title: Co-culture P. oleovorans + BaP rep3

city: Berlin

first: Lisa

middle: Lotte

last: Lemoine

address: Max-Dohrnstraße 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

hyb_protocol: Hybridization was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

scan_protocol: Array scanning was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) according to the manufacturer's instruction (Affymetrix).

data_processing:
Raw data were processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Further analysing was done using Transcriptome Analysis Console (TAC) Software 4.0.
RNA expression value derived from Expression Console software; core-exon analysis

source_name: Co-culture P. oleovorans + BaP

label_protocol: Labelling was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

growth_protocol: EpiDermFT™ tissues (MatTek, Ashland, MA) were cultivated in 2.5 ml maintenance medium (EPI-100-MM-ABF, MatTek). Skin models were allowed to recover by incubation at 37 °C and 5 % CO2 overnight, followed by the respective treatments.

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

treatment_protocol: 15 µl of the respective bacterial suspension was applied topically. In the control experiments, similar amounts of solvent were applied. 24 h after bacterial application, the models were treated with 50 nmol of benzoapyrene and solvent, respectively. Benzoapyrene was applied daily for 7 days. The medium was refreshed daily. Tissue samples were maintained at 37 °C in a humidified atmosphere containing 5% CO2 for a total of 8 days.

value: EpiDermFT™ (MatTek) skin tissue

value: Co-culture P. oleovorans + BaP


title: GRB2-SH3_NM_abundance_output1

status: Public on Sep 13 2021

type: SRA

city: New York

first: Julia

last: Domingo

state: NY

address: 101 6th Av

country: USA

institute: New York Genome Center

description:
from plasmid library
fitness_GRB2-SH3_Abundance_supp.txt

library_source: genomic

data_processing:
Library strategy: PCR amplicon
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary_files_format_and_content: Tabular format. Heather: aa_seq=amino acid sequence, Nham_aa=Number of amino acid substitutions, WT=True if it is the wild type sequence, fitness=Average fitness of all replicates calculated by DiMSuM, sigma=standard error of the fitness measurement

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: For each of the two protein domains (GRB2-SH3 and PSD95-PDZ) and two assays (bindingPCA and abundancePCA), each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, a second plasmid selection cycle (input) was performed by inoculating SC -URA/MET/ADE at a starting OD600nm = 0.1 with the saturated culture. Cells were grown for 4 generations at 30ºC under constant agitation at 200 rpm. This allowed the pool of mutants to be amplified and enter the exponential growth phase. The competition cycle (output) was then started by inoculating cells from the input cycle into the competition media (SC -URA/MET/ADE + 200 ug/mL Methotrexate) so that the starting OD600nm was 0.05. For that, the adequate volume of cells were collected, centrifuged at 3,000 rpm for 5 minutes and resuspended in the pre-warmed output media. Meanwhile, each input replicate culture was splitted in two and harvested by centrifugation for 5 min at 5,000g at 4ºC. Yeast cells were washed with water, pelleted and stored at -20ºC for later DNA extraction. After ~5-5.2 generations of competition cycle, each output replicate culture was splitted into two and harvested by centrifugation for 5 min at 5,000g at 4ºC, washed twice with water and pelleted to be stored at -20ºC

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 4 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 4 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 4 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.4 mL of NaOAc 3M and 8.8 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 2.4 mL TE 1X and treated with 20 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (200 µL of QIAEX II beads). The samples were washed twice with PE buffer and eluted 500 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. To avoid PCR biases, PCR1 of each independent sample (input/output replicates of any of the yeast assays) was run with an excess of plasmid template 20-50 times higher than the number of expected sequencing reads per sample (Table S3). Each reaction started with a maximum of 1.25x107 template plasmid molecules per uL of PCR1, avoiding introducing more yeast genomic DNA that interfered with the efficiency of the PCR reaction. For this reason, PCR1s were scaled up in volume as specified in Table S3. The PCR1 reactions were run using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) according to the manufacturer’s protocol, with 25 pmol of pooled frame-shift primers oGJJ52/54-58 and oGJJ84-89 (forward and reverse primers were independently pooled according to the nucleotide diversity of each oligo, Table S1). The PCR reactions were set to 60ºC annealing temperature, 10 seconds (for GRB2-SH3 libraries) or 15 seconds (for PSD95-PDZ3 libraries) of extension time and run for 15 cycles. Excess primers were removed by adding 0.04 uL of ExoSAP-IT (Affymetrix) per uL of PCR1 reaction and incubated for 20 min at 37 ̊C followed by an inactivation for 15 min at 80 ̊C. The PCRs of each sample were then pooled and purified using the MinElute PCR Purification Kit (QIAGEN) according to the manufacturer’s protocol. DNA was eluted in EB to a volume 6 times lower than the total volume of PCR1. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. The total reaction of PCR2 was reduced to half of PCR1, using 0.05 uL of the previous purified PCR1 per uL of PCR2. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples, while the reverse primer (3’ P7 Illumina adapter) differed by the barcode index (oligo sequences in Table S1), to be subsequently pooled together and demultiplex them after deep sequencing (indexes used in each replicate of each sequencing run found in Table S4). 10 cycles of PCR2s were run at 62ºC of annealing temperature and 15 seconds (for GRB2-SH3 libraries) or 20 seconds (for PSD95-PDZ3 libraries) of extension time. All reactions from the same sample were pooled together and an aliquot was run on a 2% agarose gel to be quantified. After quantification, samples with different Illumina indexes that were sequenced together in the same flow-cell were pooled in an equimolar ratio, run on a gel and purified using the QIAEX II Gel Extraction Kit.

tag: strain

value: Lab strain BY4742

tag: molecule subtype

value: PCR amplicon


title: Naive_day0_1_S1

city: Bethesda

first: Amir

last: Foroushani

state: MD

address: 10 CENTER DR RM 11N306

department: NIAID

institute: NIH

library_source: transcriptomic

data_processing:
bcl2fastq v2.17.1.14 was used for base calling
Reads were aligned to mm10 by STAR (version 2.5.2a)
alignments to transcriptome were then quantified using RSEM (version 1.2.31)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited expression matrix text file. (Raw counts).

molecule: total RNA

organism: Mus musculus

extract_protocol:
Mouse T cells were resuspended in TrizolTM Reagent (Thermo Fisher Scientific). Total RNA were isolated per manufacturer’s instruction and resuspended in RNase free water. RNA was quantified with Qubit® RNA HS Assay Kit (Thermo Fisher Scientific) and RNA intergrity was verified with Agilent RNA 6000 Nano kit on the 2100 Bioanalyzer (Agilent Technologies) according to the manufacturers’ protocol.
RNA-Seq libraries were prepared from 65 ng of total RNA with ERCC ExFold RNA Spike-In Mix 1 (Life Technologies) of 1 μL of 1:5000 (v/v) dilution with TruSeq® Stranded mRNA Library Prep for NeoPrepTM kit as per the NeoPrep Library Preparation System Guide on the instrument (Illumina). The libraries were diluted 1:5 (v/v), with 1 μL used to check the expected size (~300 bp) and the samples’ purity were verified with the Agilent High Sensitivity DNA Kit as manufacturer’s recommendation (Agilent Technologies). One μL of the diluted libraries were used to quantify as recommended in the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) with standard range from 0 to 14 ng/ well. Pooled libraries of 1 nM were denatured and diluted as per the Standard Normalization Method for the NextSeq® System (Illumina). Final loading concentration of 1.7 pM and 1% (v/v) PhiX was used with the NextSeq® 500/550 High Output Kit v2 (150 cycles) (Illumina Samples were sequenced paired-end with 75 cycles of each read  and single index of 6 cycles.

tag: cell type

tag: treatment


title: GRB2-SH3_NM_abundance_input3


title: PSD95-PDZ3_NM_binding_input2

description:
from plasmid library
fitness_PSD95-PDZ3_Binding_supp.txt


title: Co-culture P. oleovorans + BaP rep2

type: RNA

label: biotin

organism: Homo sapiens

tag: tissue


title: GRB2-SH3_NM_abundance_input2


title: STL_293T_KCl_2

city: Orange

first: Matthew

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq (this step excluded for STL-seq)
Reads were trimmed using cutadapt (--minimum-length=20)
For TT-TL-seq, reads were aligned to the GRCh38 genome using HISAT2 aligned with default parameters and --mp 4,2 . For STL-seq reads were aligned with Bismark and Bowtie2 with default parameters and --local.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38 or dm6
Supplementary_files_format_and_content: bedgraph

source_name: Human embryonic kidney 293T cells

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). S2 cells were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). 293T cell cultures were maintained at 37℃. S2 cell cultures were maintained at 27℃.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For transient-transciptome-TimeLapse-seq (TT-TL-seq) genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for transient-transciptome-TimeLapse-seq RNA was enriched with MTS-biotin and treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. For Start-TimeLapse-seq, total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 using mCPBA as the oxidant and short capped RNA was enriched as described in Nechaev et al. Science 2010.
TT-TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). STL-seq libraries were generated with custom oligos following methods described in Nechaev et al. Science 2010.

treatment_protocol: S2 cells were treated with 42 µM 20-hydroxyecdysone or DMSO for 30 minutes, 500 nM flavopiridol or DMSO for 40 minutes, 10 µM triptolide or DMSO for 10 minutes, and/or 1mM s4U for 1.5, 3, 5, 7.5, 10, or 120 minutes. 293T cells were treated with 80 mM KCl for 1 hour and/or 1mM s4U for 5 minutes. In all cases the s4U labeling was the last 5 minutes of drug/stress treatment.

