title: GSC P3 cells, siNONO rep3

city: jinan

first: Xu

last: Wang

state: State...

address: wenhua west road

institute: shandong university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9. perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: GSC P3 cells, siNONO

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GSC P3

value: glioblastoma cell

tag: disease state

value: glioblastoma

value: siNONO

value: NONO knockdown


title: SMA_spinal cord-replicate 3

status: Public on Aug 03 2022

type: SRA

city: nantong

first: junjie

last: sun

state: jiangsu province

address: 19 Qixiu Road

country: China

institute: nantong university

description: Ribosome removal

library_source: transcriptomic

data_processing:
First, the raw data of bulk-seq was converted into high-quality clean reads. Then, hisat2 was used to align the clean reads to the reference genome of Mus musculus. Fragments per kilobase of exon per million mapped fragments (FPKM) expression values of genes were quantified using cufflinks software.
Assembly: mm10
Supplementary files format and content: xls files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: spinal cord

extract_protocol:
The total RNA of spinal cord tissue was extracted through the Trizol method.
Using ribosomal-depleted RNA and random hexamers to synthesize one-stranded cDNA, and then we added buffer, deoxynucleoside triphosphates, and enzymes to synthesize two-stranded cDNA. Double-stranded DNA was purified using VAHTS™ DNA Clean Beads, followed by end repair, A-tailing, and the ligation of sequencing adapters. The cDNA strand containing U was degraded by the uracil-DNA glycosylase enzyme, and finally, PCR enrichment was performed; the PCR product was purified with VAHTSTM DNA Clean Beads to obtain the final strand-specific cDNA library.

tag: tissue

value: spinal cord

tag: genotype

value: (mSmn-/-, hSMN22tg/0)

tag: age

value: postnatal day 4

tag: strain

value: FVB


title: i-SOX2-ONS76 Sample 8

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

country: USA

institute: University of Nebraska Medical Center

data_processing:
Reads were aligned and mapped to reference genome hg38 using STAR 2.7.3a
Peaks from bigwig flies were visualized using IGV
TPM values were calculated using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol: ONS76, LNCaP, and DU145 and derived cell lines engineered for the inducible overexpression of SOX2: i-SOX2-ONS76, i-SOX2-LNCaP, and i-SOX2-DU145 have been described previously (21, 22). UW228 cells were obtained from Sutapa Ray (UNMC, Omaha, NE). HCT116 cells were obtained from American Type Culture Collection (Manassas, VA). All cells, including i-SOX2-derived lines, were cultured in Dulbecco’s Modified Eagle (DME) Medium supplemented with 10% fetal bovine serum. Doxycycline (Dox, Clontech, Mountain View, CA) was suspended in phosphate buffered  saline (PBS).

extract_protocol:
RNA isolation was performed using the RNeasy kit (Qiagen, Germantown, MD). Cells were lysed using RLT buffer and Qiashredder columns (Qiagen, Germantown, MD) as outlined in the manufacturer’s protocols.
i-SOX2-ONS76, i-SOX2-LNCaP, and i-Omomyc-ONS76 cells were cultured in the presence or absence of Dox for 4 days. mRNA was harvested as outlined above. RNA samples were assessed for purity and quality. Library preparation and transcriptome sequencing on an Illumina NovaSeq 6000 platform were performed by Novogene (Beijing, China).

treatment_protocol: SOX2 overexpression was induced by adding Dox to the culture medium at the times and concentrations indicated. Tamoxifen (4-OHT, Sigma, St. Louis, MO) was dissolved in ethanol. MYC-ER nuclear translocation was induced by adding 4-OHT to the culture medium at the indicated times and concentrations. Cell proliferation was assessed by MTT assays performed on triplicate samples as described previously (19-22). Statistical significance was determined using a two-tailed students t-test with a significance threshold of p=.05. Cell lines not obtained from American Type Culture Collection were verified by genetic analysis performed by the UNMC Molecular Diagnostics Laboratory. All cell lines were tested for the presence of mycoplasma and found to be negative.

tag: cell type


title: i-Omomyc-ONS76 Sample 13


title: GSC P3 cells, siNONO rep2

tag: cell line

tag: treatment


title: Liver- p42_snRNA-seq

city: New Haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

data_processing:
The cellranger version 5.0.1 commercial software was utilized to conduct the initial data processes.
Seurat and some in-house customized scripts were used to manage the single nuclei transcriptomic datasets.
For detailed snRNAseq analysis methods see Supplementary Information.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: .Rdata file includes counts for every gene in each cell and meta information for every cell

molecule: polyA RNA

organism: Sus scrofa

source_name: Liver

extract_protocol:
After administered anesthesia, circulatory collapse was induced with ventricular fibrillation to pigs 3-4 months of age for each experimental group (0h WIT, 1h WIT, 7h WIT, ECMO and OrganEx). Following the appropriate experimental condition, regions of interest were extracted from each organ and frozen at -80 ºC. Nuclei isolation from each organ (brain, heart, liver, kidney) were treated the same according to our already established protocol. The procedures/ dissections were performed in chilled RNAase-free PBS with RNase-free sterilized instruments under RNase-free conditions. Nuclei from injured and control frozen cerebral tissues were isolated by Dounce homogenization and centrifugation. Extracted nuclei samples were placed on ice and taken to the Yale Center for Genome Analysis core facility and processed within 15 minutes for single nucleus RNA sequencing. For more detail see Supplementary Information.
RNA libraries were prepared for sequencing using standard manufacturer (Illumina) protocols

value: Liver

value: 3-4 months

tag: condition

value: 0h PMI


title: Con_spinal cord-replicate 3

description: Ribosome removal

value: (mSmn+/-, hSMN22tg/0)


title: Liver- p41_snRNA-seq


title: i-SOX2-LNCap Sample 6


title: Con_spinal cord-replicate 2

description: Ribosome removal


title: Heart- p49_snRNA-seq

source_name: Heart

value: Heart

value: OrganEx


title: i-SOX2-LNCap Sample 5


title: Con_spinal cord-replicate 1

description: Ribosome removal


title: GSC P3 cells, siNONO rep1


title: Liver- p43_snRNA-seq


title: SMA_spinal cord-replicate 2

description: Ribosome removal


title: SMA_spinal cord-replicate 1

description: Ribosome removal


title: i-SOX2-LNCap Sample 4


title: GSC P3 cells, siNC rep2

source_name: GSC P3 cells, siNC

value: siNC

value: control


title: GSC P3 cells, siNC rep3

value: GSC P3


title: Heart- p48_snRNA-seq


title: GSC P3 cells, siNC rep1

value: glioblastoma cell


title: KO-Inf-M-3_157_036_S37

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

description: Blood_CD55KO BC _rep3

data_processing:
RNAseq data were trimmed and aligned to the mouse genome ( from Ensembl), with associated annotation file using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl transcripts using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The counts generated were processed by gene set analysis (GSA).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include baseMean for each gene

source_name: Blood_CD55KO BC _rep3

extract_protocol:
Total RNA was extracted from whole blood obtained from mice 2 days post infection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: CD55 KO

value: B.crocidurae infected

tag: timepoint

value: 2 dpi


title: Heart- p46_snRNA-seq


title: U251 cells, siNONO rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9. perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: U251 cells, siNONO

value: glioblastoma

value: siNONO

value: NONO knockdown


title: Heart- p50_snRNA-seq

value: Ecmo


title: U251 cells, siNONO rep2


title: i-SOX2-LNCap Sample 2


title: KO-Inf-2_169_024_S36

description: Blood_CD55KO BC rep2

source_name: Blood_CD55KO BC rep2


title: KO-Inf-1_181_012_S35

description: Blood_CD55KO BC_rep1

source_name: Blood_CD55KO BC_rep1


title: Heart- p28_snRNA-seq

value: 3-4 months


title: i-SOX2-ONS76 Sample 7


title: Wt-Inf-M-3_098_095_S34

description: Blood_C57BL/6 wt BC_rep3

source_name: Blood_C57BL/6 wt BC_rep3

value: WT


title: U251 cells, siNC rep3

source_name: U251 cells, siNC


title: U251 cells, siNONO rep1


title: i-SOX2-LNCap Sample 1


title: Heart- p27_snRNA-seq


title: Heart- p33_snRNA-seq

value: 7h PMI


title: U251 cells, siNC rep2


title: U251 cells, siNC rep1


title: Heart- p32_snRNA-seq

value: Heart


title: Wt-Inf-1_122_071_S32

description: Blood_C57BL/6 wt BC_rep1

source_name: Blood_C57BL/6 wt BC_rep1


title: EARLI 50723_SepsisBSI

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

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

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

value: SepsisBSI

value: Plasma

tag: gender

value: Male

tag: race

value: Caucasian

tag: ethnicity


title: EARLI 50695_SepsisBSI


title: KO-Uninf-M-3_134_059_S31

value: Untreated


title: Heart- p26_snRNA-seq


title: EARLI 50692_Sepsisperiph

value: Sepsisperiph

value: Asian


title: i-SOX2-LNCap Sample 3


title: PLC/PRF/5-JIB-04

city: Seoul

first: Jina

last: Lee

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of systems biology

country: South Korea

institute: Yonsei university

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic 0.32.
Read quality was checked for each sample using FastQC v0.11.5.
High-quality reads was aligned to the reference genome (hg19) using HISAT2 version 2.0.5 and bowtie2 2.2.6.
After the read mapping, StringTie version 1.3.3b was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as FPKM (Fragment per Kilobase of transcript per Million mapped reads).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gtf files were generated by StringTie version 1.3.3b

extract_protocol:
Total RNA was extracted from PLC/PRF/5 with treatment of DMSO and JIB-04 using TRI-reagent LS (MRC). Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: PLC/PRF/5 was treated with DMSO and 6µM of JIB-04 for 24hr.

