title: HSC_P3_BASAL4

city: Singapore

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School

description:
untreated normal human hepatic stellate cells at passage 3
GENELAB-0001785-2020-NHC

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: Liver

extract_protocol:
Total RNA was extracted from either HSCs or HLFs using Trizol (Invitrogen) followed by Purelink RNA mini kit (Invitrogen) purification.
Illumina Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol: untreated

value: Hepatic stellate cells

tag: passage

value: Early

tag: rin


title: Urine_W_12mo_rep6

status: Public on Sep 28 2021

type: SRA

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

country: USA

institute: University of Kentucky

library_source: transcriptomic

data_processing:
Single-end reads for miRNA were mapped to miRbase version 21 using BowTie aligner with the following parameters: Number of Mismatches: 2, Length of the Seed: 20, Alignment Type: -n, Maximum Allowed Multiple Mappings: 10. The alignment was performed by Norgen Biotek using sRNAbench and sRNAtoolbox.
Supplementary_files_format_and_content: Tab-delimited matrix table with raw read counts for every miRNA

molecule: total RNA

organism: Rattus norvegicus

source_name: Urine

growth_protocol: Male Sprague–Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol:
Total RNA was isolated from urine samples using the Urine Cell-Free Circulating RNA Purification Mini Kit (Cat. 56900, Norgen Biotek, Thorold, ON, Canada) following manufacturer's protocol. Briefly, 2 ml of cell-free urine was mixed with Binding Solution K and transferred to spin column. RNA within the sample was bound to the spin column while the urine was discarded as flow-through. Following application of Lysis Buffer A, the flow-through was precipitated with isopropanol and subjected to repeat centrifugation through the column to allow maximum RNA binding. The column was then washed twice with Wash Solution A, centrifuged to remove left over alcohol, and transferred to a new RNAse-free tube for elution. The concentration of total RNA was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation and sequencing was performed by Norgen Biotek. Briefly, library preparation was done using the Norgen Biotek Small RNA Library Prep Kit (Cat. 63600). Sequencing was performed using the NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cycle Kit) on the Illumina NextSeq 500 platform.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

tag: gender

value: Male

tag: strain

value: Sprague-Dawley

tag: metal

value: W

tag: time


title: Urine_W_12mo_rep5


title: Urine_Co_12mo_rep1

value: Co


title: Urine_W_12mo_rep8


title: HEK293T_CHX_rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

data_processing:
(Replicate 1 only) Paired-end reads were merged using Ngmerge v0.2.
Reads were split according to the sample barcodes (ACGAT for benzamide-treated samples and TTACG for CHX-treated samples) using fastx-toolkit v0.0.14. Barcodes were trimmed and the resulting reads were filtered by length (>8 bp) by cutadapt v1.8.1.
UMIs were trimmed from the reads and attached to the fastq headers using a custom Python code (see McGlincy, N. J.; Ingolia, N. T. Methods 2017, 126, 112–129. for details).
Bases whose quality is below 15 were trimmed, and then the resulting reads shorter than 6 bp were removed by cutadapt v1.8.1. Then, artifacts were removed by fastx-toolkit v0.0.14 using fastx_artifacts_filter command.
Reads were aligned to libraries of human ribosomal RNAs, tRNAs (source: GtRNAdb) and other noncoding RNAs (source: Noncode v6 and Ensembl GRCh38) using Bowtie2 (v.2.3.2) in this order, and reads that aligned to any of those libraries were removed.
Remaining reads were aligned to hg38 genome using STAR v2.7.0e and then sorted using samtools v1.5. PCR duplicates were removed using UMI-tools v1.0.0.
Genome_build: hg38
Supplementary_files_format_and_content: Differential ribosome occupancy was analyzed by DESeq2. The baseMean, log2FoldChange, lfcSE, stat, pvalue and padj of each detected gene were summarized in a csv file.

organism: Homo sapiens

growth_protocol: HEK293T cells were grown in DMEM supplemented with 100 U mL-1 penicillin, 100  μg mL-1 streptomycin and 10% fetal bovine serum.

extract_protocol:
Ribosome profiling was carried out according to the previously described protocol (McGlincy, N. J.; Ingolia, N. T. Methods 2017, 126, 112–129.) with minor modificationsCells were lysed and the lysates were clarified by centrifugation for 10 min at 20,000g, 4 °C. For each condition, lysate containing 30 μg total RNA (determined by Qubit RNA BR Assay Kit, Thermo Fisher Scientific) was used for nuclease footprinting. The digestion was transferred to 8 x 34 mm thick wall polycarbonate ultracentrifuge tube (Beckman 343776) on top of 0.25 mL sucrose cushion. Ribosome recovery was carried out by centrifugation in a TLA 100.1 rotor at 100,000 rpm, 4 °C for 3 h 40 min. The RNA from the pelleted ribosomes was purified first using the Direct-zol RNA Miniprep kit (Zymo Research) and then by precipitating with isopropanol. Size selection by running a 15% polyacrylamide TBE-Urea gel for 65 min at 200 V in 1X TBE, staining the gel for 3 min with 1X SYBR Gold in TBE, and excising the 17 nt – 34 nt region. The size-selected RNA was extracted in the gel extraction buffer and purified by isopropanol precipitation.
The extracted RNA was resuspended in 10 μL 10 mM Tris pH 8, and end repaired by T4 polynucleotide kinase (New England Biolabs, hereafter NEB). Linker ligation was performed using T4 RNA ligase 2 truncated K227Q (NEB) and linkers preadenylated using 5’ DNA adenylatioin kit (NEB). NI-812 linker (barcode CGTAA) was used for footprints from CHX-treated cells and NI-810 (barcode ATCGT) was used for footprints from 8- treated cells. Depletion of the unligated linker from the ligation reaction was carried out by adding 1 μL yeast 5’-deadenylase 10 U/μL and 1 μL RecJ exonuclease 10 U/μL (epicenter definition) directly to the ligation reaction and incubating for 45 min at 30 °C. After pooling and purification of ligations, ribosomal RNA was depleted using RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific) according to the manufacturer’s instruction. The resulting RNA was reverse transcribed using SuperScript III RT (Invitrogen) and the reverse transcription products were separated from the unextended primers and no-insert background products by running a 15% polyacrylamide TBE-Urea gel for 40 min at 180 V. The reverse transcription products were extracted from the excised bands in the DNA gel extraction buffer and were purified by isopropanol precipitation. The resulting cDNA was circularized by CircLigase II (EpiCentre) and was quantified by qPCR. Library construction was carried out by 9 cycles of PCR using Q5 Hot Start High-Fidelity DNA Polymerase (NEB). After purification of the DNA library, library length distribution was analyzed by TapeStation 2200 (Agilent) using High Sensitivity D1000 ScreenTape. The first technical replicate was sequenced for 51 cycles (paired end) on an Illumina MiSeq, and the second replicate was sequenced for 150 cycles (single read) on an Illumina NextSeq.
Ribosome profiiling

treatment_protocol: Cells were grown on 10cm2 tissue culture plates to approximately 90% confluency and were treated for 1 minute with 350 μM benzamide or 350 μM cycloheximide (solution in 0.1% DMSO in PBS) at 37 °C.

tag: tissue

value: kidney

tag: developmental stage

value: embryonic

tag: treatment

value: cycloheximide


title: HSC_P3_BASAL2

first: Benjamin

description:
untreated normal human hepatic stellate cells at passage 3
GENELAB-0001783-2020-NHC

molecule: polyA RNA

tag: cell type


title: Urine_W_12mo_rep7


title: HSC_P3_BASAL1

description:
untreated normal human hepatic stellate cells at passage 3
GENELAB-0001782-2020-NHC


title: Urine_Fe_12mo_rep1

value: Fe


title: mRNAseq_Mock_4h_Rep3

city: Hannover

middle: Erik

last: Nilsson-Payant

address: Feodor-Lynen-Straße 7

department: Experimental Virology

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Research

description:
Sample 6
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 (Samples 1-49) or NextSeq 2000 (Samples 50-54) platform.
Samples 1-42: Raw sequencing reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA) or to the SARS-CoV-2 genome using Bowtie2. Differential gene expression analysis was performed using DESeq2 comparing infedcted samples to mock-infected samples.
Sample 43: Sequencing data were processed with CellRanger v4.0.0 (10X Genomics, Inc). Reads were mapped to a combined human (GRCh38) and SARS-CoV-2 (WuhCor1, NC_045512.2, modified to reflect the USA-WA1/2020 strain, MT246667.1) genome reference using CellRanger count. Raw gene x cell counts matrices were analyzed using Seurat (v4.0.1). After an initial filter to remove cells with fewer than 4,000 UMIs (empty droplets) or greater than 65,000 UMIs (doublets) and percent mitochondrial gene expression less than 5% or greater than 40%, counts data were subject to natural logarithm normalization, cell cycle scoring, highly variable gene selection, gene expression scaling, and dimensional reduction by principal component analysis using the developer’s defaults. UMIs, mitochondrial gene expression percentage, S cell cycle phase score, and G2M cell cycle phase score were regressed during gene expression scaling. Further processing included unsupervised clustering analysis using the FindClusters function (resolution: 0.4) and visualization with Uniform Manifold Approximation and Projection (developer’s defaults). All gene expression violin plots were plotted using natural logarithm normalized counts and heatmaps with z-scaled counts. Cells were classified as infected or uninfected by performing hierarchical clustering using Ward’s minimum variance method on a distance matrix of z-scaled, log normalized viral gene expression per cell with k set to 2. Comparing total viral UMIs per cluster separated cells into high and low viral gene expressing cells, and the cluster with higher viral gene expression was classified as infected.  Differential gene expression (DGE) analyses were conducted using edgeR v3.30.3, with additional modifications for scRNA-Seq data. Gene x cell count matrices were extracted from Seurat objects with infection information as metadata. SARS-CoV-2 viral genes were excluded from all differential gene expression analyses and cell cycle scores were calculated using Seurat’s CellCycleScoring function. For all analyses, genes expressed (i.e. greater than or equal to 1 UMI) in less than 10% of cells for at least one group were excluded from differential gene expression testing. To identify the transcriptional signature in infected cells, differential expression analysis was conducting comparing bystander cells versus infected cells. To mitigate the dramatic differences in host gene expression between infected cells and bystander cells, transcript counts from infected and bystander cells were randomly downsampled to the median transcript counts/cell of the infected cells group. All cells with counts below this value were excluded from differential expression analyses. edgeR linear models included factors for cell cycle score (S phase and G2M phase scores), cellular gene detection rate, and infection status. The resulting significant differentially expressed genes were defined by an adjusted p-value < 0.0001 and an absolute log2 fold-change of > +/-1. Gene set enrichment testing was conducted using the HALLMARK gene sets from the Molecular Signatures database (MSigDB) with the CAMERA function. The parameter ‘use.ranks’ was set to TRUE to minimize assumptions about data structure of scRNA-seq data as compared to bulk RNA-seq or microarray data. Gene set enrichment contrasts were set to compare infected cells versus bystander cells and significantly enriched gene sets were identified using an adjusted p-value of less than 0.001.
Samples 44-48: Quality and adapter filtering was applied to raw reads using ‘trim_galore’ before aligning to human assembly hg38 with bowtie2 using the default parameters. The Picard tool MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove reads with the same start site and orientation. The BEDTools suite (http://bedtools.readthedocs.io) was used to create read density profiles. Enriched regions were discovered using MACS2 and scored against matched input libraries (fold change > 2 and FDR-adjusted p-value < 0.1). A consensus peak atlas was then created by filtering out blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/) and then merging all peaks within 500 bp. A raw count matrix was computed over this atlas using featureCounts (http://subread.sourceforge.net/) with the ‘-p’ option for fragment counting. The count matrix and all genome browser tracks were normalized to a sequencing depth of ten million mapped fragments. DESeq2 was used to classify differential peaks between two conditions using fold change > 2 and FDR-adjusted p-value < 0.1. Peak-gene associations were made using linear genomic distance to the nearest transcription start site with Homer (http://homer.ucsd.edu).
Genome_build: human (hg19 or hg38), SARS-CoV-2 (MN985325.1 or MT246667.1)
Supplementary_files_format_and_content: Comma-separated value files (csv) for raw read count table, raw feature-cell matrux files and bigwig ATAC-seq peak files.

