title: ChIP WT CD40/IL4 PU1 rep1

description: ChIP WT CD40/IL4 PU1 rep1

source_name: ChIP WT CD40/IL4 PU1 rep1


title: Small intestine neuroendocrine tumor (SINET), 12

status: Public on Feb 02 2021

type: genomic

city: Gothenburg

first: Yvonne

last: Arvidsson

address: Box 425

department: Biomedicin

country: Sweden

institute: University of Gothenburg

hyb_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc

scan_protocol: Arrays were scanned using the Agilent G2565BA Microarray Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor

extract_protocol: Genomic DNA was isolated from the biopsies using the DNeasy® Blood and Tissue kit (Qiagen GmbH, Hilden, Germany).

tag: case

tag: gender male (m), female (f)

value: M

tag: tissue

value: liver metastasis

source_name: Human Reference DNA male (Agilent)

tag: gender reference

value: Male (M), Female (F):M


title: Small intestine neuroendocrine tumor (SINET), 15

label_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc

value: F

source_name: Human Reference DNA female (Agilent)

value: Male (M), Female (F):F


title: Normal donor cornea

type: SRA

city: Sewickley

first: Bharesh

middle: Kumar

last: Chauhan

state: PA

address: 400 45th St., Faculty Pavilion, Suite 5111

department: Ophthalmology

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8.2 program used for converting primary sequencing output .bcl basecall files into .fastq
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 human genome using CLC Genomics Workbench Version 9.5 with parameters: mismatches 2, maximum number of hits for a read 10.
Transcripts per million reads (TPM) were calculated using methodology and calculations from Wagner et al., Theory in Biosciences, 2012. To calculate the TPM, divide the read counts by the length of each gene in kilobases (gives reads per kilobase (RPK)). Then divide the RPK values by 1,000,000 to give TPM.
Expression values were transformed (logarithm 2) and normalized by the mean. Differential expression was then identified through Kal's test [Kal et al., Molecular Biology of the Cell, 1999] and two kinds of corrected p-values were added to the analysis (in addition to the standard p-value produced for the test statistic): Bonferroni corrected and FDR corrected, with p < 0.05 in both cases.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each donor lens (L_ATCACG_L002_R1_001.txt) and age-related affected lens (ML_GGCTAC_L001_R1_001.txt)

molecule: total RNA

source_name: Normal donor cornea

extract_protocol:
Corneal tissue was placed in RLT lysis buffer (Qiagen RNeasy) and efficiently disrupted using MagNA lyser green beads and instrument (Roche). The resulting lysate was then homogenized using QIAshredder and the homogenate supernatant run through a RNeasy mini spin column according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cornea

tag: diagnosis

value: normal

tag: age

value: pediatric


title: Small intestine neuroendocrine tumor (SINET), 4


title: Small intestine neuroendocrine tumor (SINET), 8


title: ChIP WT CD40/IL4 H3K27ac rep1

city: Basel

first: Shuang

last: Song

state: Basel

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: ChIP WT CD40/IL4 H3K27ac rep1

library_source: genomic

data_processing:
ChIP-seq and BioChIP-seq sequencing reads were aligned to the mouse genome (mm9) using the qAlign function, which internally uses Bowtie Langmead et al 2009], from Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0). Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp. Peaks of OCT1, OCT2, OBF1, PU.1, H3K27ac, H3K4me3 and H3K4me1 were called in control sample (input) with MACS2 [Zhang et al 2008] (software version 2.1.1) using default parameters. Reads were counted in each peak region using the qCount function in QuasR (with shift set to 60). The read counts per sample were normalized to the mean total mapped number of reads across all samples.
Genome_build: mm9
Supplementary_files_format_and_content: wig files containing the enrichment of IP over input

organism: Mus musculus

source_name: ChIP WT CD40/IL4 H3K27ac rep1

growth_protocol: Mature B cells were purified from spleens by MACS column using anti-mouse CD19 Microbeads (Miltenyi Biotec). Single cell suspension was prepared by smashing the spleen, and then washing in freshly prepared MACS buffer (0.5% BSA and 2mM EDTA in PBS) (20ml for two spleens) three times. After washing, cell concentration was adjusted to 108 cells/ml. To label the B cells for MACS LS column separation, 10 μl CD19 beads was added to every 107 cells (100 μl), and the mixture was incubated at 4 ℃ for 15min. The anti-CD19-labeled spleen cells were further washed with MACS buffer and then applied to MACS LS column. CD19+ mature B cells were purified according to the standard protocol of Miltenyi Biotec LS column (Cat# 130-042-401). Purified CD19+ mature B cells were subjected to in vitro culture with LPS or anti-CD40/IL4 stimulants at 2 × 106 cells/ml.

extract_protocol:
To extract the nuclei of stimulated splenic B cells: cultured CD19+ spleen B cells stimulated with either LPS or anti-CD40/IL4 were used for chromatin immunoprecipitation as described {Choukrallah, 2015 #46}. Immediately after centrifugation, supernatant was discarded, and cells were resuspended and fixed with 10 ml 1% formaldehyde in PBS at room temperature for 10min, followed by quenching with 530μl 2.5 M Glycine at room temperature for 5 min. Cells were lysed for 10 min in 10 ml lysis buffer A (10 mM HEPES, pH8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, PI). The supernatant was discarded, and pellets were incubated for 10 min in lysis buffer B (10 mM HEPES, pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, PI). Then, the nuclei were resuspended in chromatin lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS) for 30 min at 4 ℃. Subsequently, sonication was performed using Bioruptor Next Gen (Diagenode) at high output intensity for 25 cycles (30s on/30s off). Finally, the fragmented chromatin suspension was diluted 5 times with chromatin dilution buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA, 167 mM NaCl, 1.67% Triton X-100). 30-50 μg chromatin was subjected to immunoprecipitation with 5-10 μg ChIP-grade antibodies and incubated overnight. Subsequently, the samples were incubated with Dynabeads Protein G for 2 hours. The beads were washed with the following buffers: twice with low salt buffer (20 mM Tris pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), twice with high salt buffer (20 mM Tris pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), twice with LiCl buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% Na Deoxychholate) and once with TE (20 mM Tris-HCl, pH8.9, 2 mM EDTA). The protein-DNA complexes were eluted from the beads with 350 μl elution buffer (10 mM Tris-HCl, pH7.5, 1 mM EDTA, 1% SDS, 100 mM NaHCO3) and reverse crosslinked overnight at 65 ℃ with 60 μg Proteinase K and 60 μg RNase A. Immunoprecipitated DNA was recovered using AMPure XP beads.
libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions

treatment_protocol: For LPS stimulation, primary spleen mature B cells were cultured in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol (AppliChem), 50 μg/ml LPS (Sigma), 2 mM Glutamine, 1% ITS (Sigma), 1% MEM (Sigma), 1mM Sodium Pyruvate (ThermoFisher Scientific)), medium was changed every day. For anti-CD40 and Interleukin 4 (IL4), primary spleen mature B cells were cultured in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol (AppliChem), 1 ug/ml anti-murine-CD40 + 20 ng/ml IL4, 2 mM Glutamine, 1% ITS (Sigma), 1% MEM (Sigma), 1 mM Sodium Pyruvate (ThermoFisher Scientific)), medium was changed every day. For each stimulation, B cells were harvested after 72 hours.

tag: genotype

value: Wild type

tag: cell type

value: CD19+ splenic B cells

tag: sample type

value: Primary cells

tag: stimulation

tag: antibody

value: H3K27ac, Active Motif, Cat# 39133


title: Small intestine neuroendocrine tumor (SINET), 2

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 14


title: ChIP WT CD40/IL4 OBF1 rep1

description: ChIP WT CD40/IL4 OBF1 rep1

source_name: ChIP WT CD40/IL4 OBF1 rep1

value: Bio-ChIP-seq, Dynabeads M-280 Streptavidin, 11205D


title: Small intestine neuroendocrine tumor (SINET), 13


title: CNAG-01 [F-01]

city: Changchun

first: Yang

last: Chao

address: Xiantai Street

country: China

institute: China-Japan Union Hospital of Jilin University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4)
guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA
Genome_build: hg19
Supplementary_files_format_and_content: FPKM as the expression profiles of LncRNA and mRNA

source_name: CNAG_gastric mucosa

extract_protocol:
Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

tag: subject status

value: chronic nonatrophic gastritis (CNAG)

value: Gastric mucosa


title: Small intestine neuroendocrine tumor (SINET), 10


title: Small intestine neuroendocrine tumor (SINET), 11


title: Small intestine neuroendocrine tumor (SINET), 7


title: Small intestine neuroendocrine tumor (SINET), 3


title: IRF4OE_Raji_rep3

data_processing:
Sequencing reads were aligned using qAlign from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) to the mouse genome (mm9) with default parameters except for splicedAlignment = TRUE. Alignments were quantified with qCount from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) for known UCSC genes obtained from the TxDb.Mmusculus.UCSC.mm9.knownGene package (package version 3.2.2) using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing the count table

growth_protocol: Burkitt’s lymphoma cell lines (Raji) were cultured in T75 flasks in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol). B Lymphoma cells were passaged every two to three days.

extract_protocol:
QIAGEN RNeasy Micro kit
The Illumina TruSeq Stranded mRNA protocol was used for library preparation for next generation sequencing.

treatment_protocol: human IRF4 cDNA is cloned into lentivirus expression vector provided by Jeffrey Chao (FMI, Basel). To prepare lentivirus for infection, 1.3 × 106 293T cells were seeded on T25 flask with 5ml DMEM medium 24 hours before transfection and, the following day, 7 μg expression vector, together with plasmids coding for Rev, Vsv-g, Tat and Gag/Pol, was transfected into 293T cells with FuGENE HD. Supernatant was collected at 24, 48 and 72 hours post transfection, and filtered through 0.4 μm EMD Millipore Steriflip Sterile Disposable Vacuum Filter units. Lentivirus particles in this 15 ml suspension were then concentrated by adding 5 ml of LentiX concentrator (Takara), and incubated for 24 hours at 4 ℃. Post incubation, lentiviral particles were precipitated and centrifuged at 1500 g for 45 min at 4 ℃. Pelleted lentiviruses were then concentrated 150 times by resuspending with 100 μl culture medium (RPMI1640, 10% FCS, 50 μm 2-mercaptoethanol). 10 μl lentivirus suspension was added to 2 × 105 cells (Raji) in 6-well plate containing 8 μg/ml Polybrene (Millipore) in RPMI1640 medium. B Lymphoma cells with lentiviruses were infected for 5 days at 37℃ and 5% CO2. Post infection, stable integrations were selected for 7 days in the presence of 3 μg/ml Puromycin (GIBCO). Empty vector was used as a control.