value: hepatocellular carcinoma cell line

value: JIB-04 for 24 hours


title: Heart- p40_snRNA-seq

value: 1h PMI


title: KO-Uninf-2_146_047_S30

value: blood

value: CD55 KO


title: EARLI 50661_Sepsisperiph


title: KO-UnInf-1_158_035_S29


title: EARLI 50650_Sepsissuspected

value: Sepsissuspected


title: EARLI 50749_Sepsisperiph


title: Heart- p38_snRNA-seq

value: 3-4 months


title: EARLI 50623_Sepsisperiph

value: African American


title: Wt-Inf-2_110_083_S33

description: Blood_C57BL/6 wt BC_rep2

source_name: Blood_C57BL/6 wt BC_rep2

value: WT

value: B.crocidurae infected

value: 2 dpi


title: MCF7 cells, siNAT10 3

city: Jeddah

first: Mohammad

middle: Imran

last: Khan

state: Makkah

address: King Abdullah Road

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 v2.0.5 was used for alignment to reference genome
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Human breast , MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37OC

extract_protocol:
RNA was isolated using TRI Reagent (Sigma, USA). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq was checked using Qubit 2.0

treatment_protocol: Cell were knocked down using NAT10 siRNA

value: Breast adenocarcinoma

value: NAT10 knockdown

value: NAT10 siRNA

tag: time


title: MCF7 cells, siNAT10 2


title: EARLI 50621_SepsisBSI

value: SepsisBSI

value: Plasma

value: Male


title: Heart- p43_snRNA-seq

value: Heart

value: 0h PMI


title: WtUninf-2_182_011_S27

description: Blood_C57BL/6 wt_rep2

source_name: Blood_C57BL/6 wt_rep2

value: Untreated


title: MCF7 cells, siNAT10 1


title: Heart- p42_snRNA-seq


title: WtUninf-1_099_094_S26

description: Blood_C57BL/6 wt_rep1

source_name: Blood_C57BL/6 wt_rep1

value: blood


title: EARLI 50618_SepsisBSI

value: Caucasian


title: Heart- p41_snRNA-seq


title: Shh KO rep5

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:
Quality control for raw reads involved trimming the first 13bp with FastQ Groomer to ensure a median quality score of 36 or above for each sample.
Fastq files were aligned to the UCSC mouse genome (mm9) (Kent et al., 2002) using TopHat (Cole Trapnell, 2009) (version 2.0.10) with the following parameters: (--segment-length 19 --segment-mismatches 2 --no-coverage-search).
Samples were then analyzed for differential gene expression using Cuffdiff (Trapnell et al., 2013) (version 2.1.1) with quartile normalization. Significantly differentially expressed genes were identified using thresholds of FDR <0.05 and fold change > 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited text file includes FPKM values for each sample and log2 fold change between WT and KO

source_name: embryonic posterior second heart field (pSHF)

extract_protocol:
pSHFs were microdissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent and RNeasy Mini RNA Isolation Kit (Qiagen 74104).
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 HiSeq2500 in Rapid Run Mode following the manufacturer's protocols to generate stranded single-end reads of 50bp.

value: mixed background

value: posterior second heart field (pSHF)

value: Shh KO


title: Hippocampus-p49_snRNA-seq

source_name: Hippocampus

value: Hippocampus

value: 3-4 months

value: OrganEx


title: Shh KO rep4

description: polyA mRNA-seq


title: PLC/PRF/5-DMSO

value: hepatocellular carcinoma cell line

value: untreated


title: EARLI 50611_Sepsisperiph

value: Sepsisperiph

value: African American


title: Heart- p39_snRNA-seq

value: 1h PMI


title: Hippocampus-p48_snRNA-seq


title: Shh KO rep3

description: polyA mRNA-seq


title: EARLI 50604_Sepsisperiph

value: Plasma

value: Female


title: WtUninfM-3_170_023_S28

description: Blood_C57BL/6 wt_rep3

source_name: Blood_C57BL/6 wt_rep3

value: WT


title: EARLI 50593_SepsisBSI

value: SepsisBSI


title: Shh KO rep2

description: polyA mRNA-seq


title: Hippocampus-p46_snRNA-seq


title: EARLI 50586_Sepsissuspected

value: Sepsissuspected

value: Asian


title: PE+IFNy replicate 4 [THP-1]

city: Ann Arbor

first: Joseph

last: Holoshitz

state: MI

address: 1150 W Medical Center Dr

department: Internal Medicine - Rheumatology

institute: University of Michigan

description: Labeled P

data_processing:
Raw counts were attained using featureCounts from the Rsubread-1.6.1 package.
Gencode28-hg38 gene annotations using only uniquely aligned reads.
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05.
Genome_build: Gencode28-hg38
Supplementary_files_format_and_content: deSeq2_counts THP-1_IFNy LE_SE_PE.txt

source_name: THP-1 cells

growth_protocol: THP-1 cells were grown with PMA (85 nM) for 3 days followed by 5 additional days without PMA prior to the experiments.

extract_protocol:
Total RNA was isolated with RNeasy mini kit from Qiagen. Genomic DNA was removed using the Turbo DNA-Free kit from Ambion. 200 ng total RNA was used to generate libraries with the Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Differentiated THP-1 cells were treated with or without IFNγ (5 ng/ml) in the presence or absence of 15-mer peptides 65-79*0301 (LE), 65-79*0401 (SE) or 65-79*0402 (PE) (100 μg/ml) for 72 hrs. Medium was refreshed once at 48 hrs.

value: cell line, macrophage

value: 65-79*PE peptide and IFNy (10ng/ml)

tag: treatment duration

value: 72 hours


title: PE+IFNy replicate 3 [THP-1]

description: Labeled L


title: EARLI 50576_Sepsisperiph


title: Hippocampus-p28_snRNA-seq

value: Hippocampus

value: Ecmo


title: PE+IFNy replicate 2 [THP-1]

description: Labeled H


title: Shh KO rep1

description: polyA mRNA-seq

value: mixed background

value: posterior second heart field (pSHF)

value: Shh KO


title: Hippocampus-p50_snRNA-seq

value: 3-4 months


title: EARLI 50562_No-Sepsis

value: No-Sepsis

value: Male

value: African American


title: MCF7 cells, siC 3

value: Breast adenocarcinoma

value: control siRNA


title: MCF7 cells, siC 1

value: WT


title: MCF7 cells, siC 2


title: EARLI 50561_SepsisBSI

value: SepsisBSI

value: Plasma

value: Female

value: Caucasian


title: PE+IFNy replicate 1 [THP-1]

description: Labeled D

value: cell line, macrophage

value: 65-79*PE peptide and IFNy (10ng/ml)

value: 72 hours


title: Shh WT rep3

description: polyA mRNA-seq

value: mixed background

value: Shh WT


title: SE+IFNy replicate 4 [THP-1]

description: Labeled O

value: 65-79*SE peptide and IFNy (10ng/ml)


title: Hippocampus-p33_snRNA-seq

value: Hippocampus

value: 3-4 months

value: 7h PMI


title: EARLI 50552_No-Sepsis

value: No-Sepsis

value: Male

value: Asian


title: Shh WT rep2

description: polyA mRNA-seq

value: posterior second heart field (pSHF)


title: SE+IFNy replicate 3 [THP-1]

description: Labeled K


title: Hippocampus-p32_snRNA-seq


title: SE+IFNy replicate 2 [THP-1]

description: Labeled G


title: Hippocampus-p26_snRNA-seq


title: Shh WT rep1

description: polyA mRNA-seq


title: SE+IFNy replicate 1 [THP-1]

description: Labeled C


title: EARLI 50540_Sepsissuspected

value: Sepsissuspected

value: African American


title: Shh WT rep4

description: polyA mRNA-seq


title: Hippocampus-p39_snRNA-seq

value: 1h PMI


title: Hippocampus-p27_snRNA-seq

value: Ecmo


title: PE+IFNy replicate 4 [RAW264.7]

description: Labeled HLA8

data_processing:
Raw counts were attained using featureCounts from the Rsubread1.5.0p3 package.
Gencode-M12 gene annotations using only uniquely aligned reads.
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05.
Genome_build: Gencode-M12 (GRCm38.p5)
Supplementary_files_format_and_content: deSeq2_counts RAW264.7 cells_IFNy LE_SE_PE.txt

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells grown in DMEM.