source_name: A549-ACE2 cells

extract_protocol:
Samples 1-42: Cells were homogenized in TRIzol reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit according to the manufacturer's instructions. Sample 43: Cells were trypsinized with 0.25% trypsin and collected as a single cells suspension. Cells were then washed twice with ice cold 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and viability were determined using trypan blue stain and a Countess II automatic cell counter (Thermfisher Scientific). Based on this cell count, a target cell input volume of 3,000 cells was loaded into a Chromium Controller using Chromium Next Gem (Gel Bead-In Emulsion) Single Cell 5’ Library & Gel Bead Kit v1.1 (10x Genomics) according to manufacturer’s instructions.. Samples 44-48: Cells were trypsinized and collected as a single cell suspension in complete DMEM. 50,000 cells were isolated and washed twice with ice cold PBS. Nuclei from washed cell pellets were extracted using lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was performed at 37°C for 30 min using the Nextera DNA Library Prep Kit (Illumina) and transposed DNA was purified using the QIAgen MinElute PCR Purification kit according to the manufacturers’ instructions.
Samples 1-42: TruSeq Stranded mRNA Library Prep Kit (Illumina); Sampls 43: Chromium Single Cell 5’ Library Kit v1.1 (10x Genomics); Samples 44-48: Nextera DNA Library Prep Kit (Illumina)
Samples 1-42: RNA-seq; Sample 43: scRNA-seq; Samples 44-48: ATAC-seq

treatment_protocol: Cells were infected with SARS-CoV-2 (USA-WA1/2020) at the indicated MOI and for the indicated amount of time. Alternatively, mock infected cells were treated with

value: Lung adenocarcinoma

tag: virus

value: Mock

tag: time point

value: 4 h


title: HSC_P6_BASAL2

description:
untreated normal human hepatic stellate cells at passage 6
GENELAB-0001779-2020-NHC

value: Late


title: HSC_P6_BASAL4

description:
untreated normal human hepatic stellate cells at passage 6
GENELAB-0001781-2020-NHC


title: HSC_P6_BASAL1

description:
untreated normal human hepatic stellate cells at passage 6
GENELAB-0001778-2020-NHC


title: Urine_W_12mo_rep3


title: Urine_Co_12mo_rep4


title: Urine_W_12mo_rep2


title: HSC_P3_BASAL3

description:
untreated normal human hepatic stellate cells at passage 3
GENELAB-0001784-2020-NHC


title: Urine_Ta_12mo_rep8

value: Ta


title: NHLF_P6_BASELINE4

description:
untreated normal human lung fibroblasts at passage 6
GENELAB-0001777-2020-NHC

source_name: Lung

value: Lung fibroblasts


title: HSC_P6_BASAL3

description:
untreated normal human hepatic stellate cells at passage 6
GENELAB-0001780-2020-NHC


title: Urine_W_12mo_rep4


title: Urine_Co_12mo_rep2


title: Urine_Ta_12mo_rep6


title: Urine_W_12mo_rep1


title: mRNAseq_Mock_12h_Rep2

description:
Sample 14
TruSeq Stranded mRNA Library Prep Kit
mRNAseq_RawReadCounts.CSV


title: Urine_Ta_12mo_rep7


title: Urine_Ta_12mo_rep5


title: Urine_Ta_12mo_rep4


title: Urine_Ta_12mo_rep3


title: NHLF_P6_BASELINE2

description:
untreated normal human lung fibroblasts at passage 6
GENELAB-0001775-2020-NHC


title: NHLF_P6_BASELINE3

description:
untreated normal human lung fibroblasts at passage 6
GENELAB-0001776-2020-NHC


title: Urine_Ta_12mo_rep1


title: HC_rep05 [L3002_Neu_023]

type: RNA

city: New Delhi

first: Pragyan

last: Acharya

state: Delhi

address: Sri Aurobindo Marg, Ansari Nagar East

department: Biochemistry

country: India

institute: All India Institute of Medical Sciences

description: Gene expression of circulating neutrophil from enriched PMN of Healthy controls (HC)

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sure Print G3 human gene expression array kit (G4851C) for 17 hours at 65°C in a Agilent hybridization system.  The Gene expression wash buffers were pre-warmed at 37°C in water bath. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting, with 3 micron resolution. Dye channel was set to Green (one-color)

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.0.3 (Agilent) using default parameters. The proccessed signal intensiies were further used for gene expression analysis.

source_name: Enriched PMN, Healthy control, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labelling Kit, One-color  (Agilent) according to the manufacturer's instructions, followed by RNAeasy Mini kit column purification (QIAGEN, Valencia, CA).  Dye incorporation (Cyanine 3 dye concentration pmol/L), and cRNA yield and quality (cRNA concentration ng/ul and RNA absorbance ratio 260nm/280nm) were checked with the NanoDrop ND-1000 Spectrophotometer. All samples had specific activity >6.

extract_protocol: RNA was extracted from 1 x10^6 PMN enriched cells, by TRIZOL method. Cleanup of RNA was done using Rneasy Mini Kit (Qiagen). RNA quantification was done using Bioanalyzer.

tag: age

tag: disease state

value: Healthy


title: Urine_Ta_12mo_rep2


title: HC_rep02 [L3002_Neu_020]

source_name: Enriched PMN, Healthy control, replicate 2

value: Female


title: HC_rep03 [L3002_Neu_021]

source_name: Enriched PMN, Healthy control, replicate 3


title: Urine_DU_6mo_rep2

value: DU


title: Urine_Pb_6mo_rep2

value: Male

value: Pb


title: Urine_DU_6mo_rep3

value: Sprague-Dawley


title: NHLF_P3_BSL2

description:
untreated normal human lung fibroblasts at passage 3
GENELAB-0001771-2020-NHC

value: Early


title: Urine_Al_6mo_rep3

value: Al


title: Urine_Pb_6mo_rep3


title: NHLF_P3_BSL1

description:
untreated normal human lung fibroblasts at passage 3
GENELAB-0001770-2020-NHC


title: Urine_Pb_6mo_rep1


title: Urine_Al_6mo_rep1


title: Urine_Al_6mo_rep2


title: NHLF_P3_BSL4

description:
untreated normal human lung fibroblasts at passage 3
GENELAB-0001773-2020-NHC


title: Urine_Cu_6mo_rep3

value: Cu


title: NHLF_P3_BSL3

description:
untreated normal human lung fibroblasts at passage 3
GENELAB-0001772-2020-NHC


title: E9

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Raw sequences were trimmed in order to remove adapter sequences and random nucleotides introduced during the library preparation.
Reads shorter than 15 nucleotides (nt) and larger than 28 nt after trimming were discarded.
We used QuickMIRSeq to align against reference miRNAs
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file with raw counts for each miRNA (rows) and all samples (columns)

source_name: Peripheral venous blood

extract_protocol:
Plasma exosomes and total RNA were obtained using "Total Exosome Isolation Kit (from plasma)" (Invitrogen) and "Total Exosome RNA and Protein Isolation Kit" (Invitrogen)
Illumina TruSeq® Small RNA Library Prep Kit (Illumina Inc) was used to generate sequencing libraries, according to the manufacturer's instructions.

treatment_protocol: Peripheral blood samples were collected in sodium citrate BD Vacutainer® tubes

value: Plasma blood

value: Exosomes

value: Hereditary hemorrhagic telangiectasia type 1 (HHT1)


title: HC_rep04 [L3002_Neu_022]

source_name: Enriched PMN, Healthy control, replicate 4


title: CLD_rep05 [L3002_Neu_017]

description: Gene expression of circulating neutrophil from enriched PMN of CLD patient

source_name: Enriched PMN, CLD patient, sterile, replicate 5

value: Chronic liver disease (CLD)


title: Urine_DU_6mo_rep1


title: CLD_rep04 [L3002_Neu_016]

source_name: Enriched PMN, CLD patient, sterile, replicate 4


title: HC_rep01 [L3002_Neu_019]

source_name: Enriched PMN, Healthy control, replicate 1


title: Urine_Fe_6mo_rep2

value: Fe


title: CLD_rep02 [L3002_Neu_014]

source_name: Enriched PMN, CLD patient, sterile, replicate 2


title: NHLF_P6_BASELINE1

description:
untreated normal human lung fibroblasts at passage 6
GENELAB-0001774-2020-NHC

value: Late


title: Urine_Cu_6mo_rep2


title: Urine_Co_6mo_rep3

value: Co


title: E8


title: Urine_Cu_6mo_rep1


title: Urine_Ni_6mo_rep2

value: Ni


title: Urine_Ni_6mo_rep3


title: E2


title: ACLF_sterile_inflammation_rep05 [L3002_Neu_011]

description: Gene expression of circulating neutrophil from enriched PMN of ACLF patient_sterile inflammation condition

source_name: Enriched PMN, ACLF patient, sterile, replicate 5

value: Acute-on-chronic liver failure (ACLF) sterile inflammation


title: CLD_rep06 [L3002_Neu_018]

