title: HKU Meningioma 160 (methylation)

description:
meningioma
QM160
204365950077_R08C01


title: SVP 72H STAT rep1

status: Public on Jan 10 2022

type: SRA

city: Milano

first: Gaia

last: Spinetti

address: Via Fantoli 16/15

country: Italy

institute: IRCCS MultiMedica

description: 2x100 paired-end sequence reads

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed to remove adaptor contaminations, using Cutadapt (version 1.18) with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --trim-n --pair-filter=any --minimum-length 20.
Read quality was checked for each sample using FastQC v0.11.8
Sequencing reads were, then, aligned to GENCODE’s human reference genome (GRCh38 primary assembly v31) and quantified at gene level using STAR (version 2.7.3a), with default parameters and allowing up to 3 mismatches.
Genome_build: GRCh38 v.31
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: saphenous vein

growth_protocol: Isolation of cells for in vitro experiments was performed as previously described, using two consecutive immunomagnetic selections to obtain CD31negative/CD34positive homogenous cell populations (Campagnolo P, Cesselli D, Haj Zen A Al, Beltrami AP, Kränkel N, Katare R, Angelini G, Emanueli C, & Madeddu P. Human adult vena saphena contains perivascular progenitor cells endowed with clonogenic and proangiogenic potential. Circulation 2010 121 1735–1745. (doi:10.1161/CIRCULATIONAHA.109.899252))

extract_protocol:
For RNA-Seq analysis, total RNA was extracted from 5 different donors of SVPs using TRIzol, treated with DNase I, and quantified by using NanoDrop-1000 spectrophotometer before integrity assessment with Agilent 2100 Bioanalyzer (RNA Integrity Number values >8).
RNA libraries were prepared for sequencing from 500ng purified RNA with TruSeq Stranded totalRNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To investigate the effect of mechanical strain on cultured cells, SVPs were subjected to cyclic strain using the FlexCell Tension Plus FX-5000T system. Before cell seeding, six-well Bioflex plates were surface-coated with human fibronectin (10μg/ml) in PBS after covalent crosslinking with a crosslinking reagent (sulfosuccinimidyl 6-(4'-azido-2'-nitrophenylamino) hexanoate; Sulfo-SANPAH) at 0.2 mg/ml in Hepes 50 mM (pH 8.5), photo-activated by exposure to UV-light (365 nm). Cells were subjected to uniaxial cyclic deformation protocol (0-10% deformation, 1 Hz frequency), for 24 and 72 hours, while static controls were provided by seeding an equal amount of cells, under the same atmospheric conditions, but without mechanical stimulation.

tag: treatment

value: static culture

tag: timepoint

value: 72 hours

tag: cell type

value: saphenous vein progenitors


title: SVP 24H DYN rep2

description: 2x100 paired-end sequence reads

value: cyclic uniaxial strain

value: 24 hours


title: SVP 72H STAT rep4

description: 2x100 paired-end sequence reads


title: HKU Meningioma 16 (methylation)

type: genomic

city: San Francisco

first: Abrar

last: Choudhury

state: California

country: USA

institute: University of California, San Francisco

description:
meningioma
QM16
203064760075_R08C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Analysis was performed in R v3.5.3 with the SeSAMe package. Probes were filtered and analyzed using the standard SeSAMe preprocessing pipeline, including normal-exponential out-of-band background correction, nonlinear dye bias correction, p-value with out-of-band array hybridization masking, and beta value calculation
Processed data file meningioma_betas.csv represents SeSAMe-computed average beta values.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and DNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)

tag: tissue

value: meningioma

tag: institution

value: HKU

tag: age

tag: Sex

tag: grade


title: HKU Meningioma 157 (methylation)

description:
meningioma
QM157
204365950077_R06C01


title: SVP 24H DYN rep1

description: 2x100 paired-end sequence reads


title: HKU Meningioma 156 (methylation)

description:
meningioma
QM156
204365950077_R05C01


title: TGA1_replica1

city: Valencia

first: Imelda

last: Ontoria-Oviedo

address: Avda Fernando Abril Martorell 106

department: Regeneration and Heart transplantation Unit

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

data_processing:
sequences were filtered and trimmed using the cutAdapt tool [http://journal.embnet.org/index.php/embnetjournal/article/view/200]
fastq.gz files were treated with Cutadapt and aligned with Kallisto to obtain the count table for each gene
Differential expression analysis of RNAseq expression profiles was done with the EdgeR package
Supplementary_files_format_and_content: Matrix table with raw RNA counts for every RNA and every sample

source_name: induced pluripotent stem cells

extract_protocol:
Total RNA was isolated through the RNeasy Plus kit  (Qiagen)
RNA libraries were prepared for sequencing using standard strand specific total RNA seq Illumina protocols; KAPA Library Quantification Kit KK4835

value: Endothelial cells derived from iPSC

tag: disease state

value: TGA


title: Ctrl2_replica1

value: control


title: Ctrl1_replica1


title: HKU Meningioma 153 (methylation)

description:
meningioma
QM153
204365950077_R04C01


title: HKU Meningioma 152 (methylation)

description:
meningioma
QM152
204365950077_R03C01


title: HKU Meningioma 151 (methylation)

description:
meningioma
QM151
203219750225_R04C01


title: HKU Meningioma 162 (methylation)

description:
meningioma
QM162
203219760007_R01C01


title: HKU Meningioma 150 (methylation)

description:
meningioma
QM150
204365950077_R02C01


title: hchlD219

city: Vancouver

first: Robert

middle: EW

last: Hancock

state: BC

address: 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Samples were assessed for quality using fastqc (v0.11.7) and multiqc (v1.6).
Reads were aligned to the Ensembl GRCh38.92 human genome using STAR (v2.6.0a). Reads aligned to genes were counted using htseq-count (v(0.11.0).
Globin genes and lowly expressed genes were removed (less than 10 average counts across cohorts). Libraries with fewer than one million counts were not analyzed further.
Where required, a variance stabilizing transformation was performed using the DESeq2 package and batch correction uding ComBat/sva.
Genome_build: GRCh38.92
Supplementary_files_format_and_content: Matrix with raw counts for each gene and sample.

source_name: Whole Blood

extract_protocol:
During routine blood collection in suspected sepsis patients, 3 mL of blood was collected into PAXgene Blood RNA tubes (BD Biosciences). Total RNA was extracted using PAXgene Blood RNA Kit (Qiagen). Quantification and quality measures of total RNA were obtained using an Agilent 2100 Bioanalyzer (Agilent). Samples with RNA Integrity Numbers less than 6.5 were discarded. Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
cDNA libraries were prepared using the KAPA Total RNA HyperPrep Kit (Roche) for Illumina sequencing.

value: healthy

value: M

tag: collection location

value: vancouver

tag: collection site

value: Healthy/Pre-surgical

tag: sofa 24h post admisssion

tag: in hospital mortality

value: Whole Blood


title: hchlD218

value: F


title: hchlD187


title: hchlD044


title: HKU Meningioma 15 (methylation)

description:
meningioma
QM15
203064760075_R07C01


title: HKU Meningioma 148 (methylation)

description:
meningioma
QM148
204365950077_R01C01


title: sepcv703W1

value: sepsis

value: toronto

value: ICU

value: Survived


title: HKU Meningioma 147 (methylation)

description:
meningioma
QM147
203219750225_R03C01


title: sepcv702W1


title: HKU Meningioma 146 (methylation)

description:
meningioma
QM146
204081560154_R08C01


title: sepcv087T1

value: Died


title: HKU Meningioma 158 (methylation)

description:
meningioma
QM158
203219750225_R07C01


title: sepcv085T1


title: SVP 72H DYN rep1

description: 2x100 paired-end sequence reads

value: cyclic uniaxial strain

value: 72 hours

value: saphenous vein progenitors


title: HKU Meningioma 141 (methylation)

description:
meningioma
QM141
204081560154_R05C01

value: meningioma

value: HKU


title: HKU Meningioma 155 (methylation)

description:
meningioma
QM155
203219750225_R06C01


title: HKU Meningioma 140 (methylation)

description:
meningioma
QM140
203219750225_R01C01


title: sepcv083T0


title: HKU Meningioma 154 (methylation)

description:
meningioma
QM154
203219750225_R05C01


title: HKU Meningioma 159 (methylation)

description:
meningioma
QM159
204365950077_R07C01


title: HKU Meningioma 145 (methylation)

description:
meningioma
QM145
204081560154_R07C01


title: HKU Meningioma 143 (methylation)

description:
meningioma
QM143
204081560154_R06C01


title: sepcv086T1


title: sepcv082T1


title: SVP 24H STAT rep1

description: 2x100 paired-end sequence reads

value: static culture

value: 24 hours


title: HKU Meningioma 139 (methylation)

description:
meningioma
QM139
203219750127_R08C01


title: HKU Meningioma 14 (methylation)

description:
meningioma
QM14
203064760075_R06C01


title: sepcv078T1


title: HKU Meningioma 137 (methylation)

description:
meningioma
QM137
204081560154_R03C01


title: TGA2_replica1

value: Endothelial cells derived from iPSC

value: TGA


title: HKU Meningioma 142 (methylation)

description:
meningioma
QM142
203219750225_R02C01


title: sepcv077T1

value: M


title: sepcv084T0

value: Whole Blood


title: HKU Meningioma 138 (methylation)

description:
meningioma
QM138
204081560154_R04C01


title: hchlD204

value: healthy

value: vancouver

value: Healthy/Pre-surgical


title: sepcv079T1

value: sepsis

value: toronto

value: ICU


title: sepcv076T1

value: Survived


title: sepcv080T1


title: HKU Meningioma 136 (methylation)

description:
meningioma
QM136
204081560154_R02C01


title: HKU Meningioma 134 (methylation)

description:
meningioma
QM134
204081730105_R08C01


title: HKU Meningioma 133 (methylation)

description:
meningioma
QM133
204081730105_R07C01


title: HKU Meningioma 132 (methylation)

description:
meningioma
QM132
203219750127_R07C01


title: sepcv072T1


title: HKU Meningioma 135 (methylation)

description:
meningioma
QM135
204081560154_R01C01


title: sepcv071T1


title: sepcv068T1a

value: F


title: sepcv075T1


title: sepcv065T0


title: HKU Meningioma 125 (methylation)

description:
meningioma
QM125
204081730105_R04C01


title: sepcv074T1


title: HKU Meningioma 127 (methylation)

description:
meningioma
QM127
203219750127_R04C01


title: sepcv063T1

value: Died


title: sepcv062T1


title: HKU Meningioma 129 (methylation)

description:
meningioma
QM129
204081730105_R05C01

value: meningioma


title: sepcv073T1


title: HKU Meningioma 130 (methylation)

description:
meningioma
QM130
204081730105_R06C01

value: HKU


title: sepcv069T1


title: sepcv070T1


title: HKU Meningioma 128 (methylation)

description:
meningioma
QM128
203219750127_R05C01


title: HKU Meningioma 131 (methylation)

description:
meningioma
QM131
203219750127_R06C01


title: HKU Meningioma 13 (methylation)

description:
meningioma
QM13
203064760075_R05C01


title: sepcv066T1


title: sepcv059T1


title: HKU Meningioma 121 (methylation)

description:
meningioma
QM121
204081730105_R02C01


title: HKU Meningioma 120 (methylation)

description:
meningioma
QM120
204081730105_R01C01


title: HKU Meningioma 12 (methylation)

description:
meningioma
QM12
203064760075_R04C01


title: sepcv057T1


title: sepcv061T1


title: sepcv058T1


title: HKU Meningioma 124 (methylation)

description:
meningioma
QM124
203219750127_R03C01


title: sepcv060T1


title: sepcv067T1


title: HKU Meningioma 119 (methylation)

description:
meningioma
QM119
203219750127_R02C01


title: HKU Meningioma 118 (methylation)

description:
meningioma
QM118
204081730061_R08C01


title: sepcv055T1


title: HKU Meningioma 117 (methylation)

description:
meningioma
QM117
204081730061_R07C01


title: sepcv056T1


title: HKU Meningioma 116 (methylation)

description:
meningioma
QM116
204081730061_R06C01


title: HKU Meningioma 114 (methylation)

description:
meningioma
QM114
204081730061_R04C01


title: HKU Meningioma 123 (methylation)

description:
meningioma
QM123
204081730105_R03C01


title: HKU Meningioma 115 (methylation)

