title: whole blood-Healthy-17


title: whole blood-Healthy-16

status: Public on Apr 22 2020

type: RNA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Data was scanned on Illumina Beadstation 500

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood-Healthy

label_protocol: Following extraction, a LabChip GX instrument (Caliper Life Sciences Inc.) was used to measure the RNA Quality Score (RQS) for each sample. RNA concentration was measured using a Nanodrop 8000 (Nanodrop Technologies). Following RNA extraction and quality control analysis, Globin mRNA was depleted from a portion of each total RNA sample using the GLOBINclear™ 96-well format kit (Ambion). This was followed by another round of RQS and concentration determinations for quality control purposes. 250ng of globin reduced RNA from all samples passing quality control were then amplified and labeled using the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion).

extract_protocol: Blood was collected in Tempus tubes (Applied Biosystems, Foster City, CA), immediately placed on ice and stored within 2-4 hours at -20°C until further analyses in batches. RNA was extracted, amplified, quantified and globin reduced according to manufacturer’s instructions [ref]. Subsequently RNA was converted to cDNA and hybridized into Illumina Human HT-12 v4 microarray chips (47,323 probes; Illumina, San Diego, CA) as described (ref). After hybridization data was scanned on Illumina Beadstation 500 and Illumina BeadStudio/GenomeStudio software were used for background subtraction and to scale average signal intensities (average normalization)

tag: gender

value: Female

tag: race

value: White

tag: sample collection date

tag: age (mos)

tag: condition

value: Healthy

tag: cohort

value: Discovery

tag: globin reduction

tag: tissue

value: whole blood


title: whole blood-Healthy-23

data_processing: Illumina BeadStudio/GenomeStudio software were used for background subtraction and to scale average signal intensities (average normalization)

value: Male


title: whole blood-Healthy-7

value: Black


title: whole blood-Healthy-15


title: whole blood-Healthy-12

value: Hispanic


title: whole blood-Healthy-11


title: whole blood-Healthy-9


title: whole blood-Healthy-13

value: Other


title: whole blood-RSV Inpatient-24

source_name: whole blood-RSV Inpatient

value: RSV Inpatient


title: whole blood-Healthy-18


title: whole blood-Healthy-8


title: whole blood-Healthy-4


title: whole blood-Healthy-6


title: whole blood-Healthy-14


title: whole blood-Healthy-3


title: whole blood-Healthy-1

value: Asian


title: whole blood-RSV Inpatient-22


title: whole blood-RSV Inpatient-21


title: whole blood-Healthy-10


title: whole blood-RSV Inpatient-20


title: whole blood-RSV Inpatient-23


title: whole blood-Healthy-2


title: whole blood-Healthy-5


title: whole blood-RSV Inpatient-19


title: whole blood-RSV Inpatient-41

value: Validation


title: whole blood-RSV Inpatient-16


title: whole blood-RSV Inpatient-15


title: whole blood-RSV Inpatient-12


title: whole blood-RSV Inpatient-18


title: whole blood-RSV Inpatient-8


title: whole blood-RSV Outpatient-16

source_name: whole blood-RSV Outpatient

value: RSV Outpatient


title: whole blood-RSV Inpatient-1

value: Biracial


title: whole blood-RSV Inpatient-14


title: whole blood-RSV Inpatient-10


title: whole blood-RSV Outpatient-22


title: whole blood-RSV Inpatient-4


title: whole blood-RSV Inpatient-13


title: whole blood-RSV Outpatient-21


title: whole blood-RSV Inpatient-5


title: whole blood-RSV Outpatient-23


title: whole blood-RSV Outpatient-24


title: whole blood-RSV Inpatient-3


title: whole blood-RSV Inpatient-17


title: whole blood-RSV Inpatient-9


title: whole blood-RSV Inpatient-6


title: whole blood-RSV Outpatient-14


title: whole blood-RSV Outpatient-20


title: whole blood-RSV Outpatient-15


title: whole blood-RSV Outpatient-19


title: whole blood-RSV Outpatient-18


title: whole blood-RSV Inpatient-2


title: whole blood-RSV Inpatient-7


title: whole blood-RSV Inpatient-11


title: whole blood-RSV Outpatient-17


title: whole blood-Healthy-19


title: Lean_IAV_infected_Brain_4

status: Public on Apr 14 2020

type: SRA

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

library_source: transcriptomic

data_processing:
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to mouse gene annotation using Bowtie1 (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene.

organism: Mus musculus

source_name: Brain

growth_protocol: C57BL/6 male and female mice were fed either a high-fat diet consisting of 40% calories from fat or a low-fat diet consisting of 12% calories from fat (Specialty Feeds, Glen Forrest, Australia) for 10 weeks and supplied with water ad libitum.

extract_protocol:
RNA was further purified using an RNAeasy plus Minielute kit.
RNA-Seq libraries were generated using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit.

treatment_protocol: Mice were anaesthetised with isoflurane using Stinger Research Anaesthetic Gas Machine (Darvall, Payson, AZ), then inoculated intranasally with 5500 plaque forming units (PFU) of influenza A/Auckland/09(H1N1) in 50µLs.