source_name: Enriched PMN, CLD patient, sterile, replicate 6


title: ACLF_sterile_inflammation_rep06 [L3002_Neu_012]

source_name: Enriched PMN, ACLF patient, sterile, replicate 6


title: Urine_Fe_6mo_rep3


title: Urine_Co_6mo_rep2


title: Urine_W_6mo_rep2

value: W


title: Urine_W_6mo_rep3


title: E1


title: Urine_Co_6mo_rep1


title: E4


title: E17


title: E15


title: E5


title: Urine_Ta_6mo_rep2

value: Ta


title: CLD_rep03 [L3002_Neu_015]

source_name: Enriched PMN, CLD patient, sterile, replicate 3

value: Male


title: Urine_Ni_6mo_rep1


title: E7


title: Urine_Fe_6mo_rep1


title: ACLF_sterile_inflammation_rep03 [L3002_Neu_009]

source_name: Enriched PMN, ACLF patient, sterile, replicate 3


title: Urine_Ta_6mo_rep3

source_name: Urine


title: CLD_rep01 [L3002_Neu_013]

source_name: Enriched PMN, CLD patient, sterile, replicate 1


title: Urine_Ta_6mo_rep1


title: Urine_DU_3mo_rep2

value: DU


title: Urine_DU_3mo_rep3

value: Sprague-Dawley


title: ACLF_sterile_inflammation_rep04 [L3002_Neu_010]

source_name: Enriched PMN, ACLF patient, sterile, replicate 4


title: Urine_W_6mo_rep1


title: Urine_Al_3mo_rep3


title: Urine_Pb_3mo_rep3

value: Pb


title: Urine_Pb_3mo_rep1


title: Urine_Pb_3mo_rep2


title: E13


title: ACLF_sterile_inflammation_rep01 [L3002_Neu_007]

source_name: Enriched PMN, ACLF patient, sterile, replicate 1

value: Female


title: ACLF_sterile_inflammation_rep02 [L3002_Neu_008]

source_name: Enriched PMN, ACLF patient, sterile, replicate 2


title: Urine_DU_3mo_rep1


title: ACLF_sepsis_rep05 [L3002_Neu_005]

description: Gene expression of circulating neutrophil from enriched PMN of ACLF patient_sepsis condition

source_name: Enriched PMN, ACLF patient, sepsis, replicate 5

value: Acute-on-chronic liver failure (ACLF) sepsis


title: E14

source_name: Peripheral venous blood

value: Plasma blood


title: Urine_Al_3mo_rep1

value: Al


title: Urine_Al_3mo_rep2


title: C9

value: Exosomes

value: Healthy donor


title: ACLF_sepsis_rep06 [L3002_Neu_006]

source_name: Enriched PMN, ACLF patient, sepsis, replicate 6


title: Urine_Cu_3mo_rep3

value: Cu


title: C8


title: E12

value: Hereditary hemorrhagic telangiectasia type 1 (HHT1)


title: Urine_Cu_3mo_rep2


title: Urine_Cu_3mo_rep1


title: E10


title: C7


title: ACLF_sepsis_rep03 [L3002_Neu_003]

source_name: Enriched PMN, ACLF patient, sepsis, replicate 3


title: Urine_Fe_3mo_rep2

value: Fe


title: KO-MI-2

city: La Jolla

first: Rebecca

middle: J.

last: Salamon

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

description: KO MI

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files of reads (ranging ~18-28Mil per sample) and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Cutadapt (Version 3.4) was used to trim adapter sequences, remove unpaired reads, and remove reads less than 36 nucleotides. The cut reads were checked for quality and adapter removal using FastQC.
Reads were aligned to the GRCm39 mouse genome using HiSAT2 (Version 2.2.1)
Gene-level counts were generated using HTSeq (Version 0.13.5)
Differential gene expression analysis was performed DESeq2
Genome_build: GRCm39
Supplementary_files_format_and_content: Differential expression (DE) of genes for each sample group (xlsx)
Supplementary_files_format_and_content: Gene-level counts for each sample group (txt)

organism: Mus musculus

source_name: full heart ventricle

extract_protocol:
Hearts were harvested, full ventricles (above and below MI ligation) were isolated, and immediately homogenized in Trizol (Invitrogen) according to the manufacturer's protocol. Samples were lysed on ice for 20 minutes, then chloroform was added, and the resulting aqueous RNA phase was isolated. Total RNA was processed using RNeasy Fibrous Tissue MiniKit (Qiagen, #74704).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.

value: full heart ventricle

tag: genotype

value: Chrna7 KO

value: myocardial infarction (MI)


title: ACLF_sepsis_rep02 [L3002_Neu_002]

source_name: Enriched PMN, ACLF patient, sepsis, replicate 2


title: KO-MI-1

description: KO MI


title: ACLF_sepsis_rep01 [L3002_Neu_001]

source_name: Enriched PMN, ACLF patient, sepsis, replicate 1


title: WT-MI-4

description: WT MI

value: WT


title: C6


title: Urine_Fe_3mo_rep3

value: Male


title: ACLF_sepsis_rep04 [L3002_Neu_004]

source_name: Enriched PMN, ACLF patient, sepsis, replicate 4


title: KO-MI-3

description: KO MI


title: C2


title: Urine_Ni_3mo_rep3

value: Ni


title: C5


title: KO-MI-4

description: KO MI


title: Urine_W_3mo_rep3

value: Sprague-Dawley

value: W


title: Urine_Ni_3mo_rep2


title: WT-MI-2

description: WT MI


title: Urine_W_3mo_rep2


title: Urine_Ta_3mo_rep3

value: Ta


title: Urine_Fe_3mo_rep1


title: Urine_Ni_3mo_rep1


title: Urine_Co_3mo_rep1

value: Co


title: C3

value: Plasma blood


title: WT-MI-1

description: WT MI


title: A9

value: Hereditary hemorrhagic telangiectasia type 2 (HHT2)


title: Urine_Ta_3mo_rep1


title: C10

value: Exosomes


title: WT-MI-3

description: WT MI


title: Urine_Co_3mo_rep2


title: C1

value: Healthy donor


title: A6


title: A5


title: Urine_Co_3mo_rep3


title: KO-SH-3

description: KO Sham

value: Sham


title: A1


title: Urine_DU_Pre_rep2

value: DU

value: Pre


title: Urine_Cu_Pre_rep2

value: Cu


title: Urine_Ta_3mo_rep2


title: Urine_W_Pre_rep2


title: Urine_Pb_Pre_rep2

value: Pb


title: A16


title: Urine_W_3mo_rep1


title: Urine_Ni_Pre_rep2


title: Urine_Co_Pre_rep2


title: Urine_Al_Pre_rep2

value: Al


title: A4


title: WT-SH-4

description: WT Sham

value: full heart ventricle

value: WT


title: Urine_Ta_Pre_rep2

value: Male


title: KO-SH-4

description: KO Sham

value: Chrna7 KO


title: A15


title: Urine_Cu_Pre_rep1

value: Sprague-Dawley


title: Urine_Pb_Pre_rep1


title: Urine_DU_Pre_rep1


title: KO-SH-2

description: KO Sham


title: Urine_Al_Pre_rep1


title: A13


title: WT-SH-2

description: WT Sham


title: Urine_Co_Pre_rep1


title: KO-SH-1

description: KO Sham


title: A12


title: Urine_Fe_Pre_rep1

value: Fe


title: Urine_Fe_Pre_rep2


title: Urine_W_Pre_rep1

value: W


title: A11

value: Plasma blood


title: Combination_3

city: Chicago

first: Yusuke

last: Tomita

state: Illinois

address: 225 E Chicago Ave Box 18

institute: Northwestern University

description: RNA derived from brain stem

data_processing:
FASTQ files were aligned to the mm10 genome using RNA-STAR 2.7 .
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature with the following HTSeq-count parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
HTSeq-count files were imported into R (https://www.r-project.org/https://www.r-project.org/), genes with < 10 reads base mean were removed, and differential expression analysis was performed with the DESeq2 package using the DESeqDataSetFromHTSeqCount function with default settings. DESeq2 analyses were run comparing the tumors treated with ribociclib and those treated with vehicle.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table in Excel format containing DESeq2 output and DESeq2 normalized abundance measurements for each sample

growth_protocol: RCAS-PDGFA, -H3.3K27M, and -Cre were injected to postnatal day 3 Nestin Tv-a; p53 fl/fl mice, and all the mice were euthanized at the indicated endpoint.

extract_protocol:
Purified RNA was obtained by using Qiagen Rneasy extraction kit and protocol
TruSeq mRNA-Seq Library Prep

treatment_protocol: 21-day treatment with vehicle, ribociclib, trametinib, or combination with ribociclib and trametinib was performed.

value: brain stem

value: Diffuse intrinsic pontine glioma (DIPG)


title: WT-SH-3

description: WT Sham


title: Urine_Ta_Pre_rep1

value: Ta


title: Urine_Ni_Pre_rep1

value: Ni


title: Combination_1

description: RNA derived from brain stem

value: combination with ribociclib and trametinib


title: HEK293T_CHX_rep1

value: kidney

value: embryonic

value: cycloheximide


title: Myotube rep2 [KC2-MT total RNA-seq]

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

department: LBD

country: France

institute: Sorbonne Université, CNRS, Paris, France

data_processing:
Trimmomatic (v0.32.3)
Bowtie2 (v2.2.6.2)
Slice BAM (v2.0)
Filter BAM (v1.1.2)
MultiCovBed (v2.26.0.0)
STAR (Galaxy Version 2.7.8a)
DESeq2 (Galaxy Version 2.11.40.6)
Genome_build: hg19
Supplementary_files_format_and_content: small RNAseq.xlsx : raw count values for each sample
Supplementary_files_format_and_content: small ncRNA.xlsx' contains the candidate number (candidate), chromosome (chr), start position (start), end position (end), raw count for myoblasts (MB), myotubes (MT), Dystrophy myotonic type 1 cells (DM), ENCODE K562 cells (K562), genomic position (type), size of the region in nucleotide (size), the strand (Strand), intron position when available (intron N°), total intron in the gene (intron (total number)), gene name containing the candidate when available (Gene name), and the refseq ID of the gene when available (RefSeq ID)

source_name: Muscle satellite cells differentiated

growth_protocol: We used myoblast (MB) and in vitro differentiated counterpart myotubes (MT) cell lines and a cell line obtained from a patient with dystrophy myotonic type 1 disease (DM11). K562 cells were grown as previously described.