description:
meningioma
QM115
204081730061_R05C01


title: sepcv053T1


title: sepcv049T1


title: sepcv050T1


title: HKU Meningioma 112 (methylation)

description:
meningioma
QM112
204081730061_R03C01


title: sepcv052T1


title: HKU Meningioma 113 (methylation)

description:
meningioma
QM113
203219750127_R01C01


title: HKU Meningioma 111 (methylation)

description:
meningioma
QM111
204081730061_R02C01


title: HKU Meningioma 110 (methylation)

description:
meningioma
QM110
203219750100_R08C01


title: HKU Meningioma 11 (methylation)

description:
meningioma
QM11
203064760075_R03C01


title: sepcv048T1


title: HKU Meningioma 108 (methylation)

description:
meningioma
QM108
203219750100_R06C01


title: HKU Meningioma 109 (methylation)

description:
meningioma
QM109
203219750100_R07C01


title: HKU Meningioma 107 (methylation)

description:
meningioma
QM107
204081730061_R01C01


title: sepcv047T1


title: HKU Meningioma 106 (methylation)

description:
meningioma
QM106
203219750100_R05C01


title: sepcv044T0


title: sepcv045T1


title: sepcv042T0


title: sepcv054T1


title: HKU Meningioma 102 (methylation)

description:
meningioma
QM102
203219750100_R02C01


title: sepcv040T1


title: sepcv041T2


title: HKU Meningioma 105 (methylation)

description:
meningioma
QM105
203219750100_R04C01


title: HKU Meningioma 104 (methylation)

description:
meningioma
QM104
204081730051_R08C01


title: HKU Meningioma 103 (methylation)

description:
meningioma
QM103
203219750100_R03C01


title: sepcv037T0


title: HKU Meningioma 101 (methylation)

description:
meningioma
QM101
204081730051_R07C01


title: HKU Meningioma 100 (methylation)

description:
meningioma
QM100
203219750100_R01C01


title: sepcv039T1


title: sepcv051T1


title: HKU Meningioma 1 (methylation)

description:
meningioma
QM1
203064760067_R06C01


title: sepcv034T1


title: UCSF Meningioma 99 (methylation)

description:
meningioma
M99
202225190150_R06C01

value: UCSF


title: sepcv033T1


title: sepcv032T1


title: UCSF Meningioma 98 (methylation)

description:
meningioma
M98
202225190150_R05C01


title: UCSF Meningioma 97 (methylation)

description:
meningioma
M97
202225190150_R04C01


title: sepcv031T1


title: sepcv030T1


title: UCSF Meningioma 94 (methylation)

description:
meningioma
M94
202225190150_R01C01


title: sepcv029T1


title: sepcv043T1


title: UCSF Meningioma 95 (methylation)

description:
meningioma
M95
202225190150_R02C01


title: sepcv027T0


title: UCSF Meningioma 92 (methylation)

description:
meningioma
M92
202212330037_R07C01


title: UCSF Meningioma 93 (methylation)

description:
meningioma
M93
202212330037_R08C01


title: sepcv026T0


title: sepcv024T1


title: sepcv028T1


title: UCSF Meningioma 90 (methylation)

description:
meningioma
M90
202212330037_R05C01


title: UCSF Meningioma 91 (methylation)

description:
meningioma
M91
202212330037_R06C01


title: HKU Meningioma 10 (methylation)

description:
meningioma
QM10
204367410003_R02C01


title: sepcv023T1


title: UCSF Meningioma 9 (methylation)

description:
meningioma
M9
202229250100_R01C01


title: sepcv022T0


title: sepcv036T0


title: sepcv020T0


title: sepcv019T0


title: sepcv018T1


title: UCSF Meningioma 86 (methylation)

description:
meningioma
M86
202212330037_R02C01


title: UCSF Meningioma 83 (methylation)

description:
meningioma
M83
202212330004_R08C01


title: sepcv021T0


title: UCSF Meningioma 89 (methylation)

description:
meningioma
M89
202212330037_R04C01


title: UCSF Meningioma 96 (methylation)

description:
meningioma
M96
202225190150_R03C01


title: UCSF Meningioma 80 (methylation)

description:
meningioma
M80
202212330004_R07C01


title: UCSF Meningioma 8 (methylation)

description:
meningioma
M8
202229250070_R08C01


title: sepcv016T1


title: sepcv015T1


title: sepcv017T0


title: UCSF Meningioma 79 (methylation)

description:
meningioma
M79
202212330004_R06C01


title: sepcv013T1


title: UCSF Meningioma 77 (methylation)

description:
meningioma
M77
202212330004_R05C01


title: sepcv012T1


title: UCSF Meningioma 76 (methylation)

description:
meningioma
M76
202212330004_R04C01


title: UCSF Meningioma 75 (methylation)

description:
meningioma
M75
202212330004_R03C01


title: sepcv011T0


title: sepcv010T0


title: UCSF Meningioma 74 (methylation)

description:
meningioma
M74
202212330004_R02C01


title: UCSF Meningioma 87 (methylation)

description:
meningioma
M87
202212330037_R03C01


title: sepcv008T1


title: sepcv007T1


title: sepcv009T1


title: UCSF Meningioma 72 (methylation)

description:
meningioma
M72
202229250118_R08C01


title: UCSF Meningioma 73 (methylation)

description:
meningioma
M73
202212330004_R01C01


title: UCSF Meningioma 71 (methylation)

description:
meningioma
M71
202229250118_R07C01


title: UCSF Meningioma 70 (methylation)

description:
meningioma
M70
202229250118_R06C01


title: sepcv005T0


title: sepcv006T0


title: sepcv004T0


title: UCSF Meningioma 69 (methylation)

description:
meningioma
M69
202229250118_R05C01


title: UCSF Meningioma 68 (methylation)

description:
meningioma
M68
202229250118_R04C01


title: UCSF Meningioma 7 (methylation)

description:
meningioma
M7
202229250070_R07C01


title: sepcv002T0


title: UCSF Meningioma 67 (methylation)

description:
meningioma
M67
202229250118_R03C01


title: sepcv003T0


title: UCSF Meningioma 65 (methylation)

description:
meningioma
M65
202229250118_R02C01


title: sepcv001T1


title: hcwimr097

value: australia


title: hcwimr096


title: UCSF Meningioma 64 (methylation)

description:
meningioma
M64
202229250118_R01C01


title: UCSF Meningioma 63 (methylation)

description:
meningioma
M63
202229250114_R08C01


title: hcwimr093


title: UCSF Meningioma 62 (methylation)

description:
meningioma
M62
202229250114_R07C01


title: hcwes078


title: hcwimr095


title: UCSF Meningioma 61 (methylation)

description:
meningioma
M61
202229250114_R06C01


title: UCSF Meningioma 60 (methylation)

description:
meningioma
M60
202229250114_R05C01


title: hcwimr094


title: UCSF Meningioma 59 (methylation)

description:
meningioma
M59
202229250114_R04C01


title: hcwes075


title: UCSF Meningioma 57 (methylation)

description:
meningioma
M57
202229250114_R02C01


title: hcwes072


title: UCSF Meningioma 6 (methylation)

description:
meningioma
M6
202229250070_R06C01


title: UCSF Meningioma 58 (methylation)

description:
meningioma
M58
202229250114_R03C01


title: hcwes074


title: UCSF Meningioma 56 (methylation)

description:
meningioma
M56
202229250114_R01C01


title: hcwes067


title: UCSF Meningioma 55 (methylation)

description:
meningioma
M55
202229250104_R08C01


title: UCSF Meningioma 54 (methylation)

description:
meningioma
M54
202229250104_R07C01


title: hcwes064


title: hcwes066


title: hcwes063


title: UCSF Meningioma 51 (methylation)

description:
meningioma
M51
202229250104_R04C01


title: hcwes060


title: UCSF Meningioma 53 (methylation)

description:
meningioma
M53
202229250104_R06C01


title: UCSF Meningioma 52 (methylation)

description:
meningioma
M52
202229250104_R05C01


title: hcwes058


title: hcwes059


title: UCSF Meningioma 49 (methylation)

description:
meningioma
M49
202229250104_R03C01


title: hcwes056


title: hcwes062


title: UCSF Meningioma 47 (methylation)

description:
meningioma
M47
202229250104_R01C01


title: UCSF Meningioma 48 (methylation)

description:
meningioma
M48
202229250104_R02C01


title: UCSF Meningioma 46 (methylation)

description:
meningioma
M46
202229250103_R08C01


title: hcwes055


title: hcwes051


title: hcwes054


title: UCSF Meningioma 44 (methylation)

description:
meningioma
M44
202229250103_R06C01


title: UCSF Meningioma 45 (methylation)

description:
meningioma
M45
202229250103_R07C01


title: hcwes050


title: UCSF Meningioma 41 (methylation)

description:
meningioma
M41
200511490066_R01C01


title: hcwes040


title: UCSF Meningioma 43 (methylation)

description:
meningioma
M43
202229250103_R05C01


title: hcwes039


title: hcwes038


title: UCSF Meningioma 40 (methylation)

description:
meningioma
M40
200511490076_R05C01


title: UCSF Meningioma 38 (methylation)

description:
meningioma
M38
200511490066_R03C01


title: hcwes037


title: UCSF Meningioma 5 (methylation)

description:
meningioma
M5
202229250070_R05C01


title: hcwes025


title: hcwes027


title: UCSF Meningioma 36 (methylation)

description:
meningioma
M36
200511490008_R05C01


title: UCSF Meningioma 37 (methylation)

description:
meningioma
M37
200511490008_R07C01


title: hchlD201


title: UCSF Meningioma 33 (methylation)

description:
meningioma
M33
200511490066_R07C01


title: UCSF Meningioma 34 (methylation)

description:
meningioma
M34
200511490066_R05C01


title: hchlD188


title: UCSF Meningioma 3 (methylation)

description:
meningioma
M3
202229250070_R03C01


title: hchlD072


title: hchlD149


title: hccol006

value: colombia


title: hccol005


title: UCSF Meningioma 29 (methylation)

description:
meningioma
M29
200511420028_R05C01


title: UCSF Meningioma 26 (methylation)

description:
meningioma
M26
200511490109_R03C01


title: UCSF Meningioma 25 (methylation)

description:
meningioma
M25
200511420050_R05C01


title: UCSF Meningioma 24 (methylation)

description:
meningioma
M24
200511420028_R03C01


title: hccol003


title: UCSF Meningioma 235 (methylation)

description:
meningioma
M235
202229250119_R02C01


title: UCSF Meningioma 4 (methylation)

description:
meningioma
M4
202229250070_R04C01


title: hcwes036


title: hccol001


title: hccol002


title: sepwes112

value: Emergency Room


title: UCSF Meningioma 233 (methylation)

description:
meningioma
M233
202226400148_R08C01


title: UCSF Meningioma 234 (methylation)

description:
meningioma
M234
202229250119_R01C01


title: sepwes110

value: M


title: UCSF Meningioma 231 (methylation)

description:
meningioma
M231
202226400148_R06C01


title: sepwes106

value: Whole Blood


title: UCSF Meningioma 232 (methylation)

description:
meningioma
M232
202226400148_R07C01


title: sepwes105


title: UCSF Meningioma 230 (methylation)

description:
meningioma
M230
202226400148_R05C01


title: sepwes104


title: UCSF Meningioma 23 (methylation)

description:
meningioma
M23
202229250103_R04C01


title: UCSF Meningioma 228 (methylation)

description:
meningioma
M228
202226400148_R04C01


title: sepwes102


title: sepwes103


title: UCSF Meningioma 28 (methylation)

description:
meningioma
M28
200511420053_R05C01


title: UCSF Meningioma 27 (methylation)

description:
meningioma
M27
200511490008_R01C01


title: hccol004

value: healthy


title: UCSF Meningioma 226 (methylation)

description:
meningioma
M226
202226400148_R02C01


title: UCSF Meningioma 227 (methylation)

description:
meningioma
M227
202226400148_R03C01


title: UCSF Meningioma 225 (methylation)

description:
meningioma
M225
202226400148_R01C01


title: sepwes098


title: sepwes096


title: UCSF Meningioma 222 (methylation)

description:
meningioma
M222
202176300058_R07C01


title: UCSF Meningioma 224 (methylation)

