title: Vpr_SORT

first: Liane

last: Dupont

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Cambridge Institute of Therapeutic Immunology & Infectious Disease

institute: University of Cambridge

description:
CRISPR-Cas9 knockout screen
Vpr_Mageck.txt

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/LDUP92/hiv-compaction
Genome_build: GRCh38
Supplementary_files_format_and_content: CRISPR screen: Processed data is the read count statistics produced using MAGeCK. ATAC-seq: Processed data is the BigWig files generated by alignment of filtered reads using BWA-MEM

source_name: Pooled Vpr target knockout library

growth_protocol: CEM-T4 were acquired from the NIH AIDS Reagent Program (Cat. #117) and Jurkat T cells from ATCC (Clone E6-1, TIB-152). All cell lines were cultured at 37°C and 5% CO2 in Iscove's Modified Dulbecco's Medium (IMDM, Sigma-Aldrich) supplemented with 10% fetal calf serum (FCS, Gibco), 1x GlutaMAX (Gibco), and 100 U/mL penicillin/streptomycin (Gibco).

extract_protocol:
CRISPR screen: DNA was isolated using a Zymo Quick-DNA Microprep (sorted sample) or a Qiagen Gentra Puregene kit (unsorted library). ATAC-seq: Chromatin fragments were purified using a MinElute PCR purification kit (Qiagen)
CRISPR screen: sgRNA sequences were amplified and Illumina sequencing adaptors added by two sequential rounds of PCR followed by PCR purification (AMPure XP, Beckman Coulter). Next-generation sequencing was performed on a MiniSeq System (Illumina) using a custom primer. ATAC-seq: Libraries of transposed chromatin fragments were prepared by minimal PCR amplification (8 or 9 total PCR cycles) using custom indexed primers, dual size selected with AMPure XP beads (Beckman Coulter)
CRISPR-Cas9 knockout screen, ATAC-seq

treatment_protocol: For CRISPR screen: 48 x 10^6 Cas9-CEM-T4 cells were transduced with “Vpr target library” sgRNA lentivirus at MOI ~ 0.3. Transduction efficiency was verified by flow cytometry (BFP+) 72 hpi, and sgRNA containing cells were enriched by puromycin selection. On day 7, 48 x 106 cells were transduced at MOI ~ 1.5 with pHRSIN.SFFV-GFP and pHRSIN.SFFV-mCherry by spinoculation in IMDM + 1 µM raltegravir (RAL) and were subsequently maintained in 1 µM RAL for the duration of the screen. The top 0.5% GFP+/mCherry+ cells were selected by fluorescence activated cell sorting (FACS) on day 10, and cells with stably integrated virus were removed by sorting the GFP-/mCherry- population on day 16. On day 18 and 21, respectively, reporter virus infection and sorting of highly expressing cells were repeated, and DNA was isolated immediately after sorting (Zymo Quick-DNA Microprep). An uninfected, unsorted library population was maintained separately at >150-fold library coverage for the duration of the screen, and unsorted library DNA was isolated for reference (Qiagen, Gentra Puregene). For ATAC-seq:  Jurkat T cells were infected at high MOI with a GFP reporter lentivirus in the presence of 1 µM RAL. 48 h post infection,  ATAC-seq was performed following the protocol  published by  Buenrostro et al (2015) without nuclei isolation (Karabacak Calviello, 2019). Briefly, 50,000 Jurkat T cells were resuspended in 50 µL 1x Illumina Tagment DNA with 2.5 µL TDE1 Tagment DNA Enzyme (Illumina). Transposition reactions were incubated in a thermomixer (1 h, 37°C, 1,400 rpm) and chromatin fragments purified using a MinElute PCR purification kit (Qiagen).

value: CEM-T4 T cells

value: Sorted sample (Unintegrated virus GFP/mCherry high)

tag: library type

value: CRISPR-Cas9 knockout screen (High diversity amplicon)


title: Vpr_LIB

status: Public on Mar 01 2021

type: SRA

city: Cambridge

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: sample type

value: Unsorted Vpr library


title: IEC_C2: IEC high carb 2

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: polyA RNA-seq

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mm10 mouse transcriptome (GRCm38 ensembl; cDNA and ncRNA) and quantified by Kallisto (v0.45.0) with a k-mer index 25 and 60 bootstrapping (Bray et al., 2016).
The expression of transcript was calculated in TPM (transcript per million). When multiple transcripts match to the same gene, the expression of the gene is calculated by summing the TPM of all matched transcripts. TPM’s of 3–4 biological replicates were averaged for each sample.
Statistical analyses for differentially expressed genes were performed by Sleuth Pimentel et al., 2017).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM

molecule: polyA RNA

organism: Mus musculus

source_name: Intestinal epithelial cells

growth_protocol: Female C57BL/6J animals aged 7-12 weeks were maintained under specific-pathogen free conditions and were euthanized by cervical dislocation at ZT8.

extract_protocol:
RNA was isolated from sorted T-cells using RNEasy Plus Micro Kit (Qiagen). RNA was isolated from epithelial cells using DirectZol RNA Miniprep Plus Kit with on-column DNAse digestion according to the manufacturer’s instructions (Zymo).
Library preparation for sorted T-cells performed using SMART-seq2 protocol. Sequencing libraries for epithelial cells were constructed using Illumina TruSeq Library Prep Kit and sequenced on Illumina NextSeq 500 (38 x 38 bp paired-end run).

treatment_protocol: Animals were fed Envigo high carb (TD170403) or high protein (TD170405) diet for 5 days.

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

value: High carbohydrate diet

tag: surface marker

value: Intestinal epithelial cells


title: D710rna_D501rna

first: Pierre

last: Larraufie

address: Box 289, Addenbrooke's Site

department: WT-MRC Institute of Metabolic Science

institute: Metabolic Research Laboratories and MRC Metabolic Diseases Unit

data_processing:
data was demultiplexed using the Casava pipeline
data was mapped to the mouse genome GRCm38 using STAR v2.5.1 and raw counts generated simultaneously
Supplementary_files_format_and_content: Dye_Guca2a_raw_count.csv  is a csv file of number of counts for ensembl gene ids of each biological sample

molecule: total RNA

source_name: Duodenum

growth_protocol: mice were grown on a 12h dark/light cycle with ad libitum access to water and standard chow

extract_protocol:
epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer
10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara)
RNAseq SE-50 on an Illumina HiSEQ 4000

tag: tissue

value: Duodenum

tag: genotype/variation

value: GFP negative


title: IEC_C3: IEC high carb 3

description: polyA RNA-seq


title: Vehicle SeraExo#1

type: RNA

city: Hong Kong SAR

first: Jin

last: Liu

address: 7 Baptist University Road, Kowloon Tong

department: TMBJ

country: China

institute: Hong Kong Baptist University

description:
Vehicle treatment
SAMPLE 1

data_processing:
The normalization and all the data analysis was performed using the manufacturer's qPCR analysis templates https://systembio.com/wp-content/uploads/Mouse_miRNome_v14_2.xls
For the normalization it uses the Spike-in control RNA.
Target miRNA signals were normalized to the average Spike-in control RNA signals; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_control average)]
All deltadeltaCt based fold-change were calculated from the uploaded raw threshold cycle data automatically by the templates.
Fold Change worksheet reports test/control (i.e., OCExoInhib/Vehicle) ratios.

label: SYBR Green

source_name: Serum exosomes

label_protocol: Reverse transcription was performed using the Mouse Complete SeraMir Exosome RNA Amplification and Profiling Kit (System Biosciences) according to the manufacturer's instructions. Real-time qPCR was performed (Applied Biosystems ViiA7) using standard run conditions (40 cycles at 95oC for 15 seconds and 60oC for 60 seconds.)

growth_protocol: The mice with OCExoInhib treatment and control mice with vehicle treatment at 2w after ACLT.

extract_protocol: Exosomal RNA was extracted with the SeraMir Exosome RNA Column Purification Kit (System Biosciences) according to the manufacturer's instructions.

treatment_protocol: The exosomes were isolated from serum of OCExoInhib-treated mice or Vehicle-treated mice.

value: Exosomes


title: ERa_EB_CR_rep2

city: Boston

first: Bruno

last: Gegenhuber

state: MA

address: 220 Longwood Ave

department: Neurobiology

country: USA

institute: Harvard Medical School

data_processing:
Library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30). Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700. After alignment, duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial DNA or incomplete assemblies were also removed (samtools view). Peaks were called using MACS2 callpeak (q < 0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10

source_name: Limbic system

growth_protocol: 10-12 week-old C57/BL6 males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, males were treated for 4 hr prior to nuclei isolation.

extract_protocol:
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4%  IGEPAL CA-630 was added to improve binding to concanavalin  A magnetic beads.
Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle (corn oil).