tag: ectopic expression

value: IRF4 overexpression

tag: cell line

value: Raji

value: GC-derived Burkitt's lymphoma


title: IRF4OE_Raji_rep2


title: ChIP WT CD40/IL4 OCT1 rep1

description: ChIP WT CD40/IL4 OCT1 rep1

source_name: ChIP WT CD40/IL4 OCT1 rep1


title: Small intestine neuroendocrine tumor (SINET), 42

value: M

value: lymph node metastasis

value: Male (M), Female (F):M


title: Affected patient cornea

source_name: Affected patient cornea

value: cornea

value: CCO from patient with Fanconi anemia


title: Small intestine neuroendocrine tumor (SINET), 1


title: IRF4OE_Raji_rep1


title: ChIP WT LPS OCT2 rep1 rep2 input

description: ChIP WT LPS OCT2 rep1 rep2 input

source_name: ChIP WT LPS OCT2 rep1 rep2 input

value: LPS

value: none (input)


title: ChIP WT LPS H3K27ac rep1 rep2 H3K4me1 H3K4me3 input

value: Wild type

value: CD19+ splenic B cells


title: ChIP WT CD40/IL4 OCT2 rep1

description: ChIP WT CD40/IL4 OCT2 rep1

source_name: ChIP WT CD40/IL4 OCT2 rep1

value: Primary cells


title: ChIP WT CD40/IL4 OCT2 rep1 rep2 input

description: ChIP WT CD40/IL4 OCT2 rep1 rep2 input

source_name: ChIP WT CD40/IL4 OCT2 rep1 rep2 input


title: Ctrl_Raji_rep3

value: Control


title: Ctrl_Raji_rep1


title: Ctrl_Raji_rep2


title: ChIP WT LPS H3K27ac rep2

description: ChIP WT LPS H3K27ac rep2

source_name: ChIP WT LPS H3K27ac rep2


title: ChIP WT LPS OCT1 OBF1 PU1 rep1 rep2 input


title: ChIP WT LPS PU1 rep2

description: ChIP WT LPS PU1 rep2

source_name: ChIP WT LPS PU1 rep2

value: PU.1, Cell Signaling Technology, Cat# 2258


title: ChIP WT LPS OBF1 rep2

description: ChIP WT LPS OBF1 rep2

source_name: ChIP WT LPS OBF1 rep2

value: Bio-ChIP-seq, Dynabeads M-280 Streptavidin, 11205D


title: PE+IFNy replicate 2

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 H

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

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 with or without IFNγ (5 ng/ml) in the presence or absence of 65-79*0401 or 65-79*0402 (100 μg/ml) for 72 hrs. Medium was refreshed once at 48 hrs

value: THP-1 cells

value: cell line, macrophage

tag: treatment

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

tag: treatment duration

value: 72 hours


title: PE+IFNy replicate 4

description: Labeled P


title: ChIP WT LPS OCT1 rep2

description: ChIP WT LPS OCT1 rep2

source_name: ChIP WT LPS OCT1 rep2


title: ChIP WT LPS OCT2 rep2

description: ChIP WT LPS OCT2 rep2

source_name: ChIP WT LPS OCT2 rep2


title: ChIP WT LPS H3K4me3

description: ChIP WT LPS H3K4me3

source_name: ChIP WT LPS H3K4me3

value: H3K4me3, Millipore, Cat# 07-473


title: ChIP WT LPS H3K4me1

description: ChIP WT LPS H3K4me1

source_name: ChIP WT LPS H3K4me1

value: H3K4me1, Abcam, Cat# ab8895


title: SE+IFNy replicate 4

description: Labeled O

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


title: SE+IFNy replicate 2

description: Labeled G


title: PBS replicate 4, IFNy

description: Labeled 3

value: PBS


title: SE+IFNy replicate 1

description: Labeled C


title: PBS replicate 3, IFNy

description: Labeled Y


title: ChIP WT LPS OCT2 rep1

description: ChIP WT LPS OCT2 rep1

source_name: ChIP WT LPS OCT2 rep1


title: ChIP WT LPS OBF1 rep1

description: ChIP WT LPS OBF1 rep1

source_name: ChIP WT LPS OBF1 rep1


title: ChIP WT LPS PU1 rep1

description: ChIP WT LPS PU1 rep1

source_name: ChIP WT LPS PU1 rep1


title: PBS replicate 1, IFNy

description: Labeled Q


title: 122016_Cell95-G12-Dark

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Leftover clinical sample read as normal

data_processing:
All single-cell libraries were pseudo-aligned to the human Ensembl version 72 transcriptome using the Kallisto through AltAnalyze version 2.1.3. as described in our previous publication [40]. To ensure quality control, libraries with less than 300,000 paired-end reads or estimated read percentage alignment <20% were excluded. Unsupervised population discovery was performed using the software ICGS version 2 (Venkatasubramanian et al. 2019, bioRxiv) and PCA-loading gene analysis and HOPACH clustering in AltAnalyze. PCA-loading genes were selected as the top-100 correlated and top-100 anti-correlated genes associated with the first 4 principal components. Initial identified predominant gene clusters from the PCA-loading analysis were excluded prior to ICGS2, by identifying genes correlated to the centroid of the gene clusters with a Pearson rho > 0.1 (21,719 genes remaining after exclusion). ICGS2 was run using the default program parameters. To expand the cell-cluster identified from the ICGS2 analysis of SJIA with donor BM macrophages, an aggerate score (sum of the TRIM8 cluster maker genes), was used to identify additional SJIA patient cells (n=12, total) enriched in TRIM8-associated genes prior to differential expression analyses. For the identification of TRIM8-cluster specific genes, we applied empirical Bayes moderated (eBayes) t-test comparing TRIM8-cluster SJIA cells to all donor macrophage cells (AltAnalyze). Only genes with a minimum average TPM >1 in the two compared populations, eBayes t-test p<0.05 (following Benjamini-Hochberg correction) and fold > 1.5 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file

source_name: sorted bone marrow macrophages

growth_protocol: Leftover bone marrow aspirates were obtained from the clinical lab, RBC lysed, and frozen until use. Cells were then thawed and bone marrow macrophages sorted as CD14+CD163+CD15-7AAD-

extract_protocol:
This suspension was then loaded onto the Fluidigm C1 Single-Cell Auto Prep System, on a 10-17um chip.  These cells were subsequently lysed, and extracted RNA converted into cDNA per manufacterers directions using v4 chemistry.
Libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA) on cDNAs with an initial concentration>180 pg/µl that were then diluted to 100 pg/µl. In each single-cell library preparation, a total of 125pg cDNA was tagmented at 55 °C for 20 minutes. Libraries were pooled and purified on AMPure® bead-based magnetic separation before a final quality control using Qubit® dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit. We required the majority of cDNA fragments to be between 375–425bp to qualify for sequencing.
Single cell libraries were subjected to paired-end RNA-Sequencing on a HiSeq 2500 (Illumina Inc., San Diego, CA). 96 scRNA-Seq libraries were sequenced per HiSeq 2500 gel (~300 million bp/gel).

value: Macrophage (CD14+CD163+)


title: ChIP WT LPS OCT1 rep1

description: ChIP WT LPS OCT1 rep1

source_name: ChIP WT LPS OCT1 rep1

value: LPS


title: ChIP WT LPS H3K27ac rep1

description: ChIP WT LPS H3K27ac rep1

source_name: ChIP WT LPS H3K27ac rep1

value: H3K27ac, Active Motif, Cat# 39133


title: PBS replicate 2, IFNy

description: Labeled U


title: PE+IFNy replicate 3

description: Labeled L


title: 122016_Cell94-F12

description: Leftover clinical sample read as normal


title: Huh7-L rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
rybkayu_fpkm.txt.gz
140821And_D14-6434

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to transcripts derived from the hg19 assembly and the ensembl version 68 non-coding RNA annotation (non-coding genes) using bowtie version 1.01  and gene expression was summarized using rsem version 1.2.3
Genome_build: hg19 with ensembl 68 non-coding genes
Supplementary_files_format_and_content: rybkayu_fpkm.txt.gz is a tab delimited text file of non-coding transcript FPKM values.
Supplementary_files_format_and_content: hg19_GRCh37_68_noncoding.fa.gz is the fasta file of non-coding transcripts that was used as an alignment target in this analysis.

molecule: polyA RNA

source_name: hepatocellular carcinoma HUH7 cells

growth_protocol: Human hepatocellular carcinoma HUH7 cell line was grown in Dulbecco's modified Eagle's medium with L-glutamine (DMEM, Gibco™) supplemented with 4.5 mg/ml glucose, 50 ug/ml gentamicin sulfate (Sigma), 25 mM HEPES (Gibco™) and 10% heat-inactivated fetal bovine serum (FBS, Gibco™). All cells were cultured at 37oC, 5% CO2.

extract_protocol:
Qiagen RNAeasy extraction
Strand-Specific Ribozero

value: hepatocellular carcinoma HUH7 cells


title: Huh7-H rep2

description:
rybkayu_fpkm.txt.gz
140821And_D14-6433


title: Huh7-L rep1

description:
rybkayu_fpkm.txt.gz
140821And_D14-6432


title: 122016_Cell93-E12

description: Leftover clinical sample read as normal


title: PE+IFNy replicate 1

description: Labeled D


title: selected rep3

description:
rybkayu_061620_hp.txt.gz
d9166

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Adapter sequence GGAAAGGACGAGGTACC was trimmed from reads using cutadapt version 1.4.2. Trimmed reads were then aligned target consisting of the 7873 sequence shRNA library with bwa version 0.7.10. Mapped reads were summarized and parsed using samtools version 1.3 and custom perl scripts.
Genome_build: rybkayu_061620_oligos.fa
Supplementary_files_format_and_content: rybkayu_061620_hp.txt.gz is a tab delimited text file of hairpin counts
Supplementary_files_format_and_content: rybkayu_061620_oligos.fa.gz are the FASTA formated sequences of the hairpin library.
Supplementary_files_format_and_content: rybkayu_061620_annotation.txt.gz is a tab delimited file of hairpin annotations.

extract_protocol:
Qiagen QIAamp DNA Blood Maxi Kit
small molecule prep

value: selected


title: Huh7-H rep4

description:
rybkayu_fpkm.txt.gz
140821And_D14-6435


title: 122016_Cell92-D12

description: Leftover clinical sample read as normal


title: 122016_Cell91-C12

description: Leftover clinical sample read as normal


title: SE+IFNy replicate 3

description: Labeled K


title: selected rep2

description:
rybkayu_061620_hp.txt.gz
d9165


title: 122016_Cell90-B12

description: Leftover clinical sample read as normal


title: library rep3

description:
rybkayu_061620_hp.txt.gz
d8924

value: input library


title: 122016_Cell89-A12

description: Leftover clinical sample read as normal


title: library rep2

description:
rybkayu_061620_hp.txt.gz
d8923


title: selected rep1

description:
rybkayu_061620_hp.txt.gz
d9164


title: 122016_Cell88-H11

description: Leftover clinical sample read as normal


title: sRNA_sequencing_Aphid_72hrs_bioreplicate_3

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

institute: Swedish University of Agricultural Sciences

data_processing:
sRNAs were trimmed using Trim Galore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For sRNA seq experiments reads were aligned with bowtie with default parameters. SAM files were converted to BAM and count reads per gene or TE were assesed with ht-seq counts. Count files were used to infer differential expression using DESeq2.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: Plants were grown under standard long day conditions at 22 °C.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. mRNA for RNA and PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs). RNA for sRNA library preparation was enriched with the mirVana miRNA Isolation Kit (Life Technologies). Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014). RNA libraries were produced using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Bisulfite DNA libraries were produced and sequenced at Novogene (Hong Kong).

treatment_protocol: 5-week-old plants were infested with 40 wingless M.persicae of second to fourth larval instars and covered with net cage. After 72 hours all aphids were carefully removed by brush and all Arabidopsis rosette leaves were sampled into Falcon tubes extraction bag before being placed in liquid nitrogen. Tissue was collected from all tested mutants. Each frozen plant sample was stored at -70 °C before RNA and DNA extraction.

