title: sup45-ts_25C_rep1_RNAseq

city: Worcester

first: Kotchaphorn

last: Mangkalaphiban

state: MA

address: 368 Plantation St.

institute: University of Massachusetts Medical School

data_processing:
For ribosome profiling, de-multiplexed sequences were first processed by cutadapt (Martin, 2011) to filter out low quality reads and read lengths shorter than 23 nt while trimming adapter sequences (cutadapt -a TGGAATTCTCGGGTGCCAAGG -q 10 --trim-n -m 23). Reads aligned to non-protein coding sequences were discarded (bowtie -m 100 -3 4 -5 4 -n 2 -l 15 --un) and PCR duplicates were removed based on the 4-mer barcodes on either end of the reads. Reads were aligned to transcriptome using bowtie (Langmead et al., 2009) with settings -m 10 -n 2 -l 15 -S --best --strata and transcript levels were quantified using RSEM ((Li and Dewey, 2011)) with settings --seed-length 15 --bowtie-m 10.
Aligned ribosome profiling reads were further processed in R. Reads were counted by region of mRNAs based on the position of the P-site of the read and normalized to the length of the region to give ribosome density for each region. Readthrough efficiency was computed by dividing the ribosome density in the extension (region between canonical stop and first downstream stop in the 3'-UTR) to ribosome density in the coding region.
For RNA-Seq, RSEM program (Li and Dewey, 2011) was used to map the sequence reads to the transcriptome and to quantify individual transcript levels with settings --bowtie-m 10.
Genome_build: R64-2-1 S288C sacCer3 genome assembly (S288C_reference_genome_R64-2-1_20150113)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (output of RSEM)
Supplementary_files_format_and_content: tab-delimited text files include read count of frame 0 footprint in different mRNA regions and readthrough efficiency value for each transcript in each sample

organism: Saccharomyces cerevisiae W303

growth_protocol: Cells were grown in 1 L of YPD at 25°C until OD600 of the culture reached 0.6-0.8, at which a temperature shift was performed. Cells were harvested by rapid vacuum filtration, flash frozen in liquid nitrogen, and stored in -80°C until RNA extraction.

extract_protocol:
For ribosome profiling, lysates were digested with RNaseI and ribosomes were isolated over 1 M sucrose cushion. RNAs were isolated from ribosomes (for ribosome profiling) or from lysates (for RNA-seq) using the miRNeasy kit (QIAgen, #217004).
For ribosome profiling, ribosomal RNAs were depleted using the Yeast Ribo-Zero Gold rRNA removal kit (Illumina, #MRZY1324) and sequencing library was prepared using the NEXTFlex Small RNA-Seq Kit v3 (BIOO Scientific, #NOVA-5132-06). For RNA-seq, total RNAs were treated with BaselineZero DNase, depleted of rRNAs using the Yeast Ribo-Zero Gold rRNA removal kit (Illumina, #MRZY1324), then the sequencing library was prepared using the TruSeq Stranded mRNA sample prep kit (Illumina, #RS-122-2101)

treatment_protocol: A temperature shift was performed as follows: Cells were collected by centrifugation, resuspended in 400 ml of fresh YPD media, transferred to a new flask, and incubated in a 25°C water bath with shaking. After 20 min of incubation, 400 ml of pre-warmed YPD prewarmed to 57°C (mock: 25°C) were added to the flask, and cells were incubated in a 37°C (mock: 25°C) water bath for 30 minutes.

tag: background

tag: genotype

value: Mock temperature shift


title: sup45-ts_25C_rep2_RNAseq

status: Public on Dec 08 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: sup45-ts_37C_rep1_RNAseq

value: Temperature shift from 25°C to 37°C


title: SUP45_37C_rep2_RNAseq

value: Wild-type


title: SUP45_25C_rep2_RNAseq


title: SUP45_37C_rep1_RNAseq


title: CRLOSKM72HS2

city: Birmingham

first: Kejin

last: Hu

state: AL

address: 1825 University Blvd.

department: Department of Biochemistry and Molecular Genetics

institute: UAB School of Medicine

description: Transduced with the four reprogramming factors OSKM lentiviral preparation, RNA extracted 72 hours post transduction

data_processing:
Pre-alignment quality assessments of the raw fastq sequences were carried out using FastQC (version 0.11.7) (Andrews, 2010). The raw fastq sequences were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28). The alignments were carried out using STAR (version 2.7.1a) (Dobin et al 2013) with default parameters. Post-alignment quality assessments were carried out with RSeQC (version 2.6.3) (Wang et al 2012) and MultiQC (version 1.4) (Ewels et al 2016). Samtools (version 0.0.19) (Li et al 2009) and IGV (version 2.6.2) (Thorvaldsdóttir et al 2013) were used for indexing and viewing the alignments respectively. Gene expression was quantified as gene level counts using the htseq-count function (version 0.12.3) (Anders et al 2015); the Ensembl gene annotations for the human genome were used (genebuild-last-updated 2019-06). The htseq-count default parameters were used. Differentially expressed genes were identified using DESeq2 (version 1.28) (Love et al 2014). DESeq2 was run with default parameters (Love et al 2014).
Genome_build: The human hg38 reference genome (GenBank assembly accession: GCA_000001405.28).
Supplementary_files_format_and_content: excel file containing deseq2 normalized gene expression for each gene in each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: newborn skin, male

growth_protocol: human ESCs were grown in feeder-free/serum-free chemically defined E8 meium: E8 medium (pH 7.4) for iPSC maintenance: DMEM/nutrient mixture F-12 (F-12) (DMEM/F-12), 1.74 g/L NaHCO3, 1 g/L sodium chloride, 64 mg/L L-ascorbic acid 2-phosphate sesquimagnesium (see Note 6), 13.6 µg/L sodium selenium, 4 ng/mL FGF2, 20 μg/mL insulin, 10 μg/mL transferrin, and 2 μg/L TGFβ1 . Human fibroblasts were grown in fibroblast medium: Fibroblast growth medium: Dulbecco's Modified Eagle Medium (DMEM) with high glucose, supplemented with 10% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 1x penicillin-streptomycin (100 U/mL penicillin and 100 ug/mL streptomycin), 0.1 mM Minimum Essential Medium (MEM) Non-Essential Amino Acids (NEAA), and 4 ng/mL human basic fibroblast growth factor (bFGF, also known as FGF2)

extract_protocol:
RNA was isolated using TRIzol™ Reagent (Invitrogen, Cat. 15596026) followed by DNA digestion with DNAseI (Thermo Fisher Scientific, Cat. AM2222) and a cleanup step using Quick-RNA Miniprep (Zymo Research, Cat. R1054). RNA concentration was determined using Nanodrop spectrophotometer (Thermo Fisher Scientific).
Sequencing library was constructed by BGI using its protocol (Document #, SOP-SS-027; Version #, A0, Effective date: 2018-06-11)PolyA mRNA was purified from total RNA using the oligo(T) attached to magentic beads. The mRNA was then fragmented.  cDNA was then generated using random hexamer-primerd reverse transcription followed by the second-strand cDNA synthesis. The synthesized cDNA was then subject to end-repair, and 3' adenylated. Adapters were then ligated to the ends of these 3' adenylated cDNA fragments. The cDNA was further PCR amplified. The amplified cDNA was purified with Ampure XP Beads. The library was validated on the Agilent 2100 bioanalyzer. The double strand PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circular DNA were formated as the final library.
RNA-seq using nanoball technology, sequening was conducted by BGI

treatment_protocol: fibroblasts were transduced with the reprogramming factors OCT4, SOX2, KLF4 and MYC. RNA was extracted at  the indicated time post transduction (48 hours, 72 hours, and 96 hours). Lentiviral titers used were OCT4, 8; SOX2, 5; KLF4, 5; MYC, 3.