value: Brain (limbic system)

value: Male

tag: developmental stage

value: Adult

tag: treatment

value: estradiol benzoate


title: D708rna_D501rna

source_name: Colon

value: Colon


title: ERa_EB_CR_rep1


title: D707rna_D501rna

value: GFP positive


title: ERa_veh_CR_rep2

value: vehicle


title: 200400320017_R05C01: 5_HGDN

type: genomic

city: Mainz

first: Alicia

middle: Anna

last: Poplawski

state: Rhineland Palatinate

address: Obere Zahlbacher Straße 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics

country: Germany

institute: University Medical Center Johannes Gutenberg University Mainz

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450k BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Quality control and data pre-processisng was performed using minfi package (Bioconductor). Samples were quantile normalized. For the detection of differentially methylated CpG sites, a linear mixed-effects model was fitted by maximazing the restricted log-likelihood to the data with patient id as random effect using the nlme R package.

label: Cy3, Cy5

source_name: tissue from HCC patients with chronic hepatitis B infection

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using Qiagen Qiamp DNA Kit (Qiagen GMBH, Hilden, Germany) following the manufacturer’s instructions.

tag: patient id

tag: pathologist classification

value: high-grade dysplastic nodules

tag: patient gender

tag: patient age

value: liver


title: 200400320017_R02C01: 5_HGDN


title: ERa_veh_CR_rep1


title: D705rna_D501rna

source_name: Ileum

value: Ileum


title: 200400320017_R06C01: 5_LGDN

value: low-grade dysplastic nodules


title: D706rna_D501rna


title: 200400320017_R03C02: 5_pHCC

value: progress to advanced HCCs


title: 200400320017_R02C02: 5_LGDN


title: D704rna_D501rna

source_name: Jejunum

value: Jejunum


title: 200400320017_R03C01: 5_HGDN


title: 200400320017_R04C01: 5_eHCC

value: hearly hepatocellular carcinoma


title: 200400320017_R01C02: 5_HGDN


title: D703rna_D501rna


title: 200107460088_R01C02: 8_HGDN

value: Female


title: D702rna_D501rna

value: Duodenum

value: GFP negative


title: D701rna_D501rna


title: IEC_C1: IEC high carb 1

description: polyA RNA-seq

source_name: Intesitnal epithelial cells

value: Wildtype C57BL/6J

value: female

value: High carbohydrate diet

value: Intesitnal epithelial cells


title: cd41gfp_WT3

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM, Cufflinks (version 2.2.1) was used.
Genome_build: GRcz10
Supplementary_files_format_and_content: tab-delimited text file include gene counts for each sample

organism: Danio rerio

source_name: hematopoietic stem and progenitor cells

extract_protocol:
cd41-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo).
Libraries were made at BGI following their low-input RNA protocol.

tag: develpmental stage

value: 40 hours post fertilization

tag: genotype

value: wildtype


title: cd41gfp_WT2


title: 200107460088_R03C01: 6_eHCC

value: Male


title: 200400320017_R01C01: 5_CL

value: cirrhotic liver


title: 200107460088_R06C01: 8_eHCC

value: liver


title: D709rna_D501rna

value: GFP positive


title: cd41gfp_WT1


title: cd41gfp_mut3

value: ddx41 mutant


title: cd41gfp_mut2


title: 200107460088_R02C01: 6_CL


title: 200107460078_R06C02: 7_CL


title: Sham_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts

source_name: Brain microvessels from sham operated healthy mice

extract_protocol:
RNA was isolated from  brain microvessels using the Rneasy plus micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Brain microvessels were isolated from tumor bearing brain region of treated or untreated mice at 21-day post tumor cell transplanantation.

tag: region

value: healthy

tag: agent

value: sham

value: Brain microvessels


title: Sham_2


title: cd41gfp_mut1


title: 200107460078_R03C02: 3_HGDN

value: high-grade dysplastic nodules

value: Female


title: 200107460088_R05C01: 8_pHCC

value: progress to advanced HCCs


title: Het_Sample_4

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Genome_build: human reference genome (GRCh37)

organism: Rattus norvegicus

source_name: Placental disc

extract_protocol:
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age).  Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: placental disc

value: Ascl2 mutant

value: Holtzman

tag: gestation day


title: Aflibercept-AMG386-aPD-1_3

source_name: Brain microvessels from tumor bearing region from mice treated with Aflibercept-AMG386 and anti-PD1

value: tumor bearing region

value: Aflibercept-AMG386 and anti-PD1


title: Aflibercept-AMG386-aPD-1_2


title: 200107460078_R05C02: 4_HGDN


title: 200107460088_R01C01: 7_eHCC

value: hearly hepatocellular carcinoma


title: 200107460078_R04C02: 4_CL

value: Male


title: Het_Sample_3

tag: strain


title: Aflibercept-AMG386-aPD-1_1


title: Het_Sample_1


title: Wild_Type_Sample_5

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: wild type


title: Het_Sample_2


title: 200107460078_R02C02: 3_CL

value: cirrhotic liver

value: liver


title: IgG-CTRL_3

source_name: Brain microvessels from contralateral non-tumor bearing region from mice treated with control IgG

value: contralateral non-tumor bearing region

value: control IgG


title: GBM S22

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 fannine St

institute: University of Texas Health Science Center at Houston

description:
GBM
small-RNA

hyb_protocol: Hybridization was performed according to hybridization protocol for nCounter Human miRNA Expression Assays Including Panels. Briefly, hybridization buffer and reporter codeset were mixed first, and this mastermix was added to samples (total RNA), finally hybridization reaction was completed by adding capture probeset.

scan_protocol: The cartridge was read with maximum sensitivity (280 FOV)

data_processing: Data from all runs were imported into nSolver version 4.0 (NanoString Technologies), matched to corresponding Reporter Library File (RLF), and subjected to quality control using the software quality metrics with default cutoff criteria

label: NanoString

source_name: Brain

label_protocol: standard NanoString protocol

extract_protocol: Total RNA was extracted from GBM tumor tissue using QIAshredder and miRNeasy Mini Kit (Qiagen, Germantown, MD), and 100 ng of total RNA was used for hybridization.

tag: diagnosis

value: GBM


title: IgG_3

source_name: Brain microvessels from tumor bearing region from mice treated with control IgG

value: Brain microvessels


title: Wild_Type_Sample_4


title: GBM S19

description:
GBM
small-RNA


title: 200107460078_R03C01: 1_LGDN

value: low-grade dysplastic nodules


title: 200107460078_R01C02: 2_HGDN

value: high-grade dysplastic nodules


title: IgG_2


title: Wild_Type_Sample_3


title: GBM S14

description:
GBM
small-RNA


title: IgG-CTRL_2


title: Wild_Type_Sample_2


title: 200107460078_R06C01: 2_HGDN


title: IgG_1


title: 200107460078_R01C01: 1_CL


title: Wild_Type_Sample_1


title: GBM S12

description:
GBM
small-RNA


title: GBM S11

description:
GBM
small-RNA


title: 200107460078_R02C01: 1_HGDN


title: IgG-CTRL_1


title: 200107460078_R05C01: 2_eHCC


title: healthy donor 2 si_NS Teffs

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description: Expression value derived using Expression Console software; Exon analysis summarized using PLIER

hyb_protocol: The fragmented/labeled single-strand cDNA (with hybridization controls) was hybridized to the Affymetrix Human Gene 2.0 ST Array at 45°C for 16h with rotation (60rpm). After the hybridization step, each of the arrays has been washed and stained on the GeneChip Fluidics Stations 450 (Affymetrix), using the GeneChip® Hybridization Wash and Stain Kit.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G with GeneChip Command Console software (Affymetrix). The software generates the .CEL files containing the probe cell intensity data and enables sample and array registration, data management, instrument control as well as automatic and manual image gridding.

data_processing: The expression signal at the exon level was summarized by the Affymetrix PLIER approach using the sketch approximation of quantile normalization with the option PM-GCBG (a GC content based background correction) using Affymetrix Expression Console v1.3.1.187. Before performing differential analysis, we first pre-processed the data with certain filtering steps. The filtering steps following the PLIER summary method included: 1) first removing any probeset whose cross-hyb type was not equal to 1; 2) removing any probeset corresponding to no identified gene or multiple genes according to the annotation (the file HuGene-2_0-st-v1.na33.2.hg19.transcript) and the library version r4 (May 23, 2012); 3), excluding the probesets with the average expression value in both groups (si_NS and si_VIMP) ≤ 2 times of the median value of the arrays (in our case, 2x the median was equal to the intensity value of 170); 4) if the mean intensity of the probesets in one group was higher, the number of absent calls among the three biological replicates should not be ≥ 1 in the group with higher mean intensity. To secure more robust analysis, we also analyzed the dataset using another model-based method(Berchtold et al. 2008, Weigand et al. 2012), i.e., RMA-sketch summary/normalization method (of note, the filtering steps mentioned above did not apply to the data resulted by the RMA-sketch summary method). We selected the probeset for further analysis only if the two-sided pair-wised T-test generated a P-value lower than 0.05 from the datasets summarized by both PLIER and RMA methods as demonstrated somewhere else (Weigand et al. 2012). To obtain a certain number of starting candidates, we lowered the threshold of the change fold to 1.2, which have to recurrently show in all the three donors, for our further analysis in consideration of both facts that VIMP is not a (co)transcription factor and the siRNA knockdown efficiency was not 100%. The database of mammalian transcription factors or cofactors, or chromatin remodeling factors was downloaded from the work of others (Zhang et al. 2012).