description:
meningioma
M224
202176300058_R08C01


title: sepwes097


title: UCSF Meningioma 219 (methylation)

description:
meningioma
M219
202176300058_R05C01


title: sepwes095


title: sepwes111


title: UCSF Meningioma 221 (methylation)

description:
meningioma
M221
202176300058_R06C01


title: sepwes090


title: sepwes092


title: UCSF Meningioma 216 (methylation)

description:
meningioma
M216
202176300058_R02C01


title: sepwes091


title: UCSF Meningioma 218 (methylation)

description:
meningioma
M218
202176300058_R04C01


title: UCSF Meningioma 215 (methylation)

description:
meningioma
M215
202176300058_R01C01


title: sepwes089


title: UCSF Meningioma 214 (methylation)

description:
meningioma
M214
202184990168_R08C01


title: UCSF Meningioma 212 (methylation)

description:
meningioma
M212
202184990168_R06C01


title: sepwes086


title: sepwes099


title: sepwes083


title: UCSF Meningioma 213 (methylation)

description:
meningioma
M213
202184990168_R07C01


title: UCSF Meningioma 210 (methylation)

description:
meningioma
M210
202184990168_R05C01


title: UCSF Meningioma 21 (methylation)

description:
meningioma
M21
202229250103_R03C01


title: sepwes082


title: sepwes084


title: sepwes101


title: UCSF Meningioma 209 (methylation)

description:
meningioma
M209
202184990168_R04C01


title: sepwes080


title: sepwes074


title: sepwes072


title: sepwes076


title: sepwes077


title: sepwes070


title: UCSF Meningioma 208 (methylation)

description:
meningioma
M208
202184990168_R03C01


title: UCSF Meningioma 207 (methylation)

description:
meningioma
M207
202184990168_R02C01


title: UCSF Meningioma 206 (methylation)

description:
meningioma
M206
202184990168_R01C01


title: sepwes087


title: UCSF Meningioma 202 (methylation)

description:
meningioma
M202
202184990103_R06C01


title: UCSF Meningioma 200 (methylation)

description:
meningioma
M200
202184990103_R04C01


title: UCSF Meningioma 20 (methylation)

description:
meningioma
M20
202229250103_R02C01


title: sepwes073


title: sepwes067


title: UCSF Meningioma 198 (methylation)

description:
meningioma
M198
202184990103_R02C01


title: UCSF Meningioma 217 (methylation)

description:
meningioma
M217
202176300058_R03C01


title: UCSF Meningioma 204 (methylation)

description:
meningioma
M204
200511420050_R03C01


title: sepwes063


title: sepwes069


title: sepwes066


title: sepwes068


title: UCSF Meningioma 2 (methylation)

description:
meningioma
M2
202229250070_R02C01


title: UCSF Meningioma 205 (methylation)

description:
meningioma
M205
202184990103_R08C01


title: UCSF Meningioma 203 (methylation)

description:
meningioma
M203
202184990103_R07C01


title: sepwes061


title: sepwes060


title: UCSF Meningioma 194 (methylation)

description:
meningioma
M194
202193490131_R08C01


title: sepwes058


title: UCSF Meningioma 193 (methylation)

description:
meningioma
M193
202193490131_R07C01


title: sepwes071


title: sepwes062


title: UCSF Meningioma 192 (methylation)

description:
meningioma
M192
202193490131_R06C01


title: UCSF Meningioma 191 (methylation)

description:
meningioma
M191
202193490131_R05C01


title: UCSF Meningioma 190 (methylation)

description:
meningioma
M190
202193490131_R04C01


title: UCSF Meningioma 189 (methylation)

description:
meningioma
M189
202193490131_R03C01


title: UCSF Meningioma 199 (methylation)

description:
meningioma
M199
202184990103_R03C01


title: UCSF Meningioma 201 (methylation)

description:
meningioma
M201
202184990103_R05C01


title: sepwes065


title: sepwes051


title: sepwes049


title: sepwes064


title: sepwes046


title: sepwes044


title: UCSF Meningioma 187 (methylation)

description:
meningioma
M187
202193490131_R01C01


title: UCSF Meningioma 188 (methylation)

description:
meningioma
M188
202193490131_R02C01


title: UCSF Meningioma 19 (methylation)

description:
meningioma
M19
202229250103_R01C01


title: UCSF Meningioma 184 (methylation)

description:
meningioma
M184
202193490063_R06C01


title: sepwes052


title: sepwes059


title: UCSF Meningioma 186 (methylation)

description:
meningioma
M186
202193490063_R08C01


title: UCSF Meningioma 185 (methylation)

description:
meningioma
M185
202193490063_R07C01


title: sepwes056


title: sepwes043


title: UCSF Meningioma 182 (methylation)

description:
meningioma
M182
202193490063_R04C01


title: sepwes041


title: UCSF Meningioma 183 (methylation)

description:
meningioma
M183
202193490063_R05C01


title: sepwes040


title: UCSF Meningioma 180 (methylation)

description:
meningioma
M180
202193490063_R02C01


title: sepwes039


title: sepwes036


title: UCSF Meningioma 179 (methylation)

description:
meningioma
M179
202193490063_R01C01


title: UCSF Meningioma 178 (methylation)

description:
meningioma
M178
202193490035_R08C01


title: UCSF Meningioma 181 (methylation)

description:
meningioma
M181
202193490063_R03C01


title: sepwes038


title: UCSF Meningioma 18 (methylation)

description:
meningioma
M18
202229250100_R08C01


title: sepwes034


title: sepwes047


title: UCSF Meningioma 176 (methylation)

description:
meningioma
M176
202193490035_R07C01


title: sepwes033


title: UCSF Meningioma 174 (methylation)

description:
meningioma
M174
202193490035_R05C01


title: UCSF Meningioma 175 (methylation)

description:
meningioma
M175
202193490035_R06C01


title: sepwes032


title: sepwes031


title: sepwes027


title: sepwes030


title: UCSF Meningioma 171 (methylation)

description:
meningioma
M171
202193490035_R03C01


title: UCSF Meningioma 170 (methylation)

description:
meningioma
M170
202193490035_R02C01


title: sepwes025


title: UCSF Meningioma 173 (methylation)

description:
meningioma
M173
202193490035_R04C01


title: UCSF Meningioma 168 (methylation)

description:
meningioma
M168
202242410193_R08C01


title: sepwes023


title: sepwes021


title: sepwes026


title: UCSF Meningioma 167 (methylation)

description:
meningioma
M167
202242410193_R07C01


title: UCSF Meningioma 165 (methylation)

description:
meningioma
M165
202242410193_R05C01


title: UCSF Meningioma 169 (methylation)

description:
meningioma
M169
202193490035_R01C01


title: sepwes020


title: sepwes029


title: UCSF Meningioma 163 (methylation)

description:
meningioma
M163
202242410193_R03C01


title: sepwes019


title: sepwes024


title: sepwes018


title: sepwes017


title: UCSF Meningioma 162 (methylation)

description:
meningioma
M162
202242410193_R02C01


title: UCSF Meningioma 161 (methylation)

description:
meningioma
M161
202242410193_R01C01


title: sepwes016


title: UCSF Meningioma 160 (methylation)

description:
meningioma
M160
202242420083_R08C01


title: sepwes015


title: sepwes014


title: sepwes013


title: UCSF Meningioma 158 (methylation)

description:
meningioma
M158
202242420083_R06C01


title: UCSF Meningioma 157 (methylation)

description:
meningioma
M157
202242420083_R05C01


title: UCSF Meningioma 166 (methylation)

description:
meningioma
M166
202242410193_R06C01


title: UCSF Meningioma 153 (methylation)

description:
meningioma
M153
202242420083_R02C01


title: UCSF Meningioma 159 (methylation)

description:
meningioma
M159
202242420083_R07C01


title: sepwes009


title: sepwes011


title: sepwes007


title: UCSF Meningioma 164 (methylation)

description:
meningioma
M164
202242410193_R04C01


title: UCSF Meningioma 152 (methylation)

description:
meningioma
M152
202242420083_R01C01


title: UCSF Meningioma 156 (methylation)

description:
meningioma
M156
202242420083_R04C01


title: sepwes003


title: UCSF Meningioma 151 (methylation)

description:
meningioma
M151
200511490076_R01C01


title: sepwes006


title: UCSF Meningioma 147 (methylation)

description:
meningioma
M147
202242420024_R07C01


title: UCSF Meningioma 150 (methylation)

description:
meningioma
M150
202242420024_R08C01


title: sepvh050

value: vancouver


title: UCSF Meningioma 145 (methylation)

description:
meningioma
M145
202242420024_R05C01


title: UCSF Meningioma 146 (methylation)

description:
meningioma
M146
202242420024_R06C01


title: sepvh047


title: UCSF Meningioma 155 (methylation)

description:
meningioma
M155
202242420083_R03C01


title: sepvh044


title: sepwes008


title: UCSF Meningioma 142 (methylation)

description:
meningioma
M142
202242420024_R02C01


title: sepwes012


title: sepvh033


title: sepvh037


title: UCSF Meningioma 14 (methylation)

description:
meningioma
M14
202229250100_R05C01


title: sepvh029


title: UCSF Meningioma 15 (methylation)

description:
meningioma
M15
202229250100_R06C01


title: UCSF Meningioma 141 (methylation)

description:
meningioma
M141
202242420024_R01C01


title: sepvh006


title: sepvh043


title: UCSF Meningioma 139 (methylation)

description:
meningioma
M139
202242420008_R08C01


title: UCSF Meningioma 144 (methylation)

description:
meningioma
M144
202242420024_R04C01


title: UCSF Meningioma 134 (methylation)

description:
meningioma
M134
202242420008_R05C01


title: sepnet9019

value: netherlands


title: UCSF Meningioma 133 (methylation)

description:
meningioma
M133
202242420008_R04C01


title: sepvh040

value: sepsis


title: sepnet9018


title: UCSF Meningioma 135 (methylation)

description:
meningioma
M135
202242420008_R06C01


title: sepnet9017


title: sepvh024


title: UCSF Meningioma 130 (methylation)

description:
meningioma
M130
202242420008_R02C01


title: sepnet9016


title: UCSF Meningioma 13 (methylation)

description:
meningioma
M13
202229250100_R04C01


title: UCSF Meningioma 129 (methylation)

description:
meningioma
M129
202242420008_R01C01


title: sepnet9014


title: sepnet9015


title: UCSF Meningioma 127 (methylation)

description:
meningioma
M127
202225190165_R07C01


title: sepvh019


title: sepnet9013


title: sepnet9012


title: UCSF Meningioma 137 (methylation)

description:
meningioma
M137
202242420008_R07C01


title: UCSF Meningioma 128 (methylation)

description:
meningioma
M128
202225190165_R08C01


title: UCSF Meningioma 143 (methylation)

description:
meningioma
M143
202242420024_R03C01


title: sepnet9011


title: UCSF Meningioma 126 (methylation)

description:
meningioma
M126
202225190165_R06C01


title: sepwes010


title: sepnet9010


title: UCSF Meningioma 125 (methylation)

description:
meningioma
M125
202225190165_R05C01


title: sepnet9009


title: sepnet9007


title: sepnet9008


title: UCSF Meningioma 124 (methylation)

description:
meningioma
M124
202225190165_R04C01


title: UCSF Meningioma 123 (methylation)

description:
meningioma
M123
202225190165_R03C01


title: UCSF Meningioma 122 (methylation)

description:
meningioma
M122
202225190165_R02C01


title: sepnet9006


title: UCSF Meningioma 120 (methylation)

description:
meningioma
M120
202225190165_R01C01


title: UCSF Meningioma 132 (methylation)

description:
meningioma
M132
202242420008_R03C01


title: sepnet9005


title: UCSF Meningioma 12 (methylation)

description:
meningioma
M12
202229250100_R03C01


title: sepnet9004


title: sepnet9002


title: sepnet9003


title: sepnet9001


title: UCSF Meningioma 119 (methylation)

description:
meningioma
M119
202225190152_R08C01


title: UCSF Meningioma 116 (methylation)

description:
meningioma
M116
202225190152_R06C01


title: UCSF Meningioma 115 (methylation)

description:
meningioma
M115
202225190152_R05C01


title: sepnet155a


title: UCSF Meningioma 117 (methylation)

description:
meningioma
M117
202225190152_R07C01


title: UCSF Meningioma 114 (methylation)