tag: cell line

value: CCD-1079Sk, ATCC Cat# is CRL-209

tag: time

value: 72 hours post transduction

tag: growth protocol

value: grown in fibroblast media


title: SUP45_25C rep1_RNAseq


title: sup45-ts_37C_rep1_Riboseq

data_processing:
Library strategy: Ribo-Seq
For ribosome profiling, de-multiplexed sequences were first processed by cutadapt (Martin, 2011) to filter out low quality reads and read lengths shorter than 23 nt while trimming adapter sequences (cutadapt -a TGGAATTCTCGGGTGCCAAGG -q 10 --trim-n -m 23). Reads aligned to non-protein coding sequences were discarded (bowtie -m 100 -3 4 -5 4 -n 2 -l 15 --un) and PCR duplicates were removed based on the 4-mer barcodes on either end of the reads. Reads were aligned to transcriptome using bowtie (Langmead et al., 2009) with settings -m 10 -n 2 -l 15 -S --best --strata and transcript levels were quantified using RSEM ((Li and Dewey, 2011)) with settings --seed-length 15 --bowtie-m 10.
Aligned ribosome profiling reads were further processed in R. Reads were counted by region of mRNAs based on the position of the P-site of the read and normalized to the length of the region to give ribosome density for each region. Readthrough efficiency was computed by dividing the ribosome density in the extension (region between canonical stop and first downstream stop in the 3'-UTR) to ribosome density in the coding region.
For RNA-Seq, RSEM program (Li and Dewey, 2011) was used to map the sequence reads to the transcriptome and to quantify individual transcript levels with settings --bowtie-m 10.
Genome_build: R64-2-1 S288C sacCer3 genome assembly (S288C_reference_genome_R64-2-1_20150113)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (output of RSEM)
Supplementary_files_format_and_content: tab-delimited text files include read count of frame 0 footprint in different mRNA regions and readthrough efficiency value for each transcript in each sample


title: sup45-ts_37C_rep2_Riboseq


title: sup45-ts_25C_rep1_Riboseq


title: SUP45_37C_rep2_Riboseq


title: SUP45_25C_rep2_Riboseq


title: SUP45_25C rep1_Riboseq


title: sup45-ts_37C_rep2_RNAseq


title: SUP45_37C_rep1_Riboseq


title: ALKKO_rep2_RRBS

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

library_source: genomic

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://github.com/DanieleBarreca/picard/)
Reads were quality-controlled using fastQC (106) and pre-processed using trimgalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to trim adapter and low quality sequences.
Reads were aligned to mouse genome (mm10) and processed further using STAR (107).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: thymocytes

extract_protocol:
RNA and DNA were isolated using the QIAGEN AllPrep DNA/RNA mini isolation kit to enable simultaneous isolation of nucleic acids from the same specimen. Tissues were homogenized using EPPI-Mikropistills (Schuett-biotec) and RNA and DNA isolation was performed according to the manufacturer’s protocol. RNA and DNA were eluted in nuclease free ddH2O.
Standard Illumina protocol

tag: age

value: 21 weeks

value: NPM-ALK+, DNMT1 fl/fl CD4-CRE

tag: Sex

value: male

tag: cell type

value: thymocytes


title: ALKKO_rep3_RRBS

value: 19 weeks


title: ALKKO_rep1_RRBS

value: 25 weeks


title: ALK_rep2_RRBS

source_name: T cell lymphoma cells

value: 22 weeks

value: NPM-ALK+

value: T cell lymphoma cells


title: ALK_rep1_RRBS

value: 24 weeks


title: wt_rep1_RRBS

value: DNMT1 fl/fl


title: KO_rep1_RRBS

value: 20 weeks

value: DNMT1 fl/fl CD4-CRE


title: KO_rep2_RRBS

value: female


title: wt_rep3_RRBS


title: KO_rep3_RRBS


title: wt_rep2_RRBS


title: ALK_rep3_RRBS

value: 31 weeks


title: ALKKO_rep2_RNA

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://github.com/DanieleBarreca/picard/)
Reads were quality-controlled using fastQC (106) and pre-processed using trimgalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to trim adapter and low quality sequences.
Reads were aligned to mouse genome (mm10) and processed further using STAR (107).
Differential gene expression levels of the transcripts were quantified by HTSeq (108) and analyzed using the Bioconductor package DESeq2 (109).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file reports abundance measurements


title: KO_rep1_RNA


title: ALK_rep2_RNA


title: ALK_rep3_RNA


title: KO_rep3_RNA


title: ALK_rep1_RNA


title: ALKKO_rep1_RNA


title: wt_rep3_RNA


title: sup45-ts_25C_rep2_Riboseq

value: Mock temperature shift


title: KO_rep2_RNA


title: wt_rep1_RNA


title: wt_rep2_RNA


title: ALKKO_rep3_RNA


title: Diffuse midline glioma, K27M mutant, Case 78

type: genomic

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: BRAF and FGFR1 WT

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting

data_processing: 'preprocessIllumina',  R package minfi v1.32.0

label: Cy3, Cy5

source_name: genomic DNA of a diffuse midline glioma, K27M mutant

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA isolation from FFPE tissue, 10 x 10 µm sections were cut and DNA isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, either the HumanMethylation450 BeadChip array or the Infinium MethylationEPIC BeadChip Kit (both Illumina) were used to quantify the methylation status of 450,000 or 850,000 CpG sites, respectively, on an iScan device (Illumina).

tag: tumor entity

value: Diffuse midline glioma, K27M mutant

tag: age (years)

tag: methylation score

tag: histology


title: Diffuse midline glioma, K27M mutant, Case 13

description: FGFR1 MU


title: Diffuse midline glioma, K27M mutant, Case 48

description: BRAF and FGFR1 WT

value: MG


title: Diffuse midline glioma, K27M mutant, Case 33

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 4

description: FGFR1 MU


title: Diffuse midline glioma, K27M mutant, Case 41

description: FGFR1 MU


title: Diffuse midline glioma, K27M mutant, Case 56

description: BRAF MU


title: Diffuse midline glioma, K27M mutant, Case 73

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 69

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 79

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 40

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 72

description: BRAF and FGFR1 WT


title: SLE_P85_T0

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

description: Patient 85 Timepoint 0

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: DNA methylation data analysis was performed in the R statistical computing environment (v.3.6.3). Raw .idat files were generated for each sample and read into the R package minfi (v.1.32.0) for quality control and downstream analysis. Probes with less than three beads and zero intensity values across all samples were removed according to best practices as implemented by the DNAmArraypackage (v.0.1.1). Then, background signal and dye bias were corrected followed by normalization of signal intensities using functional normalization in the preprocessFunnorm.DNAmArray function. This method uses the first three principal component values calculated from signal intensities of control probes present on all array spots to correct for technical variation. Probes with detection P-values < 0.01 were removed as were probes that returned signal intensities in fewer than 98% of samples. Signal intensities were then converted to M-values with a maximum bound of ±16. We masked any probes with potential technical issues if the probe met any one of the following criteria described by Zhou, Laird & Shen (2017): A unique probe sequence of less than 30bp, mapping to multiple sites in the genome, polymorphisms that cause a color channel switching in type I probes, inconsistencies in specified reporter color channel and extension base, mapping to the Y chromosome, and/or having a polymorphism within 5bp of the 3’ end of the probe with a minor allele frequency (MAF) > 1% with exception of CpG-SNPs with C>T polymorphisms which we retained for analysis. Batch correction was performed using the ComBatfunction in the sva (v.3.34.0) package.

label: Cy5 and Cy3

source_name: Neutrophil DNA

label_protocol: standard protocol

extract_protocol: Whole blood was collected from each patient at each time point during clinic visits in vials containing EDTA. Granulocyte fractions were isolated using density centrifugation with Ficoll-Histopaque (GE Healthcare, Chicago, IL, USA). Genomic DNA was isolated from the enriched granulocyte layer using either phenol-chloroform extraction or Qiagen DNEasy Blood and Tissue kit (Qiagen, Germantown, MD, USA), or following the removal of red blood cells using dextran (Sigma-Aldrich, St. Lois, MS, USA) and hypotonic lysis. DNA was eluted in water and quantified using Qubit DNA fluorescence quantification assays (Thermo-Fisher, Waltham, MA, USA). 350ng of DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo, Irvine, CA, USA) following the manufacturer’s instructions.