extract_protocol:
Total RNA was isolated with Trizol and the Direct-ZolTM RNA miniprep from Zymo research. Genomic DNA was removed using the Turbo DNA-Free kit from Ambion. 200 ng total RNA was used to generate libraries with the Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were treated with or without IFNγ (5 ng/ml) in the presence or absence of 15-mer peptides 65-79*0301 (LE), 65-79*0401 (SE) or 65-79*0402 (PE) (100 μg/ml) for 72 hrs. Medium was refreshed once at 48 hrs.

value: cell line, macrophage

value: 65-79*PE peptide and IFNy (5ng/ml)


title: EARLI 50525_No-Sepsis

value: Plasma

value: Female


title: PE+IFNy replicate 6 [RAW264.7]

description: Labeled HLA24

value: 72 hours


title: LE+IFNy replicate 3 [THP-1]

description: Labeled J

value: 65-79*LE peptide and IFNy (10ng/ml)


title: Hippocampus-p38_snRNA-seq

value: Hippocampus


title: PE+IFNy replicate 3 [RAW264.7]

description: Labeled X


title: EARLI 50514_Sepsisperiph

value: Sepsisperiph


title: EARLI 50515_Sepsisperiph


title: PE+IFNy replicate 5 [RAW264.7]

description: Labeled HLA16


title: Hippocampus-p43_snRNA-seq

value: 3-4 months

value: 0h PMI


title: EARLI 50511_SepsisBSI

value: SepsisBSI

value: Male


title: LE+IFNy replicate 2 [THP-1]

description: Labeled F


title: PE+IFNy replicate 2 [RAW264.7]

description: Labeled P


title: LE+IFNy replicate 1 [THP-1]

description: Labeled B


title: PE+IFNy replicate 1 [RAW264.7]

description: Labeled H


title: Hippocampus-p42_snRNA-seq


title: EARLI 50542_No-Sepsis

value: No-Sepsis

value: Asian


title: EARLI 50478_No-Sepsis

value: African American


title: IFNy replicate 4 [THP-1]

description: Labeled M

value: IFNy (10ng/ml)


title: Hippocampus-p41_snRNA-seq


title: Hippocampus-p40_snRNA-seq

value: 1h PMI


title: EARLI 50471_Sepsisperiph


title: SE+IFNy replicate 6 [RAW264.7]

description: Labeled HLA23

value: cell line, macrophage

value: 65-79*SE peptide and IFNy (5ng/ml)


title: LE+IFNy replicate 4 [THP-1]

description: Labeled N


title: IFNy replicate 3 [THP-1]

description: Labeled I


title: SE+IFNy replicate 5 [RAW264.7]

description: Labeled HLA15


title: EARLI 50469_No-Sepsis

value: Plasma

value: Other

value: LatinX


title: SE+IFNy replicate 4 [RAW264.7]

description: Labeled HLA7

value: 72 hours


title: EARLI 50452_Indeterm

value: Indeterm

value: Female


title: IFNy replicate 2 [THP-1]

description: Labeled E


title: EARLI 50445_SepsisBSI


title: PE replicate 4 [THP-1]

description: Labeled 6


title: A549 cells transiently transfected with 100 pmol siRNA APEX1, replicate 3

type: RNA

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: A549 adenocarcinomic human alveolar basal epithelial cell line treated with siAPEX1

data_processing: Transcript counts were normalized through the normalization method incorporated in the model framework, estimating parameters from positive controls, negative controls, and housekeeping genes embedded in the nCounter system, using the NanoStringDiff package within Bioconductor. The quality of the data was checked by the mean expression and SD values for housekeeping miRNAs and positive/negative controls. Differential expression of genes was assessed on log2-normalized data with a generalized linear model likelihood ratio test, using the glm.LRT function within the NanoStringDiff package. A q-value cutoff of 0.1 was used to determine statistical significance.

label: not provided

label_protocol: Samples were prepared for nCounter miRNA expression profiling using the human v3 miRNA expression panel, according to the manufacturer’s recommendations (NanoString, Seattle, Washington, USA) for hybridization, detection, and scanning.

growth_protocol: A549 cells were grown in RPMI medium (Euroclone, Milan, Italy). Cells were supplemented with 10% fetal bovine serum (Euroclone), 1% penicillin streptomycin solution (100 U/mL penicillin, 100 mg/mL streptomycin), 2 mM L-glutamine (Euroclone) and cultured in a humidified incubator at 5% CO2 at 37 °C. Cells were tested and free of mycoplasma contamination (N-GARDE Mycoplasma PCR Reagent, Euroclone).

extract_protocol: RNA was isolated using the miRNeasy kit (Qiagen, USA).

treatment_protocol: One day before silencing, cells were seeded in 10-cm plates at a density of 3 × 106 cells per plate. Cells were then transiently transfected with 100 pmol siRNA APE1 5ʹ-UACUCCAGUCGUACCAGACCU-3ʹ or the scramble control siRNA 5ʹ-CCAUGAGGUCAUGGUCUGdTdT-3ʹ (Dharmacon, Lafayette, CO) using DharmaFECT reagent (Dharmacon). After 72 h upon transfection, cells were collected and RNA extracted using miRNeasy kit (Qiagen, USA).  30 nM mimic has-miR-33a-5p, mimic has-miR-130b-3p or mimic negative control (Ambion) was transfected into A549 cells using Lipofectamine RNAi max (Invitrogen). Cells were incubated at 37°C, 5% CO2 for 24 h.


title: A549 cells transiently transfected with 100 pmol siRNA APEX1, replicate 2

source_name: A549 adenocarcinomic human alveolar basal epithelial cell line


title: PE replicate 3 [THP-1]

description: Labeled 2


title: EARLI 50435_SepsisBSI


title: SE+IFNy replicate 2 [RAW264.7]

description: Labeled O


title: EARLI 50444_Sepsissuspected

value: Sepsissuspected


title: A549 cells transiently transfected with 100 pmol siRNA APEX1, replicate 1


title: SE+IFNy replicate 1 [RAW264.7]

description: Labeled G


title: PE replicate 2 [THP-1]

description: Labeled X


title: LE+IFNy replicate 6 [RAW264.7]

description: Labeled HLA22

value: 65-79*LE peptide and IFNy (5ng/ml)


title: PE replicate 1 [THP-1]

description: Labeled T


title: A549 cells transiently transfected with 100 pmol scramble control siRNA, replicate 2

description: A549 adenocarcinomic human alveolar basal epithelial cell line treated with siCTRL

value: siCTRL


title: EARLI 50418_SepsisBSI

value: SepsisBSI

value: Male

value: Caucasian


title: LE+IFNy replicate 5 [RAW264.7]

description: Labeled HLA14


title: A549 cells transiently transfected with 100 pmol scramble control siRNA, replicate 1


title: SM3

city: Yinchuan

first: Shuxia

last: Li

state: Ningxia

address: 489 Helan mountain West Road

department: College of Agriculture

institute: Ningxia University

data_processing:
The adaptor contamination reads were removed using Cutadapt software.
The low-quality bases and undetermined bases were removed from raw data.
The HISAT2 software (version: 2.0.4) was used to map clean reads to the genome.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
StringTie and ballgown software were used to estimate the expression levels of all transcripts and perform gene expression level by calculating fragments per kilobase of transcripts per million (FPKM) mapped reads
Assembly: cultivated alfalfa
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Medicago sativa

source_name: Leaves

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Sequencing library construction and sequencing were performed using Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Salt plus melatonin


title: SE replicate 4 [THP-1]

description: Labeled 5


title: SM2


title: LE+IFNy replicate 4 [RAW264.7]

description: Labeled HLA6


title: EARLI 50417_SepsisBSI


title: EARLI 50400_Sepsisperiph

value: Sepsisperiph

value: Asian


title: SE replicate 3 [THP-1]

description: Labeled 1

value: cell line, macrophage


title: IFNy replicate 1 [THP-1]

description: Labeled A

value: IFNy (10ng/ml)


title: SE+IFNy replicate 3 [RAW264.7]

description: Labeled W

value: 65-79*SE peptide and IFNy (5ng/ml)


title: LE+IFNy replicate 3 [RAW264.7]

description: Labeled V


title: SM1


title: A549 cells transiently transfected with 100 pmol scramble control siRNA, replicate 3


title: S3

value: Salt treatment


title: SE replicate 2 [THP-1]

description: Labeled W


title: SE replicate 1 [THP-1]

description: Labeled S


title: EARLI 50375_Indeterm

value: Plasma


title: S2


title: LE+IFNy replicate 1 [RAW264.7]

description: Labeled F

value: 72 hours


title: EARLI 50398_SepsisBSI


title: LE replicate 4 [THP-1]

description: Labeled 4


title: EARLI 50366_SepsisBSI


title: LE replicate 3 [THP-1]

description: Labeled Z


title: IFNy replicate 5 [RAW264.7]

description: Labeled HLA13

value: IFNy


title: M3

value: Melatonin treatment


title: EARLI 50360_No-Sepsis

value: No-Sepsis


title: S1


title: LE replicate 2 [THP-1]