extract_protocol:
Tri Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/type

value: Myotube

value: Muscle satellite cells differentiated


title: HEK293T_benzamide_rep1

value: C13-benzamidyl cycloheximide


title: Combination_4

description: RNA derived from brain stem


title: Myotube rep1 [MT total RNA-seq]


title: 17618X9

city: Salt Lake City

first: Vedran

last: Radojcic

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

description: Bulk RNA sequencing

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

source_name: Sorted CD8-positive T cells

extract_protocol:
Trizol, followed by GeneJet Micro kit
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

value: No GVHD


title: 17618X8

description: Bulk RNA sequencing


title: Combination_2

description: RNA derived from brain stem


title: 17618X6

description: Bulk RNA sequencing


title: Myoblast rep2 [KC1-MB total RNA-seq]

source_name: Muscle satellite cells undifferentiated

value: Myoblast

value: Muscle satellite cells undifferentiated


title: 17618X30

description: Bulk RNA sequencing

source_name: Sorted CD4 Treg T cells


title: 17618X3

description: Bulk RNA sequencing

value: GVHD


title: A10

value: Exosomes

value: Hereditary hemorrhagic telangiectasia type 2 (HHT2)


title: 17618X29

description: Bulk RNA sequencing


title: WT-SH-1

description: WT Sham

value: full heart ventricle

value: WT

value: Sham


title: Ribociclib_4

description: RNA derived from brain stem

value: brain stem

value: Ribociclib

value: Diffuse intrinsic pontine glioma (DIPG)


title: Trametinib_2

description: RNA derived from brain stem

value: Trametinib


title: Trametinib_3

description: RNA derived from brain stem


title: 17618X5

description: Bulk RNA sequencing


title: 17618X7

description: Bulk RNA sequencing


title: 17618X4

description: Bulk RNA sequencing


title: Sample 21_421_MAM

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description:
21_S21
Donor 421 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

data_processing:
Illumina bcl2fastq v2.18.0.12 used for basecalling
Sequenced reads were trimmed for adaptor sequence, unknown bases and low quality regions, then mapped to hg19 and AF004394.1 using STAR aligner.
TPM (Transcripts Per Kilobase Million) was calculated for each of the samples.
Genome_build: hg19; AF004394.1 (HIV)
Supplementary_files_format_and_content: Text files (mapped to human and HIV genome respectively) including raw count, FPKM and TPM for each sample.
Supplementary_files_format_and_content: Matrix table with raw count for every gene and every sample

source_name: hMDM_Methamphetamine before and after infection

growth_protocol: Elutriated human monocytes were cultured in a serum-free media consisting of Macrophage-SFM supplemented with 10 mM HEPES, 50 mg/mL gentamicin, 2 μg/mL ciporflaxin, 1% Nutridoma-SP and 10 ng/mL of recombinant human macrophage colony stimulating factor (MCSF). Complete culture media was half-exchanged on day three and completely exchanged on day five.

extract_protocol:
Day 5 post HIVADA infected hMDM RNA was harvested using Trizol reagent. Post isolation, RNA was cleaned using the RNAeasy clean-up kit. RNA intactness assessed on a Fragment Analyzer. A DNA library was constructed from the RNA using TrueSeq mRNA sample prep V2.
Next Generation Sequencing performed on the Illumina Illumina Nextseq 500

treatment_protocol: Cells were differentiated in the growth protocol media for seven days +/- 100μM methamphetamine (Meth) before infection with HIVADA. At day seven, media was removed, and cells were exposed to serum-free inoculum containing HIVADA for four hours. After four hours, all media containing the virus was removed, and monocytes were washed four times with serum-free media. HIV-1 inoculated hMDMs were placed into a serum-free media consisting of Macrophage-SFM supplemented with 10 mM HEPES, 50 mg/mL gentamicin, 2 μg/mL ciporflaxin, 1% Nutridoma-SP +/- 100μM Meth. A full media exchange was completed on day three post- HIVADA infection with the supernatant reserved for a p24 assay. On day five post-HIVADA infection, all cells and supernatants were harvested. In brief, media was removed, and adherent cells were washed with ice-cold Dulbecco’s phosphate-buffered saline (DPBS). Trizol was added to each well and cells were scraped and transferred to Eppendorf tubes and transferred to -80°C for storage.

tag: subject id

value: Donor 421

value: Human monocyte-derived macrophages (hMDM)

value: Elutriated monocytes

tag: infection

value: human immunodeficiency virus (HIVADA)


title: Myoblast rep1 [MB total RNA-seq]


title: 17618X2

description: Bulk RNA sequencing


title: Trametinib_1

description: RNA derived from brain stem


title: Ribociclib_3

description: RNA derived from brain stem


title: 17618X28

description: Bulk RNA sequencing

value: No GVHD


title: Sample 20_421_CAM

description:
20_S20
Donor 421 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

source_name: hMDM_Methamphetamine after infection

value: Methamphetamine after infection


title: 17618X22

description: Bulk RNA sequencing


title: 17618X23

description: Bulk RNA sequencing


title: Ribociclib_1

description: RNA derived from brain stem


title: 17618X1

description: Bulk RNA sequencing


title: 17618X20

description: Bulk RNA sequencing

source_name: Sorted CD4 Tconv T cells


title: Ribociclib_2

description: RNA derived from brain stem


title: Sample 18_406_MAM

description:
18_S18
Donor 406 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Donor 406

value: Methamphetamine before and after infection


title: Sample 19_421_CAC

description:
19_S19
Donor 421 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection

source_name: hMDM_No Methamphetamine Control

value: No Methamphetamine Control


title: 17618X19

description: Bulk RNA sequencing


title: Vehicle_4

description: RNA derived from brain stem

value: Vehicle


title: Sample 16_406_CAC

description:
16_S16
Donor 406 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection


title: 17618X18

description: Bulk RNA sequencing


title: Sample 17_406_CAM

description:
17_S17
Donor 406 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection


title: Vehicle_3

description: RNA derived from brain stem


title: Sample 15_164_MAM

description:
15_S15
Donor 164 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Donor 164


title: 17618X27

description: Bulk RNA sequencing


title: 17618X17

description: Bulk RNA sequencing


title: 17618X21

description: Bulk RNA sequencing

value: GVHD


title: Sample 14_164_CAM

description:
14_S14
Donor 164 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection


title: 17618X16

description: Bulk RNA sequencing


title: 17618X14

description: Bulk RNA sequencing


title: 17618X11

description: Bulk RNA sequencing


title: 17618X12

description: Bulk RNA sequencing


title: Vehicle_2

description: RNA derived from brain stem


title: 17618X13

description: Bulk RNA sequencing


title: Sample 12_222_MAM

description:
12_S12
Donor 222 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Donor 222


title: Vehicle_1

description: RNA derived from brain stem

value: brain stem


title: Sample 13_164_CAC

description:
13_S13
Donor 164 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection


title: Sample 11_222_CAM

description:
11_S11
Donor 222 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection


title: E4BP4_IgG_CM_RevDKO_ZT22

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

library_source: genomic

data_processing:
The ChIP-Seq data was processed by standard ChIP-Seq pipeline: In brief, the fastq files were first trimmed by cutadapt and aligned by BWA mem, low MAPQ (<=10) and read duplicates were removed by samtools  and picard (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute.). The filtered bam files were used for peak calling by MACS2 for HA-REV-ERBa (FDR<0.05 and FC>2 over DKO) and E4BP4 (FDR < 0.05). ChIPseeker and Homer were used for peak annotation and motif search and plots were visualized by customized R/python scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER V4.9;

molecule: genomic DNA

source_name: Heart

growth_protocol: Hearts from 2-months-old mice were harvested at ZT10 and ZT22 and atria were trimmed.

extract_protocol:
Dual-crosslinked heart cells from 3xHA-Rev-erba or aMHC-Cre(+vs-)/Rev-erba/b ff/ff mice were used for ChIP pull down by anti-HA Magnetic Beads (Thermo Fisher Scientific, #88837) or anti-E4BP4 (CST, #14312).
Immunoprecipitated DNA was subjected to Tn5 (Illumina, 20034197) tagmentation, and PCR amplification (Illumina, #FC-121-1031). PCR products were subjected to SPRIselect (Beckman coulter, #B23318) for size selection and pair-end sequencing on Illumina Hiseq platform.

tag: chip antibody

value: Rabbit IgG CST#3900

value: heart

value: CM-RevDKO

tag: zt


title: E4BP4_IgG_CM_RevDKO_ZT10


title: 17618X15

description: Bulk RNA sequencing


title: 17941x35

description:
Bulk RNA sequencing
17941R_counts.txt

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 98 .
The reference database was created using STAR version 2.7.2c with splice junctions optimized for 125 base pair reads.
Optical duplicates removed from NovaSeq runs via Clumpify v38.34
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

source_name: Sorted NK cells

extract_protocol:
Trizol, column, on column DNase digestion
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

value: GVHD, No Relapse


title: 17941x32

description:
Bulk RNA sequencing
17941R_counts.txt

value: GVHD, Relapse


title: 17941x33

description:
Bulk RNA sequencing
17941R_counts.txt


title: new title

city: qq

first: Pierre

middle: X

last: Ledoux

address: qq

institute: werty

data_processing: asdfasdf

source_name: liver

extract_protocol: sdfasdf

tag: strain

value: normal diet


title: Sample 10_222_CAC

description:
10_S10
Donor 222 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection

value: Human monocyte-derived macrophages (hMDM)

value: Elutriated monocytes

value: human immunodeficiency virus (HIVADA)


title: E4BP4_IgG_RevFloxed_Control_ZT10

value: control


title: 17941x31

description:
Bulk RNA sequencing
17941R_counts.txt

value: No GVHD, No Relapse


title: Sample 9_410_MAM

description:
9_S9
Donor 410 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Donor 410

value: Methamphetamine before and after infection


title: 17941x30

description:
Bulk RNA sequencing
17941R_counts.txt


title: E4BP4_CM-RevDKO_ZT22.Rep2


title: 17941x34

description:
Bulk RNA sequencing
17941R_counts.txt


title: Sample 8_410_CAM

description:
8_S8
Donor 410 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Methamphetamine after infection


title: Paragastric cancer tissue_daiweijing_b

city: Haikou

first: JIAN

last: SONG

state: Hainan

address: 6 Changbin West 4th Street, Xiuying District

country: China

institute: the Affiliated cancer Hospital of Hainan Medical 6 University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Paragastric cancer tissue, More than 5cm away from cancer tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from tissue and gastric fluid samples were extracted using TRIzol reagent

value: Paragastric cancer tissue

tag: gender

value: male


title: Paragastric cancer tissue_pingxueyi_b


title: 17941x29

description:
Bulk RNA sequencing
17941R_counts.txt


title: E4BP4_CM-RevDKO_ZT22.Rep1


title: Sample 7_410_CAC

description:
7_S7
Donor 410 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection

value: No Methamphetamine Control


title: E4BP4_CM-RevDKO_ZT10.Rep3


title: 17941x28

description:
Bulk RNA sequencing
17941R_counts.txt


title: Sample 3_160_MAM

description:
3_S3
Donor 160 hMDMs differentiated in serum free media in the presence of rhMCSF with 100µM METH. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM METH supplemented serum-free media. hMDMs were isolated day 5 post HIV infection

value: Donor 160


title: Paragastric cancer tissue_lincaifu_b

value: female


title: E4BP4_CM-RevDKO_ZT10.Rep2

value: heart

value: CM-RevDKO


title: 17941x27

description:
Bulk RNA sequencing
17941R_counts.txt


title: Paragastric cancer tissue_fufangdi_b


title: Sample 2_160_CAM

description:
2_S2
Donor 160 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA. Post infection, hMDMs and cultured in 100µM methamphetamine (METH) supplemented serum-free media. hMDMs were isolated day 5 post HIV infection


title: E4BP4_CM-RevDKO_ZT10.Rep1


title: 17941x26

description:
Bulk RNA sequencing
17941R_counts.txt


title: Sample 1_160_CAC

description:
1_S1
Donor 160 hMDMs differentiated in serum free media in the presence of rhMCSF. Differentiated hMDMs were infected with HIV-ADA.hMDMs were cultured in serum-free media and isolated day 5 post HIV infection


title: Gastric cancer tissue_daiweijing_a

source_name: Surgical specimens of gastric cancer

value: Gastric cancer tissue


title: Gastric cancer tissue_pingxueyi_a


title: Gastric cancer tissue_lincaifu_a


title: 17941x23

description:
Bulk RNA sequencing
17941R_counts.txt

value: No GVHD, Relapse


title: E4BP4_RevFloxed_Control_ZT22_Rep1


title: U8 - thymus pool 4 - repl. 2

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

description: C015_RSS87_15_U8 S4

data_processing:
All samples passed basic quality check through FASTQC v0.11.5.
FASTQ files were mapped using STAR v2.6.0c based on ENSEMBL reference GRCm38 and ENSEMBL mouse annotation release 92.
Gene counts were directly obtained from STAR using the parameter --quantMode GeneCounts.
Post-mapping quality check was done though QoRTs v1.3.0 14 with additional parameter --genomeBufferSize 50000.
All commands were run using the UNIX command parallel v20161222.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with gene counts (normalized for sequencing depth) for every gene and every sample

source_name: CD4+CD8+TCRb- (DP)

extract_protocol:
Thymi, mediastinal adipose tissuse and aortic arches of five female, 8 week old C57BL/6J mice were collected and pooled. Aortic arches and mediastinal adipose tissue were digested as previously described (PMID: 14597735) and single cell suspensions were generated from all three tissues. 400 viable CD4+CD8b+TCR- cells were sorted into 8ul low-input lysis buffer containing RNaseH inhibitor, dNTPs, and 0.1% Triton X-100 in replicates
Libraries of 200 cells (4 ul) were prepared according to Illuminas's instruction with previously published modifications (PMID: 29956159). In brief, cDNA was amplified for 18 cycles to generate sufficient material for sequencing. Librariers were sequenced at 50 bp single end reads

value: Thymus

value: CD4+CD8+TCRb- (DP)


title: E4BP4_RevFloxed_Control_ZT10_Rep3


title: Gastric cancer tissue_fufangdi_a


title: 17941x22

description:
Bulk RNA sequencing
17941R_counts.txt


title: E4BP4_RevFloxed_Control_ZT22_Rep3


title: U5 - thymus pool 3 - repl. 2

description: C013_RSS87_13_U5 S3


title: E4BP4_RevFloxed_Control_ZT22_Rep2


title: U7 - thymus pool 4 - repl. 1

description: C014_RSS87_14_U7 S4


title: U2 - thymus pool 2 - repl. 2

description: C011_RSS87_11_U2 S2


title: U4 - thymus pool 3 - repl. 1

description: C012_RSS87_12_U4 S3


title: E4BP4_RevFloxed_Control_ZT10_Rep2


title: U1 - thymus pool 2 - repl. 1

description: C010_RSS87_10_U1 S2


title: E4BP4_RevFloxed_Control_ZT10_Rep1


title: KU-Lu-MPPt3 CS cell

city: Sagamihara

first: Dai

last: Sonoda

state: Kanagawa

address: 1-15-1 Kitasato, Minami-ku

country: Japan

institute: Kitasato University School of Medicine

hyb_protocol: 5.2 μg of the cDNA were hybridized for 16 hr at 45℃ on Clariom™ D human Array. The microarrays were washed and stained in a GeneChip Fluidics Station 450 with AGCC software version 3.2.4.

scan_protocol: The microarrays were scanned using a GeneChip Scanner 3000 7G with AGCC software version 3.2.4.

data_processing: The data were analyzed with Transcriptome Analysis Console Software version 4.0.1 (Thermo Fisher Scientific) using SST-RMA algorithm with default analysis settings.

label: biotin

source_name: Lung cancer cell line

label_protocol: Biotinylated and fragmented cDNA were prepared with GeneChip™ WT PLUS Reagent Kit according to the user guide (Thermo Fisher Scientific) from 100 ng total RNA.

growth_protocol: The cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 (Nacalai Tesque, Kyoto, Japan) media supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from the KU-Lu-MPPt3 AD and CS cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

tag: cell line

tag: phenotype

value: clumpy and suspended (CS)

tag: donor age

value: 73years old female


title: E0771 mouse 71

city: Birmingham

middle: M

last: Larimer

state: AL

address: 1824 6th AVE S, WTI 399S

department: Radiology

institute: University of Alabama at Birmingham

description: mouse PanCacner Immune Panel

scan_protocol: Nanostring mouse PanCancer Immune Panel - 20 housekeeping genes, 8 negative controls, 6 positive controls

data_processing: nSolver Advanced Analysis

label: NanoString

source_name: E0771 Breast Cancer

growth_protocol: cells were grown according to manufacturer recommendation. Implanted in mice rght shoulder at 500,000 cells with matrigel.

extract_protocol: Tumors excised post imaging, placed in RNAlater for 24hrs at 4C. Delivered to core.

treatment_protocol: immunotherapy - PD-1 and CTLA-4

tag: imaging point

value: Post-Treatment (Day 5)

tag: hypoxia status

value: Normoxic


title: 17941x24

description:
Bulk RNA sequencing
17941R_counts.txt


title: T3 - thymus pool 1 - repl. 3

description: C003_RSS87_3_T3 S1

tag: tissue

tag: cell type


title: 17941x19

description:
Bulk RNA sequencing
17941R_counts.txt

value: GVHD, Relapse


title: HA-REV-ERBa_Input

tag: age

value: HA Magnetic Beads (Thermo Fisher Scientific, #88837)


title: HA-REV-ERBa_HA-Rev-erba_Rep3


title: 17941x18

description:
Bulk RNA sequencing
17941R_counts.txt

tag: disease state


title: T2 - thymus pool 1 - repl. 2

description: C002_RSS87_2_T2 S1


title: 17941x20

description:
Bulk RNA sequencing
17941R_counts.txt

value: GVHD, No Relapse


title: E0771 mouse 55

description: mouse PanCacner Immune Panel

value: Hypoxic


title: KU-Lu-MPPt3 AD cell

value: adhesive (AD)


title: E0771 mouse 65

description: mouse PanCacner Immune Panel


title: 17941x21

description:
Bulk RNA sequencing
17941R_counts.txt


title: 17941x13

description:
Bulk RNA sequencing
17941R_counts.txt


title: 17941x14

description:
Bulk RNA sequencing
17941R_counts.txt


title: E0771 mouse 17

description: mouse PanCacner Immune Panel


title: F8 - mediastinal adipose tissue  pool 4 - repl. 2

description: C021_RSS87_21_F8 S8

value: Fat


title: F7 - mediastinal adipose tissue  pool 4 - repl. 1

description: C020_RSS87_20_F7 S8


title: E0771 mouse 38

description: mouse PanCacner Immune Panel


title: 17941x12

description:
Bulk RNA sequencing
17941R_counts.txt


title: F5 - mediastinal adipose tissue  pool 3 - repl. 2

description: C019_RSS87_19_F5 S7


title: 17941x15

description:
Bulk RNA sequencing
17941R_counts.txt


title: PC9

value: not provided

value: 45years old male


title: 17941x11

description:
Bulk RNA sequencing
17941R_counts.txt


title: HA-REV-ERBa_HA-Rev-erba_Rep2

value: heart

tag: genotype


title: HA-REV-ERBa_WT_Rep3


title: 17941x10

description:
Bulk RNA sequencing
17941R_counts.txt


title: T1 - thymus pool 1 - repl. 1

description: C001_RSS87_1_T1 S1


title: F1 - mediastinal adipose tissue  pool 2 - repl. 1

description: C016_RSS87_16_F1 S6


title: MC38 mouse 25

description: mouse PanCacner Immune Panel

source_name: MC38 colorectal cancer


title: MC38 mouse 21

description: mouse PanCacner Immune Panel


title: MC38 mouse 17

description: mouse PanCacner Immune Panel


title: 17941x8

description:
Bulk RNA sequencing
17941R_counts.txt

value: No GVHD, No Relapse


title: F4 - mediastinal adipose tissue  pool 3 - repl. 1

description: C018_RSS87_18_F4 S7


title: B3 - mediastinal adipose tissue  pool 1 - repl. 3

description: C006_RSS87_6_B3 S5


title: HA-REV-ERBa_HA-Rev-erba_Rep1


title: E0771 mouse 4

description: mouse PanCacner Immune Panel


title: age-matched virgin mouse mammary gland fibroblasts (non-cultured) replicate 3

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

description:
9482914088_F
amplified total RNA
Ctrl 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation. Processed data file includes p-values, median values and fold-change values.

source_name: fibroblasts from mouse mammary glands, virgin, 12-13 weeks of age

label_protocol: Biotinylated cDNA was prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Mice (strain C57/BL6) were kept in conventional M3 cages bedded with wood chips and paper nesting material in a temperature-controlled environment at 21±1°C, 45-55 % humidity on a 12-hr light/dark cycle. Food and water were provided ad libitum. Mice were allowed a 7-day acclimatisation period after arrival on site prior to experimental use. At 12 weeks of age, females were mated overnight and investigated for plug formation to indicate successful mating. Males were removed at this stage. In parallel, age-matched littermates were kept seperate. Plugged females were left for 72 hours after plug formation before sacrificing them using schedule 1 method. 2nd, 3rd, and 4th mammary glands were immediately removed and one flank used for fibroblast isolation. Fibroblasts were isolated as described by Ibrahim et al., 2017.