tag: cell type

value: whole brain

tag: treatment protocol

value: low fat diet, two days after influenza infection

tag: donor


title: Obese_IAV_infected_Brain_2

value: high fat diet, two days after influenza infection


title: Obese_IAV_infected_Brain_4


title: Lean_IAV_infected_Brain_3


title: Lean_IAV_infected_Brain_1


title: Obese_Naive_Brain_4

value: high fat diet, no infection


title: Obese_Naive_Brain_3


title: Lean_IAV_infected_Brain_2


title: Obese_IAV_infected_Brain_1


title: Lean_Naive_Brain_1

value: low fat diet, no infection


title: Lean_Naive_Brain_4


title: Obese_Naive_Brain_1


title: Lean_Naive_Brain_3


title: Obese_Naive_Brain_2


title: Lean_Naive_Brain_2


title: whole blood-RSV Outpatient-12


title: whole blood-RSV Outpatient-13


title: whole blood-RSV Outpatient-8

value: Female


title: whole blood-RSV Outpatient-10

value: Discovery


title: whole blood-RSV Outpatient-11

value: whole blood


title: whole blood-RSV Outpatient-7


title: whole blood-RSV Outpatient-3


title: whole blood-RSV Outpatient-1


title: whole blood-RSV Outpatient-6


title: Obese_IAV_infected_Brain_3


title: whole blood-RSV Outpatient-5


title: Obese_IAV_infected_Heart_4

source_name: Heart

value: whole heart


title: whole blood-RSV Outpatient-2


title: whole blood-RSV Outpatient-4

value: Black


title: whole blood-RSV Outpatient-9

value: Male


title: Lean_IAV_infected_Heart_2


title: Obese_IAV_infected_Heart_3


title: Obese_IAV_infected_Heart_1


title: Obese_Naive_Heart_2


title: Lean_IAV_infected_Heart_1


title: Lean_Naive_Heart_4


title: Obese_IAV_infected_Lung_4

source_name: Lung

value: whole lung tissue


title: Lean_IAV_infected_Heart_4


title: Lean_IAV_infected_Heart_3


title: Obese_IAV_infected_Lung_3


title: Obese_Naive_Heart_1


title: Obese_IAV_infected_Lung_1


title: Lean_IAV_infected_Lung_4


title: Lean_IAV_infected_Lung_3


title: Lean_Naive_Heart_1


title: Lean_IAV_infected_Lung_2


title: Obese_Naive_Lung_4


title: Lean_IAV_infected_Lung_1


title: Obese_IAV_infected_Heart_2


title: Obese_Naive_Lung_3


title: Obese_Naive_Lung_2


title: Obese_Naive_Lung_1


title: Obese_Naive_Heart_4


title: Obese_Naive_Heart_3


title: Lean_Naive_Lung_2


title: Lean_Naive_Lung_3


title: Lean_Naive_Heart_3


title: Lean_Naive_Heart_2


title: Lean_Naive_Lung_4


title: 042203_2-0dpi

status: Public on Mar 25 2020

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

data_processing:
all data was processed using the default parameters for 10X genomics CellRanger software to align the reads to the mouse genome and create count matrices of genes for each cell
Data was subsequently pooled and analyzed using Seurat's SCTransform() function in R
Cells with more than 15% mitochondrial reads and less than 200 UMIs were excluded from downstream analysis
Data was normalized using Seurat's SCTransform function and clusters were formed based on the top 20 PCAs
Cells were then visualized using UMAP. Current datafile is embedded in 2-dimensions. 3D embedding available upon request
Genome_build: mm10, Grc38m
Supplementary_files_format_and_content: all data is in a .rds file that contains @ metadata slot which references the cell barcode number and sample, cell type, and contains the normalized count matricies

source_name: tibialis anterior 2 days post CTX injury

extract_protocol:
mononuclear cells were isolated from msucle at the indicated timepoints following a published protocl (Liu et al., 2015). Cells were sorted using a live/dead stain to exclude debris or dead cells
libraries were prepared following 10X Genomics protocol for v3 3' single-cell sequencing and samples were prepared for high throughput sequencing following Illumina's specifications. Prior to sequencing all samples were evaluated using an Agilent Bioanalyzer high sensitivity chip

tag: strain

tag: number of mice

tag: age

value: 3 months

tag: Sex

value: male


title: 042204_3-5dpi

source_name: tibialis anterior 3.5 days post CTX injury


title: Lean_Naïve_Lung_1


title: 042202_0-5dpi

source_name: tibialis anterior 0.5 days post CTX injury


title: 042207_21dpi

source_name: tibialis anterior 21 days post CTX injury


title: Obese_IAV_infected_Lung_2


title: 042201_non-inj

description: Noninjured

source_name: tibialis anterior non-injured SM


title: 042206_10dpi

source_name: tibialis anterior 10 days post CTX injury


title: UHR 5pg Original aRNA method 16

status: Public on Jan 25 2020

city: Los Angeles

first: Hugo

middle: Jae Mun

last: Kim

state: CA

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
5pg Reference RNA processed with Original aRNA method
processed data file: UHR5pg_Expression_profile_Gene.csv

data_processing:
Illumina Casava software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to Human genome using STAR aligner as a module in Partek Flow
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Mapping rates and other parameters calculated
Downsampled data
Genome_build: hg38
Supplementary_files_format_and_content: transcript_counts

molecule: polyA RNA

source_name: UHR 5pg Original aRNA method

extract_protocol:
UHR RNA was bought from Agilent.(74000). UHR samples (5 or 10 pg) were diluted in water to final volume of 5 µl. Alternatively, a whole volume of single cell lysate (5 µl) was used as a starting material for the protocol.
RNA were amplified using either Modified aRNA protocol, Original aRNA protocol, NuGEN protocol. For modified aRNA protocol, To the 5 ul of each sample, we added: 4.9 µl of RNase free water, 2.4 µl of 5x First Strand buffer (Life Technology, included with Superscript III), 1.2 µl of dNTPs (Thermo Fisher, R0193, 10 mM), 0.45 µl of 100 mM DTT (Life Technology, included with Superscript III) and 0.3 µl of dt-T7 oligo (Invitrogen, GGAGGCCGGAGAATTGTAATACGACTCACTATAGGGAGACGCGTGTTTTTTTTTTTTTTTTTTTTTTTTV, 10 ng/µl). This entire mixture was incubated for 5 minutes at 70 degrees to denature the RNA, then immediately placed on ice and the first strand enzyme mix was added: 0.3 µl of Rnasin (Promega, N2111, 2500 unit), 0.45 µl of Superscript III (Life Technology, 18080044), 1 µl of RNAse-free water. First strand synthesis was performed at 42 °C for 30 minutes, followed by 70 °C for 15 minutes. To the 9.35 ul of the above reaction, we added second strand mix (5.56 µl of 5X Second strand buffer (Life Technology, 10812014), 0.75 µl of dNTP mix, 1 µl of DNA polymerase I (10 U/µl, Life Technology, 18010017), 0.25 µl of RNase H (2 U/µl, Life Technology, 18021071), 8.26 µl of RNase-free water) and incubated for exactly 2 hours at 16 °C. After incubation, 1 µl of T4 DNA polymerase (5 U/µl, Life Technology, 18005025) was added and samples incubated for an additional 10 minutes at 16 °C. Double stranded DNA was then purified using 52 µl of Agencourt XP RNAclean beads (Agencourt, A63987) according to manufacturer’s protocol and eluted in 4 µl of water.Reagents from Ambion MEGAscript® T7 Transcription Kit (Life Technology, AMB13345) were used for aRNA amplification. The 1 µl of each ATP, GTP, CTP, TTP, 10X reaction buffer, 10x Enzyme mix were added to each sample followed by incubation at 37 °C for 14 hours. Amplified RNA was purified with 18 µl of Agencourt RNACleanXP Beads and eluted in 4 µl of water. We amplified two cycles
For samples processed with Ovation® RNA-Seq System V2 (NuGEN, 7102-32), sequencing libraries were made using NuGEN Encore Rapid Library system (NuGEN, 0319, 0320) according to the protocol previously reported[19].
For bulk RNA samples (100 ng of UHR) and 10 pg UHR samples processed with modified aRNA protocol libraries were generated using Illumina Truseq Stranded mRNA Library Preparation kit (Illumina, RS-122-2101 and 2102). Samples from aRNA (round 2) were dried with SpeedVac (Savant, SVC100D) into low volume (less than 1ul) and added to the Elute-Prime-2 stage of the TruSeq Stranded mRNA protocol (Illumina, 20020594) to bypass the poly-A mRNA selection process. Rest of the steps were performed, following the manufacturer’s protocol using TruSeq RNA Single Indexes Set A and B (Illumina, 20020492 and 20020493).