description:
meningioma
M114
202225190152_R04C01


title: UCSF Meningioma 113 (methylation)

description:
meningioma
M113
202225190152_R03C01


title: sepnet1453


title: UCSF Meningioma 112 (methylation)

description:
meningioma
M112
202225190152_R02C01


title: sepnet1447


title: UCSF Meningioma 111 (methylation)

description:
meningioma
M111
202225190152_R01C01


title: sepnet1443


title: UCSF Meningioma 108 (methylation)

description:
meningioma
M108
202225190151_R07C01


title: sepnet1440


title: UCSF Meningioma 107 (methylation)

description:
meningioma
M107
202225190151_R06C01


title: sepnet1426


title: UCSF Meningioma 110 (methylation)

description:
meningioma
M110
202225190151_R08C01


title: sepnet1425


title: UCSF Meningioma 197 (methylation)

description:
meningioma
M197
202184990103_R01C01


title: UCSF Meningioma 105 (methylation)

description:
meningioma
M105
202225190151_R04C01


title: UCSF Meningioma 106 (methylation)

description:
meningioma
M106
202225190151_R05C01


title: sepnet1422


title: sepnet1416


title: UCSF Meningioma 104 (methylation)

description:
meningioma
M104
202225190151_R03C01


title: sepnet1415


title: UCSF Meningioma 103 (methylation)

description:
meningioma
M103
202225190151_R02C01


title: sepnet1413


title: sepnet1411


title: UCSF Meningioma 101 (methylation)

description:
meningioma
M101
202225190150_R08C01


title: sepnet1409


title: UCSF Meningioma 100 (methylation)

description:
meningioma
M100
202225190150_R07C01


title: UCSF Meningioma 102 (methylation)

description:
meningioma
M102
202225190151_R01C01


title: UCSF Meningioma 10 (methylation)

description:
meningioma
M10
202229250100_R02C01


title: transcriptome of blood of patient with COVID-19 99Cb

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

data_processing:
3 different pipelines were used in the process of data processing.
Pipeline 1 - Fastq files for each sample were aligned to the GRCh38 genome (Gencode, release 37) using HISAT2 (v2.6.1b) with default parameters. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counting reads was done using featureCounts.
Pipeline 2 - Human reference genome assembly GRCh38 (hg38) and gene model annotation files were downloaded from Gencode website (https://www.gencodegenes.org/human/) directly (release 37). Adapters were removed by Cutadapt (v3.4). HISAT2 (v2.2.1) [18] was used with default parameters to building of the index of the reference genome and mapping reads to genome. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counts the number of sequencing reads mapping to each gene after the alignment step was done using htseq-count function from HTSeq framework (v.0.6.1).
Pipeline 3 – Ambiguous and low-quality bases were removed from the files obtained during the FASTQ sequencing process. Removal was done with AdapterRemoval V2. The trimmed files were aligned to the human reference genome GRCH38 and GRCH38.92 gene annotation using RSEM with rsem-prepare-reference and rsem-calculate-expression commands  and the -star option to also generate STAR indices.
Genome_build: GRCH38
Supplementary_files_format_and_content: Processed count files  were obtained using each of 3 pipelines and contains 3 columns with respective pipeline counts.

source_name: blood of patient with COVID-19 99 – replication 2

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories).
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

value: blood

tag: batch

value: Batch 1

tag: survival status

value: survived

tag: sample extraction time

tag: rna extraction time

tag: rin


title: sepnet1407

value: Survived


title: UCSF Meningioma 1 (methylation)

description:
meningioma
M1
202229250070_R01C01


title: sepnet1406

value: Died


title: sepnet1378


title: transcriptome of blood of patient with COVID-19 98Ca

source_name: blood of patient with COVID-19 98 – replication 1

value: deceased


title: transcriptome of blood of patient with COVID-19 99Ca

source_name: blood of patient with COVID-19 99 – replication 1


title: sepnet1385

value: F


title: sepnet1405


title: transcriptome of blood of patient with COVID-19 96Cb

source_name: blood of patient with COVID-19 96 – replication 2


title: sepnet1377


title: transcriptome of blood of patient with COVID-19 96Ca

source_name: blood of patient with COVID-19 96 – replication 1


title: sepnet1370


title: sepnet1375


title: sepnet1362


title: transcriptome of blood of patient with COVID-19 51Cb

source_name: blood of patient with COVID-19 51 – replication 2


title: transcriptome of blood of patient with COVID-19 98Cb

source_name: blood of patient with COVID-19 98 – replication 2


title: transcriptome of blood of patient with COVID-19 51Ca

source_name: blood of patient with COVID-19 51 – replication 1


title: sepnet1359


title: sepnet1361


title: transcriptome of blood of patient with COVID-19 38Cb

source_name: blood of patient with COVID-19 38 – replication 2


title: transcriptome of blood of patient with COVID-19 126Cb

source_name: blood of patient with COVID-19 126 – replication 2


title: sepnet1355


title: sepnet1356


title: transcriptome of blood of patient with COVID-19 126Ca

source_name: blood of patient with COVID-19 126 – replication 1


title: UCSF Meningioma 17 (methylation)

description:
meningioma
M17
202229250100_R07C01

value: meningioma

value: UCSF


title: transcriptome of blood of patient with COVID-19 114Ca

source_name: blood of patient with COVID-19 114 – replication 1


title: transcriptome of blood of patient with COVID-19 114Cb

source_name: blood of patient with COVID-19 114 – replication 2


title: sepnet1347


title: sepnet1351


title: sepnet1345


title: sepnet1381


title: sepnet1340


title: sepnet1344


title: Normo-D28_S6

city: Toon

first: Tomohisa

last: Sakaue

state: Ehime

address: Shitsukawa

department: Proteo-Science center

country: Japan

institute: Ehime University

data_processing:
Sequence data were mapped on the hman genome (hg38) using Tophat and analyzed by Cufflinks.
Normalizations were performed  using iDEGES/edgeR
Genome_build: hg38

source_name: Primary human valve interstitial cells (normoxia at day28)

growth_protocol: VICs were maintained without passage in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% fetal bovine serum, penicillin, and streptomycin at 37°C.

extract_protocol:
Total RNA was purified using ISOGEN II (Nippon Gene, Tokyo, Japan) according to the manufacturer’s protocol.  Purified total RNA was quantified using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA integrity score was evaluated using the Bioanalyzer RNA 6000 Nano Assay Kit (Agilent Technologies, Santa Clara, CA, USA).
RNA-Seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   kit, NEBNext Poly(A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos for Illumina according to the manufacturer's instructions and subsequently validated for an average size of about 360 bp using  the Agilent DNA1000 kit.

treatment_protocol: VICs were cultured  in an atmosphere containing 2% oxygen for 7, 14, and 28 d.

value: Aortic valve

tag: culture

value: normoxia

tag: Stage


title: Normo-D14_S4

source_name: Primary human valve interstitial cells (normoxia at day14)

tag: tissue


title: sepnet1332

value: Emergency Room


title: transcriptome of blood of patient with COVID-19 101Ca

source_name: blood of patient with COVID-19 101 – replication 1


title: sepnet1335

source_name: Whole Blood

value: M

value: Whole Blood


title: Hypo-D28_S5

source_name: Primary human valve interstitial cells (hypoxia at day28)

value: hypoxia


title: sepnet1330

value: netherlands


title: sepnet1331

value: sepsis


title: sepnet1493


title: Hypo-D14_S3

source_name: Primary human valve interstitial cells (hypoxia at day14)


title: Normo-D7_S2

source_name: Primary human valve interstitial cells (normoxia at day7)


title: sepnet1326


title: sepnet1329


title: Hypo-D7_S1

source_name: Primary human valve interstitial cells (hypoxia at day7)


title: transcriptome of blood of patient with COVID-19 38Ca

source_name: blood of patient with COVID-19 38 – replication 1

value: blood


title: sepnet1319


title: sepnet1323


title: T-MSC D14-2

city: Seoul

first: Sung-Chul

last: Jung

address: 25, Magokdong-ro 2-gil, Gangseo-gu

department: Department of Biochemistry

country: South Korea

institute: Ewha Womans University

description: differentiated T-MSCs into PTH-releasing cells

data_processing:
Ion S5xl sequencer (Thermo-Fisher) add-in software was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: tonsil-derived MSCs

growth_protocol: T-MSCs were subcultured in DMEM-high glucose supplemented with 10% FBS at 37˚C in 5% CO2 chamber

extract_protocol:
Total RNA was isolated using Rneasy kit according to the manufacturer's protocol (Qiagen, Hilden, Germany).
Ion Torrent sequencing libraries were prepared according to the AmpliSeq Library prep kit protocol (Thermo Fisher). A total of 50 ng of total RNA was reverse transcribed, and the resulting cDNA was amplified for 11 cycles by adding PCR Master Mix and the AmpliSeq human transcriptome gene expression primer pool (over 20,000 human RefSeq genes). Amplicons were digested with the proprietary FuPa enzyme, and then, barcoded adapters were ligated onto the target amplicons. The library amplicons were bound to magnetic beads, and residual reaction components were washed off. The libraries were eluted and individually quantitated by qPCR using Ion Torrent P1, a sequencing primer, and TaqMan Probe master mix. Individual libraries were diluted to an 85 pM concentration, then combined in batches for further processing. Emulsion PCR, templating and 550 chip loading were performed with an Ion Chef Instrument (Thermo-Fisher). RNA sequencing was performed on an Ion S5xl sequencer (Thermo-Fisher)

treatment_protocol: T-MSCs were seeded at high (100% of confluence) cell density, and incubated in DMEM-high glucose supplemented with 10% FBS in the presence or absence of 100 ng/mL of activin A and sonic hedgehog (Shh) for 7 or 14 days.

tag: cell source

value: human tonsil tissues

tag: cell types

value: mesenchymal stem cells

tag: treatments

value: DMEM supplemented with 100 ng/mL of sonic hedgehog (Shh) and activin A for 14 days


title: 2143_Maternal_GD21 [SP0224-H06]

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

data_processing:
Sequencing alignment and data analysis were conducted using Partek Flow build 9.0.20.1104 (Partek Incorporated, St. Louis, MO, USA)
Raw FASTQ files provided from BioSpyder were uploaded into Partek Flow and aligned to the reference genome rn6 using STAR v.2.7.3a with default settings.
Aligned reads were then quantified to rn6-Ensembl Transcripts release 100 by Partek Expectation Maximization. Following quantification, low expression gene features with a mean count ≤ 10 across all samples were removed, a 0.0001 prior count was added to adjust for zero counts in the dataset, samples were normalized using count per million mapped reads (CPM), and finally log2 transformed.
Samples were separated by life stage into four groups: maternal GD18, maternal GD21, fetal GD18 and fetal GD21. Principle component analysis of sample gene counts from each group revealed three outlier samples (F07, B02, and G07) which were removed prior to downstream gene expression analysis.
Differentially expressed genes (DEGs) were identified for each life stage using Partek Gene Specific Analysis algorithm (GSA) on pairwise groups (Treated vs. vehicle control). GSA fit data from each gene feature to multiple models: negative binomial, log-normal, normal, and log-normal with shrinkage models. The best fit model was selected for each feature based on the lowest Akaike Information Criterion value. Significant DEGs for each life stage were identified based on a false discovery rate (FDR) adjusted p-value < 0.05 (Benjamini and Hochberg 1995) and an absolute fold change ≥ 2.
Genome_build: rn6, Ensembl build 100
Supplementary_files_format_and_content: raw count matrix in .txt format
Supplementary_files_format_and_content: Low expression filtered, 0.0001 count offset added, counts per million (CPM) normalized, and log2 transformed count matrix prior to outlier removal in .txt format

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Time-mated Sprague-Dawley rats (Crl:CD(SD)), approximately 90 days old, were purchased from Charles River Laboratories (Raleigh, NC, USA) and shipped to USEPA (Research Triangle Park, NC, USA) on GD2 (GD0 = bred date; GD1 = plug positive date). Dams and their offspring were housed individually in clear polycarbonate cages (20 × 25 × 47 cm) with heat-treated, laboratory-grade pine shavings (Northeast Products, Warrensburg, NY) and fed NIH07 Rat Chow and filtered (5 µm) municipal tap water (Durham, NC) ad libitum. Dams were weight-ranked and stratified then randomly assigned to treatment groups to produce similar mean weights and variances given the range of dam body weights (typically ∼10% coefficient of variation). This study was conducted in accordance with a protocol approved by the USEPA Center for Public Health and Environmental Assessment Institutional Animal Care and Use Committee. Animals were housed in a facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care and maintained at 20–22 °C, 45–55% humidity, and a 12:12 h photoperiod (06:00 – 18:00 EST).