label: biotin

source_name: Donor 2 Teffs si_NS (control)

label_protocol: Single-strand cDNA was labeled and fragmented using the WT Terminal Labeling, polyA and hyb Controls Kit.

growth_protocol: Buffy coats from healthy donors were provided by the Red Cross Luxembourg. The RosetteSep™ Human CD4+ T cell Enrichment Cocktail (15062, Stemcell) was added to undiluted blood at a concentration of 50 µl/ml and incubated for 30 min at 4°C. The blood was then dilued 2 times with FACS buffer (PBS + 2% FBS) and the CD4+ cells were isolated by gradient centrifugation at 1200g for 20 min, using Lympoprep (07801, StemCell) and SepMate™-50 tubes (85450, Stemcell). CD4+ cells were stained with mouse monoclonal [RPA-T4] anti-human CD4 FITC (555346, BD Biosciences) (dilution 1:20), mouse monoclonal [M-A251] anti-human CD25 APC (555434, BD Biosciences) (dilution 1:20), mouse monoclonal [HIL-7R-M21] anti-human CD127 V450 (560823, BD Biosciences) (dilution 1:20)  and LIVE/DEAD® Fixable Near-IR Dead Cell Stain (L10119, ThermoFisher Scientific) (dilution 1:500). Primary effector T cells (CD4+CD25-) were then sorted on a BD Aria III Flow cytometry cell sorter (BD Biosciences).    Sorted Teff were cultured in IMDM (21980-032, ThermoFisher Scientific) complete medium, supplemented with 10% heat-inactivated (56°C, 45 min) fetal bovine serum (FBS) (10500-064, ThermoFisher Scientific), 1x Penicillin+Streptomycin (15070-063, ThermoFisher Scientific), 1x MEM non-essential amino acids (M7145, Sigma-Aldrich) and 1x β-mercaptoethanol (21985-023, ThermoFisher Scientific). Every 7 days for two weeks, Teffs isolated from indvidual donors were restimulated with irradiated Epstein–Barr virus (EBV) transformed B-cells (EBV-B cells), at a 1:1 ratio to expand and maintain the culture. The EBV-B cells were irradiated in RS2000 X-Ray Biological Irradiator (Rad Source Technologies) for 30 minutes with a total of 90Gy.

extract_protocol: Teffs were first lysed with RLT buffer, supplemented with 1% beta-Mercaptoethanol and RNA were extracted using RNeasy Mini Kit following the manufacturer’s instructions including the digestion of genomic DNA with DNAse I.

treatment_protocol: Targeted gene’s expression was knocked-down in up to 5 x 106 cells using the P3 Primary Cell 4D-Nucleofector X Kit L (V4XP-3024, Lonza) with 90µl P3 Primary cell solution and 100 pmol of corresponding si_RNA (resuspend in 10ul RNAse-free H2O): si_Non-Specific (si_NS) (sc-37007, Santa Cruz), si_VIMP/SELS (SI03053512, Qiagen). The Amaxa 4D-Nucleofector™ X System (Lonza) was used to perform the electroporation and siRNA transfection according to the manufacturer’s recommended program for primary human T cells. After transfection, the Teffs were transferred into a 12-well plate with pre-warmed complete medium and kept at 37°C for 24 hours before being stimulated with Dynabeads® Human T-Activator CD3/CD28 for T Cell Expansion and Activation (11131D, ThermoFischer Scientific) in a 24-well plate for 24 hours.

tag: cell type

value: CD4 effector T cells

tag: Sex

value: not collected


title: Aflibercept-AMG386_3

source_name: Brain microvessels from tumor bearing region from mice treated with Aflibercept-AMG386

tag: tissue


title: OCmiR-KD OC#3

description:
Osteoclast-miRNA knockdown
SAMPLE 6

data_processing:
The normalization and all the data analysis was performed using the manufacturer's qPCR analysis templates https://systembio.com/wp-content/uploads/Mouse_miRNome_v14_2.xls
For the normalization it uses the mouse U6 snRNA.
Target miRNA signals were normalized to the average U6 snRNA signals of OCs; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_U6 average)]
All deltadeltaCt based fold-change were calculated from the uploaded raw threshold cycle data automatically by the templates.

source_name: Bone marrow-derived OSCAR+CTR+ osteoclasts

label_protocol: Reverse transcription was performed using the QuantiMir RT Kit (System Biosciences) according to the manufacturer's instructions Real-time qPCR was performed (Applied Biosystems ViiA7) using standard run conditions (40 cycles at 95oC for 15 seconds and 60oC for 60 seconds.)

growth_protocol: The mice with osteoclast-miRNA knockdown and control mice with intact osteoclast-miRNA

extract_protocol: Total RNA was extracted with Trizol Reagent

treatment_protocol: The osteoclasts (Ocs) were isolated from bone marrow cells of OCmiR-KD or OCmiR-Intact mice by magnetic-activated cell sorting.

value: OSCAR+CTR+ osteoclasts


title: healthy donor 1 si_NS Teffs

source_name: Donor 1 Teffs si_NS (control)


title: GBM S9

description:
GBM
small-RNA


title: OCmiR-KD OC#2

description:
Osteoclast-miRNA knockdown
SAMPLE 5


title: GBM S7

description:
GBM
small-RNA


title: healthy donor 1 si_VIMP Teffs

source_name: Donor 1 Teffs si_VIMP


title: Aflibercept-AMG386_1


title: 200107460088_R04C01: 2_pHCC

value: progress to advanced HCCs


title: GBM S5

description:
GBM
small-RNA


title: 200107460078_R04C01: 2_CL


title: Control S21

description:
Control
small-RNA

value: Normal


title: OCmiR-KD OC#1

description:
Osteoclast-miRNA knockdown
SAMPLE 4


title: OCmiR-Intact OC#2

description:
Osteoclast-miRNA intact
SAMPLE 2


title: healthy donor 2 si_VIMP Teffs

source_name: Donor 2 Teffs si_VIMP


title: Control S17

description:
Control
small-RNA


title: Control S18

description:
Control
small-RNA


title: Control S16

description:
Control
small-RNA


title: OCmiR-Intact OC#3

description:
Osteoclast-miRNA intact
SAMPLE 3


title: OCmiR-Intact OC#1

description:
Osteoclast-miRNA intact
SAMPLE 1


title: JAK00034 Tofacitinib Day 84

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_90

data_processing:
Demultiplex to FastQ using bcl2fastq version 2.17.1
Map to hg19 using Tophat 2.1.1
Calculate RPKM using Partek 7.18.0723
ANOVA comparison using Partek 7.18.0723
Paired T-test using Partek 7.18.0723
Genome_build: hg19
Supplementary_files_format_and_content: Excel RPKM, ANOVA and Paired T-test results

source_name: whole blood (paxgene tube)

extract_protocol:
PAXgene Blood RNA Kit (Qiagen)
TruSeq Stranded mRNA NeoPrep Kit (Illumina)

value: Tofacitinib

tag: stat4 risk allele

value: Negative

value: FEMALE


title: JAK00034 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_89


title: BRD4_ChIPSeq

city: Sydney

first: Jingwei

last: Chen

address: High Street

country: Australia

institute: Children's Cancer Institute

data_processing:
ChIP-Seq raw reads were aligned using the Burrows Wheeler Aligner (BWA) with default parameters. Files were further processed using SAMtools, BEDtools  and bedGraphToBigWig. Peaks were called with MACS2 ‘callpeak’ (version macs2 2.1.1.20160309) against input controls, with default parameters.  Common peaks of NMYC or JMJD6 were selected if a ChIP-seq peak was identified in all three replicates of either NMYC or JMJD6.
Genome_build: hg19

source_name: TERT-rearranged neuroblastoma PDX cells

growth_protocol: TERT rearranged neuroblastoma PDX cells were maintained in IMEM medium with 20% FBS and kept in 5% oxygene incubator