tag: rna source

value: Universal Human RNA,Agilent, 740000

tag: rna amount

value: 5pg Reference RNA

tag: processing method

value: Original aRNA from Single cell amount of UHR


title: UHR 5pg Original aRNA method 13


title: UHR 5pg Original aRNA method 14


title: UHR 5pg Original aRNA method 12


title: UHR 5pg Original aRNA method 15


title: UHR 5pg Original aRNA method 8


title: UHR 5pg Original aRNA method 7


title: UHR 5pg Original aRNA method 6


title: UHR 5pg Original aRNA method 9


title: UHR 5pg Original aRNA method 10


title: UHR 5pg Original aRNA method 4


title: UHR 5pg Original aRNA method 5


title: UHR 5pg Original aRNA method 3


title: UHR 5pg Original aRNA method 2


title: UHR 5pg Modified aRNA method 17

description:
5pg Reference RNA processed with Modified aRNA method
processed data file: UHR5pg_Expression_profile_Gene.csv

source_name: UHR 5pg Modified aRNA method

value: Modified aRNA from Single cell amount of UHR


title: UHR 5pg Original aRNA method 1


title: 042205_5dpi

source_name: tibialis anterior 5 days post CTX injury


title: UHR 5pg Modified aRNA method 14


title: UHR 5pg Modified aRNA method 16


title: UHR 5pg Modified aRNA method 15


title: UHR 5pg Modified aRNA method 13


title: UHR 5pg Modified aRNA method 12


title: UHR 5pg Modified aRNA method 11


title: UHR 5pg Modified aRNA method 8


title: UHR 5pg Modified aRNA method 9


title: UHR 5pg Modified aRNA method 10


title: UHR 5pg Modified aRNA method 7


title: UHR 5pg Modified aRNA method 5


title: UHR 5pg Original aRNA method 11


title: UHR 5pg Modified aRNA method 4


title: UHR 5pg Modified aRNA method 2


title: UHR 5pg Modified aRNA method 3


title: UHR 5pg Modified aRNA method 1


title: UHR 10pg Modified aRNA method 25

description:
10pg Reference RNA processed with Modified aRNA method
processed data file: Partek_Hugo_SCUHRDS_transcript_counts.xlsx

source_name: UHR 10pg Modified aRNA method

value: 10pg Reference RNA


title: UHR 10pg Modified aRNA method 20


title: UHR 10pg Modified aRNA method 22


title: UHR 10pg Modified aRNA method 18


title: UHR 10pg Modified aRNA method 24


title: UHR 10pg Modified aRNA method 16


title: UHR 10pg Modified aRNA method 23


title: UHR 10pg Modified aRNA method 19


title: UHR 10pg Modified aRNA method 17


title: UHR 10pg Modified aRNA method 10


title: UHR 10pg Modified aRNA method 11


title: UHR 5pg Modified aRNA method 6


title: UHR 10pg Modified aRNA method 12


title: UHR 10pg Modified aRNA method 14


title: UHR 10pg Modified aRNA method 15


title: UHR 10pg Modified aRNA method 9


title: UHR 10pg Modified aRNA method 13


title: UHR 10pg Modified aRNA method 8


title: UHR 10pg Modified aRNA method 4


title: UHR 10pg Modified aRNA method 6


title: UHR 10pg Modified aRNA method 2


title: UHR 10pg Modified aRNA method 5


title: UHR 10pg Modified aRNA method 3


title: UHR 10pg Modified aRNA method 7


title: UHR 10pg Modified aRNA method 21


title: UHR 10pg Modified aRNA method 1


title: UHR 10pg Original aRNA method 1

description:
10pg Reference RNA processed with Original aRNA method
processed data file: Partek_Hugo_SCUHRDS_transcript_counts.xlsx

source_name: UHR 10pg Original aRNA method


title: UHR 10pg NuGEN RNAseq V2 method 8

description:
10pg Reference RNA processed with NuGEN method
processed data file: Partek_Hugo_SCUHRDS_transcript_counts.xlsx

source_name: UHR 10pg NuGEN RNAseq V2 method

value: NuGEN RNAseq method for Single cell amount of UHR


title: UHR 10pg NuGEN RNAseq V2 method 7


title: UHR 10pg Original aRNA method 2


title: UHR 10pg NuGEN RNAseq V2 method 5


title: UHR 10pg NuGEN RNAseq V2 method 2


title: UHR 10pg NuGEN RNAseq V2 method 4


title: UHR 10pg NuGEN RNAseq V2 method 1


title: UHR 10pg NuGEN RNAseq V2 method 3


title: UHR 10pg NuGEN RNAseq V2 method 9


title: UHR Bulk Total RNA method 1

description:
Bulk Reference RNA processed with Total RNA method
processed data file: Partek_Hugo_SCUHRDS_transcript_counts.xlsx

source_name: UHR Bulk Total RNA method

value: Bulk Reference RNA

value: Total RNA method


title: UHR Bulk PolyA method 1

description:
Bulk Reference RNA processed with Poly A method
processed data file: Partek_Hugo_SCUHRDS_transcript_counts.xlsx

source_name: UHR Bulk PolyA method

value: PolyA method


title: UHR Bulk PolyA method 2


title: UHR Bulk Total RNA method 2


title: A3

status: Public on Jan 01 2020

first: Bennett

last: Novitch

state: California

address: 650 Charles E Young Dr. S, CHS 66-200

department: Department of Neurobiology

institute: University of California, Los Angeles

description:
processed data file:
Watanabe2019_ExonExpression_Normalized.csv
Watanabe2019_lncRNAExpression_Normalized.csv
Watanabe2019_ExonExpression_RawCounts.csv
Watanabe2019_lncRNAExpression_RawCounts.csv
Watanabe2019_ExonExpression_Regressed.csv
Watanabe2019_lncRNAExpression_Regressed.csv

data_processing:
STAR (version 2.4.0j; Dobin et al., 2013) was used to align RNA reads to the human genome (GRCh37/hg19).
Subsequent read quantification (exon or lncRNA counts) was performed with HTSeq (version 0.6.1p1; Anders et al., 2014), also using the human genome assembly GRCh37/hg19.
Genes (exon or lncRNA counts) were filtered such that only genes with a count greater than 10 in at least 80% of samples were retained.
The DESeq2 package (Love et al., 2014) was used to obtain normalized gene expression data (using varianceStabilizingTransform).
To generate a regressed dataset for data visualization and other analyses, we removed the effects of the following technical covariates from the normalized gene expression data using a linear model: RIN, RNA concentration, and the first principal component of the Picard QC statistics.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: CSV files with either HTSC counts (exon or lncRNA), normalized expression data (exon or lncRNA), or regressed expression data (exon or lncRNA).

growth_protocol: Every 3-5 days, hPSCs were passaged at a 1:10-1:15 dilution with partial dissociation using ReLeSR (Stemcell Technologies, 5872). Cerebral and basal ganglionic eminence (GE) organoid formation was then performed as described in Watanabe et al., 2017. Of note, Knockout Serum Replacement (KSR) is known to affect differentiation efficiency and we carried out the differentiation protocol using the same KSR lot (KSR, Invitrogen, 10828010 and 10828028) lot (1670543) as in Watanabe et al., 2017. For the differentiation of the dorsomedial telencephalic tissue (DMT), we used the modified methods as previously described in (Sakaguchi et al., 2015). From day 18-24, BMP4 (6.5 ng/ml, Invitrogen, P2026055) and GSK3 inhibitor (3 μM of CHIR 99021, Fisher Scientific, 442310) were added with DMEM/F-12 (Hyclone) supplemented with 1 % N2 (Invitrogen), 1 % chemically defined lipid concentrate (CDLC, Invitrogen), 10 % fetal bovine serum (FBS qualified source US region, Invitrogen, 10437028) under 40 % O2 and 5 % CO2 conditions at 37 °C. On day 42, DMT organoids were cut in half and the base media was changed to Neurobasal medium (Invitrogen), supplemented with 1 % N2 (Invitrogen), 1 % CDLC, 10 % FBS, 2 % B-27 supplement without vitamin A (Invitrogen), GlutaMAX (Invitrogen), 100 μg/ml of Primocin (InvivoGen). After day 42, every two weeks, DMT organoids were cut into half. From day 56, DMT organoids were cultured in a Lumox dish (SARSTEDT, cell suspension). The media was subsequently changed every 2-3 days until the organoids were used.