extract_protocol:
Subsamples of liver tissue (∼30–50 mg) were collected from NBP2-exposed dams (GD18 and GD21) and fetuses (GD18 and GD21) were placed in polypropylene microcentrifuge tubes containing 500 µL TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) on ice, then individually homogenized using a Bullet Blender (Next Advance, Troy, NY, USA) with 1 mm zirconium oxide beads and stored at −80 °C prior to RNA extraction. RNA extraction was conducted according to TRIzol Reagent manufacturer specifications using chloroform and isopropanol. Following extraction, RNA was purified using RNeasy Mini Kit (Cat no. 74104; Qiagen, Hilden, Germany). RNA concentration and purity (260:280 ratio ≥ 1.8) were determined with a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA).
Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). Purified RNA was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,119 protein coding genes in the rat genome (Rat Whole Transcriptome Assay on the Templated Oligo Detection Assay platform; TempO-Seq, BioSpyder Technologies, Carlsbad, CA, USA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500  platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads.

treatment_protocol: Rat dams were exposed to NBP2 from GD14-18 (0, 0.1, 0.3, 1, 3, 10, or 30 mg/kg/d, n = 4 per dose except n = 6 for controls) or GD17-21 (0, 1, 3, 10, or 30 mg/kg/d, n = 3 per dose).  Dams and fetuses were euthanized by decapitation 2–4 h after the final oral dose (∼08:30–10:30 EST). Euthanasia order was stratified such that the timing of necropsy was equally distributed across dose groups. Maternal and fetal liver mRNA underwent targeted RNA-sequencing.

value: Liver

tag: treatment

value: Nafion byproduct 2

tag: dose (mg/kg/d)

tag: age

value: Maternal

tag: strain

value: Sprague Dawley

tag: study block

tag: dam id


title: sepnet1317

tag: disease state

tag: Sex

value: F

tag: collection location

tag: collection site

tag: sofa 24h post admisssion

tag: in hospital mortality

value: Survived


title: 2142_Maternal_GD21 [SP0224-H05]

tag: Stage


title: sepnet1315

value: Died

tag: tissue


title: sepnet1310

value: Emergency Room


title: transcriptome of blood of patient with COVID-19 101Cb

source_name: blood of patient with COVID-19 101 – replication 2

tag: batch

value: Batch 1

tag: survival status

value: deceased

tag: sample extraction time

tag: rna extraction time

tag: rin


title: sepnet1304

tag: age

value: M

value: Whole Blood


title: T-MSC C14-2

description: undifferentiated T-MSCs

tag: cell source

tag: cell types

tag: treatments

value: DMEM culture for 14 days


title: sepnet1287

tag: disease state

value: sepsis

value: netherlands


title: T-MSC C14

description: undifferentiated T-MSCs

value: human tonsil tissues

value: mesenchymal stem cells


title: 2140_Maternal_GD21 [SP0224-H03]

value: Liver

tag: treatment

tag: dose (mg/kg/d)

tag: strain

tag: study block

tag: dam id


title: sepnet1286

tag: Sex

tag: collection location

tag: collection site

tag: sofa 24h post admisssion

tag: in hospital mortality


title: 2141_Maternal_GD21 [SP0224-H04]

tag: tissue

value: Nafion byproduct 2

tag: Stage


title: sepnet1283

tag: age


title: sepnet1282


title: sepnet1267


title: T-MSC C7

description: undifferentiated T-MSCs

tag: cell source

value: DMEM culture for 7 days


title: sepnet1266


title: sepnet1251


title: 2138_Maternal_GD21 [SP0224-H01]

value: Maternal

value: Sprague Dawley


title: T-MSC D14

tag: cell types

value: DMEM supplemented with 100 ng/mL of sonic hedgehog (Shh) and activin A for 14 days


title: sepnet1244

value: Survived


title: sepnet1245

value: Emergency Room


title: 2137_Maternal_GD21 [SP0224-G12]


title: 2136_Maternal_GD21 [SP0224-G11]


title: sepnet1243


title: T-MSC D7

tag: treatments

value: DMEM supplemented with 100 ng/mL of sonic hedgehog (Shh) and activin A for 7 days


title: sepnet1230

tag: disease state


title: sepnet1221

value: F


title: T naïve donor3

type: RNA

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

description: total RNA

data_processing: Data were processed with nSolver software obtained with the instrument.

source_name: Primary human T cells

label_protocol: No label

growth_protocol: Cells were sorted as described in the summary from healthy donor and stored in TRI-reagent

extract_protocol: Total RNA was extracted using Zymo Spin columns from Zymo Research according to manufacurer's protocols.

treatment_protocol: No treatment

tag: type

value: resting

tag: cell type

value: T naïve


title: 2135_Maternal_GD21 [SP0224-G10]

tag: treatment

tag: dose (mg/kg/d)

tag: strain


title: T naïve donor4

description: total RNA


title: T naïve donor2

description: total RNA


title: T naïve donor1

description: total RNA


title: 2134_Maternal_GD21 [SP0224-G09]

tag: study block

tag: dam id


title: sepnet1214a

tag: Sex

tag: collection location

tag: collection site

value: Whole Blood


title: sepnet1220

value: sepsis

tag: sofa 24h post admisssion

tag: in hospital mortality

tag: tissue


title: 2139_Maternal_GD21 [SP0224-H02]

tag: age

tag: Stage


title: 2133_Maternal_GD21 [SP0224-G08]


title: sepnet1205

value: M

value: netherlands


title: 2132_Maternal_GD21 [SP0224-G07]


title: T effector memory donor4

description: total RNA

value: T effector memory


title: sepnet1209


title: sepnet1201


title: 2131_Maternal_GD21 [SP0224-G06]

value: Liver

value: Control


title: sepnet1199


title: T effector memory donor2

description: total RNA


title: T effector memory donor3

description: total RNA


title: T effector memory donor1

description: total RNA


title: sepnet1196


title: T central memory donor4

description: total RNA

value: T central memory


title: 2130_Maternal_GD21 [SP0224-G05]

value: Maternal


title: sepnet1222


title: sepnet1191


title: sepnet1195


title: 2129_Maternal_GD21 [SP0224-G04]

value: Sprague Dawley


title: sepnet1185


title: sepnet1183


title: T central memory donor3

description: total RNA


title: sepnet1182


title: T central memory donor2

description: total RNA


title: sepnet1206


title: 2142_Fetal_GD21 [SP0224-G02]

value: Nafion byproduct 2

value: Fetal


title: 2143_Fetal_GD21 [SP0224-G03]


title: sepnet1170

value: Emergency Room

value: Survived


title: sepnet1204


title: 2141_Fetal_GD21 [SP0224-G01]


title: sepnet1169


title: sepnet1140


title: 2140_Fetal_GD21 [SP0224-F12]


title: sepnet1093


title: sepnet1051

value: Died


title: 2139_Fetal_GD21 [SP0224-F11]


title: sepnet0904


title: 2138_Fetal_GD21 [SP0224-F10]


title: sepnet0738


title: sepnet0537


title: sepnet0375


title: sepnet0344

value: F


title: 2136_Fetal_GD21 [SP0224-F08]


title: T central memory donor1

description: total RNA

value: resting


title: sepnet0186

value: Whole Blood


title: sepcol108

value: sepsis

value: colombia


title: sepnet1179a

value: M

value: netherlands


title: 2135_Fetal_GD21 [SP0224-F07]

value: Liver


title: sepcol109


title: sepcol106


title: sepnet1094


title: 2134_Fetal_GD21 [SP0224-F06]


title: sepcol105


title: 2133_Fetal_GD21 [SP0224-F05]


title: sepcol103


title: sepcol097


title: sepcol104


title: 2132_Fetal_GD21 [SP0224-F04]


title: 2137_Fetal_GD21 [SP0224-F09]


title: sepcol096


title: sepcol094


title: Patient 18 lesional skin week 12

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

description: gene expression data from Patient 18 lesional skin week 12

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the human Clariom D GeneChip according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 system.

data_processing: The microarray data were summarized applying the SST-RMA (signal space transformation - robust multi-array average) gene level method as implemented in the Transcriptome Analysis Console (TAC) 4.0 software.

label: Biotin

source_name: skin biopsy from Patient 18 lesional week 12

label_protocol: Biotinylated cRNA was prepared according to the protocol for the human Clariom D assay (ThermoFisher Scientific).

extract_protocol: Total RNA from skin biopsies was isolated using the SV Total RNA Isolation System according to the manufacturer's instructions.

tag: diagnosis

value: psoriasis

value: skin

tag: disease state (nl/l)

value: L

tag: week

tag: dose (mg)

tag: skin rash (no/yes)

value: yes

tag: pasi_percent_change (week12-week0)


title: Patient 18 lesional skin week 8

description: gene expression data from Patient 18 lesional skin week 8

source_name: skin biopsy from Patient 18 lesional week 8


title: Patient 18 lesional skin week 4

description: gene expression data from Patient 18 lesional skin week 4

source_name: skin biopsy from Patient 18 lesional week 4


title: Patient 17 lesional skin week 12

description: gene expression data from Patient 17 lesional skin week 12

source_name: skin biopsy from Patient 17 lesional week 12

value: no


title: 2131_Fetal_GD21 [SP0224-F03]

tag: treatment

value: Control

tag: dose (mg/kg/d)

value: Fetal

tag: strain

value: Sprague Dawley


title: Patient 18 lesional skin week 0

description: gene expression data from Patient 18 lesional skin week 0

source_name: skin biopsy from Patient 18 lesional week 0


title: Patient 18 non-lesional skin week 0

description: gene expression data from Patient 18 non-lesional skin week 0

source_name: skin biopsy from Patient 18 non-lesional week 0

value: NL


title: sepcol093

tag: disease state

tag: Sex

value: Emergency Room

value: Survived


title: sepcol092

tag: collection location

tag: collection site

value: Whole Blood


title: sepcol089

value: sepsis

value: F

tag: sofa 24h post admisssion

tag: in hospital mortality


title: 2130_Fetal_GD21 [SP0224-F02]

tag: tissue

tag: age

tag: study block

tag: dam id


title: sepcol087

value: M

value: colombia


title: Patient 17 lesional skin week 0

description: gene expression data from Patient 17 lesional skin week 0

source_name: skin biopsy from Patient 17 lesional week 0

tag: diagnosis

tag: disease state (nl/l)

tag: week


title: sepcol077

source_name: Whole Blood


title: Patient 17 non-lesional skin week 0

description: gene expression data from Patient 17 non-lesional skin week 0

source_name: skin biopsy from Patient 17 non-lesional week 0

tag: dose (mg)

