1.broadPeak
Cph_TaDa_2_vs_Dam_TaDa_2.broadPeak
Cph_TaDa_peaks_FDR5.mergePeak


title: EARLI_11522_No-Sepsis

value: No-Sepsis


title: Neural Stem Cell - NanoDamOnly Replicate 2

description:
Cph_NanoDam_1_vs_Dam_NanoDam_2.bw
Cph_NanoDam_2_vs_Dam_NanoDam_2.bw
Dam_NanoDam_2_vs_Dam_NanoDam_1.bw
Cph_NanoDam_1_vs_Dam_NanoDam_2.bedgraph
Cph_NanoDam_2_vs_Dam_NanoDam_2.bedgraph
Dam_NanoDam_2_vs_Dam_NanoDam_1.bedgraph
Cph_NanoDam_1_vs_Dam_NanoDam_2.broadPeak
Cph_NanoDam_2_vs_Dam_NanoDam_2.broadPeak
Cph_NanoDam_peaks_FDR5.mergePeak
Dam_NanoDam_2_vs_Dam_NanoDam_1.broadPeak

value: NanoDam


title: Patient 11_mes13

value: F

value: epithelioid

value: dead


title: Patient 17_mes23

value: M


title: Leukemia-863


title: Leukemia-856


title: Neural Stem Cell - NanoDamOnly Replicate 1

description:
Cph_NanoDam_1_vs_Dam_NanoDam_1.bw
Cph_NanoDam_2_vs_Dam_NanoDam_1.bw
Dam_NanoDam_2_vs_Dam_NanoDam_1.bw
Cph_NanoDam_1_vs_Dam_NanoDam_1.bedgraph
Cph_NanoDam_2_vs_Dam_NanoDam_1.bedgraph
Dam_NanoDam_2_vs_Dam_NanoDam_1.bedgraph
Cph_NanoDam_1_vs_Dam_NanoDam_1.broadPeak
Cph_NanoDam_2_vs_Dam_NanoDam_1.broadPeak
Cph_NanoDam_peaks_FDR5.mergePeak
Dam_NanoDam_2_vs_Dam_NanoDam_1.broadPeak

value: Embryo

value: Embryonic stage 10-16

value: Embryonic Neural Stem Cells


title: Patient 10_mes12

value: biphasic

value: alive

value: professional


title: EARLI_11486_Sepsisperiph

value: Sepsisperiph

value: Caucasian


title: Neural Stem Cell - Chronophage::YFP NanoDam Replicate 2

description:
Cph_NanoDam_2_vs_Dam_NanoDam_1.bw
Cph_NanoDam_2_vs_Dam_NanoDam_2.bw
Cph_NanoDam_2_vs_Dam_NanoDam_1.bedgraph
Cph_NanoDam_2_vs_Dam_NanoDam_2.bedgraph
Cph_NanoDam_2_vs_Dam_NanoDam_1.broadPeak
Cph_NanoDam_2_vs_Dam_NanoDam_2.broadPeak
Cph_NanoDam_peaks_FDR5.mergePeak

value: Cph::YFP, NanoDam


title: EARLI_11498_SepsisBSI

value: SepsisBSI

value: Plasma

value: Female


title: Patient 9_mes11


title: EARLI_11474_No-Sepsis

value: No-Sepsis

value: Male


title: Leukemia-854

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Leukemia-866


title: Patient 8_mes10

value: M

value: dead


title: EARLI_11476_No-Sepsis


title: Patient 7_mes9

value: F


title: Leukemia-832


title: EARLI_11467_No-Sepsis


title: WT24_3

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

data_processing:
illuma casava 1.7 software  used for basecalling
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum tricornutum cells 24 h

extract_protocol:
12h light, 12h dark
RNA was harvested using Trizol reagent illumina truseq RNA sample kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction
RNA libraries for RNA-seq were prepared using standard illumia protocols

tag: time

tag: strain

value: Phaeodactylum tricornutum CCAP 1055

tag: genotype

value: WT

value: dark period


title: EARLI_11489_Sepsisperiph

city: San Francisco


title: Neural Stem Cell - Chronophage::YFP NanoDam Replicate 1

description:
Cph_NanoDam_1_vs_Dam_NanoDam_1.bw
Cph_NanoDam_1_vs_Dam_NanoDam_2.bw
Cph_NanoDam_1_vs_Dam_NanoDam_1.bedgraph
Cph_NanoDam_1_vs_Dam_NanoDam_2.bedgraph
Cph_NanoDam_1_vs_Dam_NanoDam_1.broadPeak
Cph_NanoDam_1_vs_Dam_NanoDam_2.broadPeak
Cph_NanoDam_peaks_FDR5.mergePeak