tag: ecotype

value: Columbia 0

value: wild type

tag: tag

value: Aphid


title: sRNA_sequencing_Aphid_72hrs_bioreplicate_2


title: 122016_Cell83-C11

description: Leftover clinical sample read as normal


title: 122016_Cell85-E11-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell82-B11

description: Leftover clinical sample read as normal


title: sRNA_sequencing_Control_bioreplicate_2

value: Control


title: 122016_Cell80-H10-Dark

description: Leftover clinical sample read as normal


title: sRNA_sequencing_Control_bioreplicate_1


title: 122016_Cell86-F11

description: Leftover clinical sample read as normal


title: sRNA_sequencing_Control_bioreplicate_3


title: RNA_sequencing_Aphid_72hrs_bioreplicate_2

description:
mRNA
DESeq2_RNA_seq_genes.tabular
DESeq2_RNA_seq_TEs.tabular

data_processing:
sRNAs, PARE and RNA libraries  were trimmed using Trim Galore. For bisulfite sequencing libraries adapters and 10 bases from 5' ends from reads were trimmed using Trimgalore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches. PARE and RNA seq libaries were mapped using bowtie2 with default parameters. For bisulfite libraries Clean reads were mapped to the reference genome TAIR 10 using bismark, allowing one mismatch per 25 nt seed. Forward and reverse reads were mapped independently. Alignments at the same position were removed using deduplicate_bismark script, including alignments of reads 1 and 2 together.Conversion rate of cytosines were obtained using bismark_methylation_extractor, the first 7 bases from 5' end and 13 from 3' end of each read were ignored.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For RNA seq experiments reads were aligned with bowtie with default parameters. SAM files were converted to BAM and count reads per gene or TE were assesed with ht-seq counts. Count files were used to infer differential expression using DESeq2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. mRNA for RNA and PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs). RNA for sRNA library preparation was enriched with the mirVana miRNA Isolation Kit (Life Technologies). Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014). RNA libraries were produced using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Bisulfite DNA libraries were produced and sequenced at Novogene (Hong Kong).
sRNA-sequencing, RNA sequencing, PARE sequencing and Bisulfite sequencing

tag: strain

value: Columbia 0 wild type


title: 122016_Cell8-H1

description: Leftover clinical sample read as normal


title: 122016_Cell74-B10

description: Leftover clinical sample read as normal


title: RNA_sequencing_Control_bioreplicate_2


title: RNA_sequencing_Control_bioreplicate_1


title: 122016_Cell81-A11

description: Leftover clinical sample read as normal


title: 122016_Cell9-A2

description: Leftover clinical sample read as normal


title: library rep1

description:
rybkayu_061620_hp.txt.gz
d8922


title: 122016_Cell77-E10

description: Leftover clinical sample read as normal


title: RNA_sequencing_Aphid_72hrs_bioreplicate_1


title: DBA-CTRL-F-rep5

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

country: Italy

institute: Fondazione Santa Lucia IRCCS

data_processing:
base calling and de-multiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline.
Adapter sequences are masked with Cutadapt v1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimum-length 35 --mask-adapter
Color Space sequence reads were mapped against the most recent version of the mouse reference genome (GRCm38/mm10) from UCSC, using RefSeq as the gene structure and annotation database.
The software for mapping and quantification of transcripts was Lifetech Lifescope version 2.5.1
Quality control of the aligned reads were performed with the FastQC software
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file including raw gene counts values for each sample in a matrix

extract_protocol:
Brains were removed, flash frozen on dry ice, and VTA punmches dissected.  RNA was extracted using Norgen minicolumn ( Total RNA purification Kit)  and quality checked via Agilent   2100 bioanalyzer assay
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand) . sequenced on single-end 75 bp mode on NextSeq 500 (Illumina, San Diego, CA)

treatment_protocol: The RCF procedure (D'Amato et al., 2011) consists in fostering mouse litters by adoptive mothers changing every day form PD1 to PD4.

value: DBA

tag: Sex

value: female

value: adult

value: Unhandled control

tag: tissue

value: Brain - Ventral tegmental area


title: DBA-CTRL-F-rep4


title: 122016_Cell78-F10

description: Leftover clinical sample read as normal


title: 122016_Cell73-A10

description: Leftover clinical sample read as normal


title: 122016_Cell72-H9

description: Leftover clinical sample read as normal


title: DBA-CTRL-F-rep3


title: 122016_Cell71-G9

description: Leftover clinical sample read as normal


title: sRNA_sequencing_Aphid_72hrs_bioreplicate_1


title: 122016_Cell70-F9

description: Leftover clinical sample read as normal


title: DBA-CTRL-F-rep1


title: 122016_Cell79-G10

description: Leftover clinical sample read as normal


title: 122016_Cell69-E9-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell7-G1

description: Leftover clinical sample read as normal


title: 122016_Cell67-C9

description: Leftover clinical sample read as normal


title: 122016_Cell65-A9

description: Leftover clinical sample read as normal


title: 122016_Cell66-B9

description: Leftover clinical sample read as normal


title: DBA-RCF-F-rep3

value: Repeated Cross Fostered (RCF)


title: DBA-RCF-F-rep1


title: DBA-RCF-F-rep4


title: DBA-RCF-F-rep2


title: DBA-CTRL-M-rep4

value: male


title: DBA-CTRL-M-rep5


title: 122016_Cell64-H8

description: Leftover clinical sample read as normal

value: Macrophage (CD14+CD163+)


title: 122016_Cell62-F8

description: Leftover clinical sample read as normal


title: 122016_Cell61-E8

description: Leftover clinical sample read as normal


title: DBA-CTRL-M-rep3


title: DBA-CTRL-M-rep2


title: 122016_Cell60-D8-Dark

description: Leftover clinical sample read as normal


title: DBA-CTRL-M-rep1


title: DBA-CTRL-F-rep2


title: 122016_Cell59-C8-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell58-B8

description: Leftover clinical sample read as normal


title: DBA-RCF-F-rep5


title: DBA-RCF-M-rep4


title: DBA-RCF-M-rep3


title: DBA-RCF-M-rep2


title: DBA-RCF-M-rep1


title: 122016_Cell56-H7-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell55-G7-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell63-G8

description: Leftover clinical sample read as normal


title: C57-CTRL-F-rep5


title: C57-CTRL-F-rep4


title: C57-CTRL-F-rep3


title: C57-CTRL-F-rep2


title: 122016_Cell53-E7

description: Leftover clinical sample read as normal


title: 122016_Cell52-D7

description: Leftover clinical sample read as normal


title: C57-CTRL-F-rep1


title: 122016_Cell5-E1

description: Leftover clinical sample read as normal


title: DBA-RCF-M-rep5


title: C57-RCF-F-rep5


title: 122016_Cell49-A7

description: Leftover clinical sample read as normal


title: 122016_Cell54-F7

description: Leftover clinical sample read as normal


title: 122016_Cell48-H6

description: Leftover clinical sample read as normal


title: 122016_Cell6-F1

description: Leftover clinical sample read as normal


title: 122016_Cell47-G6

description: Leftover clinical sample read as normal


title: 122016_Cell50-B7

description: Leftover clinical sample read as normal


title: C57-RCF-F-rep2


title: 122016_Cell46-F6-Dark

description: Leftover clinical sample read as normal


title: C57-RCF-F-rep1


title: 122016_Cell57-A8

description: Leftover clinical sample read as normal


title: 122016_Cell45-E6

description: Leftover clinical sample read as normal


title: C57-CTRL-M-rep5


title: 122016_Cell44-D6

description: Leftover clinical sample read as normal


title: C57-CTRL-M-rep4

value: unhandled control


title: C57-CTRL-M-rep3


title: C57-CTRL-M-rep2


title: C57-RCF-M-rep5


title: 122016_Cell41-A6

description: Leftover clinical sample read as normal


title: C57-RCF-M-rep3


title: 122016_Cell4-D1

description: Leftover clinical sample read as normal


title: 122016_Cell38-F5-Dark

description: Leftover clinical sample read as normal


title: C57-RCF-M-rep4


title: 122016_Cell39-G5

description: Leftover clinical sample read as normal


title: C57-RCF-M-rep2


title: C57-RCF-F-rep3


title: 122016_Cell33-A5

description: Leftover clinical sample read as normal


title: 122016_Cell35-C5

description: Leftover clinical sample read as normal


title: C57-RCF-F-rep4

value: repeated Cross Fostered (RCF)


title: 122016_Cell36-D5

description: Leftover clinical sample read as normal


title: C57-CTRL-M-rep1


title: C57-RCF-M-rep1

value: Male


title: wt and PGC1a/b cardiomyocyte (mixed sample; non-demultiplexed)

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

data_processing:
alignment - zUMIs (uses STAR and Subread featureCounts)
Genome_build: mm10
Supplementary_files_format_and_content: We added the phenotype table containing the cell names, treatment group, and timepoint. The counts table has the raw mRNA counts.

source_name: control and PGC1a/b null cardiomyocyte

growth_protocol: Mice were maintained according to NIH guidelines.

extract_protocol:
Harvested hearts were placed in a Langendorff setup and perfused with a Type II Collagenase and Protease digestion buffer and stepped up with Calcium to 1 mM. Viable CMs were sorted using LP-FACS. The Union Biometrica COPAS Flow Platform was used to select CMs based on extinction, time of flight, and red fluorescence.
SCRB-seq was used to construct the libraries.

treatment_protocol: Mice were injected with 2e10gc of AAV9-cTnT-Cre

tag: genotype/variation

value: floxed PGC1a, floxed PGC1b, Rosa-TdTomato

value: ventricular heart tissue

value: cardiomyocyte


title: 122016_Cell31-G4

description: Leftover clinical sample read as normal


title: 122016_Cell30-F4

description: Leftover clinical sample read as normal


title: 122016_Cell43-C6

description: Leftover clinical sample read as normal


title: 122016_Cell32-H4

description: Leftover clinical sample read as normal


title: CB cells - efnA5-FC_3

city: Aachen

first: Daniel

last: Pensold

state: Nordrhein-Westfalen

address: Worringerweg 3

department: Institute for Biology II

country: Germany

institute: RWTH Aachen

description:
52F
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed

data_processing:
The paired-end FASTA files have been processed by the nextflowpipeline nfcore/rnaseq v1.4.2 mainly using the standard settings. The only changes that have been made to the default settings are specifying the strandedness of the library as reverse stranded and setting the aligner and pseudoaligner tools. The nfcore/rnaseq pipeline used Cutadept v2.9 for adapter trimming and executed an extensive quality control that was summarized in a MultiQC report by MultiQC v1.7.
The reads were aligned to the reference genome MM10 (Gencode M24) using STAR v2.6.1d.
The gene counts were determined by using featureCounts v1.6.4. Gencode M24 was used as a reference transcriptome. In addition to the alignment, a pseudoalignment providing transcript expression quantification was performed with Salmon v0.14.1.
We used the "filterByExpr" function of the limma v3.40.6 package to filter out lowly and non-expressed genes.
Next, we performed a Voom transformation of the RNA-seq count matrix adjusting for sample importance.
Genome_build: mm10
Supplementary_files_format_and_content: filtered, TMM normalized, voom transformed and sample weigthed gene counts

source_name: immortalized cerebellar granular cells

growth_protocol: CB cells [68] were cultured in Dulbecco’s modified Eagle’s medium with high glucose (DMEM, #41965-039, Thermo Fisher Scientific,Waltham, MA, USA) supplemented with 10% FBS (Biowest, Nuaillé; France), 1X GlutaMAX, 28 mM KCl at 33 °C, 5% CO2, and 95% relative humidity. Upon thawing of cells, the medium additionally contained 100 U/mL penicillin and 100 µg/mL streptomycin until the first passage. The cells were split after reaching a confluence of 75%.