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: 2127_Maternal_GD18 [SP0224-E11]

value: Liver

tag: treatment

value: Nafion byproduct 2

tag: dose (mg/kg/d)

tag: Stage

value: Maternal

tag: strain


title: sepcol091

tag: disease state

tag: Sex

tag: collection location

tag: collection site


title: sepcol082

tag: age

tag: sofa 24h post admisssion

tag: in hospital mortality

tag: tissue


title: Patient 17 lesional skin week 8

description: gene expression data from Patient 17 lesional skin week 8

source_name: skin biopsy from Patient 17 lesional week 8

tag: diagnosis

value: psoriasis

value: skin

tag: disease state (nl/l)

value: L


title: Patient 16 lesional skin week 4

description: gene expression data from Patient 16 lesional skin week 4

source_name: skin biopsy from Patient 16 lesional week 4

tag: week

tag: dose (mg)

value: yes


title: sepcol075


title: sepcol073


title: sepcol070


title: 2083_Maternal_GD18 [SP0224-B03]

tag: study block

tag: dam id


title: sepcol071


title: Patient 16 lesional skin week 0

description: gene expression data from Patient 16 lesional skin week 0

source_name: skin biopsy from Patient 16 lesional week 0

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: Patient 16 non-lesional skin week 0

description: gene expression data from Patient 16 non-lesional skin week 0

source_name: skin biopsy from Patient 16 non-lesional week 0


title: 2082_Maternal_GD18 [SP0224-B02]

tag: treatment

tag: dose (mg/kg/d)

tag: Stage

tag: strain


title: sepcol069

tag: disease state

tag: Sex

tag: collection location

tag: collection site


title: Patient 15 lesional skin week 12

description: gene expression data from Patient 15 lesional skin week 12

source_name: skin biopsy from Patient 15 lesional week 12

tag: tissue

value: no


title: sepcol065

tag: age

tag: sofa 24h post admisssion

tag: in hospital mortality


title: Patient 15 lesional skin week 8

description: gene expression data from Patient 15 lesional skin week 8

source_name: skin biopsy from Patient 15 lesional week 8

tag: diagnosis

tag: disease state (nl/l)

tag: week

tag: dose (mg)


title: sepcol064


title: sepcol067


title: 2125_Maternal_GD18 [SP0224-E09]

source_name: Liver

value: Sprague Dawley

tag: study block

tag: dam id


title: sepcol063


title: 2126_Maternal_GD18 [SP0224-E10]

tag: treatment

tag: dose (mg/kg/d)


title: 2081_Maternal_GD18 [SP0224-B01]

tag: Stage

tag: strain


title: sepcol062

tag: disease state

tag: Sex


title: Patient 15 lesional skin week 0

description: gene expression data from Patient 15 lesional skin week 0

source_name: skin biopsy from Patient 15 lesional week 0

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: Patient 15 lesional skin week 4

description: gene expression data from Patient 15 lesional skin week 4

source_name: skin biopsy from Patient 15 lesional week 4

tag: tissue


title: sepcol060

tag: age

tag: collection location

tag: collection site

tag: sofa 24h post admisssion

value: Died


title: 2080_Maternal_GD18 [SP0224-A12]


title: 2124_Maternal_GD18 [SP0224-E08]


title: sepcol061

value: Emergency Room

tag: in hospital mortality


title: 2128_Maternal_GD18 [SP0224-E12]


title: sepcol059


title: sepcol056

value: Survived


title: sepcol058

value: Whole Blood


title: 2123_Maternal_GD18 [SP0224-E07]


title: Patient 14 lesional skin week 4

description: gene expression data from Patient 14 lesional skin week 4

source_name: skin biopsy from Patient 14 lesional week 4

tag: diagnosis

tag: disease state (nl/l)

tag: week

tag: dose (mg)


title: sepcol050

value: sepsis


title: 2079_Maternal_GD18 [SP0224-A11]

tag: treatment

tag: dose (mg/kg/d)

tag: study block

tag: dam id


title: sepcol046

tag: disease state

tag: Sex


title: Patient 14 lesional skin week 12

description: gene expression data from Patient 14 lesional skin week 12

source_name: skin biopsy from Patient 14 lesional week 12

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: sepcol045

tag: age

value: F

tag: tissue


title: Patient 15 non-lesional skin week 0

description: gene expression data from Patient 15 non-lesional skin week 0

source_name: skin biopsy from Patient 15 non-lesional week 0

value: NL


title: Patient 14 lesional skin week 8

description: gene expression data from Patient 14 lesional skin week 8

source_name: skin biopsy from Patient 14 lesional week 8


title: 2129_Fetal_GD21 [SP0224-F01]

value: Control

tag: Stage

value: Fetal

tag: strain


title: 2078_Maternal_GD18 [SP0224-A10]

value: Liver

value: Nafion byproduct 2


title: Patient 14 lesional skin week 0

description: gene expression data from Patient 14 lesional skin week 0

source_name: skin biopsy from Patient 14 lesional week 0

value: psoriasis


title: Patient 17 lesional skin week 4

description: gene expression data from Patient 17 lesional skin week 4

source_name: skin biopsy from Patient 17 lesional week 4

value: skin


title: sepcol040

source_name: Whole Blood

value: M

tag: collection location

value: colombia

tag: collection site

tag: sofa 24h post admisssion

tag: in hospital mortality


title: sepcol044


title: sepcol055


title: 2122_Maternal_GD18 [SP0224-E06]

value: Maternal


title: Patient 13 lesional skin week 4

description: gene expression data from Patient 13 lesional skin week 4

source_name: skin biopsy from Patient 13 lesional week 4

tag: diagnosis

tag: disease state (nl/l)

value: L

tag: week

tag: dose (mg)

value: yes


title: sepcol034

value: Emergency Room


title: sepcol032

value: Survived


title: sepcol027

value: Whole Blood


title: sepcol028

value: sepsis


title: sepcol110


title: Patient 13 lesional skin week 0

description: gene expression data from Patient 13 lesional skin week 0

source_name: skin biopsy from Patient 13 lesional week 0


title: sepcol026

value: F


title: 2121_Maternal_GD18 [SP0224-E05]

tag: treatment

tag: dose (mg/kg/d)

value: Sprague Dawley

tag: study block

tag: dam id


title: sepcol024

tag: disease state

tag: Sex


title: sepcol025

tag: age

tag: tissue


title: Patient 14 non-lesional skin week 0

description: gene expression data from Patient 14 non-lesional skin week 0

source_name: skin biopsy from Patient 14 non-lesional week 0

value: NL

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: sepcol022

tag: collection location

tag: collection site


title: 2120_Maternal_GD18 [SP0224-E04]

tag: Stage

tag: strain


title: Patient 13 non-lesional skin week 0

description: gene expression data from Patient 13 non-lesional skin week 0

source_name: skin biopsy from Patient 13 non-lesional week 0

tag: diagnosis

tag: disease state (nl/l)


title: Patient 11 lesional skin week 12

description: gene expression data from Patient 11 lesional skin week 12

source_name: skin biopsy from Patient 11 lesional week 12

tag: week

tag: dose (mg)

value: no


title: Patient 11 lesional skin week 8

description: gene expression data from Patient 11 lesional skin week 8

source_name: skin biopsy from Patient 11 lesional week 8


title: sepcol019

tag: sofa 24h post admisssion

tag: in hospital mortality


title: 2119_Maternal_GD18 [SP0224-E03]

value: Liver

tag: treatment

tag: dose (mg/kg/d)

tag: study block

tag: dam id


title: sepcol018

tag: disease state

tag: age

tag: Sex

tag: tissue


title: sepcol017

tag: collection location

tag: collection site


title: 2074_Maternal_GD18 [SP0224-A06]

value: Nafion byproduct 2

tag: Stage

tag: strain


title: sepcol016


title: 2075_Maternal_GD18 [SP0224-A07]


title: sepcol014

value: Died


title: sepcol015


title: sepcol020


title: 2077_Maternal_GD18 [SP0224-A09]


title: sepcol021


title: sepcol086


title: 2076_Maternal_GD18 [SP0224-A08]


title: Patient 11 lesional skin week 4

description: gene expression data from Patient 11 lesional skin week 4

source_name: skin biopsy from Patient 11 lesional week 4

tag: diagnosis

value: psoriasis

value: skin

tag: disease state (nl/l)

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: sepcol010

value: colombia

tag: sofa 24h post admisssion

tag: in hospital mortality


title: 2117_Maternal_GD18 [SP0224-E01]

source_name: Liver

tag: treatment

tag: dose (mg/kg/d)

value: Maternal


title: 2118_Maternal_GD18 [SP0224-E02]

tag: study block

tag: dam id


title: sepcol009

tag: disease state

tag: age


title: Patient 11 lesional skin week 0

description: gene expression data from Patient 11 lesional skin week 0

source_name: skin biopsy from Patient 11 lesional week 0

tag: tissue

value: L

tag: week

tag: dose (mg)


title: Patient 10 lesional skin week 12

description: gene expression data from Patient 10 lesional skin week 12

source_name: skin biopsy from Patient 10 lesional week 12


title: Patient 11 non-lesional skin week 0

description: gene expression data from Patient 11 non-lesional skin week 0

source_name: skin biopsy from Patient 11 non-lesional week 0


title: sepcol008

tag: Sex

value: M

tag: collection location

tag: collection site


title: 2073_Maternal_GD18 [SP0224-A05]

tag: Stage

tag: strain


title: Patient 10 lesional skin week 4

description: gene expression data from Patient 10 lesional skin week 4

source_name: skin biopsy from Patient 10 lesional week 4

tag: diagnosis

tag: disease state (nl/l)

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: sepcol007

value: Emergency Room

tag: sofa 24h post admisssion

tag: in hospital mortality


title: sepcol006


title: sepcol004

value: Survived


title: 2116_Maternal_GD18 [SP0224-D12]

tag: treatment

value: Control

tag: dose (mg/kg/d)

tag: study block

tag: dam id


title: sepcol005

tag: disease state

value: sepsis

tag: age

tag: tissue

value: Whole Blood


title: sepcol003

tag: Sex

tag: collection location


title: sepcol001

tag: collection site


title: 2115_Maternal_GD18 [SP0224-D11]

tag: Stage

tag: strain

value: Sprague Dawley


title: Patient 10 lesional skin week 8

description: gene expression data from Patient 10 lesional skin week 8

source_name: skin biopsy from Patient 10 lesional week 8

tag: diagnosis

tag: disease state (nl/l)

tag: week

tag: dose (mg)


title: sepcol002

tag: sofa 24h post admisssion

tag: in hospital mortality


title: 2114_Maternal_GD18 [SP0224-D10]

tag: treatment

tag: dose (mg/kg/d)


title: MCF-7 C1 Ribociclib Rep2 RNA seq

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
Genome_build: Hg38
Supplementary_files_format_and_content: raw_counts_ribociclib.csv

source_name: MCF-7 C1

growth_protocol: MCF7, MCF7 C1 and MCF7 C8 were maintained in DMEM + 10%FCS + 1%P/S.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)

treatment_protocol: Cells were treated with ribociclib (600 nM) or vehicle for 5 days in full medium.

tag: cell line

value: MCF-7 C1

tag: cell type

value: Breast cancer cells

tag: er status

value: Mutant

value: Ribociclb (600 nM)

tag: replicate


title: sepcol012

tag: disease state

tag: age

tag: Sex

tag: tissue


title: MCF-7 C8 Ribociclib Rep2 RNA seq

source_name: MCF-7 C8

value: MCF-7 C8


title: 2072_Maternal_GD18 [SP0224-A04]

value: Liver

value: Nafion byproduct 2

tag: Stage

tag: strain

tag: study block

tag: dam id


title: MCF-7 Ribociclib Rep2 RNA seq

value: WT


title: 2071_Maternal_GD18 [SP0224-A03]

value: Maternal


title: Patient 10 non-lesional skin week 0

description: gene expression data from Patient 10 non-lesional skin week 0

source_name: skin biopsy from Patient 10 non-lesional week 0

tag: diagnosis

value: psoriasis

value: skin

tag: disease state (nl/l)

value: NL

tag: week

tag: dose (mg)

tag: skin rash (no/yes)

value: no

tag: pasi_percent_change (week12-week0)


title: Patient 10 lesional skin week 0

description: gene expression data from Patient 10 lesional skin week 0

source_name: skin biopsy from Patient 10 lesional week 0

value: L


title: Patient 08 lesional skin week 12

description: gene expression data from Patient 08 lesional skin week 12

source_name: skin biopsy from Patient 08 lesional week 12


title: MCF-7 C8 Vehicle Rep2 RNA seq

tag: cell line

tag: cell type

tag: treatment

value: Vehicle


title: Patient 08 lesional skin week 8

description: gene expression data from Patient 08 lesional skin week 8

source_name: skin biopsy from Patient 08 lesional week 8


title: Patient 08 lesional skin week 4

description: gene expression data from Patient 08 lesional skin week 4

source_name: skin biopsy from Patient 08 lesional week 4


title: 2070_Maternal_GD18 [SP0224-A02]

value: Control

tag: dose (mg/kg/d)


title: MCF-7 C1 Vehicle Rep2 RNA seq

tag: er status

tag: replicate


title: Patient 08 lesional skin week 0

description: gene expression data from Patient 08 lesional skin week 0

source_name: skin biopsy from Patient 08 lesional week 0

tag: tissue


title: MCF-7 Vehicle Rep2 RNA seq


title: MCF-7 C8 Ribociclib Rep1 RNA seq


title: 2069_Maternal_GD18 [SP0224-A01]

tag: age

tag: Stage

value: Sprague Dawley


title: MCF-7 C8 Vehicle Rep1 RNA seq


title: Patient 08 non-lesional skin week 0

description: gene expression data from Patient 08 non-lesional skin week 0

source_name: skin biopsy from Patient 08 non-lesional week 0


title: 2128_Fetal_GD18 [SP0224-D09]

value: Fetal

tag: strain

tag: study block


title: MCF-7 Vehicle Rep1 RNA seq

value: Breast cancer cells


title: 2127_Fetal_GD18 [SP0224-D08]

tag: dam id


title: 2083_Fetal_GD18 [SP0224-C06]


title: MCF-7 Ribociclib Rep1 RNA seq


title: MCF-7 C1 Vehicle Rep1 RNA seq

value: MCF-7 C1

value: Mutant


title: (+RA)_DDX17 ChIP-seq rep1

city: Bangkok

first: Praewa

last: Suthapot

address: 272 Rama VI Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University, Thailand

library_source: genomic

data_processing:
Basecalls performed using RTA v1.17.21.3
Demultiplexing and alignment using CASAVA package v1.8.2, which uses the aligner ELANDv2
Peak calling performed using MACS1.4, which generated bed files
Genome_build: hg19

growth_protocol: The hPSC culture of NTERA2 was maintained in DMEM high glucose medium supplemented with 10% EmbryoMax fetal bovine serum. For neural induction, hPSCs seeded at low density (1.0x10^4 cells/cm2) were treated with 10 uM retinoic acid and continuously grew for 14 days.