tag: cell line

value: WT 293T

tag: s4u feed status

value: Yes

tag: rna population

value: short, capped RNA


title: STL_293T_KCl_1


title: GRB2-SH3_NM_abundance_input1


title: Naive_day0_2_S6


title: STL_293T_UT_2


title: Co-culture P. oleovorans + BaP rep1


title: Co-culture M. luteus + BaP rep3

source_name: Co-culture M. luteus + BaP

value: Co-culture M. luteus + BaP


title: STL_293T_UT_1


title: TT_TL_S2_Ecd_2

organism: Drosophila melanogaster

source_name: Drosophila Schneider 2 cells

value: WT S2

value: s4U nascent RNA


title: Co-culture M. luteus + BaP rep1


title: Co-culture M. luteus + BaP rep2


title: TT_TL_S2_Ecd_1


title: GRB2-SH3_epPCR_binding_output2

description:
from plasmid library
fitness_GRB2-SH3_Binding_supp.txt


title: TT_TL_S2_UT_2


title: TT_TL_S2_UT_1


title: STL_293T_KCl_unlab

value: No


title: GRB2-SH3_epPCR_binding_output3


title: GRB2-SH3_epPCR_binding_output1


title: BaP treated skin rep2

source_name: BaP treated skin

value: BaP treated skin


title: BaP treated skin rep1


title: totRNA_S2_UT_unlab

value: total RNA


title: STL_S2_ts_120m_2


title: GRB2-SH3_epPCR_binding_input3


title: BaP treated skin rep3


title: Co-culture P. oleovorans rep2

source_name: Co-culture P. oleovorans

value: Co-culture P. oleovorans


title: Co-culture P. oleovorans rep1


title: STL_293T_UT_unlab


title: STL_S2_ts_10m


title: SKBR3 Control rep III

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon [reference Patroet al 2017] to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fasta file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR

source_name: SKBR3 Control

growth_protocol: Breast cancer cells (MDA-MB-231 and SKBR3) were passed and seeded in 10 cm dish plates with 70% confluency, and cultured in DMEM containing 4.5 g/L glucose and GlutaMax (Gibco), 10% (v/v) FBS, in a humidified atmosphere with 95% O2 and 5% CO2 at 37°C.

extract_protocol: After treatment, RNA was extracted using the commercial kit NucleoSpin RNA (Macherey-Nagel), including DNAse treatment in the intermediary steps.

treatment_protocol: Breast cancer cells (MDA-MB-231 and SKBR3) were treated with 500 nM of MitoQ for 48h.

tag: tissue source

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: passage

tag: disease

value: adenocarcinoma

value: control


title: Co-culture M. luteus rep1

source_name: Co-culture M. luteus

value: EpiDermFT™ (MatTek) skin tissue

value: Co-culture M. luteus


title: Uncolonized skin rep2

source_name: Uncolonized skin

value: Uncolonized skin


title: SKBR3 MitoQ rep III

source_name: SKBR3 MitoQ

value: 500 nM MitoQ for 48h


title: GRB2-SH3_epPCR_binding_input2

value: Lab strain BY4742

value: PCR amplicon


title: Mus musculus UUO day 5 rep3

city: Seattle

first: Daryl

last: Okamura

state: Washington

address: 1900 9th Ave

department: Center for Developmental Biology & Regenerative Medicine

institute: Seattle Children’s Research Institute

data_processing:
Salmon used for indexing and mapping to transcriptome (mm9 for Mus musculus, Tr2aacds from Mamrot et al 2017 for Acomys).
The transcript counts were imported into R (r-project.org) using the Bioconductor tximport package, and subsequently summarized at the gene level, generating counts per gene. The Bioconductor edgeR package was used to filter out genes with consistently low levels of expression, and to fit a linear model using the count data.
We made comparisons between UUO and sham treatment at each time point as well as between UUO treatment at the two time points using quasi-likelihood F-tests, incorporating a log fold change of 0.585, (1.5-fold on the linear scale, or a 50% difference), and a false discovery rate (FDR) of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with log fold change and FDR for every gene, sham vs treated kidney samples as labeled.

source_name: Kidney

extract_protocol:
Age-matched adult male C57BL/6J (B6) and A. cahirinus (2-4 months) were subjected to unilateral ureter obstruction (UUO) procedure at the left ureter. Kidneys from sham operated controls and UUO-treated animals after 2 and 5 days were collected after perfusion with ice-cold normal saline and flash frozen in liquid nitrogen. Total RNA was extracted from kidney using Trizol (Invitrogen) and Direct-zol RNA Kit (R2072, Zymo Research) according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: age

value: 14.0 weeks

tag: genotype

value: wild type

value: day 5 UUO


title: STL_S2_ts_120m_1

value: WT S2

value: Yes

value: short, capped RNA


title: STL_S2_ts_3m_2


title: GRB2-SH3_epPCR_binding_input1


title: SKBR3 Control rep I


title: IPF-derived_primary_lung_fibroblasts_TGFb1_rep2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1, biological replicate 2

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

extract_protocol: RNA extraction from cultured phLFs was performed using the PeqGold RNA kit (Peqlab) according to the manufacturer’s instruction

treatment_protocol: Cells were seeded with 150000 cells/well in 6-well plates. Following overnight incubation, cells were starved in serum-reduced medium (1% FBS with 0.1mM 2-phosphoascorbate) for 24h. Afterwards, cells were treated with TGFβ1 (1 ng/ml) or vehicle, and additionally small molecules or appropriate vehicle controls were added. After 72h of incubation cells were harvested.


title: BY4742 rep 1

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
Removed adaptor with cutadapt and kept only the 28-mers
Mapped the reads on the organism's transcriptome (for CDS) and genome (for IGORFs) - Bowtie (parameters: -v 2 -y -a -m 1 --best --strata -p 18)
Kept only the mapped reads - samtools (parameters: -F 4 -f 0,16 -h)
Genome_build: Saccer3
Supplementary_files_format_and_content: csv files with the count of reads detected per sequence

source_name: Yeast

growth_protocol: All strains were grown to mid-exponential growth phase in a synthetic medium,

extract_protocol:
the extraction is performed as previously published Baudin-Baillieu A et al. Methods Mol. Biol. 2016, 1361:105-24. briefly: Pellet cells by centrifugation at 4 °C, 4000×g for 10 min. resuspend pellet in 10 ml cold Lysis Buffer containing 50 μg/ml cycloheximide. Pulverize Cells by adding glass beads and vortexing the mix- ture for 10 min at 4 °C. Remove cells debris by centrifugation at 4 °C, 5000×g for 5 min and transfer the supernatant to chilled 1.5 ml microfuge tubes on ice. The supernatant is clarified by centrifugation at 4 °C, 15,000×g for 15 min. Recover supernatant.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

treatment_protocol: Cycloheximide is added to the medium at 50 µg/mL

value: CHX


title: MDA-MB-231 MitoQ rep III

description: MDAMB-mQIII

source_name: MDA-MB-231 MitoQ

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: BY4742 rep 2


title: SKBR3 Control rep II

value: adenocarcinoma


title: Uncolonized skin rep1


title: SKBR3 MitoQ rep II


title: STL_S2_ts_5m_2


title: STL_S2_ts_1.5m_2


title: STL_S2_ts_7.5m


title: MDA-MB-231 MitoQ rep V

description: MDAMB-mQV


title: MDA-MB-231 MitoQ rep IV

description: MDAMB-mQIV


title: Co-culture M. luteus rep2


title: MDA-MB-231 MitoQ rep I

description: MDAMB-mQI


title: IPF-derived_primary_lung_fibroblasts_TGFb1_rep3

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1, biological replicate 3


title: SKBR3 MitoQ rep I


title: STL_S2_ts_5m_1


title: Mus musculus UUO day 2 rep3

value: 10.1 weeks

value: day 2 UUO


title: STL_S2_Trp_2


title: Mus musculus UUO day 5 rep1


title: Mus musculus UUO day 2 rep1


title: IPF-derived_primary_lung_fibroblasts_TGFb1_cmp4_rep2

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1 and cmp4, biological replicate 2

value: TGFb1 and cmp4


title: MDA-MB-231 MitoQ rep II

description: MDAMB-mQII


title: Mus musculus sham rep2

value: 7.0 weeks

value: sham


title: STL_S2_ts_1.5m_1


title: Mus musculus UUO day 5 rep2


title: STL_S2_ts_3m_1


title: Mus musculus UUO day 2 rep2


title: Mus musculus sham rep3

value: 9.4 weeks


title: MDA-MB-231 Control rep V

description: MDAMB-CTRV

source_name: MDA-MB-231 Control

value: control


title: MDA-MB-231 Control rep IV

description: MDAMB-CTRIV


title: MDA-MB-231 Control rep II

description: MDAMB-CTRII


title: STL_S2_FP_Ecd_1


title: STL_S2_FP_2


title: MDA-MB-231 Control rep I

description: MDAMB-CTRI


title: SNCA

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ reads were aligned, filtered and counted through the Cell  Ranger pipeline (v3.1).
Differential gene expression, cell clustering and dimension reduction analysis were performed with Seurat.
Downstream analysis was performed within the R environment.
Genome_build: mm10
Supplementary_files_format_and_content: cellranger cloupe file

source_name: CD45+ substantia nigra cells

extract_protocol:
The brain nigral regions were carefully dissected from 2 subsequent 500μm-thick slices and  the tissue directly subjected for RNA extraction or processed for the single cell dissociation. The  dissociation was performed using Adult Brain Dissociation Kit and OctoMACS Separator (both  from Miltenyi Biotec) following manufacturer’s instructions. This procedure collected a large  fraction of different cell populations ranging from immune cells to neurons within the same  preparation. Cells were stained with 1:200 Zombie Aqua Fixable Viability Kit (Biolegend) and  subsequently with anti-CD45 PerCP-Cy5.5 antibody and anti-CD11b eFluor450 antibody (all  from eBioscience).
Cells were sorted using a FACSAria Fusion (BD) and collected in PBS 0.04%  BSA to be processed for sequencing through the Chromium platform (10X Genomics). Cells  were separated into droplet emulsion using the Chromium Single Cell 3’ Solution (V3.0) and  Single-cell RNA-seq libraries were prepared according to the Single Cell 3' Reagent Kits User  Guide (V3.0). Libraries were sequenced on a Novaseq 6000 flowcell (Illumina), with a minimum  depth of 50K reads/cell.