extract_protocol:
After cell culture incubation medium was removed and cells were washed with cold 1x PBS (pH 7.4). Total of 500 µL of cold nuclei buffer (10 mM Tris-HCl pH 7.9; 100 mM KCl 5 mM MgCl2) was added after removing PBS and incubated for 5 min on ice. About 20 µL of 10% NP40 and 0.5 µL DTT were added and were shaken at 200 rpm for 2 min on ice to perform cell lysis. Suspension was transferred to a 1.5-mL tube and centrifuged for 2 min at 1200_x0002_ g at 4 °C. After discarding of supernatant, 500 µL of nuclei buffer was added for pellet resuspension. After centrifugation for 2 min at 200 g at 4 °C, supernatant was discarded. Pellet was washed twice with 125 µL of glycerol buffer (20 mM Tris-HCl pH 7.4; 50% glycerol; 75 mM KCl; 1 mM DTT; 5 mM MgCl2) with centrifugation for 5 min at 500_x0002_ g at  4 °C. Finally, supernatant was discarded and pellet resuspended in 50 µL of nuclei buffer. After adding 450 µL of Trizol®Reagent (Thermo Fisher Scientific, Waltham, MA, USA) all samples were snap frozen on dry ice and stored at 80 °C. For RNA-sequencing the samples were subjected to standard RNA isolation procedure using Trizol®Reagent with additional application of GlycoBlue (Thermo Fisher Scientific, Waltham, MA, USA) to a final concentration of 0.2% during RNA precipitation for better visualization of the pellet. RNA and DNA quantities were determined using Qubit 4 Fluorometer (Thermo Fisher Scientific,Waltham, MA, USA).
Library preparation for RNA-Seq was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA, E7760) starting from 36 ng of total RNA as input. Ribosomal depletion was achieved by using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs, Ipswich, MA, USA, E6310) and indexing was performed by the use of NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, Ipswich, MA, USA, E7335). Accurate quantification of the input RNA was performed with the QuantiFluor® RNA System (Promega, Madison, WI, USA, E3310) and by TapeStation RNA ScreenTape Analysis (Agilent, Santa Clara, CA, USA, 5067-5576). Accurate quantification of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega, Madison, WI, USA). The size range of final cDNA libraries was determined applying the TapeStation D1000 ScreenTape (Agilent, Santa Clara, CA, USA, 5067-5582). cDNA libraries were amplified and sequenced using the NextSeq 500 with NextSeq 500/550 High Output Kit v2.5 (150 cycles; Illumina, San Diego, CA, USA, 20024907). Sequencing was performed as paired end; 2 _x0002_ 76 bp; single indexing with ~30 million reads per sample.
total RNA-Seq (nuclear enriched RNA isolation, ribosomal depletion)

treatment_protocol: For stimulation, both cell lines were treated with 5 µg/mL ephrinA5-Fc (R&D Systems, Minneapolis, MN, USA) or Fc protein as control (Rockland Immunochemicals, Gilbertsville, PA, USA) pre-clustered with 10 µg/mL Alexa488 conjugated anti human IgG (Thermo Fisher Scientific,Waltham, MA, USA) for 30 min at RT and then applied to the cells.

value: immortalized cerebellar granular cells


title: CB cells - efnA5-FC_1

description:
22F
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed


title: CB cells - efnA5-FC_2

description:
32F
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed


title: 122016_Cell40-H5

description: Leftover clinical sample read as normal


title: 122016_Cell28-D4

description: Leftover clinical sample read as normal


title: 122016_Cell3-C1

description: Leftover clinical sample read as normal


title: CB cells - control-FC_2

description:
32E
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed

value: control-FC


title: 122016_Cell27-C4

description: Leftover clinical sample read as normal


title: CB cells - control-FC_1

description:
22E
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed


title: 122016_Cell26-B4

description: Leftover clinical sample read as normal


title: 122016_Cell24-H3

description: Leftover clinical sample read as normal


title: old_A_HSPC

city: Marseille

first: Estelle

last: Duprez

state: région Sud - Provence-Alpes-Côte d'Azur

address: 27 Bd Leï Roure, CS 30059

country: France

institute: Inserm

description: hematopoietic stem and progenitor cells purified from bone marrow of pool of two young (between two and 3 months) male mice. Single cell capture and RNA sequencing performed in HalioDX facility (Marseille France).

data_processing:
reads alignment to the mm10 genomes, filtering, barcode counting and unique molecular identifier (UMI) counting were performed with cellranger version 2.2.0 with Mouse reference dataset-2.1.0
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: Filtered gene-barcode matrix in MEX format (only detected cellular barcodes) stored in the Market Exchange Format (MEX) for sparse matrices with also gzipped TSV files for genes and barcode sequences corresponding to row and column indices respectively.

source_name: bone marrow hematopoietic stem and progenitor cells of old male mice

growth_protocol: C57BL/6-CD45.2 mice were purchased from Charles River Laboratories and were aged at the CRCM animal facility under specific pathogen-free conditions and according to the current European regulation

extract_protocol:
BM cells were harvested by crushing the bones (Femur, Tibia and Hip). Then, red blood cells were lysed with Ammonium-Chloride-Potassium (ACK) buffer and the remainning cells were washed twice with PBS, lineage depleted  using the Lineage Cell Depletion Kit (Miltenyi), labelled with the following antibody cocktail: anti-cKit, anti Sca-1 and anti Flt3 antibodies and FACS sorted
FACS purified HSPCs were loaded 30 min after the sorting onto a Chromium Single Cell Chip and processed with the Chromium Controller (10x Genomics) according to the manufacturer’s instructions for single cell barcoding at a target capture rate of 4000 individual cells per sample. Libraries were prepared using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics)
single cell RNAseq library  using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics)

value: hematopoietic stem and progenitor cells

value: Bone marrow

tag: gender


title: old_B_HSPC

description: hematopoietic stem and progenitor cells purified from bone marrow of pool of two old (18 months) male mice.  Single cell capture and RNA sequencing performed in TGML facility (Marseille, France)


title: 122016_Cell21-E3

description: Leftover clinical sample read as normal


title: 122016_Cell19-C3

description: Leftover clinical sample read as normal


title: 122016_Cell2-B1-Dark

description: Leftover clinical sample read as normal


title: young_A_HSPC

source_name: bone marrow hematopoietic stem and progenitor cells of young male mice


title: CB cells - control-FC_3

description:
52E
nuclear enriched RNA was isolated and total RNA-Seq after ribosomal depletion was performed


title: 122016_Cell20-D3-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell18-B3

description: Leftover clinical sample read as normal


title: CT_Ly6c_H2

city: Philadelphia

first: Hong

last: Wang

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

data_processing:
The processed data were generated by mapping the raw read to the mouse reference transcriptome (mouse cDNA FASTA from ensembl, website http://uswest.ensembl.org/info/data/ftp/index.html) using Kallisto.
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM) values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ly6Chigh monocyte

extract_protocol:
Flow cytometry sorted CD11b+Ly6G-Ly6Chigh and CD11b+Ly6G-Ly6Clow cells from control and Cbs-/- WBC (200000/MC subset) were collected in 1400 μL QIAzol Lysis Reagent (Qiagen, Germantown, MD) for total RNA extraction.
Samples were quality checked on an Agilent Bioanalyzer 2100 using pico RNA chip for RNA integrity number.
Total RNA (50-100 ng/sample) were used for cDNA library construction after ribosomal cDNA depletion using Takara pico-input kit.
Pooled samples were run for sequencing analysis in duplication on Illumina NextSeq 500 (CT) and Illumina Hiseq 4000 sequencer (HHcy).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood monocyte

tag: genetype

value: wild type

tag: age

value: 22 weeks

tag: cell subtype


title: CT_Ly6c_L1

source_name: Ly6Clow monocyte

tag: cell type


title: 122016_Cell17-A3-Dark

description: Leftover clinical sample read as normal


title: 122016_Cell14-F2

description: Leftover clinical sample read as normal


title: CT_Ly6c_H1


title: 122016_Cell15-G2

description: Leftover clinical sample read as normal


title: 122016_Cell1-A1

description: Leftover clinical sample read as normal


title: 122016_Cell12-D2

description: Leftover clinical sample read as normal


title: 122016_Cell11-C2

description: Leftover clinical sample read as normal


title: 122016_Cell22-F3

description: Leftover clinical sample read as normal


title: A37548hctr rep3

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Lexogen 3’ mRNA-Seq sequencing reads were processed using cutadapt v1.18
Sequencing reads were then aligned using STAR aligner version 2.7
RSEM v1.3.1 was used to estimate gene expression.
Estimated read counts from different groups were compared using the R Bioconductor package DESeq2 following generalized linear model based on negative binomial distribution
Genome_build: human genome version 38

source_name: melanoma cells

growth_protocol: Human melanoma cell lines A375 were cultured in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cell cultures were maintained in cell culture incubator at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using GenElute Mammalian Total RNA Miniprep kit (Sigma cat# RTN70-1KT), with on-column DNase I digestion step included.
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library PrepKit FWD for Illumina from Lexogen, (Vienna, Austria)

treatment_protocol: A375 cells cells were plated at 50% confluency and grown overnight in 6-well plates. IMD-0354 at different concentrations were added to the plates and incubated for 24h and 48h.

value: skin

value: untreated


title: A37548hctr rep2


title: 48hIMD-063 rep1

value: treated with 0.63uM IMD-0354 for 48h


title: 48hIMD-063 rep2


title: CT_Ly6c_L2


title: young_B_HSPC

description: hematopoietic stem and progenitor cells purified from bone marrow of pool of three old (18 months) male mice. Single cell capture and RNA sequencing performed in TGML facility (Marseille, France).

value: male


title: A37548hctr rep1


title: 24hIMD-125 rep3

value: treated with 1.25uM IMD-0354 for 24h


title: 29DPI-Hypo-Drug-TBI-4

city: Bethesda

first: Aviva

middle: Jane

last: Symes

address: 4301 Jones Bridge Road

department: Pharmacology

institute: Uniformed Services University

data_processing:
Sequencing libraries were pooled and sequenced on a HiSeq 3000 System (Illumina) using a HiSeq 3000/4000 PE Cluster Kit and SBS Kit (150 cycles) with run conditions of paired-end reads at 75 bp length.
Raw sequencing data were demuxed using bcl2fastq2 conversion software 2.20.
Raw paired-end sequencing reads were aligned to the mouse reference genome (mm10) using MapSplice version 2.2.1.
Gene read counts against UCSC mouse gene models (obtained on February 21, 2016) were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: 3DPI_samples_counts_table.txt - tab-delimited text file of gene raw counts for all 3DPI samples
Supplementary_files_format_and_content: 29DPI_samples_counts_table.txt - tab-delimited text file of gene raw counts for all 29DPI samples

source_name: Hypothalamus

extract_protocol:
Animals were anesthetized and perfused with ice-cold filtered 0.9% saline solution, individual brain regions were removed (hypothalamus, thalamus, hippocampus), tissue triturated in Tri-reagent, RNA extracted utilizing Direct-zol RNA MiniPreps (Zymo Research, # R2025).
Total RNA integrity was assessed using automated capillary electrophoresis on a Fragment Analyzer (Roche).  For all samples RQI > 8.0 and a total RNA amount of >75 ng was used as input for library preparation using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA).
Sequencing libraries were quantified by PCR using KAPA Library Quantification Kit for NGS (Kapa, Wilmington, MA, USA) and assessed for size distribution on a Fragment Analyzer.