description: Labeled V


title: M2


title: EARLI 50359_Sepsissuspected

value: Sepsissuspected


title: LE replicate 1 [THP-1]

description: Labeled R


title: M1


title: IFNy replicate 3 [RAW264.7]

description: Labeled U


title: EARLI 50345_Sepsissuspected

value: Female


title: IFNy replicate 4 [RAW264.7]

description: Labeled HLA5


title: PBS replicate 4 [THP-1]

description: Labeled 3

value: PBS


title: CK3

value: Normal


title: IFNy replicate 2 [RAW264.7]

description: Labeled M


title: LE+IFNy replicate 2 [RAW264.7]

description: Labeled N

value: 65-79*LE peptide and IFNy (5ng/ml)


title: EARLI 50367_SepsisBSI

value: SepsisBSI

value: Caucasian


title: PBS replicate 3 [THP-1]

description: Labeled Y


title: IFNy replicate 1 [RAW264.7]

description: Labeled E


title: CK2


title: IFNy replicate 6 [RAW264.7]

description: Labeled HLA21


title: EARLI 50316_SepsisBSI

value: Male

value: Other

value: LatinX


title: EARLI 50302_SepsisBSI


title: CK1


title: PBS replicate 1 [THP-1]

description: Labeled Q

value: cell line, macrophage


title: PBS replicate 2 [THP-1]

description: Labeled U


title: PE replicate 6 [RAW264.7]

description: Labeled HLA20

value: 65-79*PE peptide


title: EARLI 50299_No-Sepsis

value: Plasma


title: EARLI 50292_Sepsisperiph

value: Sepsisperiph

value: African American


title: EARLI 50265_No-Sepsis


title: PE replicate 4 [RAW264.7]

description: Labeled HLA4

value: 72 hours


title: TGFBR2 knockout TIL with gRNA #4 exposed to vehicle, replicate 3

city: Tampa

first: Yunfei

state: FL

address: 12902 USF Magnolia Drive

department: Clinical Science

institute: H. Lee Moffitt Cancer Center & Research Institute

data_processing:
The reads were mapped to human hg38 genome and GENCODE V23 transcriptome using HISAT2 2.1.0 with parameters “--rna-strandness RF  --no-discordant --no-mixed –dta”.
The SAM files were then sorted and indexed using samtools 1.9. The gene expression level in transcript per million reads (TPM) was called using StringTie 1.3.5. The differential expression analysis was performed using limma-trend method.
Gene set enrichment analysis was performed using GSEA on all mSigDB genesets.
Genome_build: hg38
Supplementary_files_format_and_content: differential expression analysis result in Excel format

growth_protocol: Patient-derived ovarian cancer TIL were cultured from tumor fragments and viably frozen after an initial expansion phase in the presence of interleukin-2 and agonistic antibodies targeting CD3 (clone OKT3) and CD137/4-1BB (Urelumab). TIL were re-activated with plate-bound OKT3 for 2 days before electroporation-mediated delivery of Cas9 ribonucleoprotein complexes targeting TGFBR2. TIL were cultured for 4 days after TGFBR2 knockout, stimulated with TGF-B1 or vehicle for 24hrs, and harvested for RNA sequencing.

extract_protocol: TIL were harvested and resuspended in RNAlater. RNA extraction, quality control, and sequencing was performed by Avera Institute for Human Genetics.

treatment_protocol: TIL were exposed to TGF-B1 or vehicle for 24hrs.

value: tumor infiltrating lymphocyte (TIL)

value: TGFBR2 knockout

value: Vehicle


title: TGFBR2 knockout TIL with gRNA #4 exposed to TGF-B, replicate 3


title: PE replicate 3 [RAW264.7]

description: Labeled T


title: EARLI 50182_Sepsissuspected

value: Sepsissuspected

value: Female


title: PE replicate 2 [RAW264.7]

description: Labeled L


title: PE replicate 1 [RAW264.7]

description: Labeled D


title: TGFBR2 knockout TIL with gRNA #4 exposed to vehicle, replicate 2


title: EARLI 12113_SepsisBSI


title: TGFBR2 knockout TIL with gRNA #4 exposed to TGF-B, replicate 2


title: EARLI 50184_SepsisBSI


title: SE replicate 6 [RAW264.7]

description: Labeled HLA19

value: 65-79*SE peptide


title: 100% mutant control neuronal cells culture with DMEM (s12_98 Mt)

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: s12_98 Mt

hyb_protocol: Total RNA was extracted after lysing samples with TRIzol reagent (Life Technologies, Carlsbad, CA, U.S.A.), using the RNeasy Micro kit (Qiagen, Venlo, Netherlands)

scan_protocol: Expression BeadChips, stained and detected with the iScan system, according to the manufacturer’s protocol (Illumina, San Diego, CA, U.S.A.).

data_processing: raw data were quantile normalize and log2 using R

label: biotin

source_name: neuronal cells

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina Total Prep RNA Amplification kit (Ambion, Life Technologies, Carlsbad, CA, U.S.A.),

growth_protocol: cells were cultured in standard DMEM high glucose media (4.5 g/L)

treatment_protocol: mutant and control cells were cultured in the same standard DMEM high glucose media (4.5 g/L)

value: SH-SY5Y neuronal cell line

value: mutant


title: control neuronal cells culture with DMEM (s10_Ctrl)

extract_protocol: Total RNA was extracted after lysing samples with TRIzol reagent (Life Technologies, Carlsbad, CA, U.S.A.), using the RNeasy Micro kit (Qiagen, Venlo, Netherlands)

value: control


title: EARLI 12110_SepsisBSI

value: SepsisBSI

value: Asian


title: TGFBR2 knockout TIL with gRNA #4 exposed to vehicle, replicate 1


title: TGFBR2 knockout TIL with gRNA #4 exposed to TGF-B, replicate 1


title: PE replicate 5 [RAW264.7]

description: Labeled HLA12

value: cell line, macrophage


title: TGFBR2 knockout TIL with gRNA #3 exposed to vehicle, replicate 3


title: SE replicate 5 [RAW264.7]

description: Labeled HLA11


title: EARLI 12087_SepsisBSI

value: Male


title: SE replicate 4 [RAW264.7]

description: Labeled HLA3


title: EARLI 12070_No-Sepsis

value: No-Sepsis

value: Plasma


title: TGFBR2 knockout TIL with gRNA #3 exposed to TGF-B, replicate 3


title: 100% mutant control neuronal cells culture with DMEM (s9_98 Mt)

description: s9_98 Mt


title: SE replicate 3 [RAW264.7]

description: Labeled S


title: SE replicate 2 [RAW264.7]

description: Labeled K


title: TGFBR2 knockout TIL with gRNA #3 exposed to TGF-B, replicate 2


title: EARLI 12045_Sepsisperiph

value: Sepsisperiph

value: Unknown


title: SE replicate 1 [RAW264.7]

description: Labeled C

value: 72 hours


title: p14_wt

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

description: scRNA 10x

library_source: transcriptomic single cell

data_processing:
Fastq files aligned with cellranger
Differential gene expression and analysis performed using Seurat V4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Cells were captured using 10x protocol
10x scRNA protocol (5')

treatment_protocol: Mice were infected with LCMV Cl13 and 30 days later CD8 P14 cells were isolated by FACS

value: Spleen

value: P14  CD8 T cell

value: WT


title: 100% mutant control neuronal cells culture with DMEM (s6_98 Mt)

description: s6_98 Mt


title: control neuronal cells culture with DMEM (s4_Ctrl)


title: TGFBR2 knockout TIL with gRNA #3 exposed to vehicle, replicate 1

value: tumor infiltrating lymphocyte (TIL)

value: TGFBR2 knockout

value: Vehicle


title: EARLI 12083_No-Sepsis


title: LE replicate 6 [RAW264.7]

description: Labeled HLA18

value: 65-79*LE peptide


title: EARLI 12005_Sepsisperiph


title: p14_ko

description: scRNA 10x

value: P14 CD8 T cell

value: KO


title: OE_4

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

country: Germany

institute: IMB

data_processing:
The libraries were quantified using Qubit ds DNA HS Assay kit (Life Technologies-Invitrogen) and validated on a Agilent 4200 TapeStation System (Agilent technologies).
Based on Qubit quantification and sizing analysis multiplexed sequencing libraries were normalized, pooled and sequenced on NovaSeq 6000 with a final concentration of 300pM (spiked with 1% PhiX control)
Assembly: GRCm39
Supplementary files format and content: RPKM values for each Sample and the comparison of the reads between WT and KO
Supplementary files format and content: RPKM values for each Sample and the comparison of the reads between WT and OE

source_name: bone marrow

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
The libraries were quantified using Qubit ds DNA HS Assay kit (Life Technologies-Invitrogen)
Illumina sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's protocol.