value: substantia nigra

tag: cell markers

tag: genotype/variation

value: CX3-Cre infected with Synuclein-expressing vector


title: Control

value: infected with GFP (control)


title: Mus musculus sham rep1

value: kidney

value: 14.0 weeks

value: wild type


title: STL_S2_FP_Ecd_2

value: WT S2

value: Yes

value: short, capped RNA


title: STL_S2_Trp_1


title: STL_S2_FP_1


title: MDA-MB-231 Control rep III

description: MDAMB-CTRIII

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: adenocarcinoma


title: 17-CC-VAR

status: Public on Sep 12 2021

city: Lleida

first: Roger

last: Ros-Freixedes

address: Av Rovira Roure, 191

country: Spain

institute: Universitat de Lleida

description: barrow, 210 days old, raised in commercial farms

data_processing:
Quality of the raw sequencing data was assessed with the fastp tool
Filtered sequences were aligned to the Sus scrofa reference genome (Sscrofa 11.1) with the STAR 2.5.4b tool
Mapping statuses were analysed with qualimap and plotted by MultiQC v1.0
After the alignment, reads were counted with the Feature Counts v1.24.1 software
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Text table with read counts for each gene and sample

organism: Sus scrofa

source_name: muscle semimembranosus

growth_protocol: Pigs reared in standard commercial conditions of growth and fattening.

extract_protocol:
Direct-zolTM RNA Miniprep Plus Kit (Zymo Research, BioSystems, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pigs fed two diets (with and without vitamin A supplements)

tag: breed

value: Duroc

tag: diet

value: commercial diet without vitamin A supplement

value: TT


title: 7-CC-VA+

value: commercial diet with vitamin A supplement


title: 9-CC-VA+


title: 8-CC-VA+


title: 10-CC-VA+


title: 18-CC-VAR

value: CC


title: 16-CC-VAR


title: 13-CC-VAR


title: 11-CC-VAR


title: 6-CC-VA+


title: 15-CC-VAR


title: 12-CC-VAR


title: 14-CC-VAR


title: 23-CC-VAR


title: 21-CC-VAR


title: 22-CC-VAR


title: 19-CC-VAR


title: 20-CC-VAR


title: 4-CC-VA+


title: 3-CC-VA+


title: 5-CC-VA+


title: IPF-derived_primary_lung_fibroblasts_TGFb1_cmp4_rep1

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1 and cmp4, biological replicate 1

value: TGFb1 and cmp4


title: IPF-derived_primary_lung_fibroblasts_TGFb1_cmp4_rep3

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1 and cmp4, biological replicate 3


title: 11-TT-VAR


title: 1-CC-VA+


title: 2-CC-VA+


title: 15-TT-VAR


title: 13-TT-VAR


title: IPF-derived_primary_lung_fibroblasts_Ctrl_rep3

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast, control, biological replicate 3

value: control


title: 16-TT-VAR


title: IPF-derived_primary_lung_fibroblasts_Ctrl_rep2

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast, control, biological replicate 2


title: 14-TT-VAR


title: IPF-derived_primary_lung_fibroblasts_cmp4_rep2

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with cmp4, biological replicate 2


title: 17-TT-VAR


title: 7-TT-VA+


title: 10-TT-VAR


title: 4-TT-VA+


title: 9-TT-VAR


title: 6-TT-VA+


title: 1-TT-VA+


title: 2-TT-VA+


title: 5-TT-VA+


title: 8-TT-VA+


title: IPF-derived_primary_lung_fibroblasts_TGFb1_rep1

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with TGFb1, biological replicate 1


title: IPF-derived_primary_lung_fibroblasts_cmp4_rep3

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with cmp4, biological replicate 3


title: IPF-derived_primary_lung_fibroblasts_Ctrl_rep1

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast, control, biological replicate 1


title: 3-TT-VA+


title: IPF-derived_primary_lung_fibroblasts_cmp4_rep1

description: Gene expression data from IDF (Idiopathic Pulmonary Fibrosis)-derived primary pulmonary fibroblast treated with cmp4, biological replicate 1


title: 12-TT-VAR


title: HD7_PLX

city: Columbus

first: Parvathi

last: Ranganathan

state: Ohio

address: 460 W 12th Ave, BRT 420

department: Hematology

institute: The Ohio State Univeristy

data_processing:
Reads were aligned to the transcriptome derived from UCSC genome assembly using Expression Count (STAR) with default parameters.
Read counts for each transcript was measured using featureCounts.
Differentially expressed genes were determined using DESeq2 (compare 2 groups)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts.

source_name: Blood

growth_protocol: Human T cells were isolated from healthy donor PBMCs (n=4 donors) by negative selection.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and treated with Dnase (Qiagen). RNA quality was verified using Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA integrity number values were greater than 7 for all samples.
Sequencing libraries were generated with polyA+ RNA using the TruSeq RNA sample prep kit (Illumina).

treatment_protocol: T cells were treated with vehicle (DMSO) or PLX51107 (100 nM) for 48 hr.

value: T cells

value: PLX


title: HD17_PLX


title: HD18_PLX


title: HD17_DMSO

value: DMSO


title: HD18_DMSO


title: HD7_DMSO


title: PLC-control_AGTTCCG

city: Shanghai

first: Cun

last: Wang

address: Xietu Road

country: China

institute: Shanghai Cancer Institute

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome.  Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F  -k 5 --minins 0 --maxins 500 --fr --new-summary
Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters    Count library type stranded: true  Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf    mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: liver cancer cell line

growth_protocol: Cells were cultured in DMEM with 10% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2.

extract_protocol:
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PLC/PRF/5 cells are treated with XL413 for 96 hours.

value: liver cancer cell line


title: BRD4_PLX

data_processing:
FactorPath ChIP-Seq technology by Active Motif.
ChIP-Seq QC, Alignment (Bowtie2) through Basepair Tech
ChIP-Seq Peaks, Motif (MACS (v2), Homer) through Basepair Tech
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were created using Active Motif.

growth_protocol: Healthy donor (HD) T cells were stimulated with CD3/CD28 Dynabeads for 24 hours.

extract_protocol:
Cells were processed for chromatin immunoprecipitation (ChIP) per Active Motif kit instructions (Active Motif).
ChIP sequencing (ChIP-seq) was performed using FactorPath ChIP-Seq technology by Active Motif.

treatment_protocol: T cells were treated with vehicle (DMSO) or PLX2853 (10 nM) for 24 hours. Evaluation was performed on BRD4 binding, RNA polymerase II (Pol II) occupancy and H3K27Ac (BRD4-associated histone mark.

tag: antibody


title: HD19_PLX


title: Pol2_PLX


title: PLC-XL413_ATGTCAG

value: XL413 treatment (10uM) for 96 hours


title: H3K27Ac_PLX


title: WT_antenna_rep3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Drosophila Genome 2.0 arrays were hybridized with 11 microgrammes of fragmented biotinylated cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol Flex FS450_0002_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues separately.

label_protocol: 100 ng RNA was used to perform target preparation using the MessageAmp™ II-Biotin Enhanced aRNA Amplification Kit (ThermoFisher Scientific, Waltham, USA).

growth_protocol: Animals were grown at 25°C in 12 h light:12 h dark conditions on standard Drosophila culture media.

extract_protocol: Olfactory third antennal segments were harvested via snap-freezing adult flies with liquid nitrogen and agitating the animals in a mini-sieve. Collected antennae were homogenized manually with a tissue grinder and total RNA was extracted using a standard TRIzol/chloroform protocol.

value: Wild-Type

value: drosophila antenna (pool of 60 antennas)


title: HD19_DMSO


title: WT_antenna_rep2


title: Pol2_Stim


title: Atonal_antenna_rep3

value: Atonal


title: Cancer nodule Q_rep4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
P4_Q4_US83000181_252665243109_S01_GE2_1200_Jun14_1_1.txt
Gene expression from prostate cancer tumor

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from the two cancer nodules were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Cancer nodule Q_rep4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

extract_protocol: RNA was extracted with RNAEasy Minikit (Qiagen, Germantown, MD, USA) following the manufacturer's recommendations. RNA was quantified using a Thermo Fisher Scientific NanoDrop ND-1000 spectrophotometer (Waltham, MA, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: prostate

tag: gender

value: male


title: Cancer nodule Q_rep3

description:
P3_Q3_US83000181_252665243109_S01_GE2_1200_Jun14_1_2.txt
Gene expression from prostate cancer tumor

source_name: Cancer nodule Q_rep3


title: Amos_antenna_rep2

value: Amos


title: Cancer nodule Q_rep1

description:
P1_Q1_US83000181_252665243109_S01_GE2_1200_Jun14_1_4.txt
Gene expression from prostate cancer tumor

source_name: Cancer nodule Q_rep1


title: Atonal_antenna_rep2


title: Cancer nodule P_rep1

source_name: Cancer nodule P_rep1


title: Cancer nodule Q_rep2

description:
P2_Q2_US83000181_252665243109_S01_GE2_1200_Jun14_1_3.txt
Gene expression from prostate cancer tumor

source_name: Cancer nodule Q_rep2


title: WT_antenna_rep1


title: Cancer nodule P_rep4

source_name: Cancer nodule P_rep4


title: Cancer nodule P_rep3

source_name: Cancer nodule P_rep3


title: Amos_antenna_rep1


title: Cancer nodule P_rep2

source_name: Cancer nodule P_rep2


title: Atonal_antenna_rep1


title: Amos_antenna_rep3


title: H3K27Ac_Stim

tag: cell type


title: BRD4_Stim

tag: treatment


title: Peripheral blood sample from trauma patient S at Time T1

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: 5.5 μg of fragmented, biotin labeled ssDNA was hybridized to each Human Gene 2.1 ST microarrays according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis, The University of New South Wales.

scan_protocol: The samples were processed using the GeneTitan instrument (Affymetrix).

data_processing: The microarray data was preprocessed in R employing the RMA algorithm. A custom chip description file (CDF) file was used (hugene21sthsentrezg, version 19).

label_protocol: 250ng of total RNA was amplified (Ambion WT kit), labeled with biotin (Affymetrix terminal labelling kit) and fragmented according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis, The University of New South Wales.