value: Neutrophil

tag: disease

value: Lupus

value: Female

tag: ancestry

value: African-American

tag: sledai score


title: Diffuse midline glioma, K27M mutant, Case 68

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 76

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 77

description: BRAF and FGFR1 WT


title: SLE_P85_T5

description: Patient 85 Timepoint 5


title: SLE_P88_T2

description: Patient 88 Timepoint 2


title: SLE_P85_T1

description: Patient 85 Timepoint 1


title: SLE_P85_T4

description: Patient 85 Timepoint 4


title: Diffuse midline glioma, K27M mutant, Case 64

description: BRAF and FGFR1 WT


title: SLE_P88_T3

description: Patient 88 Timepoint 3


title: SLE_P85_T2

description: Patient 85 Timepoint 2


title: Diffuse midline glioma, K27M mutant, Case 71

description: BRAF and FGFR1 WT


title: SLE_P88_T0

description: Patient 88 Timepoint 0


title: Diffuse midline glioma, K27M mutant, Case 28

description: BRAF and FGFR1 WT


title: SLE_P85_T3

description: Patient 85 Timepoint 3


title: Diffuse midline glioma, K27M mutant, Case 43

description: BRAF and FGFR1 WT


title: Diffuse midline glioma, K27M mutant, Case 7

description: BRAF and FGFR1 WT


title: SLE_P84_T2

description: Patient 84 Timepoint 2


title: SLE_P88_T1

description: Patient 88 Timepoint 1


title: SLE_P84_T1

description: Patient 84 Timepoint 1


title: SLE_P83_T0

description: Patient 83 Timepoint 0


title: SLE_P82_T0

description: Patient 82 Timepoint 0


title: SLE_P84_T0

description: Patient 84 Timepoint 0


title: SLE_P76_T3

description: Patient 76 Timepoint 3


title: SLE_P83_T1

description: Patient 83 Timepoint 1


title: SLE_P72_T3

description: Patient 72 Timepoint 3


title: SLE_P83_T2

description: Patient 83 Timepoint 2


title: SLE_P76_T0

description: Patient 76 Timepoint 0


title: SLE_P82_T1

description: Patient 82 Timepoint 1


title: SLE_P71_T4

description: Patient 71 Timepoint 4


title: SLE_P77_T2

description: Patient 77 Timepoint 2

value: European-American


title: SLE_P77_T1

description: Patient 77 Timepoint 1


title: SLE_P71_T5

description: Patient 71 Timepoint 5


title: SLE_P75_T1

description: Patient 75 Timepoint 1


title: SLE_P72_T1

description: Patient 72 Timepoint 1


title: SLE_P75_T2

description: Patient 75 Timepoint 2


title: SLE_P71_T6

description: Patient 71 Timepoint 6


title: SLE_P72_T4

description: Patient 72 Timepoint 4


title: SLE_P75_T0

description: Patient 75 Timepoint 0


title: SLE_P76_T2

description: Patient 76 Timepoint 2


title: SLE_P71_T3

description: Patient 71 Timepoint 3


title: SLE_P71_T8

description: Patient 71 Timepoint 8


title: SLE_P77_T0

description: Patient 77 Timepoint 0


title: SLE_P71_T0

description: Patient 71 Timepoint 0


title: SLE_P72_T2

description: Patient 72 Timepoint 2


title: SLE_P71_T7

description: Patient 71 Timepoint 7


title: SLE_P76_T1

description: Patient 76 Timepoint 1


title: SLE_P72_T0

description: Patient 72 Timepoint 0


title: SLE_P71_T1

description: Patient 71 Timepoint 1


title: SLE_P69_T4

description: Patient 69 Timepoint 4


title: SLE_P69_T1

description: Patient 69 Timepoint 1


title: SLE_P71_T2

description: Patient 71 Timepoint 2


title: SLE_P70_T0

description: Patient 70 Timepoint 0


title: SLE_P69_T0

description: Patient 69 Timepoint 0


title: SLE_P69_T3

description: Patient 69 Timepoint 3


title: SLE_P69_T2

description: Patient 69 Timepoint 2


title: SLE_P68_T2

description: Patient 68 Timepoint 2


title: SLE_P70_T1

description: Patient 70 Timepoint 1


title: SLE_P67_T3

description: Patient 67 Timepoint 3


title: SLE_P68_T4

description: Patient 68 Timepoint 4


title: SLE_P68_T1

description: Patient 68 Timepoint 1


title: SLE_P67_T4

description: Patient 67 Timepoint 4


title: SLE_P67_T1

description: Patient 67 Timepoint 1


title: SLE_P67_T0

description: Patient 67 Timepoint 0


title: SLE_P57_T0

description: Patient 57 Timepoint 0


title: SLE_P67_T2

description: Patient 67 Timepoint 2


title: SLE_P60_T1

description: Patient 60 Timepoint 1


title: SLE_P63_T4

description: Patient 63 Timepoint 4


title: SLE_P63_T1

description: Patient 63 Timepoint 1


title: SLE_P67_T5

description: Patient 67 Timepoint 5


title: SLE_P62_T1

description: Patient 62 Timepoint 1


title: SLE_P63_T3

description: Patient 63 Timepoint 3


title: SLE_P60_T2

description: Patient 60 Timepoint 2


title: SLE_P63_T2

description: Patient 63 Timepoint 2


title: SLE_P62_T0

description: Patient 62 Timepoint 0


title: SLE_P68_T0

description: Patient 68 Timepoint 0


title: SLE_P55_T1

description: Patient 55 Timepoint 1


title: SLE_P63_T0

description: Patient 63 Timepoint 0


title: SLE_P60_T0

description: Patient 60 Timepoint 0


title: SLE_P57_T2

description: Patient 57 Timepoint 2


title: SLE_P55_T0

description: Patient 55 Timepoint 0


title: SLE_P57_T1

description: Patient 57 Timepoint 1


title: SLE_P53_T0

description: Patient 53 Timepoint 0


title: SLE_P52_T0

description: Patient 52 Timepoint 0


title: SLE_P53_T1

description: Patient 53 Timepoint 1


title: SLE_P52_T1

description: Patient 52 Timepoint 1


title: SLE_P49_T1

description: Patient 49 Timepoint 1


title: SLE_P46_T2

description: Patient 46 Timepoint 2


title: SLE_P49_T0

description: Patient 49 Timepoint 0


title: SLE_P43_T2

description: Patient 43 Timepoint 2


title: SLE_P42_T0

description: Patient 42 Timepoint 0


title: SLE_P68_T3

description: Patient 68 Timepoint 3


title: SLE_P46_T0

description: Patient 46 Timepoint 0


title: SLE_P45_T2

description: Patient 45 Timepoint 2


title: SLE_P51_T2

description: Patient 51 Timepoint 2


title: SLE_P51_T0

description: Patient 51 Timepoint 0


title: SLE_P43_T3

description: Patient 43 Timepoint 3


title: SLE_P42_T1

description: Patient 42 Timepoint 1


title: SLE_P52_T2

description: Patient 52 Timepoint 2


title: SLE_P39_T0

description: Patient 39 Timepoint 0


title: SLE_P43_T0

description: Patient 43 Timepoint 0


title: SLE_P39_T1

description: Patient 39 Timepoint 1


title: SLE_P41_T0

description: Patient 41 Timepoint 0


title: SLE_P41_T2

description: Patient 41 Timepoint 2


title: SLE_P51_T1

description: Patient 51 Timepoint 1


title: SLE_P43_T1

description: Patient 43 Timepoint 1


title: SLE_P39_T4

description: Patient 39 Timepoint 4


title: SLE_P41_T1

description: Patient 41 Timepoint 1


title: SLE_P45_T1

description: Patient 45 Timepoint 1


title: SLE_P46_T1

description: Patient 46 Timepoint 1


title: SLE_P46_T3

description: Patient 46 Timepoint 3


title: SLE_P45_T0

description: Patient 45 Timepoint 0


title: SLE_P39_T2

description: Patient 39 Timepoint 2


title: SLE_P38_T2

description: Patient 38 Timepoint 2


title: SLE_P38_T3

description: Patient 38 Timepoint 3


title: SLE_P39_T3

description: Patient 39 Timepoint 3


title: SLE_P38_T1

description: Patient 38 Timepoint 1


title: SLE_P35_T0

description: Patient 35 Timepoint 0


title: SLE_P36_T2

description: Patient 36 Timepoint 2


title: SLE_P36_T1

description: Patient 36 Timepoint 1


title: SLE_P36_T3

description: Patient 36 Timepoint 3


title: SLE_P38_T4

description: Patient 38 Timepoint 4


title: SLE_P37_T1

description: Patient 37 Timepoint 1


title: SLE_P31_T1

description: Patient 31 Timepoint 1


title: SLE_P30_T4

description: Patient 30 Timepoint 4


title: SLE_P36_T0

description: Patient 36 Timepoint 0


title: SLE_P31_T3

description: Patient 31 Timepoint 3


title: SLE_P30_T1

description: Patient 30 Timepoint 1


title: SLE_P37_T0

description: Patient 37 Timepoint 0


title: SLE_P30_T0

description: Patient 30 Timepoint 0


title: SLE_P29_T1

description: Patient 29 Timepoint 1


title: SLE_P28_T0