value: bone marrow

value: primary

value: Lineage negative AML sorted cells

value: WT + CaSR overexpression


title: OE_2


title: EARLI 12004_SepsisBSI

value: SepsisBSI

value: Plasma

value: Male

value: Asian


title: TGFBR2 knockout TIL with gRNA #3 exposed to TGF-B, replicate 1


title: OE_1


title: EARLI 11997_No-Sepsis

value: No-Sepsis

value: Female


title: 100% mutant control neuronal cells culture with DMEM (s3_98 Mt)

description: s3_98 Mt

value: SH-SY5Y neuronal cell line

value: mutant


title: control neuronal cells culture with DMEM (s1_Ctrl)

value: control


title: Unmodified TIL exposed to vehicle, replicate 3

source_name: Unmodified TIL exposed to vehicle

value: tumor infiltrating lymphocyte (TIL)

value: Unmodified

value: Vehicle


title: TGFBR2 knockout TIL with gRNA #3 exposed to vehicle, replicate 2

value: TGFBR2 knockout


title: LE replicate 4 [RAW264.7]

description: Labeled HLA2

value: cell line, macrophage

value: 65-79*LE peptide

value: 72 hours


title: control neuronal cells culture with DMEM (s7_Ctrl)


title: LE replicate 3 [RAW264.7]

description: Labeled R


title: EARLI 12036_Indeterm

value: Indeterm

value: Caucasian


title: OE_5

value: bone marrow

value: primary

value: Lineage negative AML sorted cells

value: WT + CaSR overexpression


title: Unmodified TIL exposed to TGF-B, replicate 3

source_name: Unmodified TIL exposed to TGF-B


title: Unmodified TIL exposed to vehicle, replicate 2


title: KO_5

value: CaSR knockout


title: KO_3


title: EARLI 11990_Sepsissuspected

value: Sepsissuspected

value: Plasma

value: Female

value: Asian


title: LE replicate 2 [RAW264.7]

description: Labeled J


title: EARLI 11983_Sepsisperiph

value: Sepsisperiph

value: Male


title: Unmodified TIL exposed to TGF-B, replicate 2

value: tumor infiltrating lymphocyte (TIL)

value: Unmodified


title: KO_2


title: EARLI 11976_No-Sepsis

value: No-Sepsis


title: LE replicate 1 [RAW264.7]

description: Labeled B

value: cell line, macrophage

value: 65-79*LE peptide

value: 72 hours


title: Unmodified TIL exposed to vehicle, replicate 1

value: Vehicle


title: EARLI 11959_Sepsissuspected

value: African American


title: Unmodified TIL exposed to TGF-B, replicate 1


title: WT_5

value: bone marrow

value: primary

value: Lineage negative AML sorted cells

value: WT


title: PBS replicate 6 [RAW264.7]

description: Labeled HLA17

value: PBS


title: KO_1

value: CaSR knockout


title: PBS replicate 5 [RAW264.7]

description: Labeled HLA9


title: N8_a549_siAPEX1_rep4

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
Transcript quantification was conducted with STAR (v2.5.3a)  (assigned to a gene using using the STAR function “quantMode GeneCounts”) mapped to the human genome version GRCh38 and with reference annotation.
Read counts generated by STAR were analysed by using DESeq2 package (Love, 2014) for detecting genes that were differentially expressed. An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Genome_build: human genome version GRCh38 and with reference annotation.
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

source_name: A549  treated with siAPEX1 condition

extract_protocol:
Total RNA was obtained from A549 cell line. The size profiles of the individual libraries were analyzed with LabChip GX II using a DNA High Sensitivity kit (both PerkinElmer, USA). Libraries were quantified on a Qubit with the DNA High Sensitivity kit (Life Technologies).
Library preparation was performed using SMARTer smRNA-Seq kit (Clontech/Takara, USA) protocol with minor changes to increase the chance of identifying also pri-miR in addition to miRNAs.
RNA-Seq on a Illumina HiSeq 2500  instrument, in rapid run mode, using a 100-bp, dual-indexed, single-end sequencing configuration


title: WT_4


title: EARLI 11796_Sepsisperiph

source_name: Plasma

value: Plasma

value: Female

value: Caucasian


title: N7_a549_siAPEX1_rep3


title: EARLI 11943_Sepsisperiph

value: Sepsisperiph

value: Male

value: Other


title: PBS replicate 4 [RAW264.7]

description: Labeled HLA1

value: cell line, macrophage


title: PBS replicate 3 [RAW264.7]

description: Labeled Q


title: WT_2


title: N6_a549_siAPEX1_rep2


title: EARLI 11781_Sepsissuspected

value: Sepsissuspected

value: Asian


title: N5_a549_siAPEX1_rep1


title: PBS replicate 1 [RAW264.7]

description: Labeled A

value: 72 hours


title: EARLI 11779_Indeterm

value: Indeterm


title: N4_a549_siCTRL_rep4

source_name: A549  treated with siCTRL condition

value: siCTRL


title: Phloridzin treatment group sample 3

city: Beijing

first: Yahong

last: Shi

address: 11 Beisanhuan Dong Lu, Chaoyang District

institute: Beijing University of Chinese Medicine

data_processing:
bcl2fastq
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3)
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie(v1.3.3b)
DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

value: liver

value: phloridzin treatment +CCL4 induced liver fibrosis modle


title: EARLI 11777_No-Sepsis

value: No-Sepsis


title: N2_a549_siCTRL_rep3


title: Phloridzin treatment group sample 2


title: mE12.5-lMZ-RNA3

city: beijing

first: wenyu

last: ding

address: 15 Datun Road Chaoyang District

institute: University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.1.0 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hypothalamus

extract_protocol:
The embryonic hypothalamus areas were microdissected from coronal slices that were vibratome-sectioned  in ice-chilled ACSF to isolate VZ, medial MZ and lateral MZ regions and total RNA was harvested using RNeasy Micro Kit (QIAGEN, 74004). Then the total RNA was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit for Illumina according to the Manuals. The mRNA libraries were sequenced on IlluminaHiseq 2500 platform with 100bp pair-end reads.
The mRNA libraries were sequenced on IlluminaHiseq 2500 platform

tag: developmental  stage

value: brain (hypothalamus)

tag: brain structure

value: lateral mantle zone


title: Phloridzin treatment group sample 1


title: mE12.5-lMZ-RNA2


title: EARLI 11764_SepsisBSI

tag: disease state

value: SepsisBSI

value: Plasma


title: mE12.5-lMZ-RNA1

tag: tissue


title: EARLI 11841_SepsisBSI

value: African American


title: PBS replicate 2 [RAW264.7]

description: Labeled I

value: PBS


title: HK-2 cells, G3

city: nanjing

first: shen

last: li

state: jiangsu

address: Xianlin Avenue №163, Qixia District

institute: Nanjing University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 (version:2.0.4) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated. In short,FPKM=total exon Fragments/[ mapped reads (Millions) x exon length(KB)]
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: HK-2 cell

growth_protocol: HK-2 cells were cultured in KSFM medium (GIBCO) in 5% CO2 incubator at 37℃.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plasmids were transfected into HK-2 cells using Fugene (PROGEMA).

tag: genotype

value: empty vetor


title: EARLI 11707_SepsisBSI

value: Female

tag: age


title: silibinin treatment group sample 3

value: silibinin treatment+CCL4 induced liver fibrosis modle


title: EARLI 11727_Sepsissuspected

value: Sepsissuspected

value: Other

value: LatinX


title: WT_1

value: bone marrow

value: primary

value: Lineage negative AML sorted cells

value: WT


title: silibinin treatment group sample 2

value: liver


title: mE12.5-mMZ-RNA3

value: brain (hypothalamus)

value: medial mantle zone

tag: strain


title: silibinin treatment group sample 1


title: mE12.5-mMZ-RNA1


title: N2_a549_siCTRL_rep2

value: siCTRL


title: mE12.5-mMZ-RNA2


title: WT_3

tag: cell type


title: modle group sample 3

value: CCL4 induced liver fibrosis modle


title: EARLI 11690_Sepsissuspected

value: Plasma

value: Male

value: Asian


title: HK-2 cells, G1

tag: cell line

value: empty vetor


title: mE12.5-VZ-RNA3

value: ventricular zone


title: EARLI 11766_Sepsisperiph

value: Sepsisperiph

value: Female

value: Caucasian


title: HK-2 cells, S3

value: SLPI overexpression


title: EARLI 11663_No-Sepsis

value: No-Sepsis


title: modle group sample 2

tag: treatment


title: mE12.5-VZ-RNA2


title: EARLI 11658_No-Sepsis


title: N1_a549_siCTRL_rep1


title: HK-2 cells, S2


title: modle group sample 1


title: HK-2 cells, G2


title: mE12.5-VZ-RNA1


title: HK-2 cells, S1


title: EARLI 11636_Sepsissuspected

value: Sepsissuspected

tag: gender description

value: Transgender

value: Other

value: LatinX


title: EARLI 11653_Indeterm

value: Indeterm


title: V-Mt VC, ATAC, rep4

city: Wuhan

first: Xiaorong

last: Huang

address: Bayi Road

institute: College of Life Science, Wuhan university

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Peaks were annotated by using homer's annotatePeaks.pl.;Count the results of the annotations and plot the distribution results using R.
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Assembly: TAIR10
Supplementary files format and content: bigwig files were generated using MACS