growth_protocol: Patients with anaphylaxis, trauma, or sepsis, were recruited from three Australian emergency departments (ED). Samples were also collected from healthy controls. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

extract_protocol: RNA was extracted with the PAXgene Blood RNA Extraction Kits (PreAnalytiX GmbH, Switzerland) by automation with the Qiacube instrument (Qiagen, Australia).

treatment_protocol: Blood samples were colected and stabilized in PAXgene tubes. The PAXgene tubes were placed immediately at 4°C then transferred to -20°C within 72 hours, before final storage at -80°C.

tag: tissue

value: peripheral blood

tag: study

value: Trauma study

tag: disease status

value: Head Trauma

tag: severity

value: DIED

tag: time point


title: Peripheral blood sample from trauma patient J at Time T2

value: ALIVE


title: Peripheral blood sample from trauma patient K at Time T1


title: Peripheral blood sample from trauma patient H at Time T1


title: Peripheral blood sample from trauma patient F at Time T1


title: Peripheral blood sample from trauma patient H at Time T0


title: Peripheral blood sample from trauma patient C at Time T2


title: Peripheral blood sample from trauma patient J at Time T1


title: Peripheral blood sample from trauma patient K at Time T0


title: Peripheral blood sample from trauma patient D at Time T0


title: Peripheral blood sample from trauma patient J at Time T0


title: Peripheral blood sample from trauma patient H at Time T2


title: Peripheral blood sample from trauma patient F at Time T0


title: Peripheral blood sample from trauma patient F at Time T2


title: Peripheral blood sample from trauma patient E at Time T2


title: Peripheral blood sample from healthy control C22

source_name: Peripheral blood sample from healthy control C at Time T0

value: Healthy control


title: Peripheral blood sample from healthy control C23


title: Peripheral blood sample from trauma patient D at Time T2


title: Peripheral blood sample from trauma patient G at Time T2


title: Peripheral blood sample from trauma patient E at Time T1


title: Peripheral blood sample from trauma patient T at Time T2


title: Peripheral blood sample from trauma patient D at Time T1


title: Peripheral blood sample from trauma patient C at Time T0


title: Peripheral blood sample from healthy control C24


title: Peripheral blood sample from trauma patient S at Time T2


title: Peripheral blood sample from trauma patient C at Time T1


title: Peripheral blood sample from trauma patient E at Time T0


title: Peripheral blood sample from healthy control C20


title: Peripheral blood sample from healthy control C21


title: Peripheral blood sample from healthy control C17


title: Peripheral blood sample from healthy control C15


title: Peripheral blood sample from healthy control C14


title: Peripheral blood sample from healthy control C19


title: Peripheral blood sample from healthy control C18


title: Peripheral blood sample from healthy control C16


title: Peripheral blood sample from healthy control C13


title: Peripheral blood sample from sepsis patient Z at Time T0

value: Sepsis study

value: Sepsis

value: Mild


title: Peripheral blood sample from trauma patient B at Time T1


title: Peripheral blood sample from trauma patient A at Time T0


title: Peripheral blood sample from sepsis patient Z at Time T1


title: Peripheral blood sample from sepsis patient Y at Time T1


title: Peripheral blood sample from trauma patient B at Time T0


title: Peripheral blood sample from trauma patient A at Time T1


title: Peripheral blood sample from sepsis patient X at Time T1


title: Peripheral blood sample from sepsis patient W at Time T2


title: Peripheral blood sample from sepsis patient Y at Time T0


title: Peripheral blood sample from sepsis patient W at Time T1


title: Peripheral blood sample from trauma patient A at Time T2


title: Peripheral blood sample from trauma patient B at Time T2


title: Peripheral blood sample from sepsis patient W at Time T0


title: Peripheral blood sample from sepsis patient Z at Time T2


title: Peripheral blood sample from sepsis patient X at Time T2


title: Peripheral blood sample from sepsis patient U at Time T1


title: Peripheral blood sample from sepsis patient V at Time T1


title: Peripheral blood sample from sepsis patient V at Time T0


title: Peripheral blood sample from sepsis patient Y at Time T2


title: Peripheral blood sample from sepsis patient U at Time T2


title: Peripheral blood sample from sepsis patient X at Time T0


title: Peripheral blood sample from sepsis patient V at Time T2


title: Peripheral blood sample from sepsis patient U at Time T0


title: Peripheral blood sample from sepsis patient T at Time T1


title: Peripheral blood sample from sepsis patient T at Time T0


title: Peripheral blood sample from sepsis patient R at Time T1


title: Peripheral blood sample from sepsis patient S at Time T2


title: Peripheral blood sample from sepsis patient T at Time T2


title: Peripheral blood sample from sepsis patient S at Time T1


title: Peripheral blood sample from sepsis patient R at Time T0


title: Peripheral blood sample from sepsis patient J at Time T2

value: Severe


title: Peripheral blood sample from sepsis patient Q at Time T2


title: Peripheral blood sample from sepsis patient S at Time T0


title: Peripheral blood sample from sepsis patient H at Time T2


title: Peripheral blood sample from sepsis patient I at Time T0


title: Peripheral blood sample from sepsis patient H at Time T0


title: Peripheral blood sample from sepsis patient H at Time T1


title: Peripheral blood sample from sepsis patient Q at Time T1


title: Peripheral blood sample from sepsis patient G at Time T0


title: Peripheral blood sample from sepsis patient Q at Time T0


title: Peripheral blood sample from sepsis patient G at Time T1


title: Peripheral blood sample from sepsis patient R at Time T2


title: Peripheral blood sample from sepsis patient J at Time T1


title: Peripheral blood sample from sepsis patient I at Time T1


title: Peripheral blood sample from sepsis patient F at Time T1


title: Peripheral blood sample from sepsis patient G at Time T2


title: Peripheral blood sample from sepsis patient J at Time T0


title: Peripheral blood sample from sepsis patient F at Time T2


title: Peripheral blood sample from sepsis patient D at Time T2


title: Peripheral blood sample from sepsis patient F at Time T0


title: Peripheral blood sample from sepsis patient E at Time T0


title: Peripheral blood sample from sepsis patient D at Time T0


title: Peripheral blood sample from sepsis patient E at Time T1


title: Peripheral blood sample from healthy control 09


title: Peripheral blood sample from healthy control 12


title: Peripheral blood sample from sepsis patient D at Time T1


title: Peripheral blood sample from healthy control 08


title: Peripheral blood sample from healthy control 10


title: Peripheral blood sample from healthy control 06


title: Peripheral blood sample from healthy control 05


title: Peripheral blood sample from healthy control 04


title: Peripheral blood sample from healthy control 07


title: Peripheral blood sample from healthy control 03


title: Peripheral blood sample from healthy control 02


title: Peripheral blood sample from sepsis patient C at Time T1


title: Peripheral blood sample from sepsis patient C at Time T2


title: Peripheral blood sample from healthy control 11


title: Peripheral blood sample from sepsis patient C at Time T0


title: Peripheral blood sample from sepsis patient B at Time T2


title: Peripheral blood sample from sepsis patient A at Time T2


title: Peripheral blood sample from sepsis patient A at Time T0


title: Peripheral blood sample from sepsis patient A at Time T1


title: Peripheral blood sample from sepsis patient B at Time T1


title: CNS_Sarcoma_FFPE_rep23

type: genomic

city: Hamburg

first: Martin

last: Mynarek

address: Martinistr. 52

department: Department for Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: R package minfi v1.32.0

label: Biotin/DNP

source_name: FFPE tumor tissue from pediatric brain tumor

label_protocol: Illumina protocol.

extract_protocol: Ectraction of high molecular weight DNA from FFPE tumor samples was carried out bz use the ReliaPrep™ FFPE gDNA Miniprep System from Promega.

value: 6.3 years-old

tag: Sex

value: m

tag: histology

value: Pleomorphic Sarcoma

tag: localization

value: Frontal

tag: resection

value: GTR

tag: staging

value: loc RT + VAC

value: Local RT

value: alive

value: 3.39 years

tag: pfs

value: 1.27 years

value: relapse/progression/death


title: Peripheral blood sample from healthy control 970

value: peripheral blood

value: Anaphylaxis study


title: CNS_Sarcoma_FFPE_rep24

tag: age

value: 3.3 years-old

value: f

value: Fusocellular Sarcoma

value: Parietal

value: STR

value: loc RT + ICE

value: local RT

value: death

value: 0.33 years

value: 0.31 years


title: CNS_Sarcoma_FFPE_rep25

value: 5.5 years-old

value: Undifferentiated pleomorphic Sarcoma

value: Parieto-temporal

value: GTR

value: loc RT + VAC

value: 2.94 years

value: no event


title: CNS_Sarcoma_FFPE_rep15

value: 6.5 years-old

value: m

value: ICE + loc RT

value: alive

value: 1.03 years


title: CNS_Sarcoma_FFPE_rep20

value: 2.1 years-old

value: f

value: Sarcoma NOS

value: Fronto-temporal

value: 2.92 years


title: CNS_Sarcoma_FFPE_rep27

value: 5.2 years-old

value: Undifferentiated Sarcoma

value: Frontal

value: STR

value: local RT

value: death

value: 1.57 years

value: 0.4 years

value: relapse/progression/death


title: CNS_Sarcoma_FFPE_rep14

value: 2.7 years-old

value: m

value: Fusocellular Sarcoma

value: Fronto-parietal

value: GTR

value: ICE + loc RT

value: 0.96 years

value: no event


title: CNS_Sarcoma_FFPE_rep28

value: 8.7 years-old

value: Cerebellum

value: loc RT + VAC

value: 1.97 years

value: 1.1 years


title: CNS_Sarcoma_FFPE_rep22

value: 6 years-old

value: f

value: Parietal

value: Bx - biopsy only

value: no therapy

value: death

value: 0.1 years


title: Peripheral blood sample from healthy control 947

value: peripheral blood

value: Anaphylaxis study

value: Healthy control


title: Tobi-OMVs_B2

city: Hanover

first: Zhongyou

last: Li

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

data_processing:
The first three nt and adapter sequences of all reads were trimmed using cutadapt before sequence alignment.
Reads were aligned to the PA14 reference genome using CLC Genomics Workbench (CLC-Bio/Qiagen) with the following modifications from the standard parameters: a) the maximum number of mismatches = zero to eliminate unspecific alignment and b) the maximum number of hits for a read = 30 to capture all sRNAs aligned to PA14 genome. Pileups of mapped reads and frequency tables for each unique sequence were exported for normalization and further analysis with the software package edgeR in the R environment
Genome_build: NC_008463.1
Supplementary_files_format_and_content: normalized abundance for every sample and every feature as well as edgeR statistics