growth_protocol: Embryos collected at 25°C; Embryos harvested at stage 16

value: Embryo

tag: expression conditions

value: Embryonic stage 10-16

value: Embryonic Neural Stem Cells


title: Patient 5_mes7

value: epithelioid

value: professional


title: WT24_1

tag: treatment


title: Leukemia-827


title: Patient 6_mes8


title: EARLI_11461_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Caucasian


title: WT20_3

source_name: Phaeodactylum tricornutum cells 20 h


title: Leukemia-814


title: EARLI_11463_SepsisBSI

value: SepsisBSI

value: Male


title: WT20_2


title: EARLI_11456_Sepsisperiph

value: Female


title: Leukemia-845

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Patient 3_mes4

value: M

value: biphasic

value: dead


title: Leukemia-813


title: Leukemia-807


title: EARLI_11452_No-Sepsis

value: No-Sepsis


title: EARLI_11453_No-Sepsis

value: Asian


title: WT20_1

value: Phaeodactylum tricornutum CCAP 1055

value: WT

value: dark period


title: WT24_2


title: Leukemia-829


title: 10 mg/L Sertraline 3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

description: Ser10 3

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism:
Pseudomonas putida
Escherichia coli
Acinetobacter baylyi

source_name: E. coli bacteria + P. putida bacteria + A.baylyi bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and A.baylyi ADP1 were supended in triplicate in 10 mL PBS containing 0 mg/L (control), 10 mg/L Duloxetine, 1 and 10 mg/L Sertraline, 50 mg/L Escitalopram, 10 mg/L Fluoxetine, 100 mg/L Bupropion and 50 mg/L Agomelatine for 2 h at room temperature, without shaking

tag: e.coli strain

tag: p. putida strain

tag: a. baylyi strain

value: 10 mg/L Sertraline


title: EARLI_11446_No-Sepsis


title: Leukemia-804

city: Memphis


title: WT16_2

source_name: Phaeodactylum tricornutum cells 16 h


title: Patient 2_mes3

tag: histology

tag: tnm

tag: status

value: professional


title: Patient 1_mes2

value: F

tag: survival (months)