extract_protocol: Direct-zol™ RNA MicroPrep (Zymo Research) for freshly isolated fibroblasts (500-2,000 cells) as per manufacturer’s instructions and further described by Ibrahim et al., 2017. RNA amplification was subsequently performed using a NuGen-RNA amplification kit according to the manufacturer's protocol with the advised alterations for use in Illumina Genebead Microarray hybridisation.

treatment_protocol: no treatment was applied

tag: Sex

value: female

value: 12-13 weeks

value: Fibroblasts

tag: culturing method

value: non-cultured

tag: condition

value: virgin


title: 17941x5

description:
Bulk RNA sequencing
17941R_counts.txt

source_name: Sorted CD8-positive T cells


title: B2 - mediastinal adipose tissue  pool 1 - repl. 2

description: C005_RSS87_5_B2 S5

value: CD4+CD8+TCRb- (DP)


title: B1 - mediastinal adipose tissue  pool 1 - repl. 1

description: C004_RSS87_4_B1 S5


title: E0771 mouse 12

description: mouse PanCacner Immune Panel

value: Post-Treatment (Day 5)


title: LHA sample pool 2

city: Chapel Hill

first: Marcus

middle: Luis

last: Basiri

state: NC

address: 115 Mason Farm Road

institute: UNC Chapel Hill

description: pooled live single-cell suspension generated from LHA tissue of two animals (male and female) prior to library generation

data_processing:
Demultiplexing was performed with 1 mismatch allowed using Illumina bcl2fastq v2.18.0.12. Initial read processing and generation of digital expression matrices was performed using 10X Genomics Cell Ranger v3.1.0 with 128 GB of memory on 24 cores. Sequences were aligned to a modified mm10 3.0.0 genome assembled with eYFP and tdTomato transgenic sequences. The reference sequences for eYFP and tdTomato were taken from Addgene plasmids #26972 and #59462, respectively and included the entire region from the start codon to the end of the 3’ UTR on the (+) strand. Coverage was assessed with SAMtools v1.10 (Li et al., 2009).
Genome_build: mm10 3.0.0
Supplementary_files_format_and_content: Data is provided as HDF5 matrices generated by Cell Ranger v3.1.0

source_name: live single-cell suspensions from fresh brain tissue

extract_protocol:
C57BL/6J mice (n = 6, 3 male/3 female, 6-8 weeks old at time of surgery) were injected bilaterally with retroAAV2-hSyn-eYFP in LHb and retroAAV2-CAG-tdTomato in VTA (300-400 µL).  Approximately six weeks later, the mice were deeply anesthetized with sodium pentobarbital and phenytoin sodium and transcardially perfused with 10 mL ice-cold NMDG-aCSF containing 96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ascorbate, 3 mM Na+pyruvate, 0.6 mM glutathione-ethyl-ester, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4; pH 7.35–7.40, 300-305 mOsm. Six 280 µm sections through the LHA were collected in NMDG-aCSF on a vibratome. Sections recovered in NMDG-aCSF containing 500 nM TTX, 10 μM APV, 10 μM DNQX (NMDG-aCSF-R) at room temperature for 40 minutes. After recovery, LHA tissue was isolated with tissue punches and incubated in NMDG-aCSF-R containing 1.0 mg/mL pronase for 50 minutes at room temperature. Following digestion, tissue from all animals was transferred to 1.0 mL NMDG-aCSF-R supplemented with 0.05% BSA (NMDG-aCSF-BSA), pooled, and mechanically dissociated with a patch pipet fire-polished to an internal diameter of 200-300 μm. The suspension was washed in 12 mL NMDG-aCSF-BSA, sedimented at 220 xg for 6 minutes at 18ºC. Dead cells and cellular fragments were removed using a MACS® Dead Cell Removal Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) using 100 μL of dead cell removal beads and one MACs LS column following the standard manufacturer protocol. Following the final wash, cells were sedimented at 220 xg for 6 minutes at 4ºC and resuspended in PBS containing 0.05% nuclease-free BSA for a final concentration of 700-800 cells/μL.
Single-cell RNA-sequencing was performed using Chromium Single Cell 3' v3 chemistry (10X Genomics, Pleasanton, CA) following manufacturer recommendations unless otherwise noted. Approximately 16,000-18,000 pooled cells were loaded into an individual well of a Single Cell B Chip, with three wells used in total for three reactions. cDNA amplification and sample indexing were each performed using 11 cycles. Library size distribution and concentrations were determined with an Agilent 4200 Tapestation High Sensitivity D5000 ScreenTape and a Thermo Scientific Qubit dsDNA HS Assay, respectively. Each reaction library was sequenced on an individual lane of an Illumina HiSeq 4000 using 2x150 chemistry following the standard 10X Genomics v3 paired-end configuration by Genewiz, Inc. (South Plainfield, NJ). Between approximately 370-430 million reads were generated per lane with a mean quality score >32 across all lanes.

value: lateral hypothalamic area


title: age-matched virgin mouse mammary gland fibroblasts (non-cultured) replicate 1

description:
9482914088_B
amplified total RNA
Ctrl 1


title: D8 - aortic arch pool 4 - repl. 2

description: C027_RSS87_27_D8 S12

value: Arch


title: LHA sample pool 3


title: MC38 mouse 10

description: mouse PanCacner Immune Panel

value: Normoxic


title: 17941x16

description:
Bulk RNA sequencing
17941R_counts.txt


title: 17941x9

description:
Bulk RNA sequencing
17941R_counts.txt


title: LG021: MAVS -/-, 24hpi TBEV Rep 3

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

description: Rep 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b) with parameter --outFilterMismatchNMax 2 --quantMode GeneCounts. Gene abundance was also determined by STAR using Ensembl GTF annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene in each sample

source_name: primary astrocytes

growth_protocol: Brains from newborn mice were dissected at day 3 post birth, meninges and blood vessels were removed using a stereomicroscope. Next, the brains were minced and digested with 0.1% trypsin and 0.25% DNAse, single cell suspensions were seeded in precoated poly-L-lysine flasks in DMEM with 1% penicillin/streptomycin supplemented with 10% FCS. Medium was changed on day 1 and subsequently every 3 days. Astrocytes were isolated after removing microglia and oligodendrocyte by over-night shaking at 37 °C (170 rpm), followed by cytosine arabinoside treatment for 3 days. Astrocytes were detached by trypsin-EDTA treatment and plated into a 24-well plate.

extract_protocol:
RNA was isolated from WT and MAVS-/- astrocytes either untreated or TBEV infected for 12 or 24 hours. RNA was extracted using Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were inoculated with a MOI of 1 of TBEV in serum- and antibiotic free DMEM medium for 1 hour at 370C, then washed with warm PBS and incubated with the respective culture media. At 12 and 24 hours post infection, supernatants were collected and the adhering cells for RNA analyses were then harvested and lysed by TRIzol.

value: Brain

value: Astrocytes

value: MAVS -/-

tag: treatment

value: 24hpi TBEV


title: D5 - aortic arch pool 3 - repl. 2

description: C025_RSS87_25_D5 S11


title: HA-REV-ERBa_WT_Rep2

tag: chip antibody

value: HA Magnetic Beads (Thermo Fisher Scientific, #88837)

tag: zt


title: E0771 mouse 22

description: mouse PanCacner Immune Panel

value: Hypoxic


title: 18740X37

description:
Bulk RNA sequencing
18740R_counts.txt

value: No GVHD, No Relapse


title: LG020: MAVS -/-, 24hpi TBEV Rep 2

description: Rep 2

tag: strain


title: D4 - aortic arch pool 3 - repl. 1

description: C024_RSS87_24_D4 S11


title: D2 - aortic arch pool 2 - repl. 2

description: C023_RSS87_23_D2 S10


title: HA-REV-ERBa_WT_Rep1

value: heart


title: 18740X36

description:
Bulk RNA sequencing
18740R_counts.txt


title: 17941x2

description:
Bulk RNA sequencing
17941R_counts.txt

value: No GVHD, Relapse


title: LG019: MAVS -/-, 24hpi TBEV Rep 1

description: Rep 1


title: 17941x4

description:
Bulk RNA sequencing
17941R_counts.txt


title: day3-pregnant mouse mammary gland fibroblasts (non-cultured) replicate 3

description:
9482914088_E
amplified total RNA
Preg 3

source_name: fibroblasts from mouse mammary glands, 3 days pregnancy, 12-13 weeks of age

value: female

value: 12-13 weeks

value: Fibroblasts


title: D1 - aortic arch pool 2 - repl. 1

description: C022_RSS87_22_D1 S10

value: CD4+CD8+TCRb- (DP)


title: Beta-TC-6 cells, siNF90-NF45-2

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: Following fragmentation and terminal biotin-labeling, 5.5 ug of biotin-labeled ss-DNA fragment were hybridized for 20 hr at 48C on GeneChip Mouse Gene 2.1 ST Array Strip. GeneChips were washed and stained in the Fluidics Station in GeneAtlas system (Affymetrix).

scan_protocol: GeneChips were scanned using the imaging station in GeneAtlas system (Affymetrix).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software (ThermoFisher, USA).

source_name: Beta-TC-6 cells, transfected with siRNA targeted to NF90-NF45

label_protocol: ssDNA were prepared according to the standard Affymetrix protocol from 250 ng of total RNA (GeneChip WT PLUS Reagent Kit, Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays, Affymetrix).

growth_protocol: Beta-TC6 cells were cultrured in  Dulbecco’s Modified Eagle’s Medium (DMEM) containing with 25 mM glucose supplemented with 15% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNAs were prepared from Beta-TC6 cells transfected with siRNAs by miRNeasy kit (QIAGEN).

treatment_protocol: Mixture of three RNAi duplexes that targeted to NF90-NF45 and siRNA negative control were transfected into Beta-TC6 cells by Lipofectamin RNAi MAX reagent (Invitrogen, USA).