organism: Pseudomonas aeruginosa

source_name: outer membrane vesicles (OMVs)

growth_protocol: PA14 was grown in LB medium for 16 h at 37°C and 225 rpm

extract_protocol:
RNA was extracted with the miRNeasy kit (Qiagen), followed by DNase digestion
Library was prepared using SMARTer smRNA-Seq Kit (Takara Bio)

treatment_protocol: tobramycin (1ug/mL) was added for Tobi-OMVs

tag: strain

value: tobramycin

tag: tissue type

value: outer membrane vesicles (OMVs)


title: CNS_Sarcoma_FFPE_rep16

value: 9 years-old

value: Chondrosarcoma

value: Fronto-parietal

value: STR

value: ICE + loc RT

value: local RT

value: alive

value: 1.87 years

value: no event


title: Tobi-OMVs_B3


title: CNS_Sarcoma_FFPE_rep21

value: 6.2 years-old

value: m

value: Fusocellular Sarcoma

value: Parietal

value: GTR

value: loc RT + VAC

value: 2.92 years

value: 1.36 years

value: relapse/progression/death


title: Tobi-OMVs_B1

value: tobramycin

value: outer membrane vesicles (OMVs)


title: ctrl-OMVs_B2

value: vehicle ctrl


title: Peripheral blood sample from healthy control 944

value: peripheral blood

value: Anaphylaxis study

value: Healthy control


title: CNS_Sarcoma_FFPE_rep6

value: 4.9 years-old

value: Chondrosarcoma

value: Frontal

value: ICE + loc RT

value: local RT

value: alive

value: 1.7 years


title: CNS_Sarcoma_FFPE_rep17

value: 8.6 years-old

value: f

value: Fusocellular Sarcoma

value: GTR

value: loc RT + ICE

value: death

value: 1.22 years

value: 1.12 years


title: CNS_Sarcoma_FFPE_rep19

value: 6.1 years-old

value: m

value: Pleomorphic Sarcoma

value: Fronto-parietal

value: loc RT only

value: 2.24 years

value: 0.84 years

value: relapse/progression/death


title: Peripheral blood sample from healthy control 967

value: peripheral blood

value: Anaphylaxis study

value: Healthy control


title: CNS_Sarcoma_FFPE_rep9

value: 11 years-old

value: Fusocellular Sarcoma

value: ICE + loc RT

value: local RT

value: alive

value: 1.36 years

value: no event


title: CNS_Sarcoma_FFPE_rep13

value: 13.6 years-old

value: m

value: Frontal

value: GTR

value: loc RT + ICE

value: 1.54 years


title: CNS_Sarcoma_FFPE_rep10

value: 7 years-old

value: Fronto-parietal

value: STR

value: 1.31 years


title: Peripheral blood sample from healthy control 943

value: peripheral blood

value: Anaphylaxis study

value: Healthy control


title: 26D-2_bursa of Fabricius

city: Chengdu

first: Xun

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

data_processing:
Clean reads were mapped to the pigeon genome (Cliv_1.0 from NCBI) using STAR (v.2.6.0c)
Mapped reads were assembled to transcripts using the Cufflinks (v.2.1.1) software . The transcripts ( ≤250 bp or FPKM < 0.1) were first excluded.The remaining transcripts were merged and compared to the reference genome by the meta-assembly tool TACO software (v0.7.3)
Those transcripts un-annotated by protein-coding genes (PCGs) were retained as putatively lncRNA transcripts.Subsequently, Coding Potential Calculator (CPC2) and PfamScan were applied to predict the coding potential of these transcripts.
After removing transcripts with coding capacities, the remaining transcripts were identified to be long non-coding RNAs.
Genome_build: Cliv_1.0
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

organism: Columba livia

source_name: bursa of Fabricius

growth_protocol: The pigeons were grouped into three developmental stages: 1 day (1D), 13 days (13D) and 26 days (26D).

extract_protocol:
Total RNA was respectively isolated from frozen BF samples collected from 9 female pigeon squabs across the three developmental stages (3 biological replicates each) by HiPure Universal RNA Kit (Magen, Guangzhou, China) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples for subsequent transcriptome sequencing were frozen in liquid nitrogen and stored at -80℃ refrigerator.

value: White-King pigeon

value: bursa of Fabricius

tag: developmental stage

value: 26 days old


title: ctrl-OMVs_B3

value: vehicle ctrl

value: outer membrane vesicles (OMVs)


title: Peripheral blood sample from healthy control 942


title: tRNA1-OMVs_B3

data_processing:
Reads were aligned to the PA14 reference genome using CLC Genomics Workbench (CLC-Bio/Qiagen) with the following modifications from the standard parameters: a) the maximum number of mismatches = zero to eliminate unspecific alignment and b) the maximum number of hits for a read = 30 to capture all sRNAs aligned to PA14 genome. Pileups of mapped reads and frequency tables for each unique sequence were exported for normalization and further analysis with the software package edgeR in the R environment
Genome_build: NC_008463.1
Supplementary_files_format_and_content: normalized abundance for every sample and every feature as well as edgeR statistics

growth_protocol: PA14 clones were grown in LB with 133 mM L-arabinose (2% w/v) and 300 μg/ml carbenicillinmedium for 16 h at 37°C and 225 rpm

extract_protocol:
RNA was extracted with the miRNeasy kit (Qiagen), followed by DNase digestion
Library was prepared using the QIAseq miRNA Library Kit (Qiagen)

tag: genotype

value: 5' tRNA-fMet1 half over-expression


title: Peripheral blood sample from healthy control 941


title: CNS_Sarcoma_FFPE_rep18

value: 5.3 years-old

value: f

value: Fusocellular Sarcoma

value: Parietal

value: local RT

value: death

value: 2.38 years

value: 1.42 years

value: relapse/progression/death


title: 26D-1_bursa of Fabricius


title: V-OMVs_B3

value: pMQ70 empty vector


title: CNS_Sarcoma_FFPE_rep5

value: Frontal

value: GTR

value: ICE + loc RT

value: alive

value: 1.71 years

value: no event


title: 13D-3_bursa of Fabricius

value: White-King pigeon

value: bursa of Fabricius

value: 13 days old


title: CNS_Sarcoma_FFPE_rep11

value: 4.3 years-old

value: m

value: Fusocellular Sarcoma

value: STR

value: loc RT + ICE

value: 2.21 years


title: tRNA1-OMVs_B1

value: 5' tRNA-fMet1 half over-expression

value: outer membrane vesicles (OMVs)


title: V-OMVs_B2

value: pMQ70 empty vector


title: CNS_Sarcoma_FFPE_rep7

value: 9 years-old

value: f

value: Fronto-parietal

value: local RT

value: 1.27 years


title: CNS_Sarcoma_FFPE_rep26

value: 10.4 years-old

value: Pleomorphic Sarcoma

value: GTR

value: alive

value: 2.24 years

value: no event


title: V-OMVs_B1


title: 13D-2_bursa of Fabricius

value: White-King pigeon

value: bursa of Fabricius

value: 13 days old


title: CNS_Sarcoma_FFPE_rep8

value: 2.8 years-old

value: Undifferentiated Sarcoma

value: Parietal

value: other

value: 5.02 years

value: 4.56 years

value: relapse/progression/death


title: 13D-1_bursa of Fabricius


title: CNS_Sarcoma_FFPE_rep3

value: 6.4 years-old

value: f

value: Fusocellular Sarcoma

value: Frontal

value: loc RT + VAC

value: local RT

value: 4.16 years

value: 2.23 years


title: 1D-3_bursa of Fabricius

value: White-King pigeon

value: bursa of Fabricius

value: 1 day old


title: 26D-3_bursa of Fabricius

value: 26 days old


title: CNS_Sarcoma_FFPE_rep12

value: 4.7 years-old

value: GTR

value: ICE + loc RT

value: alive

value: 1.48 years

value: no event


title: 1D-2_bursa of Fabricius


title: Patient ID: B012-0043 [SL462144]

city: Indianapolis

first: Milan

last: Radovich

state: IN

address: 980 W. Walnut St. Room C240

institute: Indiana University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw RNA-seq reads were mapped to the human genome (hg38) using the STAR algorithm
Read counts for expressed genes were generated using the featurecounts module within the subread package
FPLM values were generated using edgeR
For immune deconvolution, FPKM values were imported with the the web-based tool CIBERSORTx (cibersortx.stanford.edu), which outputs the relative proportion of 22 immune cell types present in each sample
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
Supplementary_files_format_and_content: Table with clinical data and CIBERSORT output for each sample

source_name: tumor

extract_protocol:
RNA was extracted from FFPE tumor blocks
Illumina TruSeq RNA Exome Library Kit

tag: patient id

tag: disease state

value: esophageal and gastroesophageal junction adenocarcinoma

value: tumor


title: Patient ID: B012-0039 [SL446531]

tag: tissue


title: Patient ID: B012-0044 [SL462145]


title: Patient ID: B012-0042 [SL462143]


title: Patient ID: B012-0038 [SL446530]


title: Patient ID: B012-0041 [SL446532]


title: Patient ID: B012-0037 [SL462142]


title: CNS_Sarcoma_FFPE_rep4

value: 3 years-old

value: f

value: Fusocellular Sarcoma

value: Frontal

value: 1.59 years


title: Peripheral blood sample from anaphylaxis patient 833 at Time T1

value: peripheral blood

tag: study

value: Anaphylaxis study

tag: disease status

value: Anaphylaxis

value: Moderate


title: 1D-1_bursa of Fabricius

value: White-King pigeon

value: bursa of Fabricius

value: 1 day old


title: Patient ID: B012-0036 [SL446529]