description: Patient 28 Timepoint 0


title: SLE_P38_T0

description: Patient 38 Timepoint 0


title: SLE_P30_T3

description: Patient 30 Timepoint 3


title: SLE_P28_T4

description: Patient 28 Timepoint 4


title: SLE_P30_T5

description: Patient 30 Timepoint 5


title: SLE_P29_T0

description: Patient 29 Timepoint 0


title: SLE_P27_T3

description: Patient 27 Timepoint 3


title: SLE_P28_T1

description: Patient 28 Timepoint 1


title: SLE_P30_T2

description: Patient 30 Timepoint 2


title: SLE_P28_T3

description: Patient 28 Timepoint 3


title: SLE_P35_T1

description: Patient 35 Timepoint 1


title: SLE_P31_T0

description: Patient 31 Timepoint 0


title: SLE_P28_T2

description: Patient 28 Timepoint 2


title: SLE_P27_T1

description: Patient 27 Timepoint 1


title: SLE_P31_T2

description: Patient 31 Timepoint 2


title: SLE_P26_T2

description: Patient 26 Timepoint 2


title: SLE_P27_T2

description: Patient 27 Timepoint 2


title: SLE_P24_T2

description: Patient 24 Timepoint 2


title: SLE_P24_T1

description: Patient 24 Timepoint 1


title: SLE_P26_T1

description: Patient 26 Timepoint 1


title: SLE_P23_T0

description: Patient 23 Timepoint 0


title: SLE_P26_T0

description: Patient 26 Timepoint 0


title: SLE_P23_T5

description: Patient 23 Timepoint 5


title: SLE_P23_T7

description: Patient 23 Timepoint 7


title: SLE_P23_T8

description: Patient 23 Timepoint 8


title: SLE_P21_T6

description: Patient 21 Timepoint 6


title: SLE_P23_T3

description: Patient 23 Timepoint 3


title: SLE_P27_T0

description: Patient 27 Timepoint 0


title: SLE_P21_T8

description: Patient 21 Timepoint 8


title: SLE_P21_T1

description: Patient 21 Timepoint 1


title: SLE_P21_T9

description: Patient 21 Timepoint 9


title: SLE_P23_T4

description: Patient 23 Timepoint 4


title: SLE_P21_T3

description: Patient 21 Timepoint 3


title: SLE_P27_T4

description: Patient 27 Timepoint 4


title: SLE_P24_T0

description: Patient 24 Timepoint 0


title: SLE_P23_T6

description: Patient 23 Timepoint 6


title: SLE_P21_T5

description: Patient 21 Timepoint 5


title: SLE_P20_T5

description: Patient 20 Timepoint 5


title: SLE_P23_T1

description: Patient 23 Timepoint 1


title: SLE_P21_T7

description: Patient 21 Timepoint 7


title: SLE_P23_T2

description: Patient 23 Timepoint 2


title: SLE_P20_T2

description: Patient 20 Timepoint 2


title: SLE_P21_T4

description: Patient 21 Timepoint 4


title: SLE_P21_T10

description: Patient 21 Timepoint 10


title: SLE_P20_T1

description: Patient 20 Timepoint 1


title: SLE_P21_T0

description: Patient 21 Timepoint 0


title: SLE_P21_T2

description: Patient 21 Timepoint 2


title: SLE_P19_T0

description: Patient 19 Timepoint 0


title: SLE_P19_T5

description: Patient 19 Timepoint 5


title: SLE_P20_T3

description: Patient 20 Timepoint 3


title: SLE_P19_T4

description: Patient 19 Timepoint 4


title: SLE_P17_T2

description: Patient 17 Timepoint 2


title: SLE_P20_T0

description: Patient 20 Timepoint 0


title: SLE_P20_T4

description: Patient 20 Timepoint 4


title: SLE_P17_T7

description: Patient 17 Timepoint 7


title: SLE_P19_T1

description: Patient 19 Timepoint 1


title: SLE_P19_T2

description: Patient 19 Timepoint 2


title: SLE_P11_T2

description: Patient 11 Timepoint 2


title: SLE_P19_T3

description: Patient 19 Timepoint 3


title: SLE_P17_T0

description: Patient 17 Timepoint 0


title: SLE_P17_T6

description: Patient 17 Timepoint 6


title: SLE_P17_T4

description: Patient 17 Timepoint 4


title: SLE_P15_T2

description: Patient 15 Timepoint 2


title: SLE_P17_T5

description: Patient 17 Timepoint 5


title: SLE_P17_T3

description: Patient 17 Timepoint 3


title: SLE_P15_T0

description: Patient 15 Timepoint 0


title: SLE_P18_T0

description: Patient 18 Timepoint 0


title: SLE_P11_T1

description: Patient 11 Timepoint 1


title: SLE_P15_T1

description: Patient 15 Timepoint 1


title: SLE_P17_T1

description: Patient 17 Timepoint 1


title: SLE_P18_T1

description: Patient 18 Timepoint 1


title: SLE_P11_T3

description: Patient 11 Timepoint 3


title: SLE_P10_T0

description: Patient 10 Timepoint 0


title: SLE_P10_T1

description: Patient 10 Timepoint 1


title: SLE_P10_T2

description: Patient 10 Timepoint 2


title: SLE_P10_T3

description: Patient 10 Timepoint 3


title: SLE_P11_T0

description: Patient 11 Timepoint 0


title: SLE_P6_T1

description: Patient 6 Timepoint 1


title: 04S050.04S7604_002

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

description:
04S7604_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Data were filtered using principal component analysis to remove outleirs.
Genome_build: hg19
Supplementary_files_format_and_content: text files that contain the  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using cufflinks 2.2.0

source_name: Remitting, untreated_PBMC

extract_protocol:
Total RNA was extracted from BALF\ and PBMC samples using Qiazol following Qiagen’s miRNeasy protocol (Qiagen 217004) and using QiaCube
cDNA libraries were made from 1ug of total RNA that had RNA Integrity Number (RINe) over 6.5 upon Poly-A selection using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Ambion 61021) and fragmentation using the AB Library Builder™ System (Life Technologies 4463592) with the Ion Total RNA-Seq Kit for AB Library Builder™ System (Life Technologies 4482416).

tag: phenotype group

value: Remitting, untreated

tag: scadding

value: I

tag: tissue

value: peripheral blood mononuclear cell


title: SLE_P10_T4

description: Patient 10 Timepoint 4


title: 03S083.03S7439_009

description:
03S7439_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: II


title: 05S023.05S7401_012RUN348

description:
05S7401_IonXpressRNA_012RUN348
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S104.03S7652_002

description:
03S7652_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: III


title: 03S086.03S7483_016

description:
03S7483_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P5_T6

description: Patient 5 Timepoint 6


title: SLE_P6_T0

description: Patient 6 Timepoint 0


title: 03S088.03S7490_008

description:
03S7490_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P4_T0

description: Patient 4 Timepoint 0


title: SLE_P4_T5

description: Patient 4 Timepoint 5


title: 03S006.03S7484_009

description:
03S7484_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P5_T1

description: Patient 5 Timepoint 1


title: SLE_P3_T0

description: Patient 3 Timepoint 0


title: SLE_P2_T1

description: Patient 2 Timepoint 1


title: SLE_P4_T4

description: Patient 4 Timepoint 4


title: SLE_P5_T3

description: Patient 5 Timepoint 3


title: SLE_P5_T0

description: Patient 5 Timepoint 0


title: SLE_P4_T3

description: Patient 4 Timepoint 3


title: 04S048.04S7470_010

description:
04S7470_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S085.03S7481_001

description:
03S7481_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P2_T7

description: Patient 2 Timepoint 7


title: SLE_P2_T6

description: Patient 2 Timepoint 6


title: SLE_P3_T1

description: Patient 3 Timepoint 1


title: SLE_P5_T4

description: Patient 5 Timepoint 4


title: SLE_P5_T7

description: Patient 5 Timepoint 7


title: 04S045.04S7381_009

description:
04S7381_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S021.03S7075_009

description:
03S7075_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S047.05S7661_015

description:
05S7661_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S036.05S7419_010

description:
05S7419_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S035.09S7587_010RUN287

description:
09S7587_IonXpressRNA_010RUN287
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P5_T5