treatment_protocol: All mice received their first dose of either candesartan (Tocris Bioscience, Minneapolis, MN # 4791) or vehicle (0.9% saline and 0.1N Na2CO3 at pH = 7.4) six hours after the CCI or sham procedure through intraperitoneal injection. Mice in the 3 day cohort received two subsequent i.p. injections at 24- and 48-hours after CCI, before sacrifice at 3 dpi. Mice in the 29-day cohort were surgically implanted with an osmotic pump (#1004, Alzet, Cupertino, CA) 24 hours after the CCI or sham procedure.

tag: time point

value: 29 Days Post-Injury

tag: drug treatment

value: Drug

tag: tbi

value: TBI


title: 110316_Cell9-G2

description: Leftover clinical sample read as normal

value: Macrophage (CD14+CD163+)


title: 29DPI-Hypo-Drug-TBI-2


title: 48hIMD-063 rep3

tag: cell line


title: 24hIMD-125 rep2

tag: treatment


title: 29DPI-Hypo-Drug-TBI-3


title: 29DPI-Hypo-Drug-TBI-1


title: 29DPI-Hypo-Drug-NoTBI-4

value: NoTBI


title: 24hIMD-125 rep1


title: 29DPI-Hypo-Drug-NoTBI-3


title: 122016_Cell10-B2

description: Leftover clinical sample read as normal


title: 29DPI-Hypo-Drug-NoTBI-2


title: 24hIMD-063 rep2

value: treated with 0.63uM IMD-0354 for 24h


title: 29DPI-Hypo-Drug-NoTBI-1


title: 110316_Cell6-H1

description: Leftover clinical sample read as normal


title: 24hIMD-063 rep3


title: 29DPI-Hypo-Veh-TBI-4

value: Vehicle


title: 29DPI-Hypo-Veh-TBI-3


title: 24hIMD-063 rep1


title: 110316_Cell5-F1

description: Leftover clinical sample read as normal


title: 24hIMD-032 rep3

value: treated with 0.32uM IMD-0354 for 24h


title: 29DPI-Hypo-Veh-TBI-1


title: 110316_Cell8-B2

description: Leftover clinical sample read as normal


title: 110316_Cell48-C12

description: Leftover clinical sample read as normal


title: 29DPI-Hypo-Veh-TBI-2


title: 29DPI-Hypo-Veh-NoTBI-3


title: 29DPI-Hypo-Veh-NoTBI-4


title: 24hIMD-032 rep2


title: 29DPI-Hypo-Veh-NoTBI-2


title: 24hIMD-032 rep1


title: 110316_Cell44-E11

description: Leftover clinical sample read as normal


title: 110316_Cell45-F11

description: Leftover clinical sample read as normal


title: 110316_Cell43-D11

description: Leftover clinical sample read as normal


title: 29DPI-Hypo-Veh-NoTBI-1


title: 110316_Cell7-A2

description: Leftover clinical sample read as normal


title: 110316_Cell42-C11

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Drug-TBI-4

source_name: Thalamus


title: 29DPI-Thal-Drug-TBI-2


title: A37524hctr rep3


title: 29DPI-Thal-Drug-TBI-1


title: 29DPI-Thal-Drug-TBI-3


title: A37524hctr rep2


title: 29DPI-Thal-Drug-NoTBI-4


title: 110316_Cell41-B11

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Drug-NoTBI-2


title: 29DPI-Thal-Drug-NoTBI-3


title: 110316_Cell40-A11

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Drug-NoTBI-1


title: 29DPI-Thal-Veh-TBI-3


title: 29DPI-Thal-Veh-TBI-1


title: 110316_Cell38-G9

description: Leftover clinical sample read as normal


title: 110316_Cell39-A10

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Veh-TBI-2


title: UPHN27B

city: Pittsburgh

first: Umamaheswar

last: Duvvuri

address: 203 Lothrop Street

data_processing:
Quality control was performed on the raw reads using RNA-SeQC (v1.1.7).
Pre-processed short reads were aligned to the human genome reference sequence assembly (GRCh37/hg19) with the STAR2 aligner using a two-pass procedure and default optuons to generate RNA-seq BAM files.
FeatureCounts from SubRead (v1.6.0) was used for counting reads.
Differential expression analysis was subsequently performed using the Empirical Analysis of Digital Gene Expression Data in R program (edgeR).
Negative binomial generalized log-linear models were applied to the gene-wise read counts for the recurrent and primary tumors adjusting for baseline differences between patients. Likelihood ratio tests were performed comparing log2 counts per million (CPM) between recurrent and primary tumors.
Genome_build: hg19
Supplementary_files_format_and_content: text-delimited processed data file contains normalized counts per million for each sample for each gene assayed
Supplementary_files_format_and_content: text-delimited raw counts file contains counts for each sample for each gene assayed

source_name: distant

extract_protocol:
Archival tissue specimens from the University of Pittsburgh tumor samples were processed via fixation in 10% neutral buffered formalin, dehydrated in ethanol and embedded with paraffin wax (FFPE). H&E slides were prepared, and areas with high tumor density (>75% tumor cells) were marked for extraction. Two-mm punch biopsies were taken from the FFPE tumor dense regions for downstream tumor RNA extraction. FFPE tissue was de-paraffinized with xylenes, washed in consecutive ethanol rinses (100% and 70%), and heated to remove formalin cross-linking. Tumor RNA was extracted using the Quick-RNA FFPE Miniprep extraction kit (Zymo Research, Irvine, CA).
University of Pittsburgh sample libraries were manually prepared via standard protocols using the Illumina TruSeq RNA Exome Library Prep Kit (Illumina, San Diego, CA)

tag: ct stage

tag: cn stage


title: 29DPI-Thal-Veh-NoTBI-4


title: UPHN29A

source_name: oropharynx


title: 29DPI-Thal-Veh-NoTBI-3


title: 110316_Cell36-D9

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Veh-NoTBI-2


title: UPHN27A


title: 110316_Cell35-C9

description: Leftover clinical sample read as normal


title: 29DPI-Thal-Veh-NoTBI-1


title: UPHN23B


title: 110316_Cell34-B9

description: Leftover clinical sample read as normal


title: A37524hctr rep1


title: UPHN23A


title: 110316_Cell33-A9

description: Leftover clinical sample read as normal


title: 29DPI-Hipp-Drug-TBI-1

source_name: Hippocampus


title: 29DPI-Hipp-Drug-TBI-3


title: UPHN22B

source_name: regional


title: UPHN29B


title: 29DPI-Hipp-Drug-NoTBI-3


title: 29DPI-Hipp-Drug-TBI-2


title: 29DPI-Thal-Veh-TBI-4


title: UPHN22A


title: 29DPI-Hipp-Drug-NoTBI-4


title: 29DPI-Hipp-Drug-NoTBI-1


title: 29DPI-Hipp-Drug-NoTBI-2


title: UPHN21B


title: UPHN21A


title: 110316_Cell26-C7

description: Leftover clinical sample read as normal

source_name: sorted bone marrow macrophages


title: 29DPI-Hipp-Veh-TBI-4


title: 29DPI-Hipp-Veh-TBI-2


title: 29DPI-Hipp-Veh-TBI-3


title: 110316_Cell3-D1

description: Leftover clinical sample read as normal


title: 29DPI-Hipp-Veh-TBI-1


title: 29DPI-Hipp-Drug-TBI-4


title: 110316_Cell25-E6

description: Leftover clinical sample read as normal


title: 29DPI-Hipp-Veh-NoTBI-4


title: 110316_Cell23-F5

description: Leftover clinical sample read as normal


title: 29DPI-Hipp-Veh-NoTBI-3


title: 110316_Cell32-H8

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Drug-TBI-4

value: 3 Days Post-Injury


title: 29DPI-Hipp-Veh-NoTBI-2


title: 29DPI-Hipp-Veh-NoTBI-1


title: 110316_Cell22-D5

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Drug-TBI-3


title: 3DPI-Hypo-Drug-TBI-2


title: UPHN7B


title: UPHN20B


title: 110316_Cell21-B5

description: Leftover clinical sample read as normal


title: UPHN7A


title: UPHN20A


title: 3DPI-Hypo-Drug-TBI-1


title: 110316_Cell27-F7

description: Leftover clinical sample read as normal


title: UPHN5B

source_name: local


title: 110316_Cell20-A5

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Drug-NoTBI-3


title: UPHN5A


title: 110316_Cell2-B1

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Drug-NoTBI-1


title: UPHN4B


title: 3DPI-Hypo-Drug-NoTBI-4


title: 3DPI-Hypo-Drug-NoTBI-2


title: 3DPI-Hypo-Veh-TBI-3


title: 110316_Cell19-F4

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Veh-TBI-4


title: 3DPI-Hypo-Veh-TBI-2


title: 110316_Cell18-E4

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Veh-TBI-1


title: UPHN4A


title: UPHN2A


title: UPHN2B


title: 110316_Cell17-C4

description: Leftover clinical sample read as normal


title: 3DPI-Hypo-Veh-NoTBI-4


title: 3DPI-Hypo-Veh-NoTBI-3


title: 3DPI-Hypo-Veh-NoTBI-2


title: 110316_Cell16-B4

description: Leftover clinical sample read as normal


title: 3DPI-Thal-Drug-TBI-3


title: 3DPI-Hypo-Veh-NoTBI-1


title: Series5_A549ACE2_SARS-CoV-2-siN-24h_3

city: New York

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
TruSeq Stranded mRNA LP
Time after treatment: 24 hours
RawReadCounts_Virus.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 comparing Infected samples to their correspondent mock treated sample, for each virus
Raw sequencing reads were aligned to the corresponding viral genome using Bowtie2
Genome_build: human (hg19), IAV (A/Puerto Rico/8/1934), SeV (KY295909.1), SARS-CoV-2 (MN985325.1)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene/viral genome for each sample.