title: Patient ID: B012-0040 [SL462113]


title: Peripheral blood sample from healthy control 927

value: Healthy control

tag: severity

tag: time point


title: Peripheral blood sample from anaphylaxis patient 833 at Time T0


title: Peripheral blood sample from healthy control 928


title: Peripheral blood sample from anaphylaxis patient 831 at Time T1

value: Severe


title: Peripheral blood sample from healthy control 938


title: ctrl-OMVs_B1

tag: treatment

value: vehicle ctrl

value: outer membrane vesicles (OMVs)


title: tRNA1-OMVs_B2

value: 5' tRNA-fMet1 half over-expression


title: Peripheral blood sample from anaphylaxis patient 831 at Time T0


title: Patient ID: B012-0032 [SL462111]

value: esophageal and gastroesophageal junction adenocarcinoma

value: tumor


title: nhm3-1+GA3-1

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

data_processing:
Illumina Hiseq 2500 sequencing platform with 150 bp paired-end reads used for sequencing cDNA libraries
All raw reads were filtered by removing reads with adaptors and low-quality reads. All clean reads were mapped to the reference database for the Brassica rapa genome (http://brassicadb.cn/, Brassica_Genome_data/Brapa3.0) using HISAT2 software
Gene expression levels were calculated using the Fragments Per Kilo bases per Million fragments (FPKM) method in nine libraries
The DESeq2 software was applied to analyze DEGs based on the FPKM-derived baseMean for each gene between samples. The screening criteria of DEGs were defined as |log2 Fold change|≥1 and FDR<0.05
Genome_build: http://brassicadb.cn/, Brassica_Genome_data/Brapa3.0
Supplementary_files_format_and_content: tab-delimited excel files include Gene ID, FPKM values,Description,Pathway,GO terms... for each gene

organism: Brassica rapa

source_name: mutant nhm3-1+GA3_rosette leaves

extract_protocol:
The rosette leaves of Chinese cabbage were sampled, total RNA was extracted using Trizol reagent
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: Chinese cabbage

value: rosette leaves

value: at the rosette stage

value: mutant nhm3-1+GA3


title: nhm3-1+GA3-2


title: nhm3-1-3

source_name: mutant nhm3-1_rosette leaves

value: mutant nhm3-1


title: Patient ID: B012-0028 [SL446528]


title: nhm3-1+GA3-3


title: Patient ID: B012-0033 [SL462112]


title: Patient ID: B012-0026 [SL463402]


title: Patient ID: B012-0035 [SL462141]


title: Patient ID: B012-0031 [SL462140]


title: Patient ID: B012-0025 [SL462137]


title: Patient ID: B012-0023 [SL446527]


title: nhm3-1-2


title: Patient ID: B012-0022 [SL446526]


title: nhm3-1-1


title: Peripheral blood sample from anaphylaxis patient 830 at Time T0

value: peripheral blood

value: Anaphylaxis study

value: Anaphylaxis


title: Patient ID: B012-0021 [SL446525]


title: Patient ID: B012-0020 [SL462136]


title: Patient ID: B012-0029 [SL462138]


title: FT-3

source_name: wild type 'FT'_rosette leaves

value: wild type 'FT'


title: Peripheral blood sample from anaphylaxis patient 828 at Time T0

value: Moderate


title: CNS_Sarcoma_FFPE_rep2

value: 6 years-old

tag: Sex

value: m

tag: histology

value: Sarcoma NOS

tag: localization

value: Frontal

value: GTR

value: ICE + loc RT

value: local RT

value: alive

value: 0.99 years

value: relapse/progression/death


title: Peripheral blood sample from anaphylaxis patient 819 at Time T1


title: Peripheral blood sample from anaphylaxis patient 830 at Time T1

value: Severe


title: Patient ID: B012-0019 [SL446524]

value: esophageal and gastroesophageal junction adenocarcinoma

value: tumor


title: Patient ID: B012-0018 [SL462114]


title: FT-1

value: Chinese cabbage

value: rosette leaves

value: at the rosette stage


title: FT-2

value: wild type 'FT'


title: Peripheral blood sample from anaphylaxis patient 819 at Time T0

value: peripheral blood

value: Anaphylaxis study

value: Anaphylaxis

value: Moderate


title: Patient ID: B012-0015 [SL446523]


title: Peripheral blood sample from anaphylaxis patient 802 at Time T1


title: si-SNHG17-1-3 [s6]

city: Guangzhou

first: YUE

last: LUO

state: Guangdong

address: No.13 Shiliugang Road

department: Cancer Center

institute: Integrated hospital of traditional Chinese Medicine, Southern Medical University

data_processing:
Total RNAs from Hep3B cells transfected with si-SNHG17-1 and si-NC were isolated by TRIzol reagent.
The quality and quantity of the total RNA that was used to construct the transcriptome RNA-seq library met the following standards: OD260/280 = 1.8~2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0 and >10 μg.
High-quality RNA from each sample was sent to for RNA-seq on the Illumina HiSeq Xten platform.
The clean reads were then aligned to the human genome (version GRCh38) using the HISAT2.
STRING TIE was used to count genes and fragments per kilo base per million mapped reads (FPKM) method was used to determine the gene expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The human HCC cell lines Hep3B) was cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNAs from Hep3B cells transfected with si-SNHG17-1 and si-NC were isolated by TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hep3b cell was transfected with si-SNHG17-1 or si-NC.

tag: cell line

tag: tag

value: hepatocellular carcinoma (HCC) cell line

tag: genotype/variation


title: si-SNHG17-1-2 [s5]


title: Patient ID: B012-0008 [SL462109]


title: Patient ID: B012-0012 [SL462146]


title: Patient ID: B012-0013 [SL446522]


title: Patient ID: B012-0011 [SL446521]


title: Patient ID: B012-0006 [SL446518]


title: Patient ID: B012-0007 [SL446519]


title: si-SNHG17-1-1 [s4]


title: Patient ID: B012-0017 [SL446534]


title: Peripheral blood sample from anaphylaxis patient 732 at Time T1


title: Patient ID: B012-0005 [SL446533]


title: si-NC-3

value: si-NC


title: Patient ID: B012-0002 [SL463401]


title: Patient ID: B012-0003 [SL446517]


title: Patient ID: B012-0004 [SL462135]


title: CNS_Sarcoma_FFPE_rep1

tag: age

value: 6 years-old

value: f

value: Sarcoma NOS

value: Cerebellum

tag: resection

value: GTR

tag: staging

value: M+

value: CSI

value: death

value: 1.25 years

tag: pfs

value: 1.08 years


title: Peripheral blood sample from anaphylaxis patient 719 at Time T0


title: si-NC-2


title: Patient ID: B012-0001 [SL462108]

tag: patient id

tag: disease state

value: esophageal and gastroesophageal junction adenocarcinoma

value: tumor


title: Peripheral blood sample from anaphylaxis patient 719 at Time T1

tag: tissue

value: peripheral blood

tag: study

value: Anaphylaxis study


title: si-NC-1


title: Peripheral blood sample from anaphylaxis patient 802 at Time T0

tag: disease status

value: Anaphylaxis

tag: severity

value: Severe


title: tRNA_input

description: input sample

data_processing:
Library strategy: eCLIP
Reads were trimmed and mapped to the human genome (UCSC version GRCh38/hg38), AGO2 binding clusters were identified by CLIPper in immunoprecipitated samples and normalized against the paired input sample to define significant peaks (log2 fold change ≥ 3 of normalized reads and P value < 0.001 determined by the Fisher exact test).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peak information files for total eCLIP and targeted chimeric eCLIP analysis.

source_name: airway epithelial cells

growth_protocol: Cells were grown in BronchiaLife basal medium (Lifeline Cell Technology) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline) as well as 10,000 U/ml Penicillin and 10,000 μg/ml Streptomycin

extract_protocol:
Cell pellets were lysed, sonicated, RNase treated before immunoprecipation.
Library was prepared using the published eCLIP protocol

treatment_protocol: Cells were transfected with 5' tRNA-fMet1 half or siNC for a day and then flash-frozen to get cell pellets

tag: cell type

value: airway epithelial cells from a CF donor

tag: transfection

value: 5’ tRNA-fMet1 half

tag: genotype

value: Phe508del homozygous

tag: ip antibody

tag: targeted sequencing

value: No


title: Peripheral blood sample from anaphylaxis patient 653 at Time T0

value: Moderate

tag: time point


title: tRNA_IP_targeted

description: IP sample

value: anti-AGO2 antibody (Eclipse BioInnovations)

value: Yes


title: tRNA_IP_total

description: IP sample


title: siNC_IP_targeted

description: IP sample

value: siNC


title: Peripheral blood sample from anaphylaxis patient 653 at Time T1


title: Peripheral blood sample from anaphylaxis patient 633 at Time T1


title: siNC_IP_total

description: IP sample


title: HTR-8/Svneo G1 rep2

city: Zhengzhou

first: Jung-Chien

last: Cheng

state: Henan

address: 40, Daxue Road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Illumina CASAVA 2.19 software was used for basecalling.
Following adapter trimming, reads with adapter sequences, low quality, or with N>10% were removed.
Clean reads were mapped to the GRCh38/hg38 genome assembly using HISAT2 (2.0.5)
Differential expression analysis was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file, Raw gene counts and FPKM values for every genes and every samples

source_name: Placenta

extract_protocol:
Total RNA from each sample was extracted using TRIzol
Sequencing libraries were generated using the NEBNext® Ultra™ II RNA Library Prep Kit from Illumina (NEB) according to the manufacturer’s protocol.