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: vegetative cell nuclei

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
The FANS-purified fresh nuclei to be used for ATAC-seq must be placed in ice prior to transposase integration reaction but kept never frozen. Approximately 100000 nuclei per sample was collected and pelleted by centrifugation at 500 g at 4°C for 10 min. The supernatant was then removed, leaving ~50 µl in the tube. The nuclei were re-suspended and washed with 1× phosphate buffered saline (PBS), centrifuged using the above setting, and the supernatant removed. Next, the Tn5 reaction was prepared and mixed well with nuclei using the Nextera reagents (Illumina, FC-121-1030) as follows: 25 µl 2 × TD buffer, 2.5 µl TDE1 (Nextera Tn5 Transposase) and nuclease-free H2O were added to total 50 µl. The reaction was placed in a thermal cycler at 37°C for 30 min. DNA fragments were purified immediately using the Minelute PCR purification kit (Qiagen) and eluted in 10 µl elution buffer which consists of 10 mM Tris-HCl (pH 8).
Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) .

treatment_protocol: The collected pollen grains were re-suspended in Galbraith buffer (30mM Trisodium citrate dehydrate, 45mM MgCl2, 20mM MOPS, 0.1% (v/v) Triton X-100, adjust pH to 7.0) and then transferred to a 1.5 ml tube containing glass beads. Vortex continuously at 2000rpm for 3 min. Filter the sample through a 10μm nylon mesh in a 2ml tube to acquire the nucleus mixture. Fluorescence-activated SN and VN sorting were performed in a BD FACSAria III cell sorter. Use GFP (488nm) and RFP (561nm) to gate VN population (GFP-positive) and SN population (RFP-positive) respectively. Gate also for both VN and SN with a uniform side scatter (SSC) profile, which allowed the exclusion of debris and incomplete nuclei. The sorted nuclei were collected directly into Galbraith buffer and kept on ice for the subsequent experiments.

tag: ecotype

tag: line

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP

value: mature pollen

value: vegetative cell


title: EARLI 11599_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

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

value: SepsisBSI

value: Plasma

tag: gender

value: Male

tag: race


title: EARLI 11620_No-Sepsis

tag: ethnicity


title: control group sample3

value: liver

value: WT


title: WT SC, ATAC, rep2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Peaks were annotated by using homer's annotatePeaks.pl.; Count the results of the annotations and plot the distribution results using R.
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using MACS.

source_name: sperm cell nuclei

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C.

extract_protocol:
The FANS-purified fresh nuclei to be used for ATAC-seq must be placed in ice prior to transposase integration reaction but kept never frozen. Approximately 100000 nuclei per sample was collected and pelleted by centrifugation at 500 g at 4°C for 10 min. The supernatant was then removed, leaving ~50 µl in the tube. The nuclei were re-suspended and washed with 1× phosphate buffered saline (PBS), centrifuged using the above setting, and the supernatant removed. Next, the Tn5 reaction was prepared and mixed well with nuclei using the Nextera reagents (Illumina, FC-121-1030) as follows: 25 µl 2 × TD buffer, 2.5 µl TDE1 (Nextera Tn5 Transposase) and nuclease-free H2O were added to total 50 µl. The reaction was placed in a thermal cycler at 37°C for 30 min. DNA fragments were purified immediately using the Minelute PCR purification kit (Qiagen) and eluted in 10 µl elution buffer which consists of 10 mM Tris-HCl (pH 8).
Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen).

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP

value: sperm cell


title: control group sample1


title: TLR9KO_TLR7WT_stimTLR7.3

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

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).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep3

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.

treatment_protocol: Bead purified B cells (5M) from three 5-7week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated.

value: spleen

value: MRL/lpr (MRL.Faslpr)

value: Bead purified B cells

value: B cells


title: EARLI 11597_No-Sepsis

value: No-Sepsis

value: Female

value: Caucasian


title: control group sample2


title: EARLI 11586_SepsisBSI

value: Asian


title: TLR9KO_TLR7WT_stimTLR7.2

source_name: B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep2


title: TLR9KO_TLR7WT_stimTLR7.1

source_name: B cells_TLR9-/- MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep1


title: WT VC, ATAC, rep2

value: mature pollen


title: TLR9KO_TLR7WT_stimNo.3

source_name: B cells_TLR9-/- MRL/lpr_unstimulated _Rep3


title: V-Mt VC, ATAC, rep3

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP

value: vegetative cell


title: EARLI 11582_No-Sepsis

value: Plasma


title: WT VC, ATAC, rep1


title: EARLI 11550_SepsisBSI

value: SepsisBSI

value: Male


title: TLR9KO_TLR7WT_stimNo.2

source_name: B cells_TLR9-/- MRL/lpr_unstimulated _Rep2


title: EARLI 11544_Sepsisperiph

value: Sepsisperiph


title: WT SC, ATAC, rep1

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP


title: EARLI 11533_SepsisBSI

value: Other

value: LatinX


title: V-Mt SC, ATAC, rep2

value: sperm cell


title: V-Mt SC, ATAC, rep1


title: TLR9KO_TLR7WT_stimNo.1

source_name: B cells_TLR9-/- MRL/lpr_unstimulated _Rep1

value: spleen

value: MRL/lpr (MRL.Faslpr)

value: Bead purified B cells


title: V-Mt VC, ATAC, rep2


title: F-2.5 stage

first: Shiqing

last: Gao

address: Shuguang Garden Middle Street

institute: Beijing Academy of Agriculture and Forestry Sciences

description: gene expression at 2.5 stage in BS366 under 20℃/14h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The rimmed The rimmed mean target intensity of each array was arbitrarily set to 100.

organism: Triticum aestivum

source_name: 2.5 mm in Fnther length under F condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

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

treatment_protocol: The plants were vernalized naturally in the field and then grew at  20 °C with a 12 h photoperiod,  10 °C with a 12 h photoperiod,  20 °C with a 14 h photoperiod, and  10 °C with a 14 h for 5 d, and then transfered to the  20 °C with a 12 h photoperiod condition to grow.

value: wheat anther, 2.5 in lenngth, 20C/14h


title: MZ_TLR9WT.US.rep2

source_name: Marginal zone B cells_TLR9WT BALB/C_unstimulated_Rep3

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina DNA prep kit followed by UDI Set B indices (Illumina, Inc).

treatment_protocol: TLR9WT or TLR9-/- BALB/c mice splenocytes (n=3 per genotypes, 12-14 week-old male mice) were stained with the live cell discriminator in PBS, washed in stem cell buffer, and stained with TCR, CD19, CD23, CD21 in stem cell buffer, as per cytometry protocol. FO and MZ B cells were sorted using FACSAria (BD Bioscience) as live singlets TCR- CD19+ CD23hi CD21lo and TCR- CD19+ CD23lo CD21hi respectively. A minimum of 100,000 cells per B cell subsets were sorted. Sorted B cell subsets were washed, resuspended in media at 0.5M/ml, warmed at 37 degree Celsius for half an hour and stimulated for 4 hours at 0.25M/ml  with TLR7 agonist CL_097  (Invivogen) at 5ug/ml or left unstimulated.

value: BALB/c

value: sorted cells

value: Marginal zone B cells


title: F-3.0 stage

description: gene expression at 3.0 stage in BS366 under 20℃/14h

source_name: 3.0 mm in Fnther length under F condition

growth_protocol: 20 °C with a 12 h photoperiod,  10 °C with a 12 h photoperiod,  20 °C with a 14 h photoperiod, and  10 °C with a 14 h for 5 d

value: wheat anther, 3.0 in lenngth, 20C/14h


title: EARLI 11526_SepsisBSI

first: Charles

address: HSE 401, 513 Parnassus Ave

institute: University of California San Francisco

value: Female

value: Caucasian


title: F-2.2 stage

description: gene expression at 2.2 stage in BS366 under 20℃/14h

source_name: 2.2 mm in Fnther length under F condition

value: wheat anther, 2.2 in lenngth, 20C/14h


title: V-Mt VC, ATAC, rep1

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP

value: mature pollen

value: vegetative cell


title: B-3.0 stage

description: gene expression at 3.0 stage in BS366 under 10℃/14h

source_name: 3.0 mm in Bnther length under B condition

value: wheat anther, 3.0 in lenngth, 10C/14h


title: MZ_TLR9WT.US.rep1

source_name: Marginal zone B cells_TLR9WT BALB/C_unstimulated_Rep2


title: F-1.5 stage

description: gene expression at 1.5 stage in BS366 under 20℃/14h

source_name: 1.5 mm in Fnther length under F condition

value: wheat anther, 1.5 in lenngth, 20C/14h


title: F-2.0 stage

description: gene expression at 2.0 stage in BS366 under 20℃/14h

source_name: 2.0 mm in Fnther length under F condition

value: wheat anther, 2.0 in lenngth, 20C/14h


title: WT SC_IgG_rep2

data_processing:
Library strategy: CUT&Tag
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing. Several regions are sampled depending on the size of the genome and number of processors to estimate the summary statistics on the fragment lengths. Properly paired reads are used for computation.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using MACS.