description: Patient 5 Timepoint 5


title: SLE_P3_T2

description: Patient 3 Timepoint 2


title: 03S031.03S7223_015

description:
03S7223_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P2_T4

description: Patient 2 Timepoint 4


title: SLE_P4_T1

description: Patient 4 Timepoint 1


title: SLE_P2_T3

description: Patient 2 Timepoint 3


title: 03S068.03S7427_005

description:
03S7427_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S002.03S7068_015

description:
03S7068_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S024.05S7402_004

description:
05S7402_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S040.09S7592_002

description:
09S7592_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S013.03S7069_011

description:
03S7069_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S044.04S7382_005

description:
04S7382_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S096.03S7570_007

description:
03S7570_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S025.05S7403_001

description:
05S7403_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S051.03S7341_016

description:
03S7341_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P2_T5

description: Patient 2 Timepoint 5


title: 05S046.05S7537_006

description:
05S7537_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S016.09S7177_014

description:
09S7177_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S019.05S7116_007

description:
05S7116_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S024.09S7178_012

description:
09S7178_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S093.03S7565_005

description:
03S7565_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P2_T0

description: Patient 2 Timepoint 0


title: 06S036.06S7218_013

description:
06S7218_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P5_T2

description: Patient 5 Timepoint 2


title: SLE_P4_T2

description: Patient 4 Timepoint 2


title: 06S037.06S7320_001

description:
06S7320_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S098.03S7572_002

description:
03S7572_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S012.06S7131_011

description:
06S7131_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S031.06S7205_007

description:
06S7205_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P2_T2

description: Patient 2 Timepoint 2


title: 06S007.06S7126_005

description:
06S7126_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S010.04S7083_005

description:
04S7083_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S037.01S7547_001

description:
01S7547_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Acute Sarcoidosis, untreated_PBMC

value: Acute Sarcoidosis, untreated


title: 08S057.08S7265_006

description:
08S7265_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: SLE_P6_T2

description: Patient 6 Timepoint 2


title: 08S049.08S7153_014

description:
08S7153_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S014.09S7176_016

description:
09S7176_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S072.08S7371_013

description:
08S7371_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S081.03S7482_003

description:
03S7482_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S061.08S7276_014

description:
08S7276_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S057.03S7350_002

description:
03S7350_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S014.06S7133_005

description:
06S7133_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S055.03S7347_007

description:
03S7347_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S102.03S7578_010

description:
03S7578_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S022.03S7076_002

description:
03S7076_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S006.08S7156_001

description:
08S7156_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S010.06S7129_009

description:
06S7129_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S016.04S7096_005

description:
04S7096_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S040.01S7312_006

description:
01S7312_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Stage IV, untreated_PBMC

value: Stage IV, untreated

value: IV


title: 02S003.02S7052_012

description:
02S7052_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S092.03S7562_016

description:
03S7562_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S051.04S7460_015

description:
04S7460_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S069.03S7430_008

description:
03S7430_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S003.04S7080_001

description:
04S7080_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S011.03S7067_014

description:
03S7067_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S008.04S7087_009

description:
04S7087_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S073.08S7368_002

description:
08S7368_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S040.04S7389_001

description:
04S7389_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S094.03S7568_010

description:
03S7568_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Stage IV, treated_PBMC

value: Stage IV, treated


title: 04S011.04S7088_014

description:
04S7088_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S009.04S7086_001

description:
04S7086_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S026.03S7079_015

description:
03S7079_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S035.03S7227_011RUN302

description:
03S7227_IonXpressRNA_011RUN302
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S095.03S7569_011

description:
03S7569_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S067.08S7360_010

description:
08S7360_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S041.01S7546_004

description:
01S7546_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S056.04S7464_016

description:
04S7464_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S037.09S7590_011

description:
09S7590_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S039.05S7526_014

description:
05S7526_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S049.03S7236_010

description:
03S7236_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S087.03S7495_016

description:
03S7495_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S004.05S7101_012

description:
05S7101_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S028.05S7408_002

description:
05S7408_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S012.02S7056_014

description:
02S7056_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S103.03S7651_001

description:
03S7651_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Stage II-III, untreated_PBMC

value: Stage II-III, untreated


title: 08S051.08S7148_002

description:
08S7148_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S107.03S7656_007

description:
03S7656_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S014.03S7070_015

description:
03S7070_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S109.03S7658_003

description:
03S7658_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 10S002.10S7181_011

description:
10S7181_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S042.08S7272_009

description:
08S7272_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S001.02S7051_007

description:
02S7051_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S082.03S7438_004

description:
03S7438_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S063.04S7618_012

description:
04S7618_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S028.09S7583_007

description:
09S7583_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S032.04S7249_002

description:
04S7249_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S007.05S7102_006

description:
05S7102_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S078.08S7625_007

description:
08S7625_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S025.06S7139_014

description:
06S7139_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S034.03S7225_005

description:
03S7225_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S041.04S7385_012

description:
04S7385_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S015.03S7071_010

description:
03S7071_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S055.08S7279_003

description:
08S7279_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S012.09S7165_007

description:
09S7165_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S052.03S7343_005

description:
03S7343_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S033.01S7303_014

description:
01S7303_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S056.03S7348_006

description:
03S7348_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S011.02S7058_006

description:
02S7058_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S006.04S7094_013

description:
04S7094_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S018.02S7047_012

description:
02S7047_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S036.04S7392_015

description:
04S7392_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S048.03S7235_009

description:
03S7235_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S041.05S7531_014

description:
05S7531_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S034.06S7208_014

description:
06S7208_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S025.09S7169_003

description:
09S7169_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S011.06S7130_010

description:
06S7130_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S033.04S7255_003

description:
04S7255_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S022.04S7240_003

description:
04S7240_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S099.03S7574_009

description:
03S7574_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S001.06S7120_002

description:
06S7120_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S002.06S7121_001

description:
06S7121_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S005.04S7093_010

description:
04S7093_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S058.03S7352_012

description:
03S7352_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S025.03S7221_016

description:
03S7221_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S027.02S7290_004

description:
02S7290_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S013.06S7132_010

description:
06S7132_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S100.03S7655_001

description:
03S7655_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Stage II-III, treated_PBMC

value: Stage II-III, treated


title: 03S016.03S7072_012

description:
03S7072_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S005.09S7162_010

description:
09S7162_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S097.03S7571_015

description:
03S7571_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S024.03S7078_003RUN348

description:
03S7078_IonXpressRNA_003RUN348
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S014.04S7084_004

description:
04S7084_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S007.01S7025_008

description:
01S7025_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S013.02S7042_014

description:
02S7042_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S006.05S7106_006

description:
05S7106_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S016.05S7111_013

description:
05S7111_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S052.04S7605_005

description:
04S7605_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S036.03S7228_001

description:
03S7228_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S053.04S7479_016

description:
04S7479_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S018.03S7073_015

description:
03S7073_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S002.04S7091_012

description:
04S7091_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S019.02S7045_011

description:
02S7045_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S021.01S7039_003

description:
01S7039_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S017.01S7034_007

description:
01S7034_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S026.06S7200_005

description:
06S7200_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S007.08S7157_004

description:
08S7157_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S018.01S7032_002

description:
01S7032_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S013.01S7029_005

description:
01S7029_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S009.01S7026_007

description:
01S7026_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S002.01S7020_008RUN251

description:
01S7020_IonXpressRNA_008RUN251
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: RY-Mn-L-3

city: Haikou

first: Zhijian

last: Chen

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

country: China

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, USA)
The cDNA libraries of the three biological replicates were sequenced using an Illumina HiseqTM 4000 platform (Illumina, San Diego, USA) and paired-end, 150 nucleotide reads were generated
Remove contaminated Reads (the number of bases contaminated with Reads is greater than 5 bp. For double-stranded sequencing, if one end is affected Connector contamination, then remove both ends of the Reads). Remove low-quality Reads (Quality Q ≤ 19 bases in Reads account for more than 50% of total bases. For double-stranded sequencing, If one end has low quality Reads, both ends will be removed). Remove Reads containing more than 5% of N (for double-ended sequencing, if the ratio of N at one end is greater than 5%, both ends will be removed Reads)
The obtained clean reads were assembled into unigenes using the Trinity software with default parameters. The clean reads were mapped back to the assembled contigs by Bowtie2 v.2.2.3
As the genome sequence for stylo remains unavailable, all unigene sequences were aligned by BLAST search (E-value<1e-5) against the databases of the NCBI non-redundant protein sequences (Nr), the NCBI non-redundant nucleotide sequences (Nt), the Universal Protein (UniProt), the Gene Ontology (GO), the Clusters of Orthologous Groups of protein database (COG), the Functional Annotation (eggNOG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Protein Family (Pfam).
All unigene sequences were aligned by BLAST search (E-value<1e-5) against the databases of the NCBI non-redundant protein sequences (Nr), the NCBI non-redundant nucleotide sequences (Nt), the Universal Protein (UniProt), the Gene Ontology (GO), the Clusters of Orthologous Groups of protein database (COG), the Functional Annotation (eggNOG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Protein Family (Pfam).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Stylosanthes guianensis