source_name: SARS-CoV-2 infected A549 cells trasnduced with a vector expressing human ACE2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit v2, TruSeq Stranded mRNA LP, or TruSeq Stranded Total RNA Kit RiboZero Gold according to the manufacturer’s instructions

value: Lung adenocarcinoma

value: siN transfected (24hrs) SARS-CoV-2 infected (MOI 0.1)


title: 3DPI-Thal-Drug-TBI-4


title: Series5_A549ACE2_SARS-CoV-2-siN-24h_2


title: 110316_Cell15-A4

description: Leftover clinical sample read as normal


title: 3DPI-Thal-Drug-NoTBI-4


title: 3DPI-Thal-Drug-TBI-1


title: 3DPI-Thal-Drug-TBI-2


title: 110316_Cell14-F3

description: Leftover clinical sample read as normal


title: 110316_Cell13-C3

description: Leftover clinical sample read as normal


title: 3DPI-Thal-Drug-NoTBI-3


title: 3DPI-Thal-Drug-NoTBI-2


title: 3DPI-Thal-Veh-TBI-4


title: 3DPI-Thal-Drug-NoTBI-1


title: 110316_Cell12-B3

description: Leftover clinical sample read as normal


title: 110316_Cell11-A3

description: Leftover clinical sample read as normal


title: 3DPI-Thal-Veh-TBI-3


title: 3DPI-Thal-Veh-TBI-2


title: 3DPI-Thal-Veh-TBI-1


title: 110316_Cell10-H2

description: Leftover clinical sample read as normal


title: 110316_Cell1-A1

description: Leftover clinical sample read as normal


title: 3DPI-Thal-Veh-NoTBI-4


title: Series5_A549ACE2_SARS-CoV-2-siN-24h_1


title: 3DPI-Thal-Veh-NoTBI-3


title: Series4_A549_SeV-NT-9h_1

description:
TruSeq Stranded Total RNA Kit RiboZero Gold
Time after treatment: 9 hours
RawReadCounts_Virus.tsv

source_name: SeV-NT infected A549 cells

value: SeV-NT infected (MOI 5)

value: Fushimi - 5T


title: 3DPI-Thal-Veh-NoTBI-1


title: Series4_A549_SeV-NT-9h_2


title: 3DPI-Thal-Veh-NoTBI-2


title: 031016_Cell8-C2

description: Leftover clinical sample read as normal


title: 031016_Cell9-D2

description: Leftover clinical sample read as normal


title: Series5_A549ACE2_SARS-CoV-2-siScr-24h_3

value: siSrc transfected (24hrs) SARS-CoV-2 infected (MOI 0.1)


title: Series4_A549_SeV-NC-9h_2

source_name: SeV-NC infected A549 cells

value: SeV-NC infected (MOI 5)

value: Fushimi - 5R


title: Series4_A549_SeV-NC-9h_1


title: Series5_A549ACE2_SARS-CoV-2-siScr-24h_2


title: 3DPI-Hipp-Drug-TBI-2


title: Series3_A549_IAV-NT-9h_2

source_name: IAV-NT infected A549 cells

value: IAV-NT infected (MOI 5)

value: A/Puerto Rico/8/1934 (H1N1) - N5T


title: 3DPI-Hipp-Drug-NoTBI-4

value: Drug


title: 3DPI-Hipp-Drug-TBI-3

value: TBI


title: 3DPI-Hipp-Drug-NoTBI-3


title: 3DPI-Hipp-Drug-TBI-1


title: Series3_A549_IAV-NT-9h_1


title: 3DPI-Hipp-Drug-TBI-4


title: 3DPI-Hipp-Drug-NoTBI-2


title: 031016_Cell64-D12

description: Leftover clinical sample read as normal

value: Macrophage (CD14+CD163+)


title: 031016_Cell7-B2

description: Leftover clinical sample read as normal


title: Series3_A549_IAV-NC-9h_2

source_name: IAV-NC infected A549 cells

value: IAV-NC infected (MOI 5)

value: A/Puerto Rico/8/1934 (H1N1)


title: 031016_Cell61-A12

description: Leftover clinical sample read as normal


title: 3DPI-Hipp-Drug-NoTBI-1

value: NoTBI


title: 3DPI-Hipp-Veh-TBI-3

value: Vehicle


title: Series5_A549ACE2_SARS-CoV-2-siScr-24h_1


title: 3DPI-Hipp-Veh-TBI-2

value: 3 Days Post-Injury


title: 031016_Cell60-E11

description: Leftover clinical sample read as normal


title: Series3_A549_IAV-NC-9h_1

value: Lung adenocarcinoma


title: Series2_A549_SeV-NT-24h_2

description:
TruSeq RNA Library Prep Kit v2
Time after treatment: 24 hours
RawReadCounts_Human.tsv


title: 3DPI-Hipp-Veh-TBI-1


title: 3DPI-Hipp-Veh-NoTBI-4


title: 3DPI-Hipp-Veh-NoTBI-3


title: Series2_A549_SeV-NC-24h_2


title: 3DPI-Hipp-Veh-NoTBI-1


title: 3DPI-Hipp-Veh-NoTBI-2


title: Series2_A549_SeV-NT-24h_1


title: Series2_A549_SeV-NC-24h_1


title: Series2_A549_Mock_3 (SeV-NC control)

source_name: Mock treated A549 cells

value: Mock treatment


title: 3DPI-Hipp-Veh-TBI-4


title: 031016_Cell56-G10

description: Leftover clinical sample read as normal


title: 031016_Cell59-C11

description: Leftover clinical sample read as normal


title: Series2_A549_Mock_1 (SeV-NC control)


title: 031016_Cell55-E10

description: Leftover clinical sample read as normal


title: 031016_Cell54-D10

description: Leftover clinical sample read as normal


title: Series1_A549_IAV-NT-9h_2

description:
TruSeq RNA Library Prep Kit v2
Time after treatment: 9 hours
RawReadCounts_Human.tsv


title: 031016_Cell6-G1

description: Leftover clinical sample read as normal


title: 031016_Cell53-C10

description: Leftover clinical sample read as normal


title: 031016_Cell58-B11

description: Leftover clinical sample read as normal


title: 031016_Cell63-C12

description: Leftover clinical sample read as normal


title: 031016_Cell52-B10

description: Leftover clinical sample read as normal


title: 031016_Cell57-A11

description: Leftover clinical sample read as normal


title: Series1_A549_IAV-NT-9h_1


title: Series2_A549_Mock_2 (SeV-NC control)


title: Series1_A549_IAV-NC-9h_1


title: Series1_A549_Mock_2


title: 031016_Cell50-F9

description: Leftover clinical sample read as normal


title: Series1_A549_Mock_1


title: 031016_Cell5-F1

description: Leftover clinical sample read as normal


title: Series1_A549_IAV-NC-9h_2


title: 031016_Cell51-A10

description: Leftover clinical sample read as normal


title: 031016_Cell49-E9

description: Leftover clinical sample read as normal


title: SUDHL4 OBF1

description: SUDHL4 OBF1

data_processing:
Library strategy: CUT&RUN
ChIP-seq sequencing reads were aligned to the mouse genome (mm9) using the qAlign function, which internally uses Bowtie [Langmead et al 2009], from Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0). Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp. Peaks of OBF1 and H3K27ac were called in control sample (input) with MACS2 [Zhang et al 2008] (software version 2.1.1) using default parameters. Reads were counted in each peak region using the qCount function in QuasR (with shift set to 60). The read counts per sample were normalized to the mean total mapped number of reads across all samples. CUT&RUN were aligned to the human genome (hg19) using  Bowtie2. Bigwig files were generated using bamCoverage in deepTools [Fidel Ramírez et al 2014].
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: bigwig files containing the enrichment of IP over input

source_name: SUDHL4 OBF1

growth_protocol: Burkitt’s lymphoma and DLBCL cell lines (Raji and SUDHL4) were cultured in T75 flasks in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol). B Lymphoma cells were passaged every two to three days.

extract_protocol:
For GC induction: mice were injected i.p. with 100ul 10% SRBC (PBS), and sacrificed at day 7. GC B cells were isolated using PNA beads by MACS. Bio-ChIP-seq was carried out with 4M cells crosslinked with 1% formaldehyde. For primary human GC B cells: MNCs were isolated from tonsils after tonsillectomy and crosslinked with 1% formaldehyde, and subjected to CUT&RUN. GC B cells were purified by FACS under gate CD19+CD38+IgD-. For GC-derived lymphoma cells: cells were crosslinked with 1% formaldehyde, and subjected to CUT&RUN.
libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions

tag: clone

value: Wild type SUDHL4

tag: other

value: 1% Formaldehyde crosslinked; CUT&RUN; paired-end


title: SUDHL4 H3K27ac

description: SUDHL4 H3K27ac

source_name: SUDHL4 H3K27ac


title: 031016_Cell48-D9

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 70

city: Gothenburg

last: Arvidsson

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: Tumor

extract_protocol: Genomic DNA was isolated from the biopsies using the DNeasy® Blood and Tissue kit (Qiagen GmbH, Hilden, Germany).

tag: case

tag: gender male (m), female (f)

value: F

value: liver metastasis

source_name: Human Reference DNA female (Agilent)

tag: gender reference

value: Male (M), Female (F):F


title: Small intestine neuroendocrine tumor (SINET), 68

tag: tissue

value: lymph node metastasis


title: Small intestine neuroendocrine tumor (SINET), 69


title: 031016_Cell47-C9

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 64


title: SUDHL4 IgG

description: SUDHL4 IgG

source_name: SUDHL4 IgG


title: Small intestine neuroendocrine tumor (SINET), 66

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 63

value: M

source_name: Human Reference DNA male (Agilent)

value: Male (M), Female (F):M


title: Small intestine neuroendocrine tumor (SINET), 100


title: 031016_Cell46-B9

description: Leftover clinical sample read as normal

value: Macrophage (CD14+CD163+)


title: Small intestine neuroendocrine tumor (SINET), 99


title: Small intestine neuroendocrine tumor (SINET), 53


title: Raji OBF1

description: Raji OBF1

source_name: Raji OBF1

value: Wild type Raji

value: Raji


title: Small intestine neuroendocrine tumor (SINET), 65


title: 031016_Cell45-A9

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 60


title: Small intestine neuroendocrine tumor (SINET), 67


title: Small intestine neuroendocrine tumor (SINET), 62


title: 031016_Cell44-H8

description: Leftover clinical sample read as normal


title: Raji IgG

description: Raji IgG

source_name: Raji IgG


title: Small intestine neuroendocrine tumor (SINET), 61


title: Small intestine neuroendocrine tumor (SINET), 59


title: Small intestine neuroendocrine tumor (SINET), 57


title: 031016_Cell43-F8

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 52


title: Small intestine neuroendocrine tumor (SINET), 55


title: Small intestine neuroendocrine tumor (SINET), 54


title: human tonsil GC OBF1 rep2

description: human tonsil GC OBF1 rep2

data_processing:
ChIP-seq sequencing reads were aligned to the mouse genome (mm9) using the qAlign function, which internally uses Bowtie [Langmead et al 2009], from Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0). Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp. Peaks of OBF1 and H3K27ac were called in control sample (input) with MACS2 [Zhang et al 2008] (software version 2.1.1) using default parameters. Reads were counted in each peak region using the qCount function in QuasR (with shift set to 60). The read counts per sample were normalized to the mean total mapped number of reads across all samples. CUT&RUN were aligned to the human genome (hg19) using  Bowtie2. Bigwig files were generated using bamCoverage in deepTools [Fidel Ramírez et al 2014].
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: bigwig files containing the enrichment of IP over input