extract_protocol:
Sheared chromatin was prepared by ChIP-IT Express kit (Active Motif, #53008) and immunoprecipitated by DDX5 or DDX17 antibody.
The library preparation was performed using MicroPlex Library Preparation kit (Diagenode, C05010010).

value: NTERA2-derived neural stem cells

tag: chip antibody

value: DDX17 (Bethyl Laboratories, A300-509A)


title: (+RA)_DDX17 ChIP-seq rep2


title: (+RA)_DDX17 ChIP-seq rep3


title: MCF-7 C1 Ribociclib Rep1 RNA seq

value: Ribociclb (600 nM)


title: 2082_Fetal_GD18 [SP0224-C05]

value: Liver

value: Nafion byproduct 2


title: (+RA)_DDX5 ChIP-seq rep3

value: DDX5 (Bethyl Laboratories, A300-523A)


title: (+RA)_DDX5 ChIP-seq rep2


title: 2126_Fetal_GD18 [SP0224-D07]


title: (-RA)_DDX17 ChIP-seq rep3

value: Pluripotent stem cells


title: (+RA)_DDX5 ChIP-seq rep1


title: sepcol049

source_name: Whole Blood

tag: disease state

value: sepsis

tag: Sex

value: M

tag: collection location

value: colombia

tag: collection site

value: Emergency Room

tag: sofa 24h post admisssion

tag: in hospital mortality

value: Survived

value: Whole Blood


title: 2125_Fetal_GD18 [SP0224-D06]

tag: treatment

value: Fetal

value: Sprague Dawley


title: Patient 06 lesional skin week 12

description: gene expression data from Patient 06 lesional skin week 12

source_name: skin biopsy from Patient 06 lesional week 12

tag: diagnosis

value: psoriasis

value: skin

tag: disease state (nl/l)

value: L

tag: week

tag: dose (mg)

tag: skin rash (no/yes)

value: no

tag: pasi_percent_change (week12-week0)


title: (-RA)_DDX17 ChIP-seq rep2

tag: cell type

value: DDX17 (Bethyl Laboratories, A300-509A)


title: Patient 06 lesional skin week 0

description: gene expression data from Patient 06 lesional skin week 0

source_name: skin biopsy from Patient 06 lesional week 0

tag: tissue


title: Patient 06 lesional skin week 8

description: gene expression data from Patient 06 lesional skin week 8

source_name: skin biopsy from Patient 06 lesional week 8


title: Patient 06 non-lesional skin week 0

description: gene expression data from Patient 06 non-lesional skin week 0

source_name: skin biopsy from Patient 06 non-lesional week 0

value: NL


title: (-RA)_DDX17 ChIP-seq rep1


title: Patient 06 lesional skin week 4

description: gene expression data from Patient 06 lesional skin week 4

source_name: skin biopsy from Patient 06 lesional week 4


title: 2081_Fetal_GD18 [SP0224-C04]

source_name: Liver

value: Liver

value: Nafion byproduct 2

tag: dose (mg/kg/d)

tag: age

tag: Stage

tag: strain

tag: study block

tag: dam id


title: Patient 03 lesional skin week 12

description: gene expression data from Patient 03 lesional skin week 12

source_name: skin biopsy from Patient 03 lesional week 12


title: (+RA)_siDDX5siDDX17_rep3

data_processing:
Adaptor trimming by Trimmomatic
Genome alignment to human genome reference (hg19) using HISAT2
Estimate the read counts abundance per gene using htseq-count
Differential gene expression was analyzed by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include log2 fold changes values and normalized abundance measurements for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

extract_protocol:
The total RNA extraction was performed using RNeasy Mini kit and then mixed with Oligo dT Beads provided by NEBNext poly(A) mRNA Magnetic Isolation kit (New England Biolabs, E7490S) to enrich the poly(A) RNAs.
RNA libraries were prepared as triplicates for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760S).

treatment_protocol: Cells were individually transfected with siCtrl, siDDX5, siDDX17 or co-treated with siDDX5/siDDX17 for double knockdown condition with 60-hour incubation time.

value: NTERA2-derived neural stem cells

value: siDDX5 and siDDX17


title: 2080_Fetal_GD18 [SP0224-C03]


title: (+RA)_siDDX17_rep3


title: (+RA)_siDDX5siDDX17_rep1


title: (+RA)_siDDX17_rep2


title: Patient 03 lesional skin week 8

description: gene expression data from Patient 03 lesional skin week 8

source_name: skin biopsy from Patient 03 lesional week 8


title: 2124_Fetal_GD18 [SP0224-D05]


title: (+RA)_siDDX5siDDX17_rep2


title: 2123_Fetal_GD18 [SP0224-D04]


title: (+RA)_siDDX5 rep2


title: (+RA)_siDDX17_rep1


title: 2079_Fetal_GD18 [SP0224-C02]


title: (+RA)_siDDX5 rep1


title: 2078_Fetal_GD18 [SP0224-C01]


title: (+RA)_siCtrl_rep3

value: siCtrl


title: (+RA)_siCtrl_rep2


title: 2122_Fetal_GD18 [SP0224-D03]


title: Patient 03 non-lesional skin week 0

description: gene expression data from Patient 03 non-lesional skin week 0

source_name: skin biopsy from Patient 03 non-lesional week 0


title: 2121_Fetal_GD18 [SP0224-D02]


title: Patient 03 lesional skin week 0

description: gene expression data from Patient 03 lesional skin week 0

source_name: skin biopsy from Patient 03 lesional week 0


title: Patient 02 lesional skin week 12

description: gene expression data from Patient 02 lesional skin week 12

source_name: skin biopsy from Patient 02 lesional week 12


title: Patient 03 lesional skin week 4

description: gene expression data from Patient 03 lesional skin week 4

source_name: skin biopsy from Patient 03 lesional week 4


title: (+RA)_siCtrl_rep1


title: (-RA)_siDDX5siDDX17_rep1

value: Pluripotent stem cells


title: (-RA)_siDDX5siDDX17_rep3


title: Patient 02 lesional skin week 8

description: gene expression data from Patient 02 lesional skin week 8

source_name: skin biopsy from Patient 02 lesional week 8


title: (-RA)_siDDX17_rep3


title: (-RA)_siDDX5siDDX17_rep2


title: 2077_Fetal_GD18 [SP0224-B12]


title: (+RA)_siDDX5 rep3


title: (-RA)_siDDX17_rep1


title: (-RA)_siDDX17_rep2


title: 2076_Fetal_GD18 [SP0224-B11]


title: Patient 02 lesional skin week 4

description: gene expression data from Patient 02 lesional skin week 4

source_name: skin biopsy from Patient 02 lesional week 4


title: (-RA)_siDDX5 rep3


title: (-RA)_siDDX5 rep2


title: (-RA)_siDDX5 rep1


title: 2120_Fetal_GD18 [SP0224-D01]


title: (-RA)_siCtrl_rep3


title: Patient 01 lesional skin week 12

description: gene expression data from Patient 01 lesional skin week 12

source_name: skin biopsy from Patient 01 lesional week 12


title: 2119_Fetal_GD18 [SP0224-C12]


title: Patient 02 lesional skin week 0

description: gene expression data from Patient 02 lesional skin week 0

source_name: skin biopsy from Patient 02 lesional week 0


title: Patient 02 non-lesional skin week 0

description: gene expression data from Patient 02 non-lesional skin week 0

source_name: skin biopsy from Patient 02 non-lesional week 0


title: (-RA)_siCtrl_rep1


title: Salt_96h_2

city: Jinan

first: Luoyan

last: Zhang

address: wenhuadong 88

country: China

institute: shandong normal university

data_processing:
The RNA sample of every accession was sequenced by the Illumina NovaSeq 6000. cDNA library was constructed, and Illumina pair-end 150 bp sequencing (PE150)
Raw reads of fastq format were firstly processed through in-house perl scripts. In this step, adapt-er-containing reads, ploy-N-containing reads, and low-quality reads were removed from raw data, yielding clean reads. Meanwhile, Q20, Q30, GC-content, and sequence duplication levels of the clean data were determined.
Reference genome (ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/) and gene model annotation files (ftp://ftp.ensemblgenomes.org/pub/release39/plants/gtf/chlamydomonas_reinhardtii/Chlamydomonas_reinhardtii.v3.1.39.gtf.gz) were downloaded from the genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5), which was adopted to align paired-end clean reads to the reference genome.
For the prediction of novel transcripts, StringTie (v1.3.3b) was adopted to assemble the mapped reads of each sample as previously described (Pertea et al., 2015).
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Chlamydomonas reinhardtii

source_name: alga cells

growth_protocol: The wild-type C. reinhardtii strain GY-D55 was obtained from LeadingTec Co., Ltd. (http://www.leadingtec.cn/) and maintained in 150 mL of BG-11 medium on a shaking table at 120 rpm under the following conditions: photoperiod 16-8 h/light-dark, temperature 23℃, and light intensity 100 μmol m-2 s-1. Under the above-mentioned conditions, C. reinhardtii cells were cultured in BG11 medium for approximately 14 days until the cell density reached 2 × 106 cells/mL. The cells of the mid-logarithmic phase were used for salt stress treatment.

extract_protocol:
Briefly, 100 mL cell cultures from different groups were subjected to centrifugation at 3,000 g for 5 min, and the cell pellet was re-suspended in 25 mL RNAlater solution (Ambion). Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. The integrity of RNA was evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and the NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, 50 mL medium containing 800 mM NaCl was added to a 150-mL culture medium, the final NaCl concentration was 200 mM, and the pH of the medium was adjusted to 7.0. Cells cultured in the absence of NaCl were used as the control group. Each experiment was conducted in triplicate. The cells of C. reinhardtii were collected at eight pre-set time points after exposure to 200 mM NaCl: 2, 4, 8,12, 24, 48, 72, and 96 h.

value: 200mM NaCl 96h


title: Ocular surface epithelial stem cell F8

city: Kizugawa

first: Toru

last: Okubo

state: Kyoto

address: 6-5-4 Kunimidai

department: Basic Research Development Division

institute: Rohto Pharmaceutical

description: F8: Flat-1

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode with Illumina Casava 1.8.2 software
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat  v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver.  0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: raw counts

source_name: Ocular surface epithelial stem cell

growth_protocol: Ocular surface epithelial stem cells, derived from 10 week SEAMs, were seeded at 100 or 200 cells /well in 6-well uncoated plates and cultured in ocular surface epithelial differentiation medium (DMEM/F12 [Thermo Fisher Scientific] containing 2% B27 supplement [Thermo Fisher Scientific], 20 ng/mL KGF, and 10 μM Y-27632) for 17 days. Domed and flat colonies were distinguished based on morphological differences under phase-contrast microscopy.

extract_protocol:
Cell were lysed using QIAzol Lysis Reagent (QIAGEN, Valencia, CA)
Briefly, cDNA was generated using a Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA), and the cDNA library was prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA, USA).