extract_protocol:
The FANS-purified nuclei must be preserved in ice to maintain fresh and good viability, but never frozen. About 100000 nuclei per sample was collected and then centrifuged at 500 g at 4°C for 10 min. Aliquots of nuclei were washed twice in 0.5 ml Wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting, then centrifuged for removing the supernatant. Concanavalin A-coated magnetic beads (Bangs Laboratories) were washed twice with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2) for activation, and then 10 μl beads were added per sample and subsequently incubated at RT for 15 min. Bead-bound cells were re-suspended in 50 μl Dig-wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2mM EDTA and a 1:50 dilution of primary antibody (anti-H3K27me3, Millipore), subsequently incubated overnight at 4°C with slow rotation. Removed primary antibody thoroughly and added secondary antibody (Santa Cruz) diluted in 50μl Dig-wash Buffer (1:100), and then incubated at RT for 1 h. Then nuclei were washed using magnet stand 3× for 5 min in 1ml Dg-Wash buffer to remove the unbound antibodies. A 1:100 dilution of pA-Tn5 adapter complex (TTE mix, 4μM, Novoprotein) was prepared in Dig-med Buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail, 0.05% Digitonin). Nuclei were incubated with 100μl 0.04 μM TTE mix at RT for 1h with gentle vortexing, and then washed 3× for 5 min in 1ml Dig-med Buffer to remove the unbound pA-Tn5 protein. The nuclei were then re-suspended in 300μl Tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37°C for 1 h. To terminate tagmentation, 10μl 0.5M EDTA, 2.5μl 20mg/ml Proteinase K and 3μl 10% SDS were added to samples and incubated at 55°C for 1h. DNA was purified using phenol-chloroform-isoamyl extraction and ethanol precipitation, as well as RNaseA treatment.
For library construction, 21 μl DNA was mixed with 2 μl of a universal i5 and a uniquely barcoded i7 primer, and then 25 μl NEB Next HiFi 2× PCR Master mix was added and mixed. A total volume of 50μl sample was placed in a PCR thermal cycler with a heated lid via the following program: 72°C for 5min; 98°C for 30s; 16 cycles of 98°C for 10s and 63°C for 30s; final extension at 72°C for 1 min and hold at 4°C. To purify PCR products, 1.5 × volumes of AMPure XP beads (Beckman Coulter) were added and incubated for 15 min at RT. Next, the libraries were washed twice gently in 80% ethanol, and eluted in 30μl 10mM Tris pH 8.0. The size distribution of libraries was determined by Agilent 2100 TapeStation analysis.

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP

value: sperm cell

tag: antibody

value: IgG


title: EARLI 11522_No-Sepsis

source_name: Plasma

value: No-Sepsis

value: Plasma

value: African American


title: MZ_TLR9WT.US.rep3

source_name: Marginal zone B cells_TLR9WT BALB/C_unstimulated_Rep1

value: spleen

value: BALB/c

value: sorted cells

value: Marginal zone B cells


title: B-2.5 stage

description: gene expression at 2.5 stage in BS366 under 10℃/14h

source_name: 2.5 mm in Bnther length under B condition

value: wheat anther, 2.5 in lenngth, 10C/14h


title: B-2.2 stage

description: gene expression at 2.2 stage in BS366 under 10℃/14h

source_name: 2.2 mm in Bnther length under B condition

value: wheat anther, 2.2 in lenngth, 10C/14h


title: B-1.5 stage

description: gene expression at 1.5 stage in BS366 under 10℃/14h

source_name: 1.5 mm in Bnther length under B condition

value: wheat anther, 1.5 in lenngth, 10C/14h


title: EARLI 11518_Sepsissuspected

value: Sepsissuspected

value: Male

value: Asian


title: WT SC_H3K27me3_rep2

source_name: sperm cell nuclei

value: mature pollen

value: anti-H3K27me3 (Millipore, 07-449)


title: EARLI 11503_Sepsisperiph

value: Sepsisperiph

value: Caucasian


title: WT SC_IgG_rep1

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP

value: sperm cell

value: IgG


title: WT SC_H3K27me3_rep1


title: EARLI 11476_No-Sepsis

value: No-Sepsis

value: Plasma

value: Female


title: WT VC_IgG_rep2

source_name: vegetative cell nuclei

value: vegetative cell


title: MZ_TLR9WT.CL097.rep1

source_name: Marginal zone B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep2

value: spleen

value: BALB/c

value: sorted cells

value: Marginal zone B cells


title: MZ_TLR9KO.US.rep3

source_name: Marginal zone B cells_TLR9-/- BALB/C_unstimulated_Rep3


title: E-2.5 stage

description: gene expression at 2.5 stage in BS366 under 20℃/12h

source_name: 2.5 mm in Enther length under E condition

value: wheat anther, 2.5 in lenngth, 20C/12h


title: EARLI 11474_No-Sepsis

value: Male


title: B-2.0 stage

description: gene expression at 2.0 stage in BS366 under 10℃/14h

source_name: 2.0 mm in Bnther length under B condition

value: wheat anther, 2.0 in lenngth, 10C/14h


title: WT VC_H3K27me3_rep2

value: mature pollen

value: anti-H3K27me3 (Millipore, 07-449)


title: E-2.2 stage

description: gene expression at 2.2 stage in BS366 under 20℃/12h

source_name: 2.2 mm in Enther length under E condition

value: wheat anther, 2.2 in lenngth, 20C/12h


title: MZ_TLR9WT.CL097.rep3

source_name: Marginal zone B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep1


title: EARLI 11467_No-Sepsis

value: Caucasian


title: WT VC_IgG_rep1

value: pACTIN11:H2B-GFP; pHTR10:HTR10-RFP


title: MZ_TLR9KO.US.rep1

source_name: Marginal zone B cells_TLR9-/- BALB/C_unstimulated_Rep1


title: EARLI 11463_SepsisBSI

value: SepsisBSI


title: EARLI 11498_SepsisBSI


title: A-3.0 stage

description: gene expression at 3.0 stage in BS366 under 10℃/12h

source_name: 3.0 mm in anther length under A condition

value: wheat anther, 3.0 in lenngth, 10C/12h


title: E-1.5 stage

description: gene expression at 1.5 stage in BS366 under 20℃/12h

source_name: 1.5 mm in Enther length under E condition

value: wheat anther, 1.5 in lenngth, 20C/12h


title: EARLI 11461_Sepsisperiph

value: Sepsisperiph

value: Plasma

value: Female


title: E-2.0 stage

description: gene expression at 2.0 stage in BS366 under 20℃/12h

source_name: 2.0 mm in Enther length under E condition

value: wheat anther, 2.0 in lenngth, 20C/12h


title: WT VC_H3K27me3_rep1

value: vegetative cell


title: V-Mt VC_IgG_rep2

value: pLat52:REF6-GFP; pHTR10:HTR13-RFP

value: IgG


title: A-2.2 stage

description: gene expression at 2.2 stage in BS366 under 10℃/12h

source_name: 2.2 mm in anther length under A condition

value: wheat anther, 2.2 in lenngth, 10C/12h


title: E-3.0 stage

description: gene expression at 3.0 stage in BS366 under 20℃/12h

source_name: 3.0 mm in Enther length under E condition

value: wheat anther, 3.0 in lenngth, 20C/12h


title: A-2.5 stage

description: gene expression at 2.5 stage in BS366 under 10℃/12h

source_name: 2.5 mm in anther length under A condition

value: wheat anther, 2.5 in lenngth, 10C/12h


title: MZ_TLR9KO.CL097.rep2

source_name: Marginal zone B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep2

value: spleen

value: BALB/c

value: sorted cells

value: Marginal zone B cells


title: LE replicate 5 [RAW264.7]

description: Labeled HLA10

data_processing:
Raw counts were attained using featureCounts from the Rsubread1.5.0p3 package.
Gencode-M12 gene annotations using only uniquely aligned reads.
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05.
Genome_build: Gencode-M12 (GRCm38.p5)
Supplementary_files_format_and_content: deSeq2_counts RAW264.7 cells_IFNy LE_SE_PE.txt

source_name: RAW264.7 cells

extract_protocol:
Total RNA was isolated with Trizol and the Direct-ZolTM RNA miniprep from Zymo research. Genomic DNA was removed using the Turbo DNA-Free kit from Ambion. 200 ng total RNA was used to generate libraries with the Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cell line, macrophage

value: 65-79*LE peptide

tag: treatment duration

value: 72 hours


title: MZ_TLR9KO.US.rep2

source_name: Marginal zone B cells_TLR9-/- BALB/C_unstimulated_Rep2


title: MZ_TLR9WT.CL097.rep2

source_name: Marginal zone B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep3


title: A-2.0 stage

description: gene expression at 2.0 stage in BS366 under 10℃/12h

source_name: 2.0 mm in anther length under A condition

value: wheat anther, 2.0 in lenngth, 10C/12h


title: EARLI 11456_Sepsisperiph

source_name: Plasma

value: Sepsisperiph

value: Plasma

value: Caucasian


title: V-Mt VC_H3K27me3_rep2

source_name: vegetative cell nuclei

value: pLat52:REF6-GFP; pHTR10:HTR12-RFP

value: mature pollen

value: vegetative cell

value: anti-H3K27me3 (Millipore, 07-449)