source_name: human tonsil GC OBF1 rep2

value: GC B cell from tonsils post tonsillectomy

value: Primary cells

value: FACS:CD19+CD38+IgD-; paired-end


title: Small intestine neuroendocrine tumor (SINET), 50


title: Small intestine neuroendocrine tumor (SINET), 51


title: Small intestine neuroendocrine tumor (SINET), 56


title: 031016_Cell42-E8

description: Leftover clinical sample read as normal

data_processing:
All single-cell libraries were pseudo-aligned to the human Ensembl version 72 transcriptome using the Kallisto through AltAnalyze version 2.1.3. as described in our previous publication [40]. To ensure quality control, libraries with less than 300,000 paired-end reads or estimated read percentage alignment <20% were excluded. Unsupervised population discovery was performed using the software ICGS version 2 (Venkatasubramanian et al. 2019, bioRxiv) and PCA-loading gene analysis and HOPACH clustering in AltAnalyze. PCA-loading genes were selected as the top-100 correlated and top-100 anti-correlated genes associated with the first 4 principal components. Initial identified predominant gene clusters from the PCA-loading analysis were excluded prior to ICGS2, by identifying genes correlated to the centroid of the gene clusters with a Pearson rho > 0.1 (21,719 genes remaining after exclusion). ICGS2 was run using the default program parameters. To expand the cell-cluster identified from the ICGS2 analysis of SJIA with donor BM macrophages, an aggerate score (sum of the TRIM8 cluster maker genes), was used to identify additional SJIA patient cells (n=12, total) enriched in TRIM8-associated genes prior to differential expression analyses. For the identification of TRIM8-cluster specific genes, we applied empirical Bayes moderated (eBayes) t-test comparing TRIM8-cluster SJIA cells to all donor macrophage cells (AltAnalyze). Only genes with a minimum average TPM >1 in the two compared populations, eBayes t-test p<0.05 (following Benjamini-Hochberg correction) and fold > 1.5 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file

source_name: sorted bone marrow macrophages


title: Small intestine neuroendocrine tumor (SINET), 49


title: human tonsil GC OBF1 rep1

description: human tonsil GC OBF1 rep1

source_name: human tonsil GC OBF1 rep1


title: Small intestine neuroendocrine tumor (SINET), 96


title: 031016_Cell41-D8

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 48


title: human tonsil GC H3K27ac

description: human tonsil GC H3K27ac

source_name: human tonsil GC H3K27ac


title: Small intestine neuroendocrine tumor (SINET), 46


title: human tonsil GC IgG

description: human tonsil GC IgG

source_name: human tonsil GC IgG


title: Small intestine neuroendocrine tumor (SINET), 94


title: Small intestine neuroendocrine tumor (SINET), 93


title: Small intestine neuroendocrine tumor (SINET), 92


title: Small intestine neuroendocrine tumor (SINET), 97


title: Small intestine neuroendocrine tumor (SINET), 58


title: 031016_Cell39-B8

description: Leftover clinical sample read as normal


title: 031016_Cell40-C8

description: Leftover clinical sample read as normal


title: RNAseq patient 40 MRD

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

data_processing:
BCL files were converted into FASTQ file format with bcl2fastq (v2.19) (Illumina, USA) and resulting reads were trimmed with cutadapt (v1.18).
Clean reads were aligned to the human genome reference (hg19) with STAR (Dobin et al., 2013) (v2.5.3)
Read counts per gene were calculated with quant3p (github.com/ctlab/quant3p)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix including gene-count values for each sample

source_name: Tumor plasma cells

extract_protocol:
Samples in RLT were defrosted and gDNA plus RNA were isolated with AllPrep DNA/RNA Micro Kit (Qiagen, USA) following manufacturer’s instructions. Samples in DMSO were defrosted, washed with PBS and suspended in lysis binding buffer (Ambion). Poly-A RNA was selected with Dynabeads Oligo (dT) (Ambion), and un-binded DNA was selected with SPRIselect beads, washed with EtOH and suspended in buffer EB.
We used a 3’ end RNAseq method optimized for generating libraries from low-input starting material (MARSeq), adapted for bulk RNAseq (Jaitin et al., 2014; Lavin et al., 2017) with minor modifications.
MARSeq

tag: cytogenetic alterations

value: standard-risk


title: 031016_Cell38-A8

description: Leftover clinical sample read as normal

extract_protocol:
This suspension was then loaded onto the Fluidigm C1 Single-Cell Auto Prep System, on a 10-17um chip.  These cells were subsequently lysed, and extracted RNA converted into cDNA per manufacterers directions using v4 chemistry.
Libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA) on cDNAs with an initial concentration>180 pg/µl that were then diluted to 100 pg/µl. In each single-cell library preparation, a total of 125pg cDNA was tagmented at 55 °C for 20 minutes. Libraries were pooled and purified on AMPure® bead-based magnetic separation before a final quality control using Qubit® dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit. We required the majority of cDNA fragments to be between 375–425bp to qualify for sequencing.
Single cell libraries were subjected to paired-end RNA-Sequencing on a HiSeq 2500 (Illumina Inc., San Diego, CA). 96 scRNA-Seq libraries were sequenced per HiSeq 2500 gel (~300 million bp/gel).


title: Small intestine neuroendocrine tumor (SINET), 90

first: Yvonne

address: Box 425

institute: University of Gothenburg


title: Small intestine neuroendocrine tumor (SINET), 47


title: Small intestine neuroendocrine tumor (SINET), 89


title: 031016_Cell37-H7

description: Leftover clinical sample read as normal


title: RNAseq patient 38 MRD


title: RNAseq patient 39 MRD


title: 031016_Cell36-F7

description: Leftover clinical sample read as normal


title: RNAseq patient 37 MRD


title: Small intestine neuroendocrine tumor (SINET), 88


title: Small intestine neuroendocrine tumor (SINET), 86


title: 031016_Cell35-E7

description: Leftover clinical sample read as normal


title: 031016_Cell34-D7

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 85


title: RNAseq patient 36 MRD

value: high-risk


title: Small intestine neuroendocrine tumor (SINET), 84


title: Raji H3K27ac

city: Basel

last: Song

description: Raji H3K27ac

source_name: Raji H3K27ac


title: RNAseq patient 35 MRD_2


title: 031016_Cell33-C7

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 82


title: RNAseq patient 35 MRD_1


title: Small intestine neuroendocrine tumor (SINET), 91


title: Small intestine neuroendocrine tumor (SINET), 79


title: 2(8+73-)

type: RNA

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

institute: INSERM U955_VRI

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: iScan Illumina scanning protocol using iScan control software

data_processing: Quality controls were checked using Illumina GenomeStudio software. Raw data were filtred both on detection average signal p-values (p≤ 0.05 and the proportion per group threshold of 0.5. The lumi Bioconductor package algorithm, through Flexarray software, was used to pre-process and normalize Illumina microarray data. Background were corrected using RMA background adjustment followed by log2 to stabilize variance and quantile normalization. Differentially expressed genes were analyzed using Local-pooled-error test (LPE) (Nitin J. et al., Bioinformatics. 2003. 19(15):1945-51). Genes with a fold change ≥ 1.5 and False Discovery Rate (FDR) ≤ 0.05 were considered statistically significant.

source_name: Blood CD8+ CD73-Tcells

label_protocol: In vitro transcription was generated from 200 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using RNeasy Plus Micro Kit (Qiagen, France) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

value: blood

value: CD8+ CD73-Tcells


title: Small intestine neuroendocrine tumor (SINET), 81


title: Small intestine neuroendocrine tumor (SINET), 83

value: F


title: 3(8+73+)

source_name: Blood CD8+ CD73+Tcells

value: CD8+ CD73+Tcells


title: RNAseq patient 34 MRD


title: Small intestine neuroendocrine tumor (SINET), 80

value: liver metastasis


title: 031016_Cell31-A7

description: Leftover clinical sample read as normal


title: 3(8+73-)


title: 031016_Cell30-D6

description: Leftover clinical sample read as normal


title: RNAseq patient 33 MRD


title: 2(8+73+)


title: RNAseq patient 32 MRD


title: 8+73-


title: 8+73+


title: 031016_Cell32-B7

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 76

value: lymph node metastasis


title: Small intestine neuroendocrine tumor (SINET), 74


title: Small intestine neuroendocrine tumor (SINET), 75

value: Male (M), Female (F):F


title: 031016_Cell3-D1

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 78

value: M


title: Small intestine neuroendocrine tumor (SINET), 77

value: Male (M), Female (F):M


title: 3(4+73-)

source_name: Blood CD4+ CD73-Tcells

value: CD4+ CD73-Tcells


title: Small intestine neuroendocrine tumor (SINET), 73


title: 2(4+73-)


title: RNAseq patient 31 MRD


title: Small intestine neuroendocrine tumor (SINET), 98


title: 031016_Cell29-C6

description: Leftover clinical sample read as normal

value: Macrophage (CD14+CD163+)


title: 4+73-


title: Small intestine neuroendocrine tumor (SINET), 72


title: 4+73+

source_name: Blood CD4+ CD73+Tcells

value: CD4+ CD73+Tcells


title: RNAseq patient 30 MRD


title: 2 (4+73+)


title: 031016_Cell28-B6

description: Leftover clinical sample read as normal


title: 3(4+73+)


title: 031016_Cell27-A6

description: Leftover clinical sample read as normal


title: Small intestine neuroendocrine tumor (SINET), 95

source_name: Tumor


title: KO3

city: Beijing

first: Wei

last: Li

address: 1st Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Sequencing was carried  out with Illumina HiSeq 2000
Raw paired-end sequencing reads were aligned to mouse GRCm38/mm10 reference genome by HISAT2 (2.1.0)
FPKMs (fragments per kilobase of  transcript per million mapped reads) were calculated using Cufflinks (v2.1.1)
The genes with FPKMs>1, fold changes >2, and FDR< 0.01 were identified as the differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: counts, FPKM

source_name: KO_reprogrammable cells

growth_protocol: Reprogrammable cells were cultured at 37˚C in a shumidified atmosphere with 5% CO2.

extract_protocol:
Total RNA of WT and Rnf20-knockout reprogrammable cells at day 3 was harvested using Trizol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

tag: strain background

tag: genotype

value: reprogrammable cells

value: untreated


title: KO1

tag: cell type


title: KO2


title: 031016_Cell25-C5

city: Cincinnati

last: Salomonis

description: Leftover clinical sample read as normal


title: RNAseq patient 27 MRD


title: RNAseq patient 29 MRD


title: Small intestine neuroendocrine tumor (SINET), 71

source_name: Human Reference DNA female (Agilent)


title: WT3

source_name: WT_reprogrammable cells

value: wild type


title: RNAseq patient 26 MRD


title: RNAseq patient 28 MRD

value: standard-risk


title: WT1


title: Small intestine neuroendocrine tumor (SINET), 87

source_name: Human Reference DNA male (Agilent)


title: 031016_Cell26-D5

description: Leftover clinical sample read as normal


title: RNAseq patient 25 MRD


title: MK2 KO M2 macrophage_rep 5

city: Cambridge

first: Michael

middle: B

last: Yaffe

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina Pipeline version RTA / OLB / CASAVA (v2.8.0 / v1.8.0 / v1.7.0) was used for base calling and trimming adaptor sequences.
Sequenced reads were mapped to mm10 transcriptome using RSEM (v1.3.0) with Bowtie 2 (v2.3.4.1) as the aligner with parameters -p 10  --append-names --bowtie2 --calc-ci --fragment-length-mean 200 --fragment-length-sd 40
Expected counts, expected counts rounded, TPM and FPKM files were generated (Li and Dewey, BMC Bioinformatics, 2011).
Gene length corrected TMM (Smid et al, BMC Bioinformatics, 2018) was used to normalize samples.
Genome_build: mm10
Supplementary_files_format_and_content: ExpectedCounts_rounded.txt  -  raw counts
Combined_RNAseq_edgeR_GETMM.txt  -  normalized abundance measurements

source_name: Bone marrow

growth_protocol: Bone marrow cells were isolated from femurs and tibias of MK2 WT and MK2 KO mice and grown in IMDM supplemeted with 10ng/ml murine M-CSF. On day 7 after seeding, cells were detached using 5mM EDTA in PBS w/o Ca and Mg, and replated in IMDM with 10% FBS and P/S.