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA immunoprecipitated by the antibodies were purified and subjected to sequencing with Illumina HiSeq 2000 at Ramaciotti Centre for Genomics, University of New South Wales, Australia

treatment_protocol: No treatment

value: Neuroblastoma PDX tumour cells

tag: tumor stage

value: Replased tumor

tag: chip seq antibody

value: BRD4 antibody (Bethyl Laboratories, A301-985A100)


title: JAK00034 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_88

tag: treatment


title: CD163-deficient, with LPS

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

description: SAMPLE 4

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray 4x44K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: macrophages, CD163-deficient, with LPS

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were cultured with 10%FBS/RPMI.

extract_protocol: Cells were treated with RNAisoPlus (Takara, Otshu, Shiga) for RNA isolation.

treatment_protocol: Cells were cultured with or without LPS (100ng/mL).

tag: strain background

tag: genotype/variation

value: macrophage

tag: treated with

value: LPS (100ng/mL)


title: H3K27ac_ChIPSeq

value: H3K27ac antibody (Abcam 4726)


title: Subject 8 - CSU v3

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

description:
SAMPLE 021
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: GCOS 4.0

source_name: blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: mRNA was isolated by miRNeasy kit extractions and contained both mRNA and miRNA. RIN values > 6 (lower allowed because of presence of miRNA).

treatment_protocol: No treatments in culture were performed, cells in their resting state after preparation.

value: chronic spontaneous urticaria (CSU)

value: purified basophils

value: pre-treatment

tag: subject


title: CD163-deficient, without LPS

description: SAMPLE 3

source_name: macrophages, CD163-deficient, without LPS

value: none (untreated control)


title: Input DNA


title: Wild type, without LPS

description: SAMPLE 1

source_name: macrophages, Wild type, without LPS

value: wild type


title: Wild type, with LPS

description: SAMPLE 2

source_name: macrophages, Wild type, with LPS


title: healthy donor 3 si_NS Teffs

source_name: Donor 3 Teffs si_NS (control)

value: CD4 effector T cells

value: not collected


title: Subject 7 - CSU v6

description:
SAMPLE 020
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls

value: mid-treatment on omalizumab


title: JAK00033 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_87

value: Tofacitinib

value: Positive


title: Control-IP-2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig normalized signal

source_name: Skin

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: technology

tag: condition

value: Control


title: JAK00033 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_85

value: FEMALE


title: JAK00033 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_86


title: Control-IP-1


title: healthy donor 3 si_VIMP Teffs

source_name: Donor 3 Teffs si_VIMP


title: Subject 6 - CSU v3

description:
SAMPLE 017
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls


title: Subject 6 - CSU v6

description:
SAMPLE 018
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls


title: As-T-IP-2

value: Tumorigenic cells from chronic arsenic treatment


title: As-T-IP-1


title: JAK00032 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_84

value: Placebo

value: Negative


title: As-IP-2

value: Chronic arsenic treatment


title: JAK00032 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_82


title: As-IP-1


title: Control-input-2

value: RNA-Seq


title: JAK00031 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_81


title: Control-input-1


title: Subject 6 - non CSU

description:
SAMPLE 014
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls

value: non-CSU

value: non-treated


title: Subject 5 - CSU v6

description:
SAMPLE 016
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls

value: chronic spontaneous urticaria (CSU)

value: purified basophils


title: JAK00031 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_80


title: Subject 5 - non CSU

description:
SAMPLE 013
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls


title: Subject 5 - CSU v3

description:
SAMPLE 015
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls

value: pre-treatment


title: Subject 4 - non-CSU

description:
SAMPLE 012
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: JAK00029 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_78


title: As-T-input-2


title: As-input-2


title: JAK00031 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_79


title: JAK00032 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_83


title: JAK00029 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_76


title: Subject 2 - non-CSU

description:
SAMPLE 010
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: As-T-input-1


title: As-input-1


title: Subject 3 - non-CSU

description:
SAMPLE 011
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: JAK00029 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_77


title: Subject 4 - CSU v6

description:
SAMPLE 008
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: Subject 1 - non-CSU

description:
SAMPLE 009
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: JAK00028 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_75


title: JAK00028 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_74


title: JAK00028 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_73


title: ZD2

city: ANKARA

first: Selda

last: Ayhan

address: SIHHIYE

country: Turkey

institute: HACETTEPE UNIVERSITY

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Data quality controls (filtering reads containing adapter or with low quality) of raw readings were evaluated with Babraham Bioinformatics FASTQC software (version 0.11.2) and quality control was performed.
RNA-seq reads were aligned to the Homo sapiens UCSC hg19 genome assembly using RNA-Seq Alignment version: 1.1.0 (Illumina, Inc.).
The gene counts, gene FPKMs, principal component analysis and a control-vs-comparison (R1-vs-R2) containing differential expression results were produced by DESeq2 version: 1.1.0. (BaseSpace Labs).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: FilteredGenes.csv
Supplementary_files_format_and_content: genes.fpkm.csv
Supplementary_files_format_and_content: genes.rlog.csv

source_name: Mesenchymal Stem Cell

growth_protocol: Bone marrow aspiration samples were obtained from 11 healthy donors of patients who received bone marrow transplantation (BMT) at the BMT Unit of İhsan Doğramacı Children's Hospital at Hacettepe University. Ethical approval of this study was obtained from the Hacettepe University Non-invasive Clinical Research Ethics Committee (GO 13/172). Informed consent forms were signed and all experiments were performed in accordance with the approved guidelines and regulations. The BMSCs isolated from the marrow aspirated from the R1 and R2 regions of each donor were named R1-hBMSC and R2-hBMSC, respectively. For the mononuclear cells (MNCs) isolation, 3mL of Ficoll-Paque Plus solution (density 1.077 g/cm3, GE Healthcare, Little Chalfont, Buckinghamshire, United Kingdom) was placed into a 15 mL conical tube and 6 mL of the diluted bone marrow carefully added then tubes were centrifuged at 400 g without brake for 30 min at room temperature. The white ring of MNCs was collected and counted (using automated CBC analysis test). Then equal numbers of MNCs from each region (10x106 MNCs) were seeded on a cell culture flask in DMEM-1X-GlutaMAX (GibcoTM Invitrogen, Grand Island, USA) supplemented with 10% FCS (GibcoTM Invitrogen, Grand Island, USA) and 1% penicillin/streptomycin (Invivogen, San Diego, USA). Cells were allowed to adhere for 3–5 days in a 37°C, 5% CO2 atmosphere. Thereafter, the culture medium was completely changed twice a week. When %80 confluence was reached, adherent cells were trypsinized (Trypsin-EDTA, Gibco, Invitrogen) and replated for culture expansion. Cell counts were performed with each passage and equal numbers of MSCs from each marrow region (R1-MSC and R2-MSC) were replated at the end of each passage. Passage 3 (P3) MSCs were used in the transcriptome analysis.

extract_protocol:
1x106 p3-hBMSCs were stored into 1.5 ml tubes with 500 µL RNA protect Cell Reagent (Qiagen76526). RNAs were extracted from hBMSCs using Qiagen RNEasy Mini- Plus kits (Cat.No. 74134). TruSeq® RNA Sample Preparation v2 (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue _ region

value: Bone Marrow-Region 2

tag: genotype

value: normal

tag: passages

value: Female

tag: age


title: ZD1

value: Bone Marrow-Region 1


title: ZA2


title: JAK00027 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_72

value: Tofacitinib


title: ZA1


title: JAK00027 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_71


title: JAK00027 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_70


title: OG2


title: OG1


title: JAK00026 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_69

value: Positive


title: Subject 4 - CSU v3

description:
SAMPLE 007
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls

tag: diagnosis

tag: cell type


title: JAK00026 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_68

tag: Sex

value: FEMALE


title: LUA2

value: Male


title: Subject 3 - CSU v6

description:
SAMPLE 006
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls

value: mid-treatment on omalizumab


title: LUA1


title: JAK00026 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_67

tag: stat4 risk allele


title: Subject 2 - CSU v6

description:
SAMPLE 004
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: LA2


title: Subject 3 - CSU v3

description:
SAMPLE 005
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: JAK00025 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_66

value: Negative


title: Subject 1 - CSU v3

description:
SAMPLE 001
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: JAK00025 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_65


title: Subject 2 - CSU v3

description:
SAMPLE 003
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: LA1


title: Subject 1 - CSU v6

description:
SAMPLE 002
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM5_normalized.xls


title: KC2


title: KC1


title: IRF2BP2 knock-down, biological rep 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Hela cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Hela cells were grown in DMEM containing 10% FBS, 2 mM L-glutamine and 1 mM sodium pyruvate medium  at 37°C and 10% CO2.

extract_protocol: RNA samples were purified using Nucleospin RNA Plus kit (Machery-Nagel).

treatment_protocol: Cells were treated with siRNA against IRF2BP1, IRF2BP2, IRF2BP1+IRF2BP2, as well as a non-targeting control siRNA for 72 hours.