tag: cell line

value: Pancreatic beta cells

value: siRNA targeted to NF90-NF45


title: LG018: MAVS -/-, 12hpi TBEV Rep 3

description: Rep 3

value: 12hpi TBEV


title: LHA sample pool 1

value: lateral hypothalamic area


title: A3 - aortic arch pool 1 - repl. 3

description: C009_RSS87_9_A3 S9

value: Arch


title: MC38 mouse 14

first: Benjamin

description: mouse PanCacner Immune Panel

value: Post-Treatment (Day 5)


title: age-matched virgin mouse mammary gland fibroblasts (non-cultured) replicate 2

description:
9482914088_D
amplified total RNA
Ctrl 2

value: non-cultured

value: virgin


title: 18740X20

description:
Bulk RNA sequencing
18740R_counts.txt


title: MC38 mouse 7

description: mouse PanCacner Immune Panel

value: Normoxic


title: 18740X19

description:
Bulk RNA sequencing
18740R_counts.txt


title: MC38 mouse 12

description: mouse PanCacner Immune Panel

value: Hypoxic


title: day3-pregnant mouse mammary gland fibroblasts (non-cultured) replicate 2

description:
9482914088_C
amplified total RNA
Preg 2


title: LG015: MAVS -/-, uninfected Rep 3

description: Rep 3

value: Brain

value: Astrocytes

value: MAVS -/-

value: uninfected


title: 17941x1

description:
Bulk RNA sequencing
17941R_counts.txt

value: No GVHD, Relapse


title: Beta-TC-6 cells, siNTC-2

source_name: Beta-TC-6 cells, transfected with siRNA negative control

value: siRNA negative control


title: AEP3

city: Beijing

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

institute: Institute of Biophysics

description:
Stromal_Immune_cells_metadata.csv.gz
Stromal_Immune_cells_normalized_expression.csv.gz
Monocyte_microglia_cells_metadata.csv.gz
Monocyte_microglia_cells_normalized_expression.csv.gz

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger( v3.0.2)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
SCANPY workflow
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with csv/tsv format

source_name: human ependymoma

extract_protocol:
Fresh ependymoma samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS;Frozen tumor tissue was homogenized into small cell pellets using a glass tissue grinder
Chromium™ Single Cell 3’ Reagent Kits v2 and v3

value: human ependymoma


title: A1 - aortic arch pool 1 - repl. 1

description: C007_RSS87_7_A1 S9

value: CD4+CD8+TCRb- (DP)


title: Donors_0min_2 [DE77NGSUKBR108979_S270]

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Batch correction
Flooring
Genome_build: mm10
Supplementary_files_format_and_content: normalized and raw counts

source_name: Microglia

growth_protocol: Primary mouse microglia were routinely isolated from neonatal mice. Cells of two brains were plated into T75 flasks and cultured for 7-10 days in DMEM supplemented with 10% FCS, 1% P/S and 1% L929 cell supernatant. Loosely attached mature microglia were shaken off the astrocytic layer and used for experiments.

extract_protocol:
RNA was isolated via Qiagen miRNeasy (micro)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 50bp single reads, 15mio reads deep per sample, Illumina HiSeq2500

treatment_protocol: Donors (typically 10 Mio. per petri dish) and Acceptors (typically 2 Mio. per T25 flask) were seed and allowed to adhere overnight. Donors were treated with 1 µM Atto-488-labeled alpha-synuclein for 14 hrs. Acceptors were labelled with CellTracer Violet for 15 min. Following labelling donor and acceptor populations were co-cultured for 15, 30, 60, 150 and 300 min. Co-cultures were sorted back into their original “donor” and “acceptor” cell populations by flow cytometrical cell sorting and RNA was collected using 700 µl Trizol.

value: primary mouse microglia

tag: passages

tag: group


title: LG016: MAVS -/-, 12hpi TBEV Rep 1

city: Hannover

description: Rep 1

value: 12hpi TBEV


title: LG014: MAVS -/-, uninfected Rep 2

description: Rep 2


title: day3-pregnant mouse mammary gland fibroblasts (non-cultured) replicate 1

description:
9482914088_A
amplified total RNA
Preg 1

value: female

value: 12-13 weeks

value: Fibroblasts


title: 18740X35

description:
Bulk RNA sequencing
18740R_counts.txt

source_name: Sorted CD4 Tconv T cells

value: No GVHD, No Relapse


title: LG017: MAVS -/-, 12hpi TBEV Rep 2

description: Rep 2


title: D7 - aortic arch pool 4 - repl. 1

description: C026_RSS87_26_D7 S12

value: Arch


title: 18740X1

description:
Bulk RNA sequencing
18740R_counts.txt


title: Beta-TC-6 cells, siNF90-NF45-1

value: Pancreatic beta cells

value: siRNA targeted to NF90-NF45


title: A2 - aortic arch pool 1 - repl. 2

description: C008_RSS87_8_A2 S9


title: LG009: WT, 24hpi TBEV Rep 3

description: Rep 3

value: Brain

value: Wild type

value: 24hpi TBEV


title: AEP2


title: MC38 mouse 4

description: mouse PanCacner Immune Panel

tag: imaging point

value: Post-Treatment (Day 5)

value: Normoxic


title: Acceptors_0min_2 [DE07NGSUKBR108978_S269]


title: 18740X3

description:
Bulk RNA sequencing
18740R_counts.txt


title: SE3


title: AEP1


title: Acceptors_150min_2 [DE88NGSUKBR108975_S266]


title: Donors_150min_2 [DE18NGSUKBR108974_S265]


title: Donors_300min_2 [DE61NGSUKBR108976_S267]


title: SE1


title: 15065X38

description: Bulk RNA sequencing

source_name: Sorted CD4 Treg T cells

value: No GVHD


title: Acceptors_300min_2 [DE34NGSUKBR108977_S268]


title: 15065X37

description: Bulk RNA sequencing


title: LG007: WT, 24hpi TBEV Rep 1

description: Rep 1

value: Astrocytes


title: LG006: WT, 12hpi TBEV Rep 3

description: Rep 3


title: 18740X26

description:
Bulk RNA sequencing
18740R_counts.txt


title: 15065X39

description: Bulk RNA sequencing


title: LG008: WT, 24hpi TBEV Rep 2

description: Rep 2


title: LG003: WT, uninfected Rep 3

description: Rep 3

value: uninfected


title: 15065X34

description: Bulk RNA sequencing


title: EPN6

value: human ependymoma


title: LG013: MAVS -/-, uninfected Rep 1

description: Rep 1

value: MAVS -/-


title: EPN9


title: 15065X35

description: Bulk RNA sequencing


title: 15065X33

description: Bulk RNA sequencing


title: Acceptors_60min_2 [DE45NGSUKBR108973_S264]

value: primary mouse microglia


title: LG002: WT, uninfected Rep 2

description: Rep 2


title: Beta-TC-6 cells, siNTC-1

value: siRNA negative control


title: 15065X32

description: Bulk RNA sequencing

value: GVHD


title: SE2


title: LG004: WT, 12hpi TBEV Rep 1

description: Rep 1

value: 12hpi TBEV


title: Acceptors_30min_2 [DE02NGSUKBR108971_S262]


title: 15065X30

description: Bulk RNA sequencing


title: EPN8


title: EPN4


title: 15065X36

description: Bulk RNA sequencing


title: EPN3


title: 2uM-R3-TERT

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

institute: Jinan University

data_processing:
Library strategy: CUT&Tag
Basecalls performed using CASAVA version 1.8
CUT&Tag reads were aligned to the mm10 genome assembly using Bowtie2
Data were filtered using PICARD with the following setting: M=0.5, REMOVE_DUPLICATES=True
Peaks were called using MACS version 2.1.2 with the following setting:  band width = 300, model fold = [5, 50], q-value cutoff = 5.00e-02, Range for calculating regional lambda = 10000 bps.
Normalized abundance was performed by MACS version 2.1.2 with the following setting: binsize=10, normalization with RPGC, extendReads p=12.
Combined three replicates peaks  using MACS version 2.1.2
Identified differentially binding peaks by MACS version 2.1.2 with the following setting: g=60, C=1.0, l=120.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of the diferentially binding peaks  in MS Excel format with content including chromosome, peak coordinates,  peak score, annotation, distance to TSS, gene id, gene names, gene description and gene types.

source_name: Embryonic primary neurons

growth_protocol: Cerebral cortices and hippocampus were dissected from the E15-18 embryos of C57 BL/6 pregnant mice. Primary neurons were normally cultured in Neurobasal medium supplemented with 2% B27 and glutamine 2 mM (Thermo Scientifics) and incubated at 37 °C in a humidified 5% CO2-containing atmosphere.

extract_protocol:
Cells  were immobilized on magnetic beads and incubated with antibodies, followed by ChiTag and tagmentation.
Libraries were prepared according to instruction from the NovoNGS CUT&Tag 2.0 High-Sensitivity Kit (for Illumina) (Cat. # N259-YH01). Briefly, DNA was purified with MinElute columns (Qiagen 28006) and eluted in 21 μL of elution buffer and mixed with 2 μL each of 10 μM indexed i5 and i7 primers and 25 μL of NEBNext HiFi 2x PCR Master mix. Libraries were amplified with the recommended conditions by the Kit. Library DNA was purified with MinElute columns (Qiagen 28006). CUT&Tag libraries were quantified by Qubit and DNA fragment size was determined by Agilent Bioanalyzer, and pair-end sequencing was performed with an Illumina NovaSeq 6000 syste following the manufacturer's protocols.

treatment_protocol: Three replicates were treated with vehicle control (DMSO) or 2 uM BIBR1532 for 24 hours.

value: brain cortical and hippocampal neurons

value: Embryonic E15-18

tag: cut&tag antibody

value: Anti-TERT ( Abcam (ab191523)


title: EPN7

tag: tissue


title: 2uM-R1-TERT


title: EPN2


title: Acceptors_15min_2 [DE56NGSUKBR108969_S260]

tag: cell type


title: LG001: WT, uninfected Rep 1

description: Rep 1

value: Brain


title: 15065X26

description: Bulk RNA sequencing


title: EPN5

tag: age


title: 15065X31

description: Bulk RNA sequencing

tag: disease state


title: LG005: WT, 12hpi TBEV Rep 2

description: Rep 2

tag: genotype

value: Wild type


title: Donors_15min_2 [DE83NGSUKBR108968_S259]


title: XN2289_LLX-CTRLsh

city: Cambridge

first: Cristina

last: Pina

address: Long Road

department: Department of Haematology Cambridge Biomedical Campus NHS - Blood and Transplant

institute: University of Cambridge

data_processing:
The raw fastq files were processed using RSEM v1.2.31 workflow.
The workflow uses STAR aligner to align processed reads to the reference human genome assembly GRCh37.
Workflow generates measures of expected count, TPM and FPKM values for gene ids in each sample.
R package edgeR was further used to obtain differentially expressed genes with 10% FDR values.
Genome_build: Human genome GRCh37
Supplementary_files_format_and_content: *.genes.results.txt: Gene abundances obtained from RSEM workflow for each sample processed.

source_name: Cord blood cells

extract_protocol:
Trizol manufacturer's protocol using linear polyacrylamide as a carrier.
NuGen Ovation RNA-seq kit with incorporated DNase treatment as per manufacturer's instructions.