source_name: Leaf

extract_protocol:
Total RNA from leaves of stylo with 5 and 400 μM Mn treatments were extracted using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. RNA integrity and concentration were determined using an Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: manganese conccentration


title: 04S065.04S7602_002

description:
04S7602_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: RY-Mn-L-2


title: 01S025.01S7300_009

description:
01S7300_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S009.06S7128_002

description:
06S7128_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: RY-CK-L-2

value: 5 mM


title: RY-Mn-L-1


title: RY-CK-L-1


title: 03S037.03S7229_010

description:
03S7229_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: RY-CK-L-3


title: 05S003.05S7100_015

description:
05S7100_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S001.01S7023_006

description:
01S7023_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S046.04S7472_011RUN248

description:
04S7472_IonXpressRNA_011RUN248
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

source_name: Non-acute, Stage I, untreated_PBMC

value: Non-acute, Stage I, untreated


title: 03S101.03S7575_012

description:
03S7575_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S027.04S7256_006

description:
04S7256_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S079.08S7637_005

description:
08S7637_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S076.08S7633_012

description:
08S7633_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 04S024.04S7253_002

description:
04S7253_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S027.01S7302_016

description:
01S7302_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S042.01S7551_004

description:
01S7551_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S005.02S7054_011

description:
02S7054_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S040.03S7232_016

description:
03S7232_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S005.05S7105_013

description:
05S7105_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S011.05S7103_005

description:
05S7103_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 08S069.08S7364_007

description:
08S7364_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb6_5.25hpf

city: Berlin

first: Jan

middle: Philipp

last: Junker

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
R1 contains only barcode information, not used for mapping, not included.
Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1, the following options were used: mask-short-adapter-reads = 12  and minimum-trimmed-read-length = 12.
The resulting reads were further demultiplexed with the R package scruff 1.2.5 (using only the first 4 bases of the barcode in the run for the biological replicate ID 1) and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference.
Normalization and differential expression analysis was done with edgeR 3.26.8
Genome_build: DanRer11v96
Supplementary_files_format_and_content: tab-delimited table with raw gene counts for all the samples at each timepoint.

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Naturally spawned embryos were collected in Trizol (Thermo Fisher) at the desired stage after an incubation at 28.5ºC.

extract_protocol:
RNA extraction was carried according to the manufacturer’s recommendations
Every sample was barcoded, pooled and the libraries were prepared according to the CEL-seq2 protocol (Hashimshony, et al., Genome Biology, 2016) with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.

tag: strain

value: TL

tag: developmental stage

value: Whole embryo

tag: biological replicate id


title: TL_emb4_5.25hpf


title: 06S032.06S7206_008

description:
06S7206_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb5_5.25hpf


title: AB_emb6_5.25hpf

value: AB


title: 01S019.01S7033_007

description:
01S7033_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 06S020.06S7138_016

description:
06S7138_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb5_5.25hpf


title: 06S030.06S7204_004

description:
06S7204_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S004.02S7055_014

description:
02S7055_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb3_5.25hpf


title: AB_emb4_5.25hpf


title: 06S027.06S7201_008

description:
06S7201_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb2_5.25hpf


title: 01S020.01S7036_010

description:
01S7036_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: C57BL/6 mice mock-treated_2

type: RNA

city: Pamplona

first: Pedro

last: Berraondo

address: Avenida Pio XII 55

department: Program of Immunology and Immunotherapy

country: Spain

institute: Cima Universidad de Navarra

hyb_protocol: A total of 2.3μg of biotinylated cRNA was fragmented and hybridized to Affymetrix Mouse Gene 1.0 ST array

scan_protocol: Arrays were scanned with  Affymetrix GeneChip Command Console (AGCC) Software

data_processing: Background correction and normalization were done using the Robust Multichip average algorithm.

label: biotin

source_name: Liver from C57BL/6

label_protocol: RNA (100ng) was used for generating biotinylated cRNA through single-round amplification using the MessageAmpIII RNA Amplification kit following the manufacturer’s recommendations (Ambion, ThermoFisher Scientific Inc.).

growth_protocol: 6 week-old C57BL/6 mice

extract_protocol: 15 days later, livers were extracted and homogenized. RNA was obtained using Maxwell 16 LEV simplyRNA purification kit (Promega Madison, WI).

treatment_protocol: We administered intravenously AAV-IFNα or AAV-IFNα + AAV-L37pA  to wild type mice

value: liver

tag: activation time

value: 15 days


title: C57BL/6 mice treated withAAV- IFNα + AAV-L37pA_1


title: TL_emb1_5.25hpf


title: C57BL/6 mice treated withAAV- IFNα + AAV-L37pA_3


title: C57BL/6 mice treated with AAV- IFNα_2


title: C57BL/6 mice mock-treated_3


title: AB_emb3_5.25hpf


title: C57BL/6 mice treated with AAV- IFNα_3


title: C57BL/6 mice mock-treated_1


title: 04S034.04S7394_001

description:
04S7394_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: I


title: 08S012.08S7155_006

description:
08S7155_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: peripheral blood mononuclear cell


title: AB_emb2_5.25hpf


title: 04S047.04S7473_012RUN248

description:
04S7473_IonXpressRNA_012RUN248
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: C57BL/6 mice treated with AAV- IFNα_1


title: 06S039.06S7324_011

description:
06S7324_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb5_4.25hpf


title: AB_emb1_5.25hpf


title: TL_emb6_4.25hpf


title: 06S017.06S7136_006

description:
06S7136_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S009.03S7065_011

description:
03S7065_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb4_4.25hpf


title: AB_emb6_4.25hpf


title: 02S015.02S7041_013

description:
02S7041_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S034.01S7307_011

description:
01S7307_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: Multi-organ


title: 02S028.02S7283_003

description:
02S7283_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb5_4.25hpf


title: AB_emb4_4.25hpf


title: 02S061.02S7446_014

description:
02S7446_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb3_4.25hpf


title: 03S066.03S7424_002

description:
03S7424_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: II


title: TL_emb2_4.25hpf


title: TL_emb1_4.25hpf


title: 05S049.05S7662_015

description:
05S7662_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb3_4.25hpf


title: 09S017.09S7167_002

description:
09S7167_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 10S003.10S7182_011

description:
10S7182_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv

value: III


title: AB_emb1_4.25hpf


title: 03S032.03S7224_006

description:
03S7224_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S065.03S7422_006

description:
03S7422_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb6_3.25hpf


title: 05S008.05S7104_015

description:
05S7104_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb5_3.25hpf


title: 06S029.06S7203_011

description:
06S7203_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb6_3.25hpf


title: TL_emb4_3.25hpf


title: 01S028.01S7301_004

description:
01S7301_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 09S001.09S7160_003

description:
09S7160_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S047.03S7234_009

description:
03S7234_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb4_3.25hpf


title: AB_emb5_3.25hpf


title: TL_emb3_3.25hpf


title: 04S031.04S7247_007

description:
04S7247_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S055.02S7287_001

description:
02S7287_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 01S008.01S7021_007

description:
01S7021_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S059.03S7357_007

description:
03S7357_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 02S020.02S7040_012

description:
02S7040_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb2_4.25hpf


title: AB_emb2_3.25hpf


title: TL_emb1_3.25hpf


title: TL_emb6_2.25hpf


title: 06S038.06S7323_008

description:
06S7323_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: AB_emb1_3.25hpf


title: TL_emb5_2.25hpf


title: 03S027.03S7220_016

description:
03S7220_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: TL_emb4_2.25hpf


title: AB_emb5_2.25hpf


title: AB_emb6_2.25hpf


title: TL_emb3_2.25hpf


title: AB_emb4_2.25hpf


title: TL_emb2_3.25hpf


title: TL_emb2_2.25hpf


title: 03S086.03B9387_005

description:
03B9387_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Remitting, untreated_BAL

value: Remitting, untreated

value: bronchoalveolar lavage


title: 03S088.03B9391_009

description:
03B9391_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S003.08S7140_009

description:
08S7140_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 03S006.03B9388_007

description:
03B9388_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: AB_emb3_2.25hpf


title: 09S035.09B9427_012

description:
09B9427_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: TL_emb1_2.25hpf


title: 03S068.03B9334_004

description:
03B9334_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: AB_emb1_2.25hpf


title: 06S035.06S7209_015

description:
06S7209_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_PBMC_clean_withannot_gradsids_added.tsv


title: 05S046.05B9349_005

description:
05B9349_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: AB_emb2_2.25hpf


title: 04S048.04B9418_007

description:
04B9418_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: C57BL/6 mice treated withAAV- IFNα + AAV-L37pA_2


title: AB_emb3_3.25hpf


title: 04S045.04B9258_005

description:
04B9258_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S050.04B9410_011

description:
04B9410_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S083.03B9380_012

description:
03B9380_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S085.03B9385_015

description:
03B9385_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 05S023.05B9116_012

description:
05B9116_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S104.03B9451_003

description:
03B9451_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G184_9_S8_L004