extract_protocol:
Samples were lysed in QIAzol and RNA was extracted following manufacturer’s instructions (Qiagen, miRNeasy Micro Kit). RNA integrity was confirmed with the Agilent 2200 TapeStation (RIN > 8) and sent to the UCLA Neuroscience Genomic Core.
The cDNA libraries were generated using TruSeq with Ribo-Zero Gold (Illumina) and sequenced using Illumina HiSeq4000, yielding about 50 million reads per sample.

treatment_protocol: Treatments for different conditions (Feeder or Feeder-free) were applied before organoid formation.

tag: cell line

tag: feeder

value: Yes

tag: mef details

value: mouse embryonic fibroblast-supported conditions (Millipore, PMEF-CF)

tag: feeder-free

value: No

tag: feeder-free details

tag: raw counts name

tag: normalized name

tag: molecule subtype

value: total RNA (rRNA depleted/Ribo-Zero)


title: C1

value: maintained with mTeSRTM1 (Stemcell Technologies, 85850) or Essential 8 medium (E8, ThermoFisher, A15117001) and where specified on hESC-qualified Matrigel substrate (Fisher Scientific, 08-774-552)


title: G2

source_name: XFiPSC

value: XFiPSC


title: F3


title: G3


title: F2


title: C2


title: C3


title: F1


title: G1


title: A1


title: C_RPMI_RPMI

status: Public on Dec 10 2019

data_processing:
MMSEQ package was used to infer gene expression levels. Reads were mapped to the genome using Bowtie1
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq.txt format, containing counts per gene and log RPKM.

growth_protocol: Monocytes were negatively selected from peripheral blood and cultured in RPMI and 10% human serum for 6 days.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared by Novogene

treatment_protocol: Cells were collected in Trizol.

tag: tissue

value: Adult Human Peripheral Blood

tag: cell type

value: macrophage

tag: treatment protocol


title: C_BG_RPMI

tag: donor


title: C_RPMI_MTB


title: UHR 10pg NuGEN RNAseq V2 method 6

value: Universal Human RNA,Agilent, 740000


title: B_RPMI_RPMI


title: B_RPMI_MTB


title: B_BG_RPMI


title: B_BG_MTB


title: A_RPMI_MTB


title: A_BG_RPMI


title: Wild type strain + ProQ overexpression 3

status: Public on Dec 08 2019

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
Total RNA library_exp4
10_wt ProQ-3

data_processing:
fastq records trimming (cutadapt 1.16)
short reads mapping and wiggle file generation (rilseq 0.60)
chimera mapping and s-chimera reporting (rilseq 0.60)
BED file genreration (rilseq 0.60)
Genome_build: ecoli-k12-MG1655-NC_000913-3
Supplementary_files_format_and_content: BED format for significant chimeric fragments of RILseq samples.
Supplementary_files_format_and_content: Wiggle format for RNAseq samples

organism: Escherichia coli K-12

source_name: MG1655 + pBAD-ProQ

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 250 rpm, in either LB rich or M63 minimal medium and samples were collected at OD~1 in experiments 1 and 3, at 150 min in experiment 2 and at 210 in experiment 4 after arabinose was added for 30 min

extract_protocol:
Standard TRIzol protocol was used for total RNA extraction and standard TRI Reagent LS protocol was used for RNA extraction in the RIL-seq protocol
Library construction was carried out based on the RNAtag-Seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)
RIL-seq

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen by liquid nitrogen.

tag: growth

value: Subcultured for 180 min in LB and then arabinose was added for 30 min


title: A_RPMI_RPMI


title: A2


title: Wild type strain + ProQ overexpression 1

description:
Total RNA library_exp4
2_wt ProQ-1


title: Wild type strain + control plasmid 2

description:
Total RNA library_exp4
5_wt pBAD-2


title: Wild type strain + control plasmid 3

description:
Total RNA library_exp4
9_wt pBAD-3


title: Wild type strain + control plasmid 1

description:
Total RNA library_exp4
1_wt pBAD-1


title: C_BG_MTB


title: Deletion of proQ RNA-Seq 6_del-proQ 3

description:
Deletion of proQ
total RNA
Total RNA library_exp3

source_name: MG1655 proQ::kan

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 250 rpm, in either LB rich or M63 minimal medium and samples were collected at OD~1 in experiments 1  and 3, and at 150 min in experiment 2.

value: Subcultured for 150 min in LB


title: Tagged Hfq RNA-Seq 3_Hfq-FLAG  1

description:
Tagged Hfq
total RNA
Total RNA library_exp2

source_name: MG1655 hfq-FLAG


title: Deletion of proQ RNA-Seq 4_del-proQ 1


title: Wild type strain RNA-Seq 3_wt 3

description:
Wild type strain
total RNA
Total RNA library_exp3


title: Wild type strain RNA-Seq 2_wt 2


title: Tagged ProQ RNA-Seq 6_ProQ-FLAG  2

description:
Tagged ProQ
total RNA
Total RNA library_exp2

source_name: MG1655 proQ-3XFLAG


title: Tagged Hfq in a proQ deletion RNA-Seq 7_Hfq-FLAG  del-proQ 1

description:
Tagged Hfq in a proQ deletion
total RNA
Total RNA library_exp2

source_name: MG1655 hfq-FLAG, proQ::kan


title: Tagged ProQ in an hfq deletion RNA-Seq 9_ProQ-FLAG del-hfq  1

description:
Tagged ProQ in an hfq deletion
total RNA
Total RNA library_exp2

source_name: MG1655 proQ-3XFLAG, hfq::cat


title: Control library of untagged Hfq and ProQ RNA-Seq 1_wt 1

description:
Control library of untagged Hfq and ProQ
total RNA
Total RNA library_exp2


title: Wild type strain RNA-Seq 1_wt 1


title: Wild type strain + ProQ overexpression 2

description:
Total RNA library_exp4
6_wt ProQ-2


title: Tagged ProQ RNA-Seq 5_ProQ-FLAG  1


title: Deletion of proQ RNA-Seq 5_del-proQ 2


title: Tagged Hfq RNA-Seq 4_Hfq-FLAG  2


title: Tagged Hfq in a proQ deletion RNA-Seq 8_Hfq-FLAG  del-proQ 2


title: Tagged ProQ in an hfq deletion other 9_ProQ-FLAG del-hfq  1

description:
Tagged ProQ in an hfq deletion
RNA after application of RIL-seq
RIL-seq library_exp2


title: A_BG_MTB


title: Tagged ProQ in an hfq deletion other 10_ProQ-FLAG del-hfq  2


title: Tagged Hfq in a proQ deletion other 7_Hfq-FLAG  del-proQ 1

description:
Tagged Hfq in a proQ deletion
RNA after application of RIL-seq
RIL-seq library_exp2


title: Control library of untagged Hfq and ProQ RNA-Seq 2_wt 2


title: Tagged Hfq other 4_Hfq-FLAG  2

description:
Tagged Hfq
RNA after application of RIL-seq
RIL-seq library_exp2


title: Control library of untagged Hfq and ProQ other 1_wt 1

description:
Control library of untagged Hfq and ProQ
RNA after application of RIL-seq
RIL-seq library_exp2