value: Trophoblast cells

tag: cell line

tag: treatment

value: Treated with 1 µM G1 for 24 hours


title: HTR-8/Svneo G1 rep3


title: HTR-8/Svneo Control rep3

value: Untreated


title: HTR-8/Svneo Control rep2


title: siNC_input

description: input sample


title: HTR-8/Svneo Control rep1


title: Peripheral blood sample from anaphylaxis patient 576 at Time T0


title: LVCtrl amyloid-beta-treated rep 3

city: La Jolla

first: Robert

last: Rissman

state: California

address: 9500 Gillman Drive

institute: University of California, San Diego

description:
Ctrl_with_AB_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

data_processing:
Paired-end FASTQ files. Extra sequencing was done on another lane to add sequencing depth; this can be found in the "L001" files, which can be merged with corresponding the "L004" files. In the raw file name, the lentiviral infection is listed (ex. "3R", "4R", "3R4R", "Ctrl"), then the treatment ("AB" = amyloid beta; "only" = DMSO), then the biological replicate ("1", "2", or "3"). "R1" and "R2" are the different paired-end files.
FastQC was run before and after adapter trimming with Bbduk (BBMap_38.73).
FASTQ files were mapped to the GRCh38 human reference genome available from Ensembl using STAR 2.7.3a and release number 98 of the GTF.
featureCounts (Subread 1.6.4) was used to determine gene counts, which were then analyzed for differential expression using DESeq (1.26.0).
GO analysis was carried out using clusterProfileR.
For transposable element quantification and analysis, TEcounts (2.0.3) was used for a global view of transposable element expression (i.e. not at locus level), while TElocal (0.1.0) was used to analyze locus-level differential expression of transposable elements. Both programs are available from Molly Hammell's lab at Cold Spring Harbor Laboratory. Genome indices and GTFs for GRCh38 that are custom-made by the Hammell lab were used in analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing gene counts output from featureCounts. File is called "featurecounts_matrix.txt".
Supplementary_files_format_and_content: csv file containing raw counts for both genes and transposable elements from TEcount. File is "TEcount_cells_raw_counts_all.csv".
Supplementary_files_format_and_content: csv file containing raw counts of only transposable elements from TEcount. File is "TEcount_cells_raw_counts_TEs_only.csv".
Supplementary_files_format_and_content: csv file containing raw counts for both genes and transposable elements from TElocal. File is "TElocal_cells_raw_counts_all.csv".
Supplementary_files_format_and_content: csv file containing raw counts of only transposable elements from TElocal. File is "TElocal_cells_raw_counts_TEs_only.csv".

molecule: polyA RNA

source_name: Neuroblastoma SHSY-5Y cells

growth_protocol: Undifferentiated SY5Y cells underwent fewer than 20 passages, were passaged weekly, and were maintained with media composed of 10% fetal bovine serum and a 1:1 mixture of Eagle’s Minimum Essential Medium (MEM) and Ham’s F12 (F12).

extract_protocol:
Cells were gently scraped and RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral infection with respective tau or control lentiviruses at MOI 20 at time of plating. Following plating, cells were differentiated into neurons and fed daily using 15 nM retinoic acid in 1:1 MEM:F12 with 3% fetal bovine serum. For 24 hours prior to collection, cells were incubated with either 50nM amyloid-beta oligomers or 50 nM DMSO (as a control).

value: Retinoic acid-differentiated SHSY-5Y cells

tag: lentiviral infection

value: Empty vector lentivirus, MOI 20 at time of plating

tag: agent

value: 50 nM amyloid-beta 42 oligomers for 24 hours prior to collection


title: Peripheral blood sample from anaphylaxis patient 568 at Time T1

value: peripheral blood

value: Anaphylaxis study


title: WL02

city: Joondalup

first: Elin

last: Gray

state: Western Australia

address: 270 Joondalup Drive

department: School of Medical and Health Sciences

institute: Edith Cowan University

data_processing:
BCL files were demultiplexed and converted into FASTQ using bcl2fastq utility of Illumina BaseSpace Sequence Hub. FASTQ files were processed using Cell Ranger 3.0.2 with refdata-cellranger-GRCh38-3.0.0 reference. Raw gene-barcode matrices from Cell Ranger output were used for downstream processing.
Genome_build: refdata-cellranger-GRCh38-3.0.0 reference
Supplementary_files_format_and_content: Raw gene-barcode matrices from Cell Ranger were provided for each sample.

source_name: liver metastasis of uveal melanoma

extract_protocol:
Tumours obtained from the surgery were freshly subjected to single-cell dissociation using Human Tumour Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, the tumours were washed with plain RPMI (ThermoFisher Scientific) supplemented with Penicillin and Streptomycin (ThermoFisher Scientific), and processed into pieces (1 mm3) using scalpels with the recommended volume of enzyme mix as per instructions. The tumour pieces and enzyme mix were then transferred into gentleMACS™ C tubes (Miltenyi Biotec), and then the tubes were loaded onto the gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec) with the program according to the manufacturer’s instructions. After incubation, digested tissues were filtered through Falcon® 70-μm strainers (Corning) and washed. Cell suspension was further filtered through 40-μm strainers to remove cell clumps. The viability was assessed by ReadyProbe® Cell Viability Imaging Kit (ThermoFisher Scientific) to ensure the viability was greater than 90%.
Single-cell RNA sequencing was performed using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to the manufacturer’s protocol. WL02 was aimed with a targeted capture of 2,000 cells due to the limited tissue obtained from the surgery, while WL03 with a targeted capture of 9,000 cells. Gel Beads-in-emulsion was generated using Chromium Single Cell B Chip Kit. Libraries were sequenced using the Illumina NovaSeq 6000 and S2 flow cells (100 cycle kit) with a read one length of 28 cycles and a read two length of 94 cycles.

treatment_protocol: Resected tumours were triaged by pathologist immediately after surgery and immersed into RPMI 1640 supplemented with 20% foetal bovine serum, 10,000 U/mL penicillin and 10,000 µg/mL streptomycin (ThermoFisher Scientific) at 4°C to maximise the viability of cells.

value: liver

tag: gender

value: male

tag: age at diagnosis of primary tumour


title: WL03


title: Sonalika_control, biological rep2

city: Mohali

first: Jitendra

last: Kumar

state: Punjab

address: National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India) C-127, Industrial Area S.A.S. Nagar, Phase 8 Mohali-160071, Punjab, India

country: India

description: Gene expression data from control Sonalika_plant leaf.

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with GeneSpring GX v12 (Agilent Technologies) and the followed on transcriptome analysis console (TAC) software (Applied Biosystems).

organism: Triticum aestivum

source_name: Sonalika_plants inoculated with agrobacterium but no virus

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

growth_protocol: Wheat plants were grown with regular watering and light conditions.

extract_protocol: Spectrum Plant Total RNA Kit (Sigma-Aldrich) was used for the extraction of total RNA follwing the manufacturer's instructions.

treatment_protocol: The control plants received agrobacterium inoculations without virus; however, the agrobacterium contained WDIV infectious clones in the virus treated plants.

value: leaf

tag: cultivar

value: Sonalika

tag: phenotype

value: resistant

value: control

tag: age

value: 28 day old wheat plants


title: Peripheral blood sample from anaphylaxis patient 583 at Time T0

tag: tissue

tag: study

tag: disease status

value: Anaphylaxis

value: Severe


title: Sonalika_virus, biological rep2

institute: National Agri-Food Biotechnology Institute

description: Gene expression data from virus infected Sonalika_plant leaf.

source_name: Sonalika_plants inoculated with agrobacterium containing infectious clone of the virus

value: virus infected


title: liver tissue-IMP-GH006

city: New York

first: George

last: Hasko

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University Medical Center

data_processing:
Real-Time Analysis software (Illumina) was used for base calling.
bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment was performed to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Testing for differentially expressed genes under various conditions was done using DESeq2 R package designed to test differential expression between two experimental groups from RNAseq counts data.
Signaling pathways were identified by Ingenuity Pathway Analysis (Qiagen IPA software).

source_name: liver tissue

extract_protocol:
Frozen liver samples were submitted to Columbia Molecular Pathology/MPSR (HICCC) core where they were homogenized with Qiagen TissueLyser II, at 25/s oscillation frequency for 2 min. RNA was extracted with Qiagen miRNeasy mini kit following the instructions of the manufacturer, and RNA was eluted at a volume of 50 ul. RNA samples with RIN 8≥ were submitted to the JP Sulzberger Columbia Genome Center for RNAseq analysis.
Poly-A pull-down was used to enrich mRNAs from total RNA samples, followed by library construction using Illumina TruSeq chemistry. Libraries were sequenced using Illumina NovaSeq 6000. Samples were multiplexed in each lane, yielding a targeted number of paired end 100-bp reads for each sample.

tag: strain

value: IMP (1000mg/kg) +LPS (10mg/kg)


title: HTR-8/Svneo G1 rep1

tag: cell type

value: Trophoblast cells

value: Treated with 1 µM G1 for 24 hours


title: Peripheral blood sample from anaphylaxis patient 633 at Time T0

tag: severity


title: Sonalika_virus, biological rep1


title: LVCtrl amyloid-beta-treated rep 1

description:
Ctrl_with_AB_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: Retinoic acid-differentiated SHSY-5Y cells

value: Empty vector lentivirus, MOI 20 at time of plating


title: LV3R4R amyloid-beta-treated rep 3

description:
3R4R_with_AB_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 0N3R and 1N4R tau lentivirus (1:1), MOI 20 each at time of plating

value: 50 nM amyloid-beta 42 oligomers for 24 hours prior to collection


title: LVCtrl amyloid-beta-treated rep 2

description:
Ctrl_with_AB_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: liver tissue-IMP-GH005

value: liver


title: Sonalika_control, biological rep1


title: Peripheral blood sample from anaphylaxis patient 568 at Time T0

value: peripheral blood

value: Anaphylaxis study


title: Peripheral blood sample from anaphylaxis patient 459 at Time T1

value: Moderate


title: WL711_virus, biological rep1

description: Gene expression data from virus WL711 plant leaf.

source_name: WL711 plants inoculated with agrobacterium containing infectious clone of the virus

value: leaf

value: susceptible


title: Peripheral blood sample from anaphylaxis patient 828 at Time T1


title: WL711_virus, biological rep2

description: Gene expression data from virus infected WL711 plant leaf.

value: 28 day old wheat plants


title: WL711_control, biological rep2

description: Gene expression data from control WL711 plant leaf.