tag: abestos exposure

value: familial


title: EARLI_11445_Sepsisperiph

value: Sepsisperiph

tag: tissue

value: Plasma

tag: gender

tag: age


title: Leukemia-790

tag: disease state


title: 10 mg/L Sertraline 2

description: Ser10 2


title: Leukemia-787


title: Patient 4_mes5

value: no


title: EARLI_11430_Sepsisperiph

value: Female

tag: race

tag: ethnicity


title: EARLI_11437_No-Sepsis

value: Male

value: African American


title: 10 mg/L Sertraline 1

description: Ser10 1


title: 1 mg/L Sertraline 3

description: Ser1 3

value: 1 mg/L Sertraline


title: Leukemia-783

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Leukemia-784


title: 1 mg/L Sertraline 2

description: Ser1 2


title: WT12_1

source_name: Phaeodactylum tricornutum cells 12 h

tag: time

tag: strain

tag: genotype

value: light period


title: WT16_3

value: Phaeodactylum tricornutum CCAP 1055

tag: treatment


title: EARLI_11422_SepsisBSI

value: SepsisBSI

value: Asian


title: EARLI_11417_SepsisBSI

value: Caucasian


title: Leukemia-782


title: 1 mg/L Sertraline 1

description: Ser1 1

tag: e.coli strain

tag: p. putida strain


title: EARLI_11424_SepsisBSI


title: WT8_3

source_name: Phaeodactylum tricornutum cells 8 h

value: 8 h

value: WT


title: 10 mg/L Fluoxetine 3

description: Flu10 3

tag: a. baylyi strain

value: 10 mg/L Fluoxetine


title: EARLI_11416_No-Sepsis

value: No-Sepsis


title: WT8_1


title: WT8_2


title: Leukemia-779


title: 10 mg/L Fluoxetine 1

description: Flu10 1

value: 0 mg/L Fluoxetine


title: Leukemia-777


title: 10 mg/L Fluoxetine 2

description: Flu10 2


title: EARLI_11412_SepsisBSI

value: Plasma


title: WT12_3


title: EARLI_11403_SepsisBSI

value: tive American


title: WT4_3

source_name: Phaeodactylum tricornutum cells 4 h

value: 4 h


title: 50 mg/L Escitalopram 3

description: Ecs50 3

value: 50 mg/L Escitalopram


title: Leukemia-753


title: WT4_2


title: Leukemia-738


title: WT12_2


title: Leukemia-734


title: 50 mg/L Escitalopram 2

description: Ecs50 2


title: EARLI_11375_No-Sepsis

value: Male

value: LatinX


title: WT4_1


title: Leukemia-728

value: Blood

value: B-cell acute lymphoblastic leukemia


title: EARLI_11373_No-Sepsis


title: 50 mg/L Escitalopram 1

description: Ecs50 1


title: WT0_3

source_name: Phaeodactylum tricornutum cells 0 h

value: 0 h

value: Phaeodactylum tricornutum CCAP 1055

value: light period


title: Leukemia-710


title: EARLI_11345_No-Sepsis

value: Female

value: Asian


title: 10 mg/L Duloxetine 2

description: Dul10 2

value: 10 mg/L Duloxetine


title: 10 mg/L Duloxetine 3

description: Dul10 3


title: WT0_2

value: WT


title: WT0_1


title: Leukemia-705


title: WT16_1

value: dark period


title: EARLI_11321_SepsisBSI

value: SepsisBSI


title: Leukemia-699


title: EARLI_11329_SepsisBSI

value: Plasma

value: African American


title: 100 mg/L Bupropion 3

description: Bup100 3

value: 100 mg/L Bupropion


title: Leukemia-696


title: EARLI_11317_Sepsisperiph

value: Sepsisperiph


title: EARLI_11309_Sepsisperiph

value: Male

value: Caucasian


title: 100 mg/L Bupropion 1

description: Bup100 1


title: Leukemia-689

value: Blood


title: 100 mg/L Bupropion 2

description: Bup100 2


title: Leukemia-653

value: B-cell acute lymphoblastic leukemia


title: Leukemia-646


title: Leukemia-683


title: 50 mg/L Agomelatine 3

description: Ago50 3

value: 50 mg/L Agomelatine


title: EARLI_11297_No-Sepsis

value: No-Sepsis


title: EARLI_11344_No-Sepsis


title: Leukemia-628


title: EARLI_11290_SepsisBSI


title: EARLI_11255_No-Sepsis


title: 50 mg/L Agomelatine 1

description: Ago50 1


title: EARLI_11254_No-Sepsis


title: Leukemia-632


title: Leukemia-625


title: 10 mg/L Duloxetine 1

description: Dul10 1


title: EARLI_11203_SepsisBSI

value: Other

value: LatinX


title: Contr 1

description: Con 1

value: Control


title: Contr 2

description: Con 2


title: EARLI_11195_No-Sepsis


title: Leukemia-580


title: Leukemia-544


title: Contr 3

description: Con 3


title: tic-2_postdusk bio3

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

description:
tic_ZT12_C
whole plant

data_processing:
150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X ten.
Low quality sequencing reads were removed. Clean reads were mapped to the Arabidopsis reference genome (TAIR10, www.arabidopsis.org) with Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software, and differential expressed genes (DEGs) was identified using edgeR in the R package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) if FoldChange > 2 and FDR < 0.05 between case group sample and control group sample. GO and KEGG pathway enrichment analysis was performed using TopGO in the R package (http://bioconductor.org/).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Plants were grown under LD conditions at 22ºC for 10 days and harvest at predawn and postdusk repsectively.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
Sequencing libraries were prepared following the protocol of the Directional RNA library Prep Kit (NEB).

tag: time point

tag: ecotype

tag: medium

value: MS+3% sucrose


title: EARLI_11299_SepsisBSI

value: Asian


title: tic-2_postdusk bio2

description:
tic_ZT12_B
whole plant


title: Leukemia-529


title: tic-2_postdusk bio1

description:
tic_ZT12_A
whole plant


title: EARLI_11182_SepsisBSI

value: Female


title: Leukemia-530


title: 50 mg/L Agomelatine 2

description: Ago50 2


title: Leukemia-508


title: Yanyan97_8h_rep3

city: Nanjing

first: zhenyu

last: luo

state: Jiangsu

address: Xuanwu

department: College of Agricuture

data_processing:
The raw sequence data were processed to remove low-quality reads using FastQC (v0.11.5) and Trim_Galore (v0.6.4). The filtered high-quality reads were mapped on the Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/) using HISAT2 (v2.0.5) with default parameters.
Reads with a mapping quality below twenty were excluded from further analyses using SAMtools (v1.9).(-q 20)
StringTie (v1.3.4d) and FeatureCounts (v1.6.4) were used to obtain transcripts per million (TPM) and read counts for all annotated genes in the tobacco genome.
Genome_build: Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcripts Per Million) values  for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene read counts for every gene and every sample