value: CD34+ HSC and progenitors

tag: shRNA

value: Control non-targeting


title: 0uM-R1-TERT

value: untreated


title: 15065X23

description: Bulk RNA sequencing

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

extract_protocol:
Trizol, followed by GeneJet Micro kit
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

value: No GVHD


title: XN2218_KAT2Ash81


title: Donors_TW_300min DE96NGSUKBR114166

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Batch correction
Flooring
Genome_build: mm10

extract_protocol:
RNA was isolated via Qiagen miRNeasy (micro)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 100bp single reads, 15mio reads deep per sample, NovaSeq 6000

treatment_protocol: Donors (typically 0.25 Mio. per Well in a 24 Well plate) and Acceptors (typically 6 Mio. in a T25 flask) were seed and allowed to adhere overnight. Donors were treated with 1 µM Atto-488-labeled alpha-synuclein for 14 hrs. Acceptors were labelled with CellTracer Violet for 15 min. Following labelling donor and acceptor populations were co-cultured for 15, 30, 60, 150 and 300 min without direct cell-cell contact. RNA of "donor" and "acceptor" cell populations was collected using 700 µl Trizol.


title: Untreated_Ctrl_2 [DE67NGSUKBR108965_S256]


title: XN2218_LLX-CTRLsh


title: aSyn_Donor_2 [DE40NGSUKBR108966_S257]


title: Donors_30min_2 [DE29NGSUKBR108970_S261]


title: 2uM-R2-TERT


title: Donors_TW_0min DE95NGSUKBR114184


title: 15065X28

description: Bulk RNA sequencing


title: 15065X27

description: Bulk RNA sequencing


title: 15065X29

description: Bulk RNA sequencing


title: Acceptors_TW_15min DE94NGSUKBR114202


title: 0uM-R3-TERT


title: EPN_20181210

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger( v3.0.2)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

extract_protocol:
Human ependymoma samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2

value: ependymoma


title: Donors_150min_1 [DE62NGSUKBR108958_S249]


title: Donors_0min_1 [DE24NGSUKBR108963_S254]


title: 15065X18

description: Bulk RNA sequencing


title: Untreated_Ctrl_2 [DE94NGSUKBR108964_S255]


title: Acceptors_30min_1 [DE46NGSUKBR108955_S246]


title: Acceptors_300min_1 [DE78NGSUKBR108961_S252]


title: SPT20_1

data_processing:
ChIP-seq reads were aligned to GRCh38 human genome assembly using BWA algorithm.
MACS2 peak-calling algorithm was used to call peaks.
P-value cut-off for peak detection was set to 0.01 and FDR value was set to 0.05.
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: Bedgraph files generated by MACS2 for each sample.

source_name: Blood cells

extract_protocol:
Samples were cross-linked with 1% formaldehyde, immunoprecipitated with immune sera raised against human SPT20 and human ZZZ3 as described (Krebs et al Mol Cell 2011; 44: 410) and captured in Invitrogen protein A/G magnetic beads. After reverse cross-link, pulled-down DNA was purified using a Zymo Research kit, in parallel with 2.5% input chromatin DNA, and used for library preparation.
NextFlex ChIP-seq library preparation kit - standard protocol

tag: antibody


title: 15065X17

description: Bulk RNA sequencing


title: 15065X19

description: Bulk RNA sequencing


title: Donors_30min_1 [DE73NGSUKBR108954_S245]


title: Acceptors_0min_1 [DE51NGSUKBR108962_S253]


title: Acceptors_TW_30min DE84NGSUKBR114188


title: Donors_60min_1 [DE19NGSUKBR108956_S247]


title: 15065X24

description: Bulk RNA sequencing


title: ZZZ3_1


title: XN2289_KAT2Ash81


title: 15065X16

description: Bulk RNA sequencing


title: Donors_300min_1 [DE08NGSUKBR108960_S251]


title: 0uM-R2-TERT


title: Acceptors_150min_1 [DE35NGSUKBR108959_S250]


title: Donors_15min_1 [DE30NGSUKBR108952_S243]


title: 15065X20

description: Bulk RNA sequencing


title: 15065X22

description: Bulk RNA sequencing


title: Donors_TW_60min DE79NGSUKBR114181


title: Acceptors_TW_60min DE74NGSUKBR114174


title: Acceptors_TW_150min DE78NGSUKBR114199


title: 15065X12

description: Bulk RNA sequencing


title: Donors_TW_30min DE89NGSUKBR114195


title: Untreated_Ctrl_1 [DE14NGSUKBR108949_S240]


title: ST88 cell, BRD2  ChIP, sh Ctr, number 1

city: Derio

first: Jose

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
The sequencing data were mapped to the hg38 genome assembly via Bowtie.
Biological replicates merged and peak calling was performed using Model-based analysis of ChIP-seq (MACS) 2 (Zhang et al., 2008) to identify regions of ChIP-Seq enrichment over background (input) with an enrichment threshold of adjusted p-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Peaks called from merged biological replicates by MACS2 are submitted as tab separated text files with ".broadPeak" extension.

source_name: Cancer cell line

growth_protocol: Human MPNST cell line were maintained in Dulbecco’s modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (Thermo Fisher Scientific) and 1% (v/v) antibiotic/antimycotic (Thermo Fisher Scientific) under standard conditions of 37 ºC and 5% CO2.

extract_protocol:
PCR purification kit (Qiagen).
Sequencing libraries were prepared following TruSeq® ChIP Sample Preparation Guide with the corresponding kit (Illumina Inc.).  ChIPseq libraries were single-read sequenced for 51 nucleotides in a HiSeq2500 (Illumina Inc.)

treatment_protocol: Chromatin immunoprecipitation was performed essentially as described (Fontanals-Cirera et al., 2017). In brief, ST88-14 cells were infected with shControl or shHuR#1 lentivirus, selected with puromycin for 2 days, replated and then 2 days later cross-linked with 1% formaldehyde for 10 min at RT and reaction quenched with 125 mM glycine for 5 min. The isolated nuclei were resuspended in nuclei lysis buffer and sonicated using a Bioruptor Sonicator (Diagenode). The samples were immunoprecipitated with the appropriate antibodies overnight at 4 ºC. Protein G beads (Thermo Fisher Scientific) were added and incubated for 1 h, and the immunoprecipitates were washed twice, each with low-salt, high-salt and LiCl buffer. The eluted DNA was reverse-crosslinked and purified using PCR purification kit (Qiagen).

value: NF1-derived MPNST

value: Anti-BRD2  Rabbit polyclonal, Bethyl, Cat# A302-583A

value: sh Ctr


title: Acceptors_60min_1 [DE89NGSUKBR108957_S248]

value: primary mouse microglia


title: SPT20_2


title: 15065X11

first: Vedran

last: Radojcic

address: 2000 Cir of Hope Dr

institute: University of Utah

description: Bulk RNA sequencing


title: Input_1


title: Input_2


title: Acceptors_TW_0min DE90NGSUKBR114177


title: Donors_0min_3 [DE68NGSUKBR108947_S238]


title: Acceptors_TW_300min DE68NGSUKBR114185


title: aSyn_Donor_1 [DE84NGSUKBR108950_S241]


title: Donors_TW_15min DE85NGSUKBR114170


title: 15065X21

description: Bulk RNA sequencing


title: ST88 cell, BRD2  ChIP, sh Ctr, number 2


title: Acceptors_15min_1 [DE03NGSUKBR108953_S244]


title: Myotube rep2 [medium RNA-seq]

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

institute: Sorbonne Université, CNRS, Paris, France

data_processing:
Trimmomatic (v0.32.3)
Bowtie2 (v2.2.6.2)
Slice BAM (v2.0)
Filter BAM (v1.1.2)
MultiCovBed (v2.26.0.0)
STAR (Galaxy Version 2.7.8a)
DESeq2 (Galaxy Version 2.11.40.6)
Genome_build: hg19
Supplementary_files_format_and_content: small RNAseq.xlsx : raw count values for each sample
Supplementary_files_format_and_content: small ncRNA.xlsx' contains the candidate number (candidate), chromosome (chr), start position (start), end position (end), raw count for myoblasts (MB), myotubes (MT), Dystrophy myotonic type 1 cells (DM), ENCODE K562 cells (K562), genomic position (type), size of the region in nucleotide (size), the strand (Strand), intron position when available (intron N°), total intron in the gene (intron (total number)), gene name containing the candidate when available (Gene name), and the refseq ID of the gene when available (RefSeq ID)

source_name: Muscle satellite cells differentiated

extract_protocol:
Tri Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/type

value: Myotube

value: Muscle satellite cells differentiated

tag: molecule subtype

value: Sized fractionated RNA


title: Ctrl_0min DE63NGSUKBR114178


title: ST88 cell, BRD2  ChIP, sh HuR#1, number 1

tag: chip antibody

tag: treatment

value: sh HuR


title: ZZZ3_2


title: Donors_150min_3 [DE79NGSUKBR108943_S234]

tag: strain


title: Myotube rep1 [medium RNA-seq]


title: Donors_TW_300min DE73NGSUKBR114192


title: Acceptors_60min_3 [DE09NGSUKBR108942_S233]


title: Donors_TW_0min DE58NGSUKBR114171


title: 15065X15

city: Salt Lake City

description: Bulk RNA sequencing

value: GVHD


title: Donors_TW_150min DE69NGSUKBR114167


title: Donors_60min_3 [DE36NGSUKBR108941_S232]


title: ST88 cell, BRD3  ChIP, sh Ctr, number 1

tag: cell line

value: Anti-BRD3  Rabbit polyclonal, Bethyl, Cat# A302-367A


title: 15065X13

description: Bulk RNA sequencing


title: Donors_300min_3 [DE25NGSUKBR108945_S236]

tag: passages


title: Donors_TW_30min DE52NGSUKBR114182


title: ST88 cell, BRD3  ChIP, sh Ctr, number 3


title: 15065X14

description: Bulk RNA sequencing


title: ST88 cell, BRD2  ChIP, sh HuR#1, number 3


title: Acceptors_TW_30min DE47NGSUKBR114175


title: ST88 cell, BRD3  ChIP, sh HuR#1, number 1


title: 15065X1

description: Bulk RNA sequencing


title: Acceptors_0min_3 [DE41NGSUKBR108948_S239]

tag: group


title: 15065X10

description: Bulk RNA sequencing


title: ST88 cell, BRD2  ChIP, sh HuR#1, number 2


title: ST88 cell, BRD2  ChIP, sh Ctr, number 3


title: Donors_TW_15min DE62NGSUKBR114196


title: ST88 cell, BRD3  ChIP, sh HuR#1, number 2


title: 15065X5

description: Bulk RNA sequencing