title: Tagged Hfq other 3_Hfq-FLAG  1


title: Tagged Hfq RNA-Seq 12_Hfq-FLAG M63 2

description:
Tagged Hfq
total RNA
Total RNA library_exp1

value: OD ~ 1 in M63


title: Control library of untagged Hfq and ProQ other 2_wt 2


title: Tagged ProQ other 5_ProQ-FLAG  1

description:
Tagged ProQ
RNA after application of RIL-seq
RIL-seq library_exp2


title: Tagged Hfq in a proQ deletion other 8_Hfq-FLAG  del-proQ 2


title: Tagged ProQ in an hfq deletion RNA-Seq 10_ProQ-FLAG del-hfq  2


title: Tagged ProQ RNA-Seq 11_ProQ-FLAG M63 2

description:
Tagged ProQ
total RNA
Total RNA library_exp1


title: Tagged Hfq RNA-Seq 9_Hfq-FLAG LB 2

value: OD ~ 1 in LB


title: Control library of untagged Hfq and ProQ RNA-Seq 7_wt LB 2

description:
Control library of untagged Hfq and ProQ
total RNA
Total RNA library_exp1


title: Control library of untagged Hfq and ProQ other 7_wt LB 2

description:
Control library of untagged Hfq and ProQ
RNA after application of RIL-seq
RIL-seq library_exp1


title: Tagged Hfq RNA-Seq 3_Hfq-FLAG LB 1


title: Tagged ProQ RNA-Seq 5_ProQ-FLAG M63 1


title: Tagged Hfq other 6_Hfq-FLAG M63 1

description:
Tagged Hfq
RNA after application of RIL-seq
RIL-seq library_exp1


title: Tagged Hfq other 12_Hfq-FLAG M63 2


title: Control library of untagged Hfq and ProQ RNA-Seq 4_wt M63 1


title: Tagged ProQ other 5_ProQ-FLAG M63 1

description:
Tagged ProQ
RNA after application of RIL-seq
RIL-seq library_exp1


title: Tagged ProQ other 11_ProQ-FLAG M63 2


title: Tagged Hfq other 9_Hfq-FLAG LB 2


title: Control library of untagged Hfq and ProQ RNA-Seq 10_wt M63 2


title: Control library of untagged Hfq and ProQ other 10_wt M63 2


title: Tagged Hfq RNA-Seq 6_Hfq-FLAG M63 1


title: Control library of untagged Hfq and ProQ RNA-Seq 1_wt LB 1


title: Tagged ProQ other 6_ProQ-FLAG  2


title: Tagged ProQ other 8_ProQ-FLAG LB 2


title: Tagged ProQ RNA-Seq 2_ProQ-FLAG LB 1


title: Tagged ProQ other 2_ProQ-FLAG LB 1


title: Control library of untagged Hfq and ProQ other 1_wt LB 1

description:
Control library of untagged Hfq and ProQ
RNA after application of RIL-seq
RIL-seq library_exp1
processed data: none (no significant s-chimeras)


title: Tagged Hfq other 3_Hfq-FLAG LB 1


title: Tagged ProQ RNA-Seq 8_ProQ-FLAG LB 2


title: t-HESC_EGR1

status: Public on Nov 26 2019

city: Houston

first: Maria

last: Szwarc

address: One Baylor Plaza

institute: Baylor College of MEdicine

library_source: genomic

data_processing:
75-nt sequence reads identified using Ilumina's NextSeq 500 were mapped to the genome using the BWA algorithm at default settings.
Only reads that passed Illumina’s purity filter, align with no more than 2 mismatches, and mapped uniquely to the genome were used. Duplicate reads were removed.
33624867 of total 33624867 EGR1 peaks aligned (42723299 of total 45719322 input peaks)
Unique alignments (-q 25): 30,319,137, Unique alignments (without duplicate reads): 14,418,837, Final number of EGR1 tags: 14,413,272 ( Final number of input tags: 35,216,489)
For peak calling, reads were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
Genomic binding sites ('intervals') were defined using MACS 2.1.0 software and following settings: effective genome size = 2.70e+09, band width = 200, model fold = [5, 50], p-value cutoff = 1.00e-07, Broad region calling is off
100752 paired peaks produced 7726 final MACS peaks. 17 intervals were ENCODE blacklisted (7709 filtered intervals)
Genome_build: GRCh37.p2-Primary Assembly
Supplementary_files_format_and_content: BED = standard BED file containing genomic position data for MACS intervals  and peak summits

molecule: genomic DNA

source_name: t-HESC cell line

growth_protocol: DMEM/F12, 10% fetal bovine serum, penicilin-streptomycin, 500 ng/ml puromycin

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody Cell Signaling 4154
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the  3'-ends. Illumina genomic adapters were ligated and the sample was  size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR  amplification step (18 cycles), the resulting DNA libraries were  quantified and sequenced on NextSeq 500.

treatment_protocol: no treament; growth medium only

value: t-HESC

tag: antibody

value: EGR1 (Cell Signaling 4154)


title: oxLDL_d6_H3K4me3

status: Public on Nov 07 2019

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the histone marks at p-value of 10-10. H3K27ac peaks were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format, DownSampled to make all files the same read depth.

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were negatively selected from peripheral blood and immediately fixed for ChIP.

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 33 µl of chromatin (1 ug) was used for immunoprecipitation.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes were cultured for 24 hours in media with or without oxLDL

value: Monocyte

value: 24 hours in media with oxLDL, then 5 days in media

tag: chip antibody

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: RPMI_d6_LPS_H3K4me3

value: 6 days in media and then LPS for 4 hours


title: RPMI_d6_H3K4me3

value: 6 days in media


title: oxLDL_24h_H3K4me3

value: 24 hours in media with oxLDL


title: oxLDL_d6_LPS_H3K4me3

value: 24 hours in media with oxLDL, then 5 days in media, then LPS for 4 hours


title: Control library of untagged Hfq and ProQ other 4_wt M63 1


title: RPMI_24h_H3K4me3

value: 24 hours in media


title: oxLDL_d6_LPS_H3K27ac

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: oxLDL_d6_H3K27ac


title: oxLDL_24h_H3K27ac


title: RPMI_24h_H3K27ac


title: oxLDL_24h

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene.

growth_protocol: Monocytes were negatively selected from peripheral blood and placed in Trizol for RNA.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes were cultured in media with or without oxLDL. Then differentiated to macrophages.


title: oxLDL_d6_LPS


title: RPMI_d6_LPS_H3K27ac


title: RPMI_d6_H3K27ac


title: Monocyte_T0_H3K4me3

value: attached for 1 hour


title: Monocyte_T0


title: RPMI_d6


title: RPMI_24h


title: SK23-DSPKR2-lightpolysome

status: Public on Nov 02 2019

first: Ya

last: Cui

state: TEXAS

address: One Baylor Plaza, Baylor College of Medicine, 529DH

institute: Baylor College of Medicine

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence by Trimmomatic v0.38.
Then mapped to mm10 whole genome using hisat2-2.1.0 with parameters -p 10 -t --dta-cufflinks -x;Then cufflinks-v2.2.1 was used to assess differentially expressed genes.
Wig files were generated using RSeQC-v2.6.5 and wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using RSeQC-v2.6.5 and wigToBigWig.