tag: cell line

value: HeLa


title: IRF2BP1 knock-down, biological rep 3


title: non-targeting control, biological rep 3


title: Subject 7 - CSU v3

description:
SAMPLE 019
mRNA & miRNA
The Sample title describes a preparation of cells (Expt xx) and the conditions of treatment, and follow naming consistent with the published report.
DM6_normalized.xls


title: Aflibercept-AMG386_2

source_name: Brain microvessels from tumor bearing region from mice treated with Aflibercept-AMG386

tag: region

value: tumor bearing region

tag: agent

tag: tissue

value: Brain microvessels


title: JAK00024 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_63

tag: treatment


title: non-targeting control, biological rep 2


title: HK1


title: HK2


title: JAK00024 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_62


title: IRF2BP1 knock-down, biological rep 2


title: JAK00024 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_61


title: IRF2BP1+IRF2BP2 knock-down, biological rep 3


title: HE2


title: non-targeting control, biological rep 1


title: HE1


title: GNK2


title: Sample 8

city: Guangzhou

first: Yingfeng

last: Zheng

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Centre

institute: Sun Yat-sen University

description: single-cell RNA

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software (v3.0.2).
Genome_build: GRCh38/macFas5/mm10.
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing cellular barcodes in MEX format

organism: Macaca fascicularis

source_name: central corneal epithelial cells

extract_protocol:
Human, monkey and mouse single cell suspensions in 0.4% BSA-PBS were processed for single-cell sequencing using the Chromium Single Cell 3’ Reagent Version 1 Kit and Chromium Controller (10xGenomics, CA, USA).
In each experiment, 20,000 cells per reaction were loaded for Gel Bead-in-Emulsion (GEM) generation in the GemCode instrument, followed by cell lysis, barcoded reverse transcription of RNA, cDNA amplification, shearing, adaptor and sample index attachment.
scRNA-Seq

treatment_protocol: The injury experiment was performed under in vivo condition for mouse and monkey eyes, and under ex vivo condition for human donor eyes. To mimic central corneal injury, an excimer laser (Allegretto Wave Eye-Q) was used to make a wounding by removing a small portion of the central epithelium and anterior stroma. The full thickness of the limbal epithelium and a layer of stroma beneath were excised to exclude the potential influence of limbal cells. Normal central corneas from contralateral eyes from the same donors without laser injury and limbal excision were used as uninjured controls.

value: central corneal epithelium

value: 24 hours after surgical injury


title: JAK00023 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_60

value: Placebo


title: IRF2BP2 knock-down, biological rep 2


title: JAK00023 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_59


title: JAK00023 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_58


title: Sham_1

source_name: Brain microvessels from sham operated healthy mice

value: healthy

value: sham


title: JAK00025 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_64


title: JAK00022 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_57


title: GD2

value: Bone Marrow-Region 2

value: normal


title: GNK1

value: Bone Marrow-Region 1

value: Female


title: Sample 6

description: single-cell RNA

value: Normal


title: IRF2BP1+IRF2BP2 knock-down, biological rep 2


title: JAK00022 Placebo Day 56 error

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_56

value: Positive

value: FEMALE


title: GD1

value: Male


title: IRF2BP1+IRF2BP2 knock-down, biological rep 1


title: RM_6_3

city: Jinan

first: Shuguo

last: Hou

state: Shandong

address: Fengming Road 1000, Shandong Jianzhu University

department: School of Municipal & Environmental Engineering

institute: Shandong Jianzhu University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values and raw counts for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Cold stratified seeds were surface-sterilized with 70% (v/v) ethanol for 5 min and were sown on ½ MS plates. Seedlings grown on plates vertically in a growth chamber at 20-23°C, 50% humidity, and 75-100 μE m-2 s-1 light with a 12-hr light/12-hr dark photoperiod.

extract_protocol: Total RNAs (5 μg) from two biological replicates were pooled for cDNA library construction. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform with 150-nucleotide pair-end reads.

treatment_protocol: Ten-day-old seedlings grown on ½ MS plates were incubated in 1 mL of liquid ½ MS medium overnight. Seedlings were then treated with or without 1 μM PIP1 for 1 or 6 hr and harvested for RNA isolation.

value: 10-day old

tag: time

value: 6 hr

value: seedling


title: JAK00022 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_55


title: RM_6_2


title: JAK00021 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_54

value: Tofacitinib

value: Negative


title: JAK00021 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_53


title: RM_6_1


title: Sample 7

description: single-cell RNA

value: central corneal epithelium

value: 24 hours after surgical injury


title: GBM S10

description:
GBM
small-RNA

source_name: Brain

value: GBM


title: a485_groseq

city: Los Angeles

first: Arnold

middle: J

last: Berk

state: CA

address: 611 Charles E. Young Dr.

institute: UCLA

description: nascent RNA

data_processing:
GRO-seq reads were aligned with HISTAT2 software to Ad5 and human (hg19) genomes and normalized to the number of reads aligned to hg19.
Pause indexes (TSS to +200 counts)/(+201 to TTS counts) were calculated using HTSeq software.
Bedgraph and wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19 human genome, Adenovirus 5 genome

source_name: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

growth_protocol: Human Bronchial/Tracheal Epithelial Cells (HBTEC, Lifeline Cell Technology Cat# FC-0035; lot# 02196) were grown at 37°C in BronchiaLife Medium Complete Kit (Lifeline Cell Technology catalog number: LL-0023) in a 5% CO2 incubator

extract_protocol:
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 12h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and the indicated antibody. 50uL of protein A/G dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
GRO-seq libraries were constructed using the Illumina Truseq Small RNA Library Prep Kit
GRO-seq

treatment_protocol: HBTEC were grown until they reached confluence. Cells were then incubated 3 days more without addition of fresh media and were Infected with the indicated Ad5-based vectors for 12h, followed by the indicated treatment (DMSO or A-485) for 2h.

tag: passage

tag: ad5 mutant

value: wt E1A


title: A1


title: dmso_groseq

description: nascent RNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: DMSO


title: JAK00021 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_52

source_name: whole blood (paxgene tube)


title: JAK00020 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_51

value: MALE


title: RM_1_2

value: 1 hr


title: RM_1_3


title: RM_1_1


title: JAK00020 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_50


title: Sample 5

description: single-cell RNA

value: Normal


title: a485_brd4

description: genomic DNA and viral DNA

data_processing:
Reads were mapped to the adenovirus 5 or hg19 human genome reference using Bowtie2 software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled into 50 base pair windows and each read was extended by 150 bases and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other.
Bedgraph and wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19 human genome, Adenovirus 5 genome

extract_protocol:
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 12h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and the indicated antibody. 50uL of protein A/G dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

tag: chip antibody

value: Rabbit polyclonal anti-BRD4 Bethyl Cat#A301-985A50


title: A2

tag: tissue _ region

value: Bone Marrow-Region 2

value: normal

value: Female


title: IRF2BP2 knock-down, biological rep 1

value: HeLa


title: JAK00020 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_49


title: JAK00019 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_48

value: Positive


title: dmso_brd4

description: genomic DNA and viral DNA

value: Male


title: dmso_k9

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-H3K9ac Millipore Cat#07-352


title: JRJ032: TP53 mutant thymocytes irradiated, replicate 4

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of biotinylated cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: thymocytes from irradiated mouse

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

extract_protocol: Total RNA was isolated using Rneasy mini columns (Qiagen)

treatment_protocol: Thymocytes were obtained from WT or p53 mutant mice 6h after treatment with 5 Gy whole body radiation

tag: strain

value: thymocytes from irradiated mouse


title: IRF2BP1 knock-down, biological rep 1


title: JRJ031: TP53 mutant thymocytes irradiated, replicate 3


title: JRJ026: TP53 mutant thymocytes non-irradiated, replicate 3

source_name: thymocytes from non-irradiated mouse

value: thymocytes from non-irradiated mouse


title: JRJ030: TP53 mutant thymocytes irradiated, replicate 2


title: RM_0_1

value: 10-day old

tag: genotype

value: untreated

value: 0 hr

value: seedling


title: WT_6_3

tag: age

value: wild type

value: 6 hr


title: a485_k27

description: genomic DNA and viral DNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: wt E1A

value: Rabbit polyclonal anti-H3K27ac Active Motif Cat#39133  Lot#31814008


title: JRJ028: TP53 mutant thymocytes irradiated, replicate 1


title: JRJ027: TP53 mutant thymocytes non-irradiated, replicate 4


title: JAK00019 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_46

value: Tofacitinib

value: MALE


title: WT_6_2


title: dmso_k27

description: genomic DNA and viral DNA

value: DMSO


title: WT_6_1


title: RM_0_3


title: JRJ025: TP53 mutant thymocytes non-irradiated, replicate 2


title: RM_0_2


title: J1a: B4_TNF_168

first: Irina

last: Budunova

state: Illinois

address: 303 E Chicago Ave, Ward Bldg, #9-132

department: Dermatology

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file with raw read counts per gene

source_name: Organotypic raft cultures

growth_protocol: Primary human keratinocytes were seeded onto collagen hydrogels and cultured at the air-liquid interface for up to 11 days. This induces the formation of epidermis tissue.