organism: Nicotiana tabacum

growth_protocol: Two cultivated tobacco (Nicotiana tabacum L.) varieties, Taiyan8 tobacco (TT) and Yanyan97 tobacco (YT), were used in this study. The seeds were sterilized in 75% ethanol for 30 s and washed with sterile water for five times. Sterilized seeds were germinated and grown in 1/2 MS medium in an illuminated incubator (16 h/8 h day/night light cycle, 22/20℃day/night temperature setting with 65% relative humidity).

extract_protocol:
Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tobacco seedlings at the five-leaf stage were used for cold treatment at 4℃. Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.

tag: developmental stage

value: five-leaf stage

value: seedlings

value: 8h cold treatment at 4 degrees centigrade


title: EARLI_11180_Sepsisperiph

tag: tissue

value: Plasma


title: Yanyan97_8h_rep2


title: Leukemia-507


title: Col_0_postdusk bio3

description:
tic_ZT0_C
whole plant

value: Wild type


title: Col_0_postdusk bio2

description:
tic_ZT0_B
whole plant


title: Leukemia-1107


title: EARLI_11168_SepsisBSI

value: SepsisBSI

tag: gender


title: Col_0_postdusk bio1

description:
tic_ZT0_A
whole plant

tag: age


title: Yanyan97_4h_rep3

value: 4h cold treatment at 4 degrees centigrade


title: EARLI_11128_No-Sepsis

tag: disease state

value: Male


title: Yanyan97_8h_rep1


title: tic-2_predawn bio2

description:
Col_ZT12_B
whole plant


title: EARLI_11122_No-Sepsis

tag: race

value: Caucasian


title: EARLI_11114_No-Sepsis

tag: ethnicity


title: Leukemia-1098

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Leukemia-1105


title: tic-2_predawn bio3

description:
Col_ZT12_C
whole plant


title: Yanyan97_2h_rep3

value: 2h cold treatment at 4 degrees centigrade


title: tic-2_predawn bio1

description:
Col_ZT12_A
whole plant


title: Leukemia-1096


title: Yanyan97_4h_rep1


title: EARLI_11184_No-Sepsis

value: No-Sepsis


title: Leukemia-1067


title: EARLI_11111_No-Sepsis


title: Col_0_predawn bio3

description:
Col_ZT0_C
whole plant


title: EARLI_11097_Sepsisperiph

value: Sepsisperiph

value: LatinX


title: Leukemia-1060


title: Yanyan97_2h_rep2


title: EARLI_11139_Sepsisperiph

value: Other


title: Col_0_predawn bio2

description:
Col_ZT0_B
whole plant

value: MS+3% sucrose


title: Leukemia-1058


title: Col_0_predawn bio1

description:
Col_ZT0_A
whole plant


title: Yanyan97_1h_rep3

value: five-leaf stage

value: 1h cold treatment at 4 degrees centigrade


title: Yanyan97_4h_rep2

value: seedlings


title: Leukemia-1056


title: EARLI_11093_No-Sepsis

value: Plasma


title: EARLI_11062_SepsisBSI

value: African American


title: Yanyan97_1h_rep2


title: EARLI_11052_Sepsisperiph

value: Female

value: Asian


title: Leukemia-1047


title: Mono_DL1_3

description: repeat 3 of 3

organism: Streptococcus gordonii

source_name: Whole cell lysate

value: grown in monoculture (TYG) to OD600 nm = 0.5

value: DL1 wild-type (reference strain)


title: EARLI_11038_Sepsisperiph

value: Male

value: Caucasian


title: Leukemia-1041

value: Blood

value: B-cell acute lymphoblastic leukemia


title: Yanyan97_1h_rep1


title: Leukemia-1033


title: Yanyan97_0.5h_rep3

value: 0.5h cold treatment at 4 degrees centigrade


title: Male_CORT M12

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using STAR (version 2.7.3a).
Gene-read quantification was perfromed using HTSeq-count (version 0.12.4) .
HTSeq-count output files were merged into the raw_gene_count_matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every feature according to Ensembl97 for each sample.