extract_protocol:
Mouse brain tissue was dissected in a cutting solution. Polysomal mRNA was isolated from WT, Ts65Dn, and Ts65Dn-Pkr-/- mice. See Methods for detail
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age (month)

tag: genotype/variation

value: Ts65Dn Pkr-/-

value: Brain

value: Ribosome associated mRNA


title: t-HESC_Input

tag: cell line


title: SK27-DSPKR3-heavypolysome


title: SK24-DSPKR2-heavypolysome


title: SK20-DSPKR1-lightpolysome


title: SK18-DS3-heavypolysome


title: SK14-DS2-lightpolysome


title: SK12-DS1-heavypolysome


title: SK15-DS2-heavypolysome


title: SK11-DS1-lightpolysome


title: SK17-DS3-lightpolysome


title: SK9-WT3-heavypolysome

value: wild type


title: RPMI_d6_LPS


title: Monocyte_T0_H3K27ac


title: SK6-WT2-heavypolysome


title: SK21-DSPKR1-heavypolysome


title: SK8-WT3-lightpolysome


title: SK3-WT1-heavypolysome


title: oxLDL_d6


title: SK2-WT1-lightpolysome


title: SK26-DSPKR3-lightpolysome


title: iPSC myotube-SDDF-RNAseq-Exp1

status: Public on Oct 29 2019

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
ATAC-seq analysis. Reads were aligned to the human genome (hg38) using Bowtie2 with the following parameters: -q -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant. Aligned reads were filtered for PCR duplicates using Samtools and then processes with MACS 2.1 with the following parameters: --nomodel --nolambda --keep-dup all --call-summits -q 0.05 -B. Bigwig files for visualization on IGV were generated by converting the bedgraph files obtained from MACS2 using the Kent tool bedGraphToBigWig. To identify peaks unique to DMSO and SDDF-treated cells, we used the BEDTools package: summits from DMSO- or SDDF-treated cells were extended 50bp in both directions and then compared pairwise with BEDTools intersect (Rep1_vs_Rep2, Rep1_vs_Rep3, Rep2_vs_Rep3). Common peaks from the 3 comparisons (DMSO or SDDF) were then combined in a unique list and filtered using BEDTools merge. DMSO and SDDF peaks were then compared using BEDTools intersect using the -v function and a minimum overlap of 60% (-f 0.6 -F 0.6). Analysis of differential accessibility was performed by generating a list of peaks representative of all samples using the peak summits identified by MACS2. Each summit was extended 50bp in both directions and the resulting lists of peaks were combined, sorted and merged to obtain a dataset of unique and non-overlapping loci. This list was then used to extrapolate the sequencing depth coverage from each sample bedgraph file. Coverage files were then analyzed using DEseq2  to identify loci with differential chromatin accessibility.
RNA-seq analysis: 75bp FastQ paired-end reads (n=20.9 Million per sample) were trimmed using Trimmomatic (v 0.33). Quality control on raw sequence data was performed with FastQC. Reads were mapped to the human genome (hg38) reference using Hisat2 (v2.1.0). Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLC genomics work bench (Qiagen) using raw read counts. We filtered the generated list based on a minimum 2X Absolute Fold Change and FDR corrected p < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq: processed files contain the list of peak summits identified by MACS2 in each replicate
Supplementary_files_format_and_content: RNA-seq: processed files contain tab-delimited expression values following analysis using EdgeR

source_name: iPSC myotube-SDDF

growth_protocol: Human iPSC were differentiated into myogenic progenitors using conditional expression of PAX7. Myogenic progenitors were induced to terminally differentiate in a serum free low nutrient medium supplemented with vehicle (DMSO) or small molecules (SDDF)

extract_protocol:
Total RNA was extracted in TRIzol reagent and column purified with DNAse treatment using the Purelink RNA mini kit as per manufacturer's instructions
RNA-seq: Dual-indexed libraries were generated using the TruSeq stranded mRNA library kit
ATAC-seq: 50,000cells from 2-day DMSO- and SDDF-treated cultures were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes, after which transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Final libraries were generated by primer extension of the transposed DNA followed by PCR amplification using Illumina-compatible adapter-barcodes.

treatment_protocol: Myotubes were generated upon a 5-day treatment with vehicle (DMSO) or small molecules (SDDF)

value: Human iPSC derived myotubes

tag: treatment

value: S/Da/De/F (SDDF)

tag: time

value: 5-day treatment


title: iPSC myotube-SDDF-RNAseq-Exp2


title: iPSC myotube-SDDF-RNAseq-Exp4


title: JY12858.K5.RANKL

status: Public on Oct 28 2019

data_processing:
The pair-ended reads were mapped to the mouse genome using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference. STAR generated read count for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: text table with counts for each sample and gene identifiers; 10 columns
Supplementary_files_format_and_content: JY12853.control.count; JY12854.control.count; JY12855.control.count; JY12856.K5.RANKL.count; JY12857.K5.RANKL.count; JY12858.K5.RANKL.count; EntrezGeneID; GeneSymbol; GeneDescription; GeneDescription2

source_name: salivary gland

extract_protocol:
Total RNA was extracted from salivary gland tissues using TRIzol reagent (ThermoFisher Scientific) and further purified with the RNeasy Plus Mini Kit (Qiagen). RNA purity was evaluated with a NanoDrop spectrophotometer (ThermoFisher Scientific) and RNA integrity was determined using a 2100 Bioanalyzer with RNA chips (Agilent Technologies).
Libraries for mRNA sequencing were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) from 250 ng of RNA. Quality analysis of libraries was performed using Agilent 4200 TapeStation with D1000 ScreenTape assays (Agilent Technologies). Libraries were pooled and then quantified by two methods: 1) on a 2100 Bioanalyzer with DNA chips using High Sensitivity DNA Kit (Agilent Technologies); and 2) with KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: Control and K5-rtTA:TetO-RANKL mice were administered doxycycline (in food and water) at 9-weeks of age for two weeks to induce transgenic RANKL expression. Each sample contains pooled salivary gland tissues from 5 mice

value: salivary gland

tag: genotype


title: JY12857.K5.RANKL


title: JY12856.K5.RANKL


title: JY12855.control

value: control


title: JY12853.control


title: WT rep2

status: Public on Oct 22 2019

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.1) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: TA muscle

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standard protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: tibialis anterior (TA) muscle

tag: age


title: KO rep1

value: Mettl21e KO


title: WT rep1


title: KO rep3


title: WT rep3


title: JY12854.control


title: KO rep2


title: Control_21

status: Public on Sep 30 2019

data_processing:
Illumina Casava software 1.8.2  used for basecalling of NextSeq500 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq.txt format, containing counts per gene.

source_name: control_Adult Peripheral Blood

growth_protocol: Monocytes were isolated from donors and placed in Trizol immediately.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase

tag: subject status

value: healthy control

tag: subject id

value: Control

value: Monocyte


title: Patient_13_v2

source_name: patient_visit 2_Adult Peripheral Blood

value: hypercholestoremia patient

value: after 3 months of Statin treatment; visit2

tag: cell type


title: Patient_3_v1

source_name: patient_visit 1_Adult Peripheral Blood

tag: treatment protocol

value: before 3 months of Statin treatment; visit1


title: Patient_22_v2


title: Patient_5_v2


title: Patient_3_v2


title: Patient_14_v1


title: Control_9


title: Patient_14_v2


title: Patient_22_v1


title: Control_6


title: Patient_13_v1


title: Control_1


title: Control_4


title: TBM_LPCSF_14 (CSF)

status: Public on Aug 06 2019

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM14.1LP

data_processing:
Trimmomatic v0.36
STAR v2.5.2a
RSEM v1.2.29
DESeq2 v1.18.1
Genome_build: GRCh38 release 88
Supplementary_files_format_and_content: NormalizedCounts

source_name: Lumbar Puncture Cerebrospinal fluid

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from patient whole blood collected in PAXgene tubes
RNA-Seq libraries were constructed using NuGen Ovation Human FFPE Library Kit