extract_protocol: total RNA was isolated using Rneasy miRNA kit from flash frozen ORC

treatment_protocol: The control group received BSA 0.1% from days 5-11. For acute TNFalpha treatment, cultures were treated with BSA 0.1% for days 5-10, then treated with TNFalpha for 24 h (acute). For chronic treatment,  tissues received TNFalpha for days 5-11. All treatments were given in the media of the air-liquid interface tissue cultures.

tag: ethnicity

value: African American

value: TNFA 168h

tag: donor

value: donor 9

value: Organotypic raft cultures (ORC) containing keratinocytes


title: JAK00018 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_43

value: Positive

tag: Sex

value: FEMALE


title: J3a: B4_C

value: BSA


title: JRJ024: TP53 mutant thymocytes non-irradiated, replicate 1

value: thymocytes from non-irradiated mouse


title: JAK00019 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_47

tag: stat4 risk allele


title: a485_k9

description: genomic DNA and viral DNA

tag: cell type

value: Male

value: Rabbit polyclonal anti-H3K9ac Millipore Cat#07-352


title: WT_1_3

value: 10-day old

value: wild type

value: 1 hr

value: seedling


title: JAK00018 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_45

value: Tofacitinib


title: JRJ019: WT thymocytes irradiated, replicate 2

value: C57BL6/J WT

value: thymocytes from irradiated mouse


title: JRJ018: WT thymocytes irradiated, replicate 1


title: JRJ017: WT thymocytes non-irradiated, replicate 4


title: JAK00017 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_42


title: H3a: B3_C

value: African American

value: donor 8


title: JAK00018 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_44


title: JAK00017 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_41


title: H2a: B3_TNF_24

value: TNFA 24h


title: JAK00017 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_40


title: H1a: B3_TNF_168

value: TNFA 168h

value: Organotypic raft cultures (ORC) containing keratinocytes


title: WT_0_3

value: untreated

value: 0 hr


title: G3a: B2_C

value: BSA

value: donor 7


title: JAK00015 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_39

value: Positive

value: FEMALE


title: G1a: B2_TNF_168


title: WT_0_2

value: 10-day old

value: wild type


title: JRJ016: WT thymocytes non-irradiated, replicate 3

value: thymocytes from non-irradiated mouse


title: WT_0_1

value: seedling


title: JAK00015 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_37

value: Tofacitinib


title: F3a: B1_C

value: donor 6


title: WT_1_2

value: 1 hr


title: JRJ015: WT thymocytes non-irradiated, replicate 2

value: C57BL6/J WT


title: JRJ014: WT thymocytes non-irradiated, replicate 1


title: tma64∆ [SM010F]

first: Nicholas

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

data_processing:
Multiple sequencing lanes were pooled together to create a single fastq file.
Base calling and demultiplexing was performed at the NIDDK DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD for samples run on theHiseq2500. Demultiplexing was performed using CutAdapt for samples run on the HiSeq3000.
Reads were aligned to a library of RNA genes and those not matching were retained.
Samples sequenced on the HiSeq3000 had PCR duplicates removed according to McGlincy and Ingolia, 2017.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Trimming of consecutive 3'As was not performed for 40S samples.
Replicates for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome). 26-45 nt 5' end aligned for 40S profiling and 25-34 nt 5' end aligned for 80S profiling.

organism: Saccharomyces cerevisiae

source_name: tma64∆_whole cells

growth_protocol: Cells were grown to an OD of ~1.5 for 40S profiling or ~0.6 for 80S profiling and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose gradients to isolate either the 40S peak (40S profiling) or the monosome peak (80S profiling). RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription (rRNA was subtracted using Ribo-Zero after ligation for 40S profiling). cDNAs were then circularized and PCR amplified. (Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos for 80S profiling).
40S ribosome profiling; 80S ribosome profiling

treatment_protocol: Cells were cross-linked with formaldehyde for 1h, spun down, resuspended in lysis buffer, and beaded into liquid nitrogen for 40S profiling. Cells were rapidly vacuum filtered and flash frozen for 80S profiling. Samples were lysed in a freezer mill with lysis buffer.

tag: molecule subtype

value: 80S Ribosome-protected RNA 25-34 nt


title: tma22∆ [SM009F]

source_name: tma22∆_whole cells


title: JAK00014 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_35

value: Placebo


title: WT_1_1


title: JAK00015 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_38


title: G2a: B2_TNF_24

value: African American

value: TNFA 24h

value: Organotypic raft cultures (ORC) containing keratinocytes


title: tma20∆ [SM008F]

source_name: tma20∆_whole cells


title: JAK00014 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_34


title: F1a: B1_TNF_168

value: TNFA 168h


title: Vitrified TE_7

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the bovien reference genome by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference. Genes with FPKM > 0.1 in at least one sample were kept in downstream analysis for Pearson correlation, Principle Component Analysis (PCA) and cluster analysis using R. Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: FASTQ

organism: Bos taurus

source_name: Day 14 embryonic cells

extract_protocol: none provided by the submitter

value: embryonic cells


title: rpl11b∆ [DY181F]

description: Biological replicate of DY180F. Wig files composed of combination of two biological replicates (DY180F and DY181F) are linked to the DY180F records.

source_name: rpl11b∆_whole cells


title: D3a: W4_C

value: Caucasian

value: BSA

value: donor 4


title: E3a: W5_C

value: donor 5


title: JAK00014 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_36

value: Positive

value: FEMALE


title: E1a: W5_TNF_168


title: JAK00013 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_33

value: Tofacitinib

value: Negative


title: JAK00013 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_32


title: Vitrified TE_6


title: Endothelium_Nondiabetic_R2

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

hyb_protocol: According to the manufacturer's instructions (Affymetrix)

data_processing: R/Bioconductor, RMA

source_name: endothelium

label_protocol: Ovation Pico WTA System V2 (NuGEN)

growth_protocol: We used an established high fat model to induce type 2 diabetes in mice. To this end, male C57BL/6J mice consumed a high fat diet containing 60kcal% fat (#D12492, Research Diets Inc) for 4 months.

extract_protocol: total RNA extraction

treatment_protocol: 5000 bone marrow endothelial cells were sorted using FACS

value: bone marrow

value: endothelial cells

value: male

tag: disease state

value: control


title: Endothelium_Diabetic_R3

scan_protocol: According to the manufacturer's instructions (Affymetrix)

tag: tissue

value: diabetes


title: rpl11b∆ [DY180F]

description: Biological replicate of DY181F. Wig files composed of combination of two biological replicates (DY180F and DY181F).

value: 80S Ribosome-protected RNA 25-34 nt


title: Endothelium_Diabetic_R1


title: Endothelium_Nondiabetic_R1


title: Endothelium_Nondiabetic_R3


title: JAK00013 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_31

tag: treatment


title: Vitrified TE_5


title: D1a: W4_TNF_168

value: Organotypic raft cultures (ORC) containing keratinocytes


title: Vitrified TE_4


title: JAK00012 Placebo Day 56 error

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_29

value: Placebo


title: JAK00012 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_30


title: tma22∆ YCplac33-tma22-A105L [DY192Ffx]

description: Biological replicate of DY161Ffx. Wig files composed of combination of two biological replicates (DY161Ffx and DY192Ffx) are linked to the DY161Ffx records.

source_name: tma22∆ YCplac33-tma22-A105L_whole cells

value: tma22{delta} YCplac33-tma22-A105L

value: 40S Ribosome-protected RNA 15-80 nt


title: tma22∆ YCplac33-tma22-C11Y [DY191Ffx]

description: Biological replicate of DY160Ffx. Wig files composed of combination of two biological replicates (DY160Ffx and DY191Ffx) are linked to the DY160Ffx records.

source_name: tma22∆ YCplac33-tma22-C11Y_whole cells

value: tma22{delta} YCplac33-tma22-C11Y


title: C3a: W3_C

value: Caucasian

value: BSA

value: donor 3


title: Vitrified TE_3

value: embryonic cells


title: JAK00012 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_28

value: FEMALE


title: Vitrified TE_2


title: C2a: W3_TNF_24

value: TNFA 24h


title: tma22∆ YCplac33 [DY189Ffx]

description: Biological replicate of DY158Ffx. Wig files composed of combination of two biological replicates (DY158Ffx and DY189Ffx) are linked to the DY158Ffx records.