extract_protocol:
RNA extration was obtained using TRIzol (Invitrogen) and further purfied using the Rneasy Mini Kit (Qiagen)
Libraries were prepared for sequencing using the Kapa Hyperprep kit for 40 bp single-end sequencing with 8+8 nucleotide indexes

treatment_protocol: To induce polarization, cells were either unstimulated or treated wit 10ng/ml murine IL-4 to obtain M0 and M2 cells respectively  and harvested 24h post-stimulation.

value: Bone marrow

value: M2 macrophage

tag: strain

value: MK2 KO


title: MK2 KO M2 macrophage_rep 6


title: MK2 KO M2 macrophage_rep 4


title: RNAseq patient 22 MRD


title: MK2 KO M2 macrophage_rep 3


title: RNAseq patient 23 MRD


title: WT2


title: 031016_Cell21-B4

description: Leftover clinical sample read as normal


title: MK2 KO M0 macrophage_rep 6

value: M0 macrophage


title: MK2 KO M2 macrophage_rep 2


title: 031016_Cell22-D4

description: Leftover clinical sample read as normal


title: MK2 KO M0 macrophage_rep 5


title: 031016_Cell23-A5

description: Leftover clinical sample read as normal


title: 031016_Cell24-B5

description: Leftover clinical sample read as normal


title: 031016_Cell20-A4

description: Leftover clinical sample read as normal


title: MK2 KO M0 macrophage_rep 3


title: RNAseq patient 20 MRD


title: 031016_Cell2-B1

description: Leftover clinical sample read as normal


title: RNAseq patient 21 MRD


title: MK2 KO M0 macrophage_rep 1


title: 031016_Cell17-E3

description: Leftover clinical sample read as normal


title: RNAseq patient 19 MRD


title: MK2 WT M2 macrophage_rep 6

value: MK2 WT


title: MK2 WT M2 macrophage_rep 5


title: 031016_Cell16-D3

description: Leftover clinical sample read as normal


title: MK2 WT M2 macrophage_rep 4


title: RNAseq patient 24 MRD

value: high-risk


title: RNAseq patient 18 MRD


title: MK2 KO M0 macrophage_rep 4


title: MK2 WT M2 macrophage_rep 2


title: MK2 WT M2 macrophage_rep 1


title: 031016_Cell14-B3

description: Leftover clinical sample read as normal


title: RNAseq patient 16 MRD


title: MK2 WT M0 macrophage_rep 5


title: 031016_Cell13-A3

description: Leftover clinical sample read as normal


title: RNAseq patient 17 MRD


title: 031016_Cell12-G2

description: Leftover clinical sample read as normal


title: MK2 WT M0 macrophage_rep 6


title: RNAseq patient 14 MRD


title: MK2 WT M0 macrophage_rep 3


title: RNAseq patient 15 MRD


title: MK2 WT M0 macrophage_rep 4


title: 031016_Cell11-F2

description: Leftover clinical sample read as normal


title: RNAseq patient 13 MRD


title: Sample L3: Stem Grandis 20°C

city: Campinas

first: Paulo

last: Mazzafera

state: Sao Paulo

address: Rua Monteiro Lobato

department: Plant Physiology

country: Brazil

institute: State University of Campinas

data_processing:
Next generation sequencing enables uncover the effects of high and low temperature and carbon dioxide in two eucalyptus species
Purpose: The use of Next generation sequence (NGS) analysis aiming to understand  changes in the expression of genes related with biosynthesis and remodeling of the cell wall, as well as genes related with carbon partitioning and hormonal regulation.
Methods: Eucalyptus stem of 35-day-old plants profile were generated by deep sequencing, in triplicate, using Illumina platform HISEQ2500 . It was considered the larger splicing variant of each loci using Bowtie2 program (Langmead and Salzberg 2012).  Avadis NGS software (Thermo Fisher) was used to visualize and analyze mapped reads. P-values (p <0,05) were calculated using the DESeq statistical method, which is based on the negative binomial distribution with variance and mean linked by local regression. For gene differential expression we used Moderate t-Test and One-way ANOVA. Multiple test correction was done using Benjamini Hochberg FDR (false discovery rate)
Results: There was an upregulation of ethylene and auxin biosynthetic genes in both species, but it was stronger under high and low temperature in E.globulus. Temperature was more effective to change cell wall biosynthetic genes than CO2 and CO2 stimulated lignin biosynthetic pathway. We also analyzed lignin composition and structure. There was an increase in F5H and COMT expression and the S/G ratio also increased under high CO2 in E.globulus. Thus, the species responded differently to treatments and stem composition and development was highly affected by temperature and CO2 concentration
Conclusion: In general our analysis using different temperatures, from low to high, associated with high CO2, as suggested in some global warming scenarios, showed an intense and diverse changes in cell wall related genes. Whether these scenarios will be confirmed or not, or in which degree and proportions changes in the temperature and atmospheric CO2 will happen is a matter of discussion, but certainly woody plants will change cell wall composition and the content of its components. Our results showed that temperature induced more genes related to cell wall formation in both species studied here and eCO2 genes related to lignin biosynthesis.
Genome_build: PhytozomeV10: Egrandis_201_v1
Supplementary_files_format_and_content: Matrix table with gene fold change for every comparisons between treatments for both species

organism: Eucalyptus grandis

source_name: eucalyptus grandis stem

growth_protocol: Six-months-old seedlings of Eucalyptus grandis and E. globulus (seedlings produced from clonal seeds obtained from Sementes Caiçara – Brazil, www.sementescaicara.com) were used in this experiment. They were grown in 1 L plastic pots containing a mixture of soil and vermiculite (2:1, V/V) and maintained under greenhouse conditions (mean air temperature of 25°C and a relative humidity of 73%).

extract_protocol:
Stem total RNA were extracted using CTAB protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the seedlings reached approximately 25 cm in height they were transferred to growth chambers and left to acclimate for one week before the temperature and CO2 treatments. At this time, they had 5-6 fully expanded leaves. The chambers were adjusted for 10 h of light, which was provided by a set of blue and red light-emitting diodes (LED, 280 µmol photons m2.s-1 at the top of the plants) positioned 30 cm above the seedlings. We combined three temperatures (10-12°C -  low, 22-24°C - normal, 33-35°C - high) with two CO2 concentrations (390 ppm - normal and 700 ppm - elevated). The plants were maintained 35 days in these conditions. A cylinder with pure CO2 was used to attain 700 ppm. The gas flow was controlled with a microvalve and we used an Infra-Red Gas Analyzer for calibration of the CO2 inside the chamber (Licor 6400 model). The temperatures were set with cooling and heating systems placed inside the chamber. The air circulation inside of the chambers was provided by two small fans positioned in opposite sides of the chamber (1.5 m x 3.0 m x 2.2 m, W x L x H). We named as control treatments those plants growing at 22oC and ambient CO2, which varied between 380-390 ppm. Plants were watered every second day. They were maintained for five weeks under these conditions.

value: stem

value: controle temperature


title: 031016_Cell10-E2

first: Nathan

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

description: Leftover clinical sample read as normal

source_name: sorted bone marrow macrophages


title: Sample L1: Stem Grandis 20°C


title: Sample L2: Stem Grandis 20°C


title: 031016_Cell15-C3

description: Leftover clinical sample read as normal


title: MK2 WT M2 macrophage_rep 3


title: MK2 KO M0 macrophage_rep 2


title: RNAseq patient 12 MRD


title: 031016_Cell1-A1

description: Leftover clinical sample read as normal


title: RNAseq patient 11 MRD


title: MK2 WT M0 macrophage_rep 1


title: MK2 WT M0 macrophage_rep 2


title: Sample J3: Stem Grandis CO2 20°C

value: carbon dioxide control temperature


title: 020717_Cell9-B2

description: New onset SJIA patient


title: Sample J1: Stem Grandis CO2 20°C


title: Sample J2: Stem Grandis CO2 20°C


title: RNAseq patient 10 MRD


title: 020717_Cell8-A2

description: New onset SJIA patient


title: Sample F3: Stem Grandis 30°C

value: high temperature


title: Sample F2: Stem Grandis 30°C


title: 020717_Cell75-G12

description: New onset SJIA patient


title: RNAseq patient 9 MRD


title: MK2 KO M2 macrophage_rep 1


title: Sample E3: Stem Grandis CO2 30°C

value: carbon dioxide high temperature


title: RNAseq patient 8 MRD


title: Sample E2: Stem Grandis CO2 30°C


title: Sample F1: Stem Grandis 30°C


title: Sample E1: Stem Grandis CO2 30°C


title: Sample D3: Stem Grandis CO2 10°C

value: carbon dioxide low temperature


title: RNAseq patient 7 MRD


title: Sample D2: Stem Grandis CO2 10°C


title: 020717_Cell70-A12

description: New onset SJIA patient

value: Macrophage (CD14+CD163+)


title: Sample C2: Stem Grandis 10°C

value: low temperature


title: Sample C3: Stem Grandis 10°C


title: 020717_Cell7-H1

description: New onset SJIA patient


title: RNAseq patient 6 MRD


title: Sample D1: Stem Grandis CO2 10°C


title: RNAseq patient 5 MRD_2


title: 020717_Cell68-G11

description: New onset SJIA patient


title: Sample C1: Stem Grandis 10°C


title: RNAseq patient 5 MRD_1


title: 020717_Cell71-B12

description: New onset SJIA patient


title: RNAseq patient 4 MRD


title: 020717_Cell73-D12

description: New onset SJIA patient


title: N39

city: shanghai

first: Qingshan

last: Chen

address: Changhai road 255

institute: Third Affiliated Hospital of Second Military Medical University

description: all.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: normal liver

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard IonPronton protocols

treatment_protocol: Male Wistar rats (180 g ± 20 g) were randomly divided into four groups (n=8 per group) as follows: 1) normal group, 2) model group, 3) 25 mg/kg Schisandrin B (Sch B) group (CCl4+ Sch B 25 mg/kg), and 4) 50 mg/kg Sch B group (CCl4+ Sch B 50 mg/kg). Liver fibrosis model was induced by CCl4(50% CCl4/olive oil; 2 mL/kg) thrice a week for 8 weeks. In Sch B-treated group, the rats were administered CCl4 for 4 weeks and then administered Sch B at a dose of 25 or 50 mg/kg daily, respectively, together with CCl4 gavage for another 4 weeks. The rats in normal group were treated with equal volume of olive oil instead of CCl4 as sham control.

value: liver

value: Wistar rat

tag: treatment time

value: 8 weeks


title: N24

description: all.counts.exp.txt

source_name: Liver fibrosis liver

value: liver fibrosis


title: N37

description: all.counts.exp.txt


title: N32

description: all.counts.exp.txt


title: RNAseq patient 3 MRD

value: standard-risk


title: 020717_Cell67-F11

description: New onset SJIA patient


title: N36

description: all.counts.exp.txt


title: 020717_Cell66-E11

description: New onset SJIA patient


title: N20

description: all.counts.exp.txt

source_name: Schisandrin B treated liver

value: Schisandrin B treated liver


title: 020717_Cell65-D11

description: New onset SJIA patient


title: RNAseq patient 2 MRD

source_name: Tumor plasma cells


title: N23

description: all.counts.exp.txt


title: 020717_Cell64-C11

description: New onset SJIA patient


title: 020717_Cell63-A11

description: New onset SJIA patient


title: RNAseq patient 40 diagnosis


title: RNAseq patient 39 diagnosis