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Illumina’s bcl2fastq program was used for conversion of base calls to FASTQ files with default settings
STAR was used to align sequences to the GRCm38/mm10 mouse genome with default settings
STAR was also used for quantification of reads per gene using -quantMode
Raw counts between tumors and days for each genotype were summed
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Processed table with summed gene counts for each replicate

source_name: breast tumor

growth_protocol: PyMT males were bred to homozygous Abi1 females to generate PyMT;Abi1 (fl/wt) males, which were then backcrossed to homozygous Abi1 females. The resulting progeny were used to establish PyMT animals with heterozygous or homozygous Abi1 floxed, with and without MMTV-cre expression

extract_protocol:
Tissue was homogenized in QIAzol reagent with a Qiagen TissueRuptor, and RNA was extracted using QIAzol/choloroform phase separation followed by purification with Qiagen RNeasy Mini Columns
Illumina TruSeq Stranded Total RNA Kit with RiboZer Gold H/M/R

tag: date

tag: lane

tag: abi1 genotype (all mice are pyvt+)

value: fl/fl

tag: cre


title: Breast tumor, 190618_G184_9_S8_L002


title: 09S040.09B9439_016

description:
09B9439_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G184_6_S7_L004


title: 03S096.03B9441_009

description:
03B9441_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G184_6_S7_L003


title: Breast tumor, 190618_G184_6_S7_L002


title: 05S047.05B9350_003

description:
05B9350_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S013.03B9065_003

description:
03B9065_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G184_6_S7_L001


title: Breast tumor, 190618_G174_6_S6_L003


title: 05S036.05B9346_008

description:
05B9346_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S021.03B9071_006

description:
03B9071_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S031.03B9078_016

description:
03B9078_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G184_9_S8_L003


title: Breast tumor, 190618_G174_1_S5_L004


title: Breast tumor, 190618_G184_9_S8_L001


title: Breast tumor, 190618_G174_1_S5_L003


title: 03S002.03B9063_004

description:
03B9063_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 05S025.05B9119_007

description:
05B9119_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S044.04B9253_004

description:
04B9253_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G174_1_S5_L002


title: Breast tumor, 190618_G174_6_S6_L004


title: Breast tumor, 190618_G174_6_S6_L001


title: Breast tumor, 190618_G174_1_S5_L001


title: Breast tumor, 190618_G164_6_S4_L004

value: fl/wt


title: Breast tumor, 190618_G174_6_S6_L002


title: 05S024.05B9117_002

description:
05B9117_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S098.03B9399_005

description:
03B9399_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 09S016.09B9431_015

description:
09B9431_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 05S019.05B9114_011

description:
05B9114_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: CrePos_Vill_Colon_4

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Fastqs generated, trimmed, aligned with STAR followed by DeSeq2, EdgeR and Cuffdiff for DEG
Genome_build: mm10

source_name: colon Il17ra vil cre+

extract_protocol:
colon were isolated and RNA was harvested using Rneasy plus Mini Kit (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: time

value: post infection day 10

tag: genotype

value: gut epithelial cells specific deficient mouse (Il17ra villin cre +)


title: CrePos_Vill_Colon_2


title: 03S051.03B9218_006

description:
03B9218_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G164_6_S4_L003


title: 09S024.09B9423_003

description:
09B9423_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G164_6_S4_L002


title: 06S031.06B9139_007

description:
06B9139_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: CrePos_Vill_Colon_1


title: 06S037.06B9227_003

description:
06B9227_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 06S012.06B9126_005

description:
06B9126_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G164_6_S4_L001


title: CreNeg_WT_Colon_3

source_name: colon Il17ra vil cre-

value: wild type


title: 08S049.08B9141_003

description:
08B9141_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Acute Sarcoidosis, untreated_BAL

value: Acute Sarcoidosis, untreated


title: 08S072.08B9304_004

description:
08B9304_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: equineSample_bone_marrow_derived_MSC_s2

city: Ithaca

first: Gerlinde

last: Van de Walle

address: 235 Hungerford Hill Road

department: Microbiology and Immunology

institute: Cornell University

data_processing:
fastq files were aligned to version 95 of the horse genome reference (with manually annotated immunoglobulins (adapted from Wagner B. Immunoglobulins and immunoglobulin genes of the horse. Developmental & Comparative Immunology. 2006;30: 155–164. doi:10.1016/j.dci.2005.06.008)) from ensembl using the count function in the cellranger suite (10X Genomics, v3.0.1)
Alignments were extracted from intermediate BAM files and modified by appending cell barcode and unique molecular identifiers to their read names
The End Sequence Analysis Toolkit(v0.1.1) was applied on the resulting BAM files to obtain gene-cell barcode expression matrices (Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016;26: 1397–1410. doi:10.1101/gr.207902.116)
Custom script was applied to identify duplicated genes and scale their expression proportionally
Genome_build: EquCab3.0
Supplementary_files_format_and_content: gene-cell barcode matrices

organism: Equus caballus

source_name: Peripheral blood mononuclear cells

growth_protocol: Equine mesenchymal stromal cells (MSCs) were isolated and cultured from the adipose tissue (AT), bone marrow (BM) and peripheral blood (PB), of a healthy adult research warmblood mare, euthanized for reasons unrelated to this study, exactly as described in Pennington et al. 2016 (10.1089/ten.TEC.2015.0403)

extract_protocol: Libraries were prepared with 10X Genomics 3' end single cell RNA sequencing library prepration protocol, version 2

tag: age

value: 10 year old

tag: Sex

value: Female

tag: breed

value: Warmblood


title: 03S057.03B9321_003

description:
03B9321_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: phenotype group


title: 06S007.06B9131_007

description:
06B9131_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: scadding

value: I


title: Breast tumor, 190618_G164_3_S3_L002


title: equineSample_peripheral_blood_derived_MSC_s3


title: equineSample_adipose_tissue_derived_MSC_s1


title: Breast tumor, 190618_G164_3_S3_L004


title: CreNeg_WT_Colon_1

tag: tissue


title: 09S014.09B9164_008

description:
09B9164_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S081.03B9384_016

description:
03B9384_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G144_8_S2_L004


title: 04S010.04B9092_010

description:
04B9092_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G164_3_S3_L003


title: 03S022.03B9072_002

description:
03B9072_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S057.08B9155_010

description:
08B9155_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S055.03B9320_007

description:
03B9320_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G144_8_S2_L002


title: 06S014.06B9127_008

description:
06B9127_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S093.03B9398_001

description:
03B9398_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S102.03B9447_013

description:
03B9447_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S061.08B9159_001

description:
08B9159_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: CreNeg_WT_Colon_2


title: DLBCL: OCT1_Ly7

city: New York

first: Chi-Shuen

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2 (v2.3.2.2) with default parameters and duplicate reads were removed by rmdup option of samtools (1.3.1)
Peaks were called using MACS2 (2.1.1.20160309) with the default setting in tabular format
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated by converting bedgraph files from MACS2 (2.1.1.20160309) by Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1).

source_name: DLBCL cell line

growth_protocol: OCI-Ly7 cells were routinely cultured by re-plating d 3 suspension cultures with IMDM supplemented with 10% fetal bovine serum and 1% of P/S