source_name: tma22∆ YCplac33_whole cells

value: tma22{delta} YCplac33


title: tma22∆ YCplac33-DENR [DY193Ffx]

source_name: tma22∆ YCplac33-DENR_whole cells

value: tma22{delta} YCplac33-DENR


title: JAK00011 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_27

value: Tofacitinib

value: Positive


title: Vitrified TE_1


title: B3a: W2_C

value: donor 2


title: Vitrified embryo_2


title: JAK00011 Tofacitinib Day 56 error

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_26


title: JAK00011 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_25


title: C1a: W3_TNF_168

value: TNFA 168h


title: D2a: W4_TNF_24

value: donor 4

value: Organotypic raft cultures (ORC) containing keratinocytes


title: JAK00010 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_24

value: Negative


title: Vitrified embryo_1


title: tma22∆ [DY187Ffx]

description: Biological replicate of DY155Ffx. Wig files composed of combination of two biological replicates (DY155Ffx and DY187Ffx) are linked to the DY155Ffx records.

value: 40S Ribosome-protected RNA 15-80 nt


title: Fresh TE_5


title: tma20∆ [DY186Ffx]

description: Biological replicate of DY154Ffx. Wig files composed of combination of two biological replicates (DY154Ffx and DY186Ffx) are linked to the DY154Ffx records.


title: tma64∆/tma22∆ [DY185Ffx]

description: Biological replicate of DY137Ffx. Wig files composed of combination of two biological replicates (DY137Ffx and DY185Ffx) are linked to the DY137Ffx records.

source_name: tma64∆/tma22∆_whole cells


title: tma22∆ YCplac33-TMA22 [DY190Ffx]

description: Biological replicate of DY159Ffx. Wig files composed of combination of two biological replicates (DY159Ffx and DY190Ffx) are linked to the DY159Ffx records.

source_name: tma22∆ YCplac33-TMA22_whole cells

value: tma22{delta} YCplac33-TMA22


title: JAK00010 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_23


title: A3a: W1_C

value: Caucasian

value: donor 1


title: tma64∆/tma20∆ [DY184Ffx]

description: Biological replicate of DY136Ffx. Wig files composed of combination of two biological replicates (DY136Ffx and DY184Ffx) are linked to the DY136Ffx records.

source_name: tma64∆/tma20∆_whole cells


title: B1a: W2_TNF_168


title: Fresh TE_4


title: JAK00010 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_22

source_name: whole blood (paxgene tube)


title: Fresh TE_3


title: tma64∆ [DY188Ffx]

description: Biological replicate of DY156Ffx. Wig files composed of combination of two biological replicates (DY156Ffx and DY188Ffx) are linked to the DY156Ffx records.


title: JAK00009 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_21

value: Placebo


title: Fresh TE_2

value: embryonic cells


title: B2a: W2_TNF_24


title: A1a: W1_TNF_168


title: hESC-derived peripheral neuron-Batch B-SARS-CoV-2 infected

city: Seoul

first: Yong Jun

last: Kim

address: 26 Kyungheedaero

department: Department of Pathology

institute: Kyung Hee University

data_processing:
Illumina Real-Time Analysis 3 (RTA3) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie 2 v2.2.5 with following parameters: Seed lenth 22, Seed mismatches 0, Seed extension attempts 15, Max re-seed attempts 2, Interval between seeds S,1.0,1.25, Ambiguous character function L,0.0,0.15, Gaps per read 15, Gap end buffer 4, Ambiguous character penalty 1, Alignment score cutoff L,-0.6,-0.6, Mismatch penalty range Max6 Min2, Rad gap penalties Open5 and extend 3penalties, Reference gap penalties Open5 and extend 3penalties
Normalized by criteria Transcripts Per Million (TPM) using a protocol from Abrams et al., BMC Bioinformatics, 2019. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (A&AC, B&BC)

source_name: Peripheral neurons

growth_protocol: Human embryonic stem cell–derived peripheral neurons were routinely generated by adherent neural crest stem cell differentiation cultures (typically 2–3 × 106 cells into a 24 well plate) on Geltrex coated plastic in Neurobasal medium (Thermo Fisher) supplemented with N2, B27,3uM 100nM LDN193189, 10uM SB431549 and CHIR99021, followed by addition of 20ng/ml NGF, 20ng/ml BDNF, 20ng/ml GDNF, 100uM dbcAMP.

extract_protocol:
Total RNA samples from SARS-CoV-2 uninfected or infected hESC-derived peripheral neurons were harvested using Trizol reagent.
The libraries were prepared for 150 bp paired-end sequencing using TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero H/M/R (Illumina, CA, USA).

treatment_protocol: SARS-CoV-2 (10^4.0 TICD 50/ml, strain NCCP43326) was incubated with peripheral neurons for initial 24 hours, and neurons were incubated for additional 72 hours after wash out of uninfected virus

value: hESC-derived peripheral neurons

value: SARS-CoV-2 infection


title: WT [DY182Ffx]

description: Biological replicate of DY134Ffx. Wig files composed of combination of two biological replicates (DY134Ffx and DY182Ffx) are linked to the DY134Ffx records.

source_name: WT_whole cells


title: Fresh embryo_6


title: hESC-derived peripheral neuron-Batch B-uninfected

value: Uninfected


title: hESC-derived peripheral neuron-Batch A-SARS-CoV-2 infected


title: JAK00009 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_19

data_processing:
Demultiplex to FastQ using bcl2fastq version 2.17.1
Map to hg19 using Tophat 2.1.1
Calculate RPKM using Partek 7.18.0723
ANOVA comparison using Partek 7.18.0723
Paired T-test using Partek 7.18.0723
Genome_build: hg19
Supplementary_files_format_and_content: Excel RPKM, ANOVA and Paired T-test results

extract_protocol:
PAXgene Blood RNA Kit (Qiagen)
TruSeq Stranded mRNA NeoPrep Kit (Illumina)

value: FEMALE


title: Fresh TE_1


title: hESC-derived peripheral neuron-Batch A-uninfected


title: tma22∆ YCplac33-tma22-A105L [DY161Ffx]

description: Biological replicate of DY192Ffx. Wig files composed of combination of two biological replicates (DY161Ffx and DY192Ffx).

value: tma22{delta} YCplac33-tma22-A105L


title: rpl11b∆ [DY183Ffx]

description: Biological replicate of DY135Ffx. Wig files composed of combination of two biological replicates (DY135Ffx and DY183Ffx) are linked to the DY135Ffx records.


title: JAK00008 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_18

value: Tofacitinib


title: JAK00009 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_20


title: tma22∆ YCplac33-TMA22 [DY159Ffx]

description: Biological replicate of DY190Ffx. Wig files composed of combination of two biological replicates (DY159Ffx and DY190Ffx).


title: JAK00008 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_17


title: Endothelium_Diabetic_R2

value: bone marrow

value: endothelial cells

value: male

value: diabetes


title: Fresh embryo_5


title: WTConVLP

city: Cambridge

first: Liane

last: Dupont

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Cambridge Institute of Therapeutic Immunology & Infectious Disease

institute: University of Cambridge

description: ATAC-seq

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/LDUP92/hiv-compaction
Genome_build: GRCh38
Supplementary_files_format_and_content: CRISPR screen: Processed data is the read count statistics produced using MAGeCK. ATAC-seq: Processed data is the BigWig files generated by alignment of filtered reads using BWA-MEM

source_name: WT Jurkat + RAL + virus + control VLP

growth_protocol: CEM-T4 were acquired from the NIH AIDS Reagent Program (Cat. #117) and Jurkat T cells from ATCC (Clone E6-1, TIB-152). All cell lines were cultured at 37°C and 5% CO2 in Iscove's Modified Dulbecco's Medium (IMDM, Sigma-Aldrich) supplemented with 10% fetal calf serum (FCS, Gibco), 1x GlutaMAX (Gibco), and 100 U/mL penicillin/streptomycin (Gibco).