title: MZ_TLR9KO.CL097.rep3

source_name: Marginal zone B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep3


title: EARLI 11453_No-Sepsis

value: No-Sepsis

value: Female

value: Asian


title: V-Mt VC_IgG_rep1

value: pLat52:REF6-GFP; pHTR10:HTR11-RFP

value: IgG


title: EARLI 11452_No-Sepsis


title: MZ_TLR9KO.CL097.rep1

source_name: Marginal zone B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep1

value: spleen

value: BALB/c

value: sorted cells

value: Marginal zone B cells


title: FO_TLR9WT.US.rep3

source_name: Follicular B cells_TLR9WT BALB/C_unstimulated_Rep3

value: Follicular B cells


title: V-Mt VC_H3K27me3_rep1

value: pLat52:REF6-GFP; pHTR10:HTR10-RFP


title: EARLI 11446_No-Sepsis

value: Plasma


title: A-1.5 stage

description: gene expression at 1.5 stage in BS366 under 10℃/12h

source_name: 1.5 mm in anther length under A condition

value: wheat anther, 1.5 in lenngth, 10C/12h


title: FO_TLR9WT.US.rep1

source_name: Follicular B cells_TLR9WT BALB/C_unstimulated_Rep1


title: EARLI 11437_No-Sepsis

value: Male

value: African American


title: FO_TLR9WT.CL097.rep2

source_name: Follicular B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep3


title: FO_TLR9WT.CL097.rep1

source_name: Follicular B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep2


title: EARLI 11428_Sepsissuspected

value: Sepsissuspected

value: Caucasian


title: Embry.63.d Le 338_(SNOWBALLs520824F)

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

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.

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).

value: liver

value: F2 based DLXPi

value: 63 dpc


title: FO_TLR9WT.CL097.rep3

source_name: Follicular B cells_TLR9WT BALB/C_in vitro stimulated with TLR7 agonists_Rep1


title: EARLI 11422_SepsisBSI

city: San Francisco

last: Langelier

value: SepsisBSI

value: Asian


title: Embry.63.d Le 307_(SNOWBALLs520824F)


title: FO_TLR9WT.US.rep2

source_name: Follicular B cells_TLR9WT BALB/C_unstimulated_Rep2

value: spleen


title: Embry.63.d Le 327_(SNOWBALLs520824F)


title: EARLI 11417_SepsisBSI

value: Female


title: EARLI 11412_SepsisBSI


title: Fibroblasts from Control subject_4

city: Genova

first: Giuseppina

last: Conteduca

state: GE

address: Largo Rosanna Benzi 10

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.
11US09453725_CTR2_4

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 Control subject

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

value: control subject


title: Fibroblasts from Control subject_5

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_257236339170_CTR2_3


title: FO_TLR9KO.US.rep1

source_name: Follicular B cells_TLR9-/- BALB/C_unstimulated_Rep1

value: BALB/c

value: sorted cells

value: Follicular B cells


title: EARLI 11371_Sepsissuspected

tag: disease state

value: Plasma


title: FO_TLR9KO.CL097.rep3

source_name: Follicular B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep3

tag: tissue


title: EARLI 11403_SepsisBSI

value: Male

value: Native American


title: FO_TLR9KO.US.rep2

source_name: Follicular B cells_TLR9-/- BALB/C_unstimulated_Rep2


title: Embry.63.d Le 324_(SNOWBALLs520824F)

tag: genotype


title: FO_TLR9KO.CL097.rep2

source_name: Follicular B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep2


title: Embry.63.d Le 297_(SNOWBALLs520824F)

tag: age


title: FO_TLR9KO.US.rep3

source_name: Follicular B cells_TLR9-/- BALB/C_unstimulated_Rep3

tag: strain


title: EARLI 11362_Indeterm

source_name: Plasma

value: Indeterm


title: Fibroblasts from Control subject_2

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.
7US09453725_CTR1_4

tag: cell type


title: EARLI 11353_Sepsissuspected

value: Sepsissuspected

value: African American


title: FO_TLR9KO.CL097.rep1

source_name: Follicular B cells_TLR9-/- BALB/C_in vitro stimulated with TLR7 agonists_Rep1


title: Embry.63.d Le 281_(SNOWBALLs520824F)

value: liver

value: F2 based DLXPi

value: 63 dpc


title: Fibroblasts from Sotos patient_13

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.
US257236337127_SoS2_2

source_name: Fibroblasts from Sotos patient

value: Sotos patient


title: Fibroblasts from Sotos patient_14

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.
US257236339170_SoS1_1


title: Embry.63.d Le 274_(SNOWBALLs520824F)


title: Embry.63.d Le 363_(SNOWBALLs520824F)


title: Fibroblasts from Control subject_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.
5US09453725_CTR1_2


title: Embry.63.d Le 355_(SNOWBALLs520824F)


title: Embry.63.d Le 360_(SNOWBALLs520824F)


title: Fibroblasts from Control subject_3

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.
9US09453725_CTR2_2


title: Embry.63.d Le 329_(SNOWBALLs520824F)


title: Embry.63.d Le 384_(SNOWBALLs520824F)


title: Fibroblasts from Sotos patient_11

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_257236339170_SoS1_3


title: ABC_TLR9WT.ATAC.rep3

description: Aged associated B cells_3-way BM chimera_TLR9WT sorted cells_Rep3

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

source_name: spleen

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

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

value: MRL/lpr (MRL.Faslpr)

value: 3-way BM chimera_sorted cells

value: Aged associated B cells


title: Embry.63.d Le 303_(SNOWBALLs520824F)


title: EARLI 11321_SepsisBSI

value: SepsisBSI

value: Female

value: Asian


title: Fibroblasts from Sotos patient_9

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_SoS2_4

value: skin sample

value: fibroblasts


title: ABC_TLR9WT.ATAC.rep2

description: Aged associated B cells_3-way BM chimera_TLR9WT sorted cells_Rep2


title: EARLI 11344_No-Sepsis

value: No-Sepsis

value: Plasma


title: EARLI 11317_Sepsisperiph

value: Sepsisperiph


title: EARLI 11299_SepsisBSI

value: Male


title: ABC_TLR9WT.ATAC.rep1

description: Aged associated B cells_3-way BM chimera_TLR9WT sorted cells_Rep1


title: Fibroblasts from Sotos patient_10

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_257236339170_SoS1_2


title: ABC_TLR9P915H.ATAC.rep1

description: Aged associated B cells_3-way BM chimera_TLR9P915H sorted cells_Rep1


title: EARLI 11284_Indeterm

value: Indeterm

value: Caucasian


title: EARLI 11203_SepsisBSI

value: Other

value: LatinX


title: ABC_TLR9P915H.ATAC.rep2

description: Aged associated B cells_3-way BM chimera_TLR9P915H sorted cells_Rep2


title: EARLI 11195_No-Sepsis


title: Embry.63.d Le 370_(SNOWBALLs520824F)

value: liver

value: F2 based DLXPi

value: 63 dpc


title: Fibroblasts from Sotos patient_6

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_1

value: Sotos patient


title: EARLI 11184_No-Sepsis


title: Fibroblasts from Sotos patient_8

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_4


title: ABC_TLR9KO.ATAC.rep3

description: Aged associated B cells_3-way BM chimera_TLR9-/- sorted cells_Rep3

value: MRL/lpr (MRL.Faslpr)

value: 3-way BM chimera_sorted cells

value: Aged associated B cells


title: Embry.63.d Le 352_(SNOWBALLs520824F)

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.


title: Fibroblasts from Sotos patient_5

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.
U257236337127_SoS2_3

value: skin sample


title: Embry.63.d Le 311_(SNOWBALLs520824F)


title: Fibroblasts from Sotos patient_12

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.
US257236337127_SoS1_2

value: fibroblasts


title: Fibroblasts from Sotos patient_3

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.
8US09453725_SoS2_1


title: Embry.63.d Le 313_(SNOWBALLs520824F)


title: EARLI 11182_SepsisBSI

value: SepsisBSI

value: Female

value: Asian


title: Embry 63 Le 283_(SNOWBALLs520824F)


title: ABC_TLR9P915H.ATAC.rep3

description: Aged associated B cells_3-way BM chimera_TLR9P915H sorted cells_Rep3


title: Embry 63 Le 272_(SNOWBALLs520824F)


title: ABC_TLR9KO.ATAC.rep2

description: Aged associated B cells_3-way BM chimera_TLR9-/- sorted cells_Rep2


title: EARLI 11164_Indeterm

value: Plasma


title: ABC_TLR9KO.ATAC.rep1

description: Aged associated B cells_3-way BM chimera_TLR9-/- sorted cells_Rep1


title: EARLI 11139_Sepsisperiph

value: Sepsisperiph

value: Male


title: Cured, replicate2, 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

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

value: 10 weeks old


title: Taf7l konckin RS (KIRS2)rep2

city: Nanjing

first: Li

last: Fangfang

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

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

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

value: testis

value: konckin