source_name: WL711 plants inoculated with agrobacterium but no virus

value: control


title: Peripheral blood sample from anaphylaxis patient 576 at Time T1

value: Anaphylaxis

value: Severe


title: Peripheral blood sample from anaphylaxis patient 459 at Time T0


title: liver tissue-IMP-GH004

value: IMP (1000mg/kg) +LPS (10mg/kg)


title: WL711_control, biological rep1


title: Peripheral blood sample from anaphylaxis patient 318 at Time T1


title: LV3R4R amyloid-beta-treated rep 1

description:
3R4R_with_AB_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: LV4R amyloid-beta-treated rep 3

description:
4R_with_AB_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 1N4R tau lentivirus, MOI 20 at time of plating


title: liver tissue-vehicle-GH003

value: vehicle+LPS (10mg/kg)


title: liver tissue-vehicle-GH002


title: Patient ID: B012-0030 [SL462139]

tag: patient id

tag: disease state

value: esophageal and gastroesophageal junction adenocarcinoma

value: tumor


title: liver tissue-vehicle-GH001


title: LV4R amyloid-beta-treated rep 2

description:
4R_with_AB_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: Retinoic acid-differentiated SHSY-5Y cells


title: pro-B cell line transfected with Lmo2 rep2

city: Isehara

first: Katsuto

last: Hozumi

state: Kanagawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai University School of Medicine

hyb_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v14.9, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

source_name: pro-B cell line transfected with Lmo2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: B cell line


title: LV3R4R amyloid-beta-treated rep 2

description:
3R4R_with_AB_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 0N3R and 1N4R tau lentivirus (1:1), MOI 20 each at time of plating

value: 50 nM amyloid-beta 42 oligomers for 24 hours prior to collection


title: Cyfip2 WT retinas_3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The raw reads were mapped to the mouse reference genome sequences (mm10) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.3.5.1 and SAMtools ver. 1.11.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Cyfip2 WT

extract_protocol:
Retinal total RNAs were isolated using TRIzol RNA extraction reagent (Invitrogen).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: retina

tag: genotype

value: Cyfip2 WT


title: LV4R amyloid-beta-treated rep 1

description:
4R_with_AB_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: LV3R amyloid-beta-treated rep 3

description:
3R_with_AB_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 0N3R tau lentivirus, MOI 20 at time of plating


title: Cyfip2 WT retinas_2


title: pro-B cell line transfected with Lmo2 rep1


title: Peripheral blood sample from anaphylaxis patient 313 at Time T1

value: peripheral blood

value: Anaphylaxis study

value: Moderate

tag: time point


title: Peripheral blood sample from anaphylaxis patient 318 at Time T0

value: Anaphylaxis


title: Cyfip2 WT retinas_1


title: LV3R amyloid-beta-treated rep 2

description:
3R_with_AB_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

tag: lentiviral infection


title: Ebf1-deficient pro-B cell lines without potential T cell lineage rep1


title: Peripheral blood sample from anaphylaxis patient 313 at Time T0


title: Peripheral blood sample from anaphylaxis patient 249 at Time T1


title: Cyfip2 CKO retinas_3

source_name: Cyfip2 CKO

value: Cyfip2 CKO


title: 155-shH19D

city: Tucson

first: Ritu

last: Pandey

state: Arizona

address: 1515 N Campbell Ave.,

department: Cellular and Molecular Medicine, Arizona Cancer Center

institute: University of Arizona

data_processing:
Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark.
Differential methylation was estimated using MethylKit (v. 1.11)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Text file containg percent methylation scores of bisulfite converted cytosines (T’s, unmethylated C’s) and  non-converted Cs (methylated C’s)

source_name: Organoid

extract_protocol: none provided by the submitter

value: prostate

value: organoid

tag: treatment


title: 155-shH19C


title: Cyfip2 CKO retinas_2


title: LVCtrl DMSO-treated rep 3

description:
Ctrl_only_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: Empty vector lentivirus, MOI 20 at time of plating

tag: agent

value: DMSO (Control group) for 24 hours prior to collection


title: 155-shH19B


title: LVCtrl DMSO-treated rep 2

description:
Ctrl_only_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: Cyfip2 CKO retinas_1


title: Peripheral blood sample from anaphylaxis patient 249 at Time T0

data_processing: The microarray data was preprocessed in R employing the RMA algorithm. A custom chip description file (CDF) file was used (hugene21sthsentrezg, version 19).

extract_protocol: RNA was extracted with the PAXgene Blood RNA Extraction Kits (PreAnalytiX GmbH, Switzerland) by automation with the Qiacube instrument (Qiagen, Australia).


title: Peripheral blood sample from anaphylaxis patient 310 at Time T1

value: Severe


title: 155C

value: Control


title: Ebf1-deficient pro-B cell lines without potential T cell lineage rep2

value: B cell line


title: Ebf1-deficient pro-B cell lines with potential T cell lineage rep2


title: pro-B cell line transfected with empty vector rep2


title: LV3R4R DMSO-treated rep 3

description:
3R4R_only_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: Retinoic acid-differentiated SHSY-5Y cells

value: 0N3R and 1N4R tau lentivirus (1:1), MOI 20 each at time of plating


title: LVCtrl DMSO-treated rep 1

description:
Ctrl_only_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: Ebf1-deficient pro-B cell lines with potential T cell lineage rep1


title: 155B


title: LV3R amyloid-beta-treated rep 1

description:
3R_with_AB_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 50 nM amyloid-beta 42 oligomers for 24 hours prior to collection


title: Keratinocytes_baby_rep6

city: Val-de-Reuil

first: Cécilia

last: Brun

address: Campus de Maigremont

department: Translational Science - Essential Health

institute: Johnson & Johnson Santé Beauté France

hyb_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.

data_processing: A background correction followed by a quantile normalization (QN) was applied using the RMA framework as implemented in the limma R package. Quality-check was performed to properly evaluate the impact of the QN and filtering using extensive data visualization before and after normalization.

source_name: Keratinocytes - Foreskin

growth_protocol: Human primary keratinocytes were provided by Sterlab (Sophia Antipolis, France) from 6 baby and 6 adult volunteers. Briefly, keratinocytes were isolated from foreskin and from abdominoplasty, for babies and adults respectively. Then, Keratinocytes were cultured in KGM gold basal medium supplemented with KGM-Gold Keratinocyte SingleQuots Kit (Lonza).

extract_protocol: One passage after thawing, RNAs were extracted using RNeasy 96 QIAcube HT Kit (Qiagen) and supernatants were collected.

tag: gender

value: Male

value: Baby

value: Keratinocytes - Foreskin


title: Keratinocytes_baby_rep5

scan_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.


title: Keratinocytes_baby_rep2

label_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.


title: Keratinocytes_baby_rep3


title: Wild-Type lungs

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gen counts obtained using the Cell Ranger workflow (version 3.1.0) using the mm10-2.1.0 reference transcriptome. Each sample was sequenced to a depth of >390 million reads, with over 9,600 called cell barcodes from each library, with >34,000 UMI per cell on average (default filtering options) (see summary metrics in Table S1). Using the default filtered cellular barcodes, the associated sparse-filtered HDF5 files were jointly processed (WT and MAS) in AltAnalyze and ICGS2 (Iterative Clustering and Guide-gene selection version 2) to obtain normalized gene counts (counts per ten thousands (CPTT) UMIs) and initial predicted cell populations (9). ICGS2 was run using the default options (cosine clustering) in addition to a PageRank down-sampling threshold of 5,000 cells. ICGS2 identified two cell populations (c20 and c34) as presumptive unknown cell types (no enrichment in its BioMarkers gene set database), that were excluded prior to downstream analyses due to a lack of protein-coding marker genes (only lncRNAs) and broad UMAP dispersion. Cell populations names were revised from the original ICGS2 predictions based on the literature (marker gene driven). The top-specific marker genes for each Macrophage and Monocyte cluster were derived using the MarkerFinder algorithm and gene set enrichments using GO-Elite, both AltAnalyze (9). Comprehensive differential expression and gene regulatory prediction analyses were performed using these alignment results in the software cellHarmony with the supplied ICGS2 groups for both WT and MAS (options --referenceType None) and eBayes p<0.05 FDR adjusted and fold>1.2 (10). Included UMAP plots were produced by cellHarmony or downstream by AltAnalyze by querying the expression of individual genes (--genes "<gene symbols>" --separateGenePlots True).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file (ICGS2 WT and MAS assigned clusters and UMAP coordinate text file) and h5 (sparse-matrix HDF5 counts)

source_name: Lungs

extract_protocol:
Lung cell dissociation. 25 mg fresh lung tissue was minced on ice and then shaken and triturated on ice for 9 minutes with 1.5 mL enzyme mix (90 uL of 100 mg/mL Collagenase A (Sigma), 150 L of 43 U/mL lyophilized Elastase (Worthington), 150 uL of 90 U/mL purified neutral Protease (Worthington), 7.5 uL of 1M CaCl2, 7.5 uL of 125 U/mL DNase I (Applichem), and 1095 uL of DPBS). After allowing to settle, the upper layer was filtered through a 30 uM filter and collected, followed by rinsing of filter with 0.04% BSA. Lich enzyme mix (1 uL of 0.5M EDTA, 100 L of 100 mg/mL Bacillus Licheniformis (Sigma), and 899 uL DPBS) was added to remaining tissue and triturated on ice for 10 minutes before being filtered and collected. Filter was again rinsed with 0.04% BSA, after which samples were lysed with RBC Lysis solution before being resuspended in 0.04% BSA.
Following dissociation, cells were diluted to 1,000 cells/mL, and 15,000 cells from wild-type and MAS mice were each loaded in a separate lane of a Chromium Controller Instrument (10x Genomics). The 10x Genomics single cell 3’ v3 assay protocol was followed as described until the cDNA amplification step.

value: Lungs

value: Wild-type


title: LV3R4R DMSO-treated rep 2

description:
3R4R_only_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: MAS lungs

value: TLR9 mouse model of Macrophage Activation Syndrome (MAS)


title: Keratinocytes_baby_rep4