extract_protocol:
CRISPR screen: DNA was isolated using a Zymo Quick-DNA Microprep (sorted sample) or a Qiagen Gentra Puregene kit (unsorted library). ATAC-seq: Chromatin fragments were purified using a MinElute PCR purification kit (Qiagen)
CRISPR screen: sgRNA sequences were amplified and Illumina sequencing adaptors added by two sequential rounds of PCR followed by PCR purification (AMPure XP, Beckman Coulter). Next-generation sequencing was performed on a MiniSeq System (Illumina) using a custom primer. ATAC-seq: Libraries of transposed chromatin fragments were prepared by minimal PCR amplification (8 or 9 total PCR cycles) using custom indexed primers, dual size selected with AMPure XP beads (Beckman Coulter)
CRISPR-Cas9 knockout screen, ATAC-seq

treatment_protocol: For CRISPR screen: 48 x 10^6 Cas9-CEM-T4 cells were transduced with “Vpr target library” sgRNA lentivirus at MOI ~ 0.3. Transduction efficiency was verified by flow cytometry (BFP+) 72 hpi, and sgRNA containing cells were enriched by puromycin selection. On day 7, 48 x 106 cells were transduced at MOI ~ 1.5 with pHRSIN.SFFV-GFP and pHRSIN.SFFV-mCherry by spinoculation in IMDM + 1 µM raltegravir (RAL) and were subsequently maintained in 1 µM RAL for the duration of the screen. The top 0.5% GFP+/mCherry+ cells were selected by fluorescence activated cell sorting (FACS) on day 10, and cells with stably integrated virus were removed by sorting the GFP-/mCherry- population on day 16. On day 18 and 21, respectively, reporter virus infection and sorting of highly expressing cells were repeated, and DNA was isolated immediately after sorting (Zymo Quick-DNA Microprep). An uninfected, unsorted library population was maintained separately at >150-fold library coverage for the duration of the screen, and unsorted library DNA was isolated for reference (Qiagen, Gentra Puregene). For ATAC-seq:  Jurkat T cells were infected at high MOI with a GFP reporter lentivirus in the presence of 1 µM RAL. 48 h post infection,  ATAC-seq was performed following the protocol  published by  Buenrostro et al (2015) without nuclei isolation (Karabacak Calviello, 2019). Briefly, 50,000 Jurkat T cells were resuspended in 50 µL 1x Illumina Tagment DNA with 2.5 µL TDE1 Tagment DNA Enzyme (Illumina). Transposition reactions were incubated in a thermomixer (1 h, 37°C, 1,400 rpm) and chromatin fragments purified using a MinElute PCR purification kit (Qiagen).

value: Jurkat T cells

tag: sample type

value: ATAC-seq

tag: library type

value: ATAC-seq (high diversity amplicon)


title: WTVprVLP

description: ATAC-seq

source_name: WT Jurkat + RAL + virus + Vpr VLP


title: Fresh embryo_4


title: tma22∆ YCplac33-tma22-C11Y [DY160Ffx]

description: Biological replicate of DY191Ffx. Wig files composed of combination of two biological replicates (DY160Ffx and DY191Ffx).

value: tma22{delta} YCplac33-tma22-C11Y

value: 40S Ribosome-protected RNA 15-80 nt


title: JAK00008 Tofacitinib Day 1

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_16

value: Negative


title: Fresh embryo_3

value: embryonic cells


title: tma22∆ YCplac33 [DY158Ffx]

description: Biological replicate of DY189Ffx. Wig files composed of combination of two biological replicates (DY158Ffx and DY189Ffx).

value: tma22{delta} YCplac33


title: Fresh embryo_2


title: JAK00007 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_15

value: Positive

value: MALE


title: WTnoVLP

description: ATAC-seq

source_name: WT Jurkat + RAL + virus


title: tma22∆ [DY155Ffx]

description: Biological replicate of DY187Ffx. Wig files composed of combination of two biological replicates (DY155Ffx and DY187Ffx).

source_name: tma22∆_whole cells


title: tma64∆ [DY156Ffx]

description: Biological replicate of DY188Ffx. Wig files composed of combination of two biological replicates (DY156Ffx and DY188Ffx).

source_name: tma64∆_whole cells


title: JAK00007 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_14


title: Fresh embryo_1

source_name: Day 14 embryonic cells


title: WTnovi

description: ATAC-seq

source_name: Uninfected WT Jurkat


title: JAK00007 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_13


title: Knockdown_Sample_4

city: Kansas City

first: Kaela

last: Varberg

address: 2401 Gillham Road; CMRI 7902.19

institute: Children's Mercy

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Genome_build: human reference genome (GRCh37)

source_name: human trophoblast stem cells

extract_protocol:
Human TS cells were transduced with shControl or shASCL2 lentiviral supernatant and incubated for 24 h. Media was changed 24 h post-transduction and selected with puromycin dihydrochloride (5mg/mL, cat. no. A11138-03, Thermo-Fisher) for two days. Cells recovered for 1-3 days in complete human TS medium prior to splitting for EVT differentiation. RNA was isolated on the eighth day of differentiation.
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: extravillous trophoblast

tag: shRNA

value: ASCL2 shRNA


title: JAK00006 Placebo Day 84

institute: NIAMS/NIH

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_12

value: Placebo


title: Knockdown_Sample_3


title: BR.h11

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw data obtained from the Illumina NextSeq 500 was trimmed and aligned as described in Yuan et al, Genome Medicine, 2018. For each read with a unique, strand specific alignment to exonic sequence, we constructed an address comprised of the sample barcode, unique molecular identifier (UMI) barcode, and gene identifier. The resulting address file only contained the addresses from reads with corresponding single index. We generated a digital gene expression matrix and filter sample barcodes as described previously (Yuan et al. 2018). Briefly, reads with the same sample barcode, UMI and aligned gene were collapsed and sequencing errors in the sample barcode and UMI were corrected to generate a  matrix of molecular counts for each cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file that contains the gene expression counts of each sample.

organism: blank sample

source_name: blank

growth_protocol: PBMCs from donors' blood were isoalted by Ficoll gradient (GE Healthcare). pDCs and pan-DCs wre enriched from PBMCs by negative selection using EasySep Human Plasmacytoid DC Enrichment Kit and EasySep Human pan-DC Pre-Enrichment Kit (STEM CELL Technologies) with ~80-90% purity and cultured in RPMI-1640 complete medium with 2 mM L-gluatamine, 1 mM sodium pyruvate, 1x MEM non-essential amino acids, 100 U/mL penicillin-streptomycin, and 10% fetal bovine serum. MRC5 human lung fibroblasts were cultured under the same conditions. All cells were incubated at 37C with 5% carbon dioxide.

extract_protocol:
pDCs were detached from plates by gentle pipetting and stained for viability with the Zombie Aqua Fixable Vaiability Kit in PBS for 20 mins at 4C. Cells were washed in 4C medium and FAC-sorted to remove MRC5 cells based on forward and side-scatter using an SH800Z sorter (SONY Biotechnology). Total RNA from sorted live pDCs was isolated using an RNeasy Mini Kit (QIAGEN).
Pooled RNA-seq was performed using the low-input RNA-seq protocol reported in Snyder et al, Science Immunology, 2019. All of the steps prior below that  come before the barcoded cDNA libraries are pooled were performed using a BioMek  4000 automated liquid handling robot (Beckman). Briefly, we added deoxyribonucleotides  (dNTPs) (ThermoFisher) to a final concentration of 2 mM and reverse transcriptase primer  to 2 uM followed by primer annealing at 72C for 3 mins. We then added 7.5 uL of reverse  transcription mixture to each well comprised of 2M betaine (Affymetrix), 2x ProtoScript  Buffer (NEB), 12 mM MgCl2 (ThermoFisher), 10 mM dithiothreitol (ThermoFisher), 5.3 U  of Protoscript II reverse transcriptase (NEB), 0.53 U of SUPERaseIN (ThermoFisher), and  2 uM template-switching oligo. The reverse transcription reaction was incubated at 42C  for 90 mins followed by 10 cycles of 50C for 2 mins, 42C for 2 mins, and 70C for 10 mins.  Next, 2 uL of exonuclease I (ThermoFisher) was added to each well (1.875 U of  exonuclease I in water) and the resulting mixture was incubated at 37C for 30 mins, 85C  for 15 mins, and 75C for 30s.

treatment_protocol: Cells were stimulated or co-cultured with 2.5 uM CpG, IL-3, 10 MOI CMV, MRC5 cells, or CMV-infected MRC5 cells for 2, 4, 8, 16, or 32 hours.

tag: donor number

value: blank

tag: time


title: BR.h12


title: Tfcp2l1_ChIPseq_repeat2

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

description:
ChIP DNA
Tfcp2l1_peaks_rep2.txt

data_processing:
Bascalling: RTA 1.8.70.0 and Sequencing Chemistry: Illumina TruSeq 2.0.
Alignment: Illumina Casava 1.8.2.
Processed files are peak files. Peak calling was performed using MACS (1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Peak files in Bed format.

source_name: embryonic stem cells

growth_protocol: A base medium made from a 1:1 mix of DMEM/F12 (Life technologies, 11032-033) and Neurobasal medium (Life Technologies, 21103-049) including N2 supplement (Life Technologies, 17502-048, 1:100 dilution), B27 supplement (Life Technologies (Life Technologies, 17504-044, 1:50 dilution), 0.1 mM 2-mercaptoethanol, 1,000 units/mL of LIF, 3 µM of CHIR99021 (Cayman Chemical) and 1 µM of PD0325901 (Cayman Chemical).

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit.

treatment_protocol: No treatment.

value: wild type

value: embryonic stem cells

tag: growth condition

value: in vitro cell culture in 2i

tag: chip antibody

tag: repeat


title: BR.h10


title: Knockdown_Sample_2