source_name: Muscle

extract_protocol:
The snap-frozen, dissected quadriceps muscle were homogenized in Tripure using a Kimble pellet pestle followed by a phase-separation with chloroform. RNA was isolated using the RNeasy kit according to manufacturer’s instructions (Qiagen 74104)
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

value: quadriceps muscle

tag: Sex

value: Corticosterone


title: Yanyan97_0.5h_rep2


title: EARLI_11035_No-Sepsis

value: No-Sepsis


title: Mono_DL1_1

description: repeat 1 of 3

tag: strain


title: EARLI_11028_No-Sepsis


title: Leukemia-1023


title: Yanyan97_2h_rep1

value: five-leaf stage

value: 2h cold treatment at 4 degrees centigrade

tag: genotype


title: EARLI_11022_No-Sepsis


title: Male_VEH M11

tag: treatment

value: Vehicle


title: Yanyan97_0.5h_rep1

value: seedlings


title: Yanyan97_0h_rep3

value: 0h cold treatment at 4 degrees centigrade


title: Male_CORT M10


title: Leukemia-1013


title: EARLI_11017_No-Sepsis

value: Plasma


title: Yanyan97_0h_rep2


title: Male_VEH M9


title: Leukemia-1012


title: EARLI_11011_No-Sepsis


title: Mono_DL1_2

description: repeat 2 of 3


title: Male_CORT M8


title: Yanyan97_0h_rep1


title: EARLI_11010_No-Sepsis


title: 997


title: Male_VEH M7


title: Taiyan8_8h_rep3

value: 8h cold treatment at 4 degrees centigrade


title: Leukemia-1019


title: Taiyan8_8h_rep2


title: EARLI_11005_No-Sepsis


title: 983


title: Male_CORT M6


title: EARLI_10993_SepsisBSI

value: SepsisBSI

value: Female

value: African American


title: Male_VEH M5

value: Male


title: Taiyan8_8h_rep1


title: 979

value: Blood


title: EARLI_10983_No-Sepsis

value: Caucasian


title: Male_CORT M4


title: Taiyan8_4h_rep3

value: 4h cold treatment at 4 degrees centigrade


title: Taiyan8_4h_rep2


title: Male_VEH M3

value: quadriceps muscle


title: EARLI_10991_Sepsisperiph

value: Sepsisperiph


title: EARLI_10979_No-Sepsis

value: No-Sepsis


title: 970

value: B-cell acute lymphoblastic leukemia


title: Male_VEH M1


title: Taiyan8_4h_rep1

value: five-leaf stage


title: Male_CORT M2

value: Corticosterone


title: EARLI_10971_SepsisBSI

value: Asian


title: 955


title: 985


title: EARLI_10958_Sepsisperiph


title: Taiyan8_2h_rep3

value: seedlings

value: 2h cold treatment at 4 degrees centigrade


title: Female_VEH F11

value: Vehicle


title: Taiyan8_2h_rep2


title: 981


title: EARLI_10957_Sepsisperiph

value: Plasma


title: Taiyan8_2h_rep1


title: Female_CORT F10

value: Female


title: 953


title: 954


title: Female_VEH F9


title: Taiyan8_1h_rep3

value: 1h cold treatment at 4 degrees centigrade


title: Female_CORT F8


title: EARLI_10856_No-Sepsis

value: African American


title: Female_VEH F7


title: 937

value: Blood


title: EARLI_10902_No-Sepsis


title: Taiyan8_1h_rep2


title: Taiyan8_1h_rep1


title: 959


title: EARLI_10825_Sepsisperiph

value: Male


title: Female_CORT F6


title: EARLI_10820_SepsisBSI

value: SepsisBSI

value: Caucasian


title: Taiyan8_0.5h_rep3

value: 0.5h cold treatment at 4 degrees centigrade


title: Female_VEH F5

value: quadriceps muscle


title: Taiyan8_0.5h_rep2


title: 914

value: B-cell acute lymphoblastic leukemia


title: EARLI_10929_SepsisBSI


title: 928


title: EARLI_10819_SepsisBSI


title: Female_CORT F4


title: Taiyan8_0.5h_rep1

value: five-leaf stage


title: EARLI_10812_No-Sepsis

value: No-Sepsis


title: 909


title: Female_VEH F3


title: 886


title: 947


title: Taiyan8_0h_rep3

value: 0h cold treatment at 4 degrees centigrade


title: Female_CORT F2

value: Corticosterone


title: EARLI_10778_No-Sepsis


title: EARLI_10755_Sepsisperiph

value: Sepsisperiph


title: Female_VEH F1

value: Vehicle


title: Taiyan8_0h_rep2

value: seedlings


title: 1100


title: 1103


title: 929


title: EARLI_10757_No-Sepsis

value: Plasma

value: Asian


title: Taiyan8_0h_rep1