value: human pluripotent stem cell-derived ocular surface epithelial stem cell

tag: source cell line

tag: culture duration

value: 17 days

tag: phenotype

value: Flat


title: Patient 01 non-lesional skin week 0

description: gene expression data from Patient 01 non-lesional skin week 0

source_name: skin biopsy from Patient 01 non-lesional week 0

tag: diagnosis


title: Patient 01 lesional skin week 0

description: gene expression data from Patient 01 lesional skin week 0

source_name: skin biopsy from Patient 01 lesional week 0

tag: disease state (nl/l)


title: Ocular surface epithelial stem cell D9

description: D9: Domed-3

value: Domed


title: Salt_96h_1

tag: treatment


title: Ocular surface epithelial stem cell F5

description: F5: Flat-3


title: 2118_Fetal_GD18 [SP0224-C11]

value: Fetal

value: Sprague Dawley


title: Ocular surface epithelial stem cell D1

description: D1: Domed-1


title: 2075_Fetal_GD18 [SP0224-B10]


title: Salt_72h_2

value: 200mM NaCl 72h


title: Salt_72h_3


title: Ocular surface epithelial stem cell F1

description: F1: Flat-2


title: 2074_Fetal_GD18 [SP0224-B09]


title: Treg treated with anti-CD3/anti-CD28 antibody beads, IL-2 and TNFR2 agonist antibody_2

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

description: CD3/CD28 + IL-2 + TNFR2 agonist rep2

data_processing:
Base calling and making fastq files were performed using software provided with the 10X Genomics Cell Ranger (cellranger mkfastq v3.0).
Count data were calculated from fastq files using software provided with the 10X Genomics Cell Ranger (cellranger count v3.0).
Count data were normalized to compare across samples using software provided with the 10X Genomics Cell Ranger (cellranger aggr v3.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each cell.

source_name: Treg isolated from PBMC

growth_protocol: CD4+CD25+ Tregs were isolated using a Dynabeads Regulatory CD4+CD25+T Cell (Thermo Fisher Scientific) following the manufacturer’s instructions. Treg were seeded into a round-bottom 96-well plate and cultured in RPMI1640 (FUJIFILM Wako Pure Chemical) containing 10% fetal bovine serum (FBS) and 500 IU/mL interleukin-2 (IL-2) (R&D Systems) in a humidified CO2 incubator at 37⁰C. Dynabeads Treg expander (anti-CD3/anti-CD28 antibody beads, Invitrogen) was added to culture medium.

extract_protocol:
Single cell RNA seq library was prepared using cell suspension.
A single-cell RNA-seq library was prepared from cultured Tregs using Chromium Single Cell 3' Library Kit v2 (10x Genomics) following the manufacturer’s instructions.

treatment_protocol: Tregs were cultured in the presence of MR2-1 TNFR2 agonist antibody  (Hycult Biotech) or mouse IgG1 (R&D Systems) for 5 days.

value: Treg isolated from PBMC

value: Anti-CD3/anti-CD28 antibody beads, IL-2 and TNFR2 agonist antibody


title: Patient 01 lesional skin week 4

description: gene expression data from Patient 01 lesional skin week 4

source_name: skin biopsy from Patient 01 lesional week 4

value: psoriasis

value: skin

value: L

tag: week

tag: dose (mg)

value: no


title: 2117_Fetal_GD18 [SP0224-C10]

source_name: Liver

value: Liver

value: Nafion byproduct 2


title: Treg treated with anti-CD3/anti-CD28 antibody beads and IL-2_1

description: CD3/CD28 + IL-2 rep1

value: Anti-CD3/anti-CD28 antibody beads and IL-2


title: Salt_72h_1


title: Treg treated with anti-CD3/anti-CD28 antibody beads, IL-2 and TNFR2 agonist antibody_1

description: CD3/CD28 + IL-2 + TNFR2 agonist rep1


title: 2073_Fetal_GD18 [SP0224-B08]


title: Patient 01 lesional skin week 8

description: gene expression data from Patient 01 lesional skin week 8

source_name: skin biopsy from Patient 01 lesional week 8

tag: skin rash (no/yes)

tag: pasi_percent_change (week12-week0)


title: (-RA)_siCtrl_rep2

tag: cell type

value: Pluripotent stem cells

value: siCtrl


title: Ocular surface epithelial stem cell D4

description: D4: Domed-2

value: human pluripotent stem cell-derived ocular surface epithelial stem cell

value: 17 days


title: Treg no treatment_1

description: NT rep1

value: No treatment


title: Treg no treatment_2

description: NT rep2


title: 2072_Fetal_GD18 [SP0224-B07]

tag: tissue

tag: dose (mg/kg/d)

value: Fetal


title: Salt_48h_3

value: 200mM NaCl 48h


title: Meningioma 99 (RNA-seq)

description:
Sex: 2
M99

data_processing:
Standard Illumina software was used for basecalling
Sequenced reads were trimmed using Trimmomatic, then mapped to hg38 transcriptome using HISAT2 2.1.0
Exon level count data were extracted from the mapped reads using featureCounts
Transcripts per million (TPM) were calculated from the count data
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPMs for every gene and every sample

source_name: Meningioma

extract_protocol:
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and RNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit v2 (CAT# RS-122-2001)

value: meningioma

tag: institution

value: UCSF

tag: age

tag: grade


title: Salt_48h_2

tag: strain


title: Meningioma 97 (RNA-seq)

description:
Sex: 2
M97


title: Meningioma 98 (RNA-seq)

description:
Sex: 1
M98


title: 2115_Fetal_GD18 [SP0224-C08]

value: Control

tag: Stage

value: Sprague Dawley

tag: study block

tag: dam id


title: Meningioma 96 (RNA-seq)

description:
Sex: 2
M96


title: 2116_Fetal_GD18 [SP0224-C09]


title: Salt_24h_3

value: 200mM NaCl 24h


title: Salt_48h_1


title: 2071_Fetal_GD18 [SP0224-B06]


title: Meningioma 92 (RNA-seq)

description:
Sex: 1
M92


title: Salt_24h_2


title: Meningioma 90 (RNA-seq)

description:
Sex: 1
M90


title: Meningioma 91 (RNA-seq)

description:
Sex: 1
M91


title: Meningioma 93 (RNA-seq)

description:
Sex: 2
M93


title: Meningioma 94 (RNA-seq)

description:
Sex: 1
M94


title: Meningioma 89 (RNA-seq)

description:
Sex: 2
M89


title: 2070_Fetal_GD18 [SP0224-B05]


title: 2114_Fetal_GD18 [SP0224-C07]


title: Salt_12h_3

value: 200mM NaCl 12h


title: Meningioma 87 (RNA-seq)

description:
Sex: 1
M87


title: Meningioma 86 (RNA-seq)

description:
Sex: 2
M86


title: Salt_12h_2


title: Meningioma 83 (RNA-seq)

description:
Sex: 2
M83


title: Salt_24h_1


title: Meningioma 95 (RNA-seq)

description:
Sex: 2
M95


title: Meningioma 80 (RNA-seq)

description:
Sex: 2
M80


title: Meningioma 79 (RNA-seq)

description:
Sex: 2
M79


title: Meningioma 8 (RNA-seq)

description:
Sex: 2
M8


title: Meningioma 77 (RNA-seq)

description:
Sex: 1
M77


title: Salt_8h_3

value: 200mM NaCl 8h


title: Salt_12h_1


title: Meningioma 76 (RNA-seq)

description:
Sex: 2
M76


title: flail3_RNAseq_rep2

city: Frederiksberg C

first: Yu

last: Jin

address: Thorvaldsensvej 40, 2nd floor

data_processing:
Basecalls performed using CASAVA version 1.4
 Trim adapters using trimmomatic v0.39 3 in paired-end mode
Align to TAIR10 using STAR v2.7.8a in local mode
Filter out MAPQ reads below 10 by Samtools v1.1.2
Convert BAM files to Bedgraph using BEDtools genomecov v2.30.0
Convert BAM files to BigWig using bamCoverage 3.5.1
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files show sequencing coverage with single base resolution (no signal smoothing, transformation or normalization were applied)

organism: Arabidopsis thaliana

source_name: Whole seedlings

extract_protocol:
Total RNA was extracted from two‐week old Arabidopsis seedlings using a RNeasy Plant Mini Kit (Qiagen, Germany). DNA in the isolated RNA were digested with TURBO DNase (Thermo Fisher Scientific, USA). Purified RNA was subsequently turned into cDNA as manufacturer’s instructions with iScript™ cDNA Synthesis Kit (Bio-Rad, USA).
RNA-seq libraries were prepared using NEXTFLEX® Rapid Directional RNA-seq Library Prep Kit (NOVA-5138-08)   RNA-seq libraries were pooled into one flow cell (NextSeq 500/550 High Output Kit v2.5) for sequencing with single-indexed, PE (2*75 bp) and sequenced on an Illumina Nextseq 500.

value: 14-day seedlings

tag: ecotype

value: Columbia (Col-0)

tag: genotype

value: untreated


title: complement_RNAseq_rep1

value: flail3 pFLAIL:gFLAIL

tag: treatment


title: Meningioma 9 (RNA-seq)

description:
Sex: 2
M9


title: flail3_RNAseq_rep3


title: Meningioma 75 (RNA-seq)

description:
Sex: 2
M75


title: Salt_96h_3

value: 200mM NaCl 96h


title: flail3_RNAseq_rep1


title: Meningioma 74 (RNA-seq)

description:
Sex: 1
M74


title: 2069_Fetal_GD18 [SP0224-B04]

value: Liver


title: WT_RNAseq_rep3

value: wild type


title: Salt_8h_2


title: Salt_8h_1


title: Salt_4h_3

value: 200mM NaCl 4h


title: WT_RNAseq_rep2


title: complement_RNAseq_rep2


title: Salt_4h_2


title: WT_RNAseq_rep1


title: Meningioma 71 (RNA-seq)

description:
Sex: 2
M71


title: Meningioma 73 (RNA-seq)

description:
Sex: 2
M73


title: Meningioma 70 (RNA-seq)

description:
Sex: 1
M70


title: Meningioma 69 (RNA-seq)

description:
Sex: 1
M69


title: Meningioma 7 (RNA-seq)

description:
Sex: 1
M7


title: ctbp-1 neurons

city: Cambridge

first: Joshua

last: Saul

state: MA

department: Biology

institute: MIT

data_processing:
Data was processed using 10X Genomics' CellRanger pipeline. Raw base call (BCL) files were demultiplexed into fastq files using CellRanger mkfastq
fastq files were aligned, filtered, barcodes and UMIs were counted,and clustering was determined using CellRanger count
cloupe files generated by CellRanger count were processed in 10X Genomics' Loupe Browser application. Cells were checked for expression of cell-specific markers and desired cells' transcriptional profiles were saved for analysis
Genome_build: WBcel235
Supplementary_files_format_and_content: comma-separated value (csv) files for each genotype were generated using 10X Genomics' Loupe Browser looking for cells expressing the desired cell-specific markers

organism: Caenorhabditis elegans

source_name: C. elegans neurons

growth_protocol: stage-synchromized animals were grown on NGM plates seeded with E. coli strain OP50 to the L4 larval stage

extract_protocol:
Whole C. elegans animals were dissociated (washed, treated with SDS-DTT, washed, treated with pronase, washed with L-15-10, and filter for size) and living, GFP+, DAPI- neurons were FACS sorted out of the dissociated mixture. Libraries were prepared using Chromium Next GEM Single Cell 3’ Kit v3.1
Libraries were prepared using Chromium Next GEM Single Cell 3’ Kit v3.1 according to manufacturer’s protocol

treatment_protocol: L4 worms were washed off plates with M9 buffer

value: neurons

value: L4 larval stage


title: Meningioma 68 (RNA-seq)

description:
Sex: 2
M68

value: meningioma


title: Meningioma 67 (RNA-seq)

description:
Sex: 2
M67

value: UCSF


title: wild-type neurons


title: Meningioma 65 (RNA-seq)

description:
Sex: 1
M65


title: Meningioma 63 (RNA-seq)

description:
Sex: 1
M63


title: Salt_2h_3

value: 200mM NaCl 2h


title: Meningioma 64 (RNA-seq)

description:
Sex: 1
M64


title: Meningioma 72 (RNA-seq)

description:
Sex: 1
M72