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3" to 5" exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected and purified by Agencourt Ampure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: DLBCL cell line

tag: cell type

value: Diffuse large B-cell lymphoma (DLBCL)

tag: chip antibody

value: sc232, Santa Cruz


title: DLBCL: EP300_Ly7

value: sc369, Santa Cruz


title: 01S037.01B9286_004

description:
01B9286_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G164_3_S3_L001


title: Breast tumor, 190618_G144_8_S2_L003


title: 08S006.08B9146_003

description:
08B9146_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II


title: DLBCL: CREBBP_Ly7

value: sc-584, Santa Cruz


title: DLBCL: MED1_Ly7

value: A300-793A, Bethyl


title: 02S003.02B9052_010

description:
02B9052_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: Breast tumor, 190618_G144_6_S1_L004

value: fl/wt


title: 03S092.03B9396_013

description:
03B9396_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Stage IV, untreated_BAL

value: Stage IV, untreated

value: IV


title: 04S016.04B9099_004

description:
04B9099_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G144_6_S1_L002


title: Breast tumor, 190618_G144_8_S2_L001


title: Breast tumor, 190618_G144_6_S1_L003


title: 06S010.06B9124_012

description:
06B9124_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S051.04B9417_009

description:
04B9417_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: DLBCL: OCT2_Ly7

value: sc-233, Santa Cruz


title: 03S069.03B9338_006

description:
03B9338_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190618_G144_6_S1_L001


title: DLBCL: OCA-B_Ly7

value: ab92315, Abcam


title: DLBCL: INPUT_Ly7

value: none (input)


title: 04S040.04B9247_009RUN302

description:
04B9247_IonXpressRNA_009RUN302
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 01S040.01B9291_014

description:
01B9291_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G184_9_S8_L004

value: fl/fl


title: 04S011.04B9084_013

description:
04B9084_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S011.03B9064_010

description:
03B9064_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S035.03B9204_008

description:
03B9204_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G184_9_S8_L003


title: 08S073.08B9314_013

description:
08B9314_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S008.04B9085_005

description:
04B9085_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: carcass of MhcGal4-driven activated Baboon expression rep3

city: Minneapolis

first: Myung-jun

last: Kim

state: MN

address: 5-235 Moos tower, 515 Delaware st. SE

department: GCD

institute: University of minnesota

description:
MhcGal4>bact-3
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx

data_processing:
The RNA-seq reads were mapped to Drosophila genome
Fragments per kilo base of transcript per million mapped reads (FPKM) valuse were generated by Cufflinks.
Gene differential expressions were tested using Cuffdiff.
Genome_build: Dm3
Supplementary_files_format_and_content: average fpkm from 3 replicates and comparisons of control vs expt

organism: Drosophila melanogaster

source_name: carcass (muscle-epidermis complex) of late foraging 3rd Drosophila larvae

growth_protocol: w1118 (used as wild-type) and smox mutants were grown on yeast-paste placed on apple-juice plate. MhcGal4 control and MhcGal4>baboACT animals were grown on standard vial food

extract_protocol:
Larvae were dissected in HL3 solution to remove the internal guts. Total RNA was extracted from the remaining carcases using TRIzol and further cleaned by RNAeasy kit.
The RNA libraries were constructed using TruSeq RNA preparation kit v2 following Illumina protocols

treatment_protocol: w1118 and smox mutants had no treatment. Tub-Gal80ts/+;MhcGal4/+ and tub-Gal80ts/+;MhcGal4/baboACT animals were heat-shocked at 30oC for 12hr before RNA extraction.

value: carcass (muscle-epidermis complex)

tag: Stage

value: 3rd late foraging

tag: treatment

value: heat-shock at 30oC for 12 hr before RNA extraction


title: carcass of MhcGal4-driven activated Baboon expression rep2

description:
MhcGal4>bact-2
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx


title: Breast tumor, 190617_G184_9_S8_L002


title: 05S039.05B9347_006

description:
05B9347_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Stage IV, treated_BAL

value: Stage IV, treated


title: Breast tumor, 190617_G184_6_S7_L004


title: 04S003.04B9080_011

description:
04B9080_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 10S002.10B9379_003

description:
10B9379_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S094.03B9397_015

description:
03B9397_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: carcass of MhcGal4 control rep3

description:
MhcGal4-3
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx


title: carcass of MhcGal4-driven activated Baboon expression rep1

description:
MhcGal4>bact-1
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx


title: 03S026.03B9074_001

description:
03B9074_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: carcass of MhcGal4 control rep2

description:
MhcGal4-2
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx


title: 03S095.03B9440_007

description:
03B9440_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S067.08B9313_006

description:
08B9313_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S056.04B9414_010

description:
04B9414_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G184_6_S7_L002


title: Breast tumor, 190617_G184_6_S7_L003


title: 03S049.03B9213_013RUN287

description:
03B9213_IonXpressRNA_013RUN287
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: carcass of MhcGal4 control rep1

description:
MhcGal4-1
MhcGal4-MhcGal4bact_Kim and O'Connor_12-8-20.xlsx


title: 09S037.09B9422_015

description:
09B9422_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G174_6_S6_L004


title: Breast tumor, 190617_G184_6_S7_L001


title: smox mutant carcass rep2

description:
smox-2
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: 05S004.05B9101_003

description:
05B9101_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: smox mutant carcass rep1

description:
smox-1
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: 04S009.04B9086_002

description:
04B9086_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 01S033.01B9288_014

description:
01B9288_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G184_9_S8_L001


title: Breast tumor, 190617_G174_6_S6_L003


title: 05S028.05B9342_016

description:
05B9342_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 01S041.01B9293_012

description:
01B9293_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S028.03B9076_010

description:
03B9076_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: wild-type carcass rep3

description:
w1118-3
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: 02S012.02B9046_001

description:
02B9046_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: wild-type carcass rep2

description:
w1118-2
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: smox mutant carcass rep3

description:
smox-3
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: 02S011.02B9044_007

description:
02B9044_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S103.03B9453_013

description:
03B9453_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Stage II-III, untreated_BAL

value: Stage II-III, untreated


title: Breast tumor, 190617_G174_6_S6_L002


title: 03S087.03B9393_001

description:
03B9393_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G174_6_S6_L001


title: wild-type carcass rep1

description:
w1118-1
w1118-smox_Kim and O'Connor_12-8-20.xlsx


title: 08S051.08B9144_012

description:
08B9144_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S014.03B9066_013

description:
03B9066_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S109.03B9452_001

description:
03B9452_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 02S001.02B9049_009

description:
02B9049_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G174_1_S5_L002


title: Breast tumor, 190617_G174_1_S5_L003


title: 08S042.08B9158_003

description:
08B9158_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S033.04B9241_011

description:
04B9241_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III


title: Breast tumor, 190617_G174_1_S5_L001


title: 03S082.03B9389_001

description:
03B9389_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II


title: 04S022.04B9098_016

description:
04B9098_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G164_6_S4_L004


title: WT intra-abdominal fat, biological rep2

city: Columbus

first: Federica

last: Accornero

state: Ohio

address: 473 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to manufacturer's instructions in the manual target preparation for GeneChip Whole Transcript (WT) Expression Arrays for the GeneChipWT Pico Reagent Kit (Applied Biosystems).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

source_name: WT C57, intra-abdominal fat

label_protocol: Fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using a DNA Labeling Reagent that is covalently linked to biotin (GeneChip Pico Reagent Kit, Applied Biosystems) according to manufacturer instructions by Ohio State Genomics Shared Resource-Comprehensive Cancer Center core facility.

extract_protocol:
tissue isolated directly from animals and placed in lysis buffer for homogenization.
RNA was isolated from the pCF and iVF depot of wild type using the Norgen Fatty Tissue RNA Purification Kit (Norgen Biotek Corp) according to the manufacturer's instructions.

value: intra-abdominal fat depot

tag: strain

tag: gender

value: male


title: WT intra-abdominal fat, biological rep3


title: 04S032.04B9259_013

description:
04B9259_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: 03S107.03B9454_015

description:
03B9454_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S063.04B9404_003

description:
04B9404_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G174_1_S5_L004

tag: date

tag: lane


title: WT intra-abdominal fat, biological rep1


title: Breast tumor, 190617_G164_6_S4_L003

tag: abi1 genotype (all mice are pyvt+)

value: fl/wt

tag: cre


title: 08S078.08B9311_011

description:
08B9311_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 09S028.09B9436_013

description:
09B9436_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G164_6_S4_L002