treatment_protocol: Not applicable

tag: individual

tag: disease state

value: Pediatric TB meningitis

tag: sample type

value: Lumbar Puncture Cerebrospinal fluid


title: TBM_LPCSF_16 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM16.1LP


title: TBM_LPCSF_6 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM6.1LP


title: TBM_LPCSF_17 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM17.1LP


title: TBM_LPCSF_13 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM13.1LP


title: TBM_LPCSF_15 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM15.1LP


title: TBM_LPCSF_20 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM20.1LP


title: TBM_LPCSF_19 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM19.1LP


title: TBM_LPCSF_18 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM18.1LP


title: TBM_LPCSF_5 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM5.1LP


title: TBM_LPCSF_3 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM3.1LP


title: TBM_LPCSF_1 (CSF)

description:
Ventricular_vs_Lumbar_NormalizedCounts
TBM1.1LP


title: Non-TB Infection Case_7 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
V04

source_name: Ventricular Cerebrospinal fluid

value: Other infection

value: Ventricular Cerebrospinal fluid


title: Non-TB Infection Case_6 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
V01


title: Non-TB Infection Case_4 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
SI2


title: Non-TB Infection Case_5 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
SI5


title: Non-TB Infection Case_2 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
BM2


title: TBM_VentCSF_17 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM17.1V


title: Non-TB Infection Case_3 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
SI1


title: Non-TB Infection Case_1 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
BM1


title: TBM_VentCSF_15 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM15.1V


title: TBM_VentCSF_20 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM20.1V


title: TBM_VentCSF_11 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM11.1V


title: TBM_VentCSF_19 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM19.1V


title: TBM_VentCSF_12 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM12.1V


title: TBM_VentCSF_14 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM14.1V


title: TBM_VentCSF_10 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM10.1V


title: No Infection Healthy Control_22

description:
TBM_Blood_RawCount.txt
VPS3

data_processing:
Trimmomatic v0.36
STAR v2.5.2a
RSEM v1.2.29
DESeq2 v1.18.1
Genome_build: GRCh38 release 88
Supplementary_files_format_and_content: Raw Counts

source_name: Whole blood

value: No Infection Healthy Control

tag: tissue

value: Whole blood


title: TBM_VentCSF_2 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM2.1V


title: No Infection Healthy Control_24

description:
TBM_Blood_RawCount.txt
VPS6


title: No Infection Healthy Control_21

description:
TBM_Blood_RawCount.txt
VPS2


title: TBM_VentCSF_3 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM3.1V


title: TBM_VentCSF_8 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM8.1V


title: No Infection Healthy Control_18

description:
TBM_Blood_RawCount.txt
LIP1


title: No Infection Healthy Control_17

description:
TBM_Blood_RawCount.txt
ICP4


title: No Infection Healthy Control_19

description:
TBM_Blood_RawCount.txt
LIP2


title: No Infection Healthy Control_16

description:
TBM_Blood_RawCount.txt
ICP3


title: No Infection Healthy Control_14

description:
TBM_Blood_RawCount.txt
ICP1


title: No Infection Healthy Control_15

description:
TBM_Blood_RawCount.txt
ICP2


title: SK5-WT2-lightpolysome

tag: strain background

value: wild type

value: Brain

tag: molecule subtype

value: Ribosome associated mRNA


title: TBM_VentCSF_9 (CSF)

description:
TBM_vs_nonTBM_NormalizedCounts
Ventricular_vs_Lumbar_NormalizedCounts
TBM9.1V


title: No Infection Healthy Control_10

description:
TBM_Blood_RawCount.txt
FFR4


title: No Infection Healthy Control_11

description:
TBM_Blood_RawCount.txt
FFR5


title: No Infection Healthy Control_12

description:
TBM_Blood_RawCount.txt
FFR6


title: No Infection Healthy Control_7

description:
TBM_Blood_RawCount.txt
ETV1


title: No Infection Healthy Control_9

description:
TBM_Blood_RawCount.txt
FFR3


title: No Infection Healthy Control_6

description:
TBM_Blood_RawCount.txt
DR4


title: No Infection Healthy Control_3

description:
TBM_Blood_RawCount.txt
CS1


title: No Infection Healthy Control_20

description:
TBM_Blood_RawCount.txt
TC1


title: No Infection Healthy Control_4

description:
TBM_Blood_RawCount.txt
DR1


title: No Infection Healthy Control_23

description:
TBM_Blood_RawCount.txt
VPS5


title: No Infection Healthy Control_1

description:
TBM_Blood_RawCount.txt
CCJ1


title: No Infection Healthy Control_2

description:
TBM_Blood_RawCount.txt
CP1


title: Non-TB Infection Case_4

description:
TBM_Blood_RawCount.txt
V1

value: Non-TB Infection


title: Non-TB Infection Case_3

description:
TBM_Blood_RawCount.txt
SI2


title: Non-TB Infection Case_2

description:
TBM_Blood_RawCount.txt
SI1


title: TBM Case_20

description:
TBM_Blood_RawCount.txt
TBM201


title: TBM Case_18

description:
TBM_Blood_RawCount.txt
TBM181


title: TBM Case_16

description:
TBM_Blood_RawCount.txt
TBM161


title: Non-TB Infection Case_1

description:
TBM_Blood_RawCount.txt
BM2


title: TBM Case_13

description:
TBM_Blood_RawCount.txt
TBM131


title: TBM Case_12

description:
TBM_Blood_RawCount.txt
TBM121


title: TBM Case_15

description:
TBM_Blood_RawCount.txt
TBM151


title: No Infection Healthy Control_8

description:
TBM_Blood_RawCount.txt
FFR2


title: No Infection Healthy Control_5

description:
TBM_Blood_RawCount.txt
DR3


title: TBM Case_11

description:
TBM_Blood_RawCount.txt
TBM111


title: No Infection Healthy Control_13

description:
TBM_Blood_RawCount.txt
HCP4


title: TBM Case_14

description:
TBM_Blood_RawCount.txt
TBM141


title: TBM Case_9

description:
TBM_Blood_RawCount.txt
TBM91


title: TBM Case_8

description:
TBM_Blood_RawCount.txt
TBM81


title: TBM Case_10

description:
TBM_Blood_RawCount.txt
TBM101


title: TBM Case_3

description:
TBM_Blood_RawCount.txt
TBM31


title: TBM Case_7

description:
TBM_Blood_RawCount.txt
TBM71


title: adult_non-ART_Donor_56

status: Public on Jul 29 2019

type: genomic

description: whole blood from naturally (non-ART) conceived individual

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

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

data_processing:
BeadStudio software v3.2
matrix processed includes: Normalized (SWAN) Average Beta and detP
matrix signal intensities includes: The Methylated and unmethylated signal intensities and detP

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the Zymo Research ZR DNA-Card Extraction Kit following manufacturer protocol

tag: gender

value: M

tag: art status

value: non-ART

tag: art subtype

tag: time of collection

value: adulthood


title: adult_non-ART_Donor_53

value: F


title: adult_non-ART_Donor_58


title: adult_non-ART_Donor_54


title: adult_non-ART_Donor_78


title: adult_non-ART_Donor_55


title: adult_non-ART_Donor_51


title: TBM Case_19

description:
TBM_Blood_RawCount.txt
TBM191


title: adult_non-ART_Donor_77


title: adult_non-ART_Donor_50


title: adult_non-ART_Donor_49


title: adult_non-ART_Donor_48


title: adult_non-ART_Donor_76


title: adult_non-ART_Donor_46


title: adult_non-ART_Donor_75


title: adult_non-ART_Donor_45


title: TBM Case_6

description:
TBM_Blood_RawCount.txt
TBM61


title: adult_non-ART_Donor_57


title: adult_non-ART_Donor_43


title: adult_non-ART_Donor_44


title: adult_non-ART_Donor_41


title: adult_non-ART_Donor_40


title: adult_non-ART_Donor_73


title: adult_non-ART_Donor_74


title: adult_non-ART_Donor_72


title: adult_non-ART_Donor_39


title: adult_non-ART_Donor_42


title: adult_non-ART_Donor_52


title: adult_non-ART_Donor_70


title: adult_non-ART_Donor_71


title: adult_non-ART_Donor_36


title: adult_non-ART_Donor_38


title: adult_non-ART_Donor_68


title: adult_non-ART_Donor_69


title: adult_non-ART_Donor_35


title: adult_non-ART_Donor_34


title: adult_non-ART_Donor_33


title: adult_non-ART_Donor_32


title: adult_non-ART_Donor_47


title: adult_non-ART_Donor_29


title: adult_non-ART_Donor_30


title: adult_non-ART_Donor_28


title: adult_non-ART_Donor_66


title: adult_non-ART_Donor_26


title: adult_non-ART_Donor_64


title: adult_non-ART_Donor_22


title: adult_non-ART_Donor_24


title: adult_non-ART_Donor_65


title: adult_non-ART_Donor_63


title: adult_non-ART_Donor_62


title: adult_non-ART_Donor_25


title: adult_non-ART_Donor_23


title: adult_non-ART_Donor_37


title: adult_non-ART_Donor_20


title: adult_non-ART_Donor_17


title: adult_non-ART_Donor_16


title: adult_non-ART_Donor_61


title: adult_non-ART_Donor_21


title: adult_non-ART_Donor_14


title: adult_non-ART_Donor_18


title: adult_non-ART_Donor_31


title: adult_non-ART_Donor_11


title: adult_non-ART_Donor_10


title: adult_non-ART_Donor_9


title: adult_non-ART_Donor_13


title: adult_non-ART_Donor_6


title: adult_non-ART_Donor_27


title: adult_non-ART_Donor_60


title: adult_non-ART_Donor_7


title: adult_non-ART_Donor_5


title: adult_non-ART_Donor_3


title: adult_non-ART_Donor_59


title: adult_non-ART_Donor_2


title: adult_ART_Donor_145

description: whole blood from ART conceived individual

value: ART

value: Frozen embryo


title: adult_ART_Donor_149


title: adult_non-ART_Donor_4


title: adult_ART_Donor_148

value: GIFT


title: adult_non-ART_Donor_67


title: adult_ART_Donor_143


title: adult_ART_Donor_147

value: Fresh embryo


title: adult_ART_Donor_142


title: Patient_5_v1

value: hypercholestoremia patient

value: before 3 months of Statin treatment; visit1

value: Monocyte


title: adult_ART_Donor_139


title: adult_ART_Donor_140


title: adult_ART_Donor_141


title: adult_ART_Donor_174


title: adult_ART_Donor_138


title: adult_ART_Donor_175


title: adult_ART_Donor_173


title: adult_ART_Donor_137


title: adult_non-ART_Donor_12


title: adult_ART_Donor_135


title: adult_ART_Donor_136


title: adult_ART_Donor_134


title: adult_non-ART_Donor_1


title: adult_ART_Donor_172


title: adult_ART_Donor_130


title: adult_ART_Donor_131


title: adult_ART_Donor_132


title: adult_ART_Donor_129


title: adult_ART_Donor_128


title: adult_ART_Donor_126


title: adult_ART_Donor_127


title: adult_ART_Donor_123


title: adult_ART_Donor_122


title: adult_ART_Donor_120


title: adult_ART_Donor_121


title: adult_ART_Donor_176


title: adult_ART_Donor_119


title: adult_ART_Donor_117


title: adult_ART_Donor_114


title: adult_ART_Donor_115


title: adult_ART_Donor_118


title: adult_ART_Donor_170


title: adult_ART_Donor_116


title: adult_ART_Donor_113


title: adult_ART_Donor_112


title: adult_ART_Donor_108


title: adult_ART_Donor_111


title: adult_ART_Donor_110


title: adult_ART_Donor_169


title: adult_ART_Donor_109


title: adult_ART_Donor_107


title: adult_ART_Donor_124


title: adult_ART_Donor_103


title: adult_ART_Donor_168


title: adult_ART_Donor_101


title: adult_ART_Donor_106


title: adult_ART_Donor_100


title: adult_ART_Donor_105


title: adult_ART_Donor_98


title: adult_ART_Donor_167


title: adult_ART_Donor_94


title: adult_ART_Donor_93


title: adult_ART_Donor_171


title: adult_ART_Donor_92


title: adult_ART_Donor_91


title: adult_ART_Donor_95


title: adult_ART_Donor_89


title: adult_ART_Donor_90


title: adult_ART_Donor_166


title: adult_ART_Donor_87


title: adult_ART_Donor_88


title: adult_ART_Donor_165


title: adult_ART_Donor_86


title: adult_ART_Donor_85


title: adult_ART_Donor_81


title: adult_ART_Donor_164


title: adult_ART_Donor_84


title: adult_ART_Donor_80


title: adult_ART_Donor_104


title: adult_ART_Donor_79


title: adult_ART_Donor_78


title: adult_ART_Donor_77


title: adult_ART_Donor_163


title: adult_ART_Donor_74


title: adult_ART_Donor_75


title: adult_ART_Donor_72


title: adult_ART_Donor_76


title: adult_ART_Donor_68


title: adult_ART_Donor_67


title: adult_ART_Donor_161


title: adult_ART_Donor_66


title: adult_ART_Donor_71


title: adult_ART_Donor_64


title: adult_ART_Donor_62


title: adult_ART_Donor_160


title: adult_ART_Donor_61


title: adult_ART_Donor_70


title: adult_ART_Donor_63


title: adult_ART_Donor_65


title: adult_ART_Donor_83


title: adult_ART_Donor_56


title: adult_ART_Donor_58


title: adult_ART_Donor_162


title: adult_ART_Donor_54


title: adult_ART_Donor_53


title: adult_ART_Donor_57


title: adult_ART_Donor_60


title: adult_ART_Donor_52


title: adult_ART_Donor_51


title: adult_ART_Donor_159


title: adult_ART_Donor_50


title: adult_ART_Donor_49


title: adult_ART_Donor_48


title: adult_ART_Donor_59


title: adult_ART_Donor_46


title: adult_ART_Donor_45


title: adult_ART_Donor_157


title: adult_ART_Donor_158


title: adult_ART_Donor_40


title: adult_ART_Donor_43


title: adult_ART_Donor_41


title: adult_ART_Donor_44


title: adult_ART_Donor_39


title: adult_ART_Donor_34


title: adult_ART_Donor_37


title: adult_ART_Donor_35


title: adult_ART_Donor_55


title: adult_ART_Donor_33


title: adult_ART_Donor_32


title: adult_ART_Donor_31


title: adult_ART_Donor_30


title: adult_ART_Donor_29


title: adult_ART_Donor_25


title: adult_ART_Donor_26


title: adult_ART_Donor_156


title: adult_ART_Donor_47


title: adult_ART_Donor_23


title: adult_ART_Donor_24


title: adult_ART_Donor_22


title: adult_ART_Donor_42


title: adult_ART_Donor_21


title: adult_ART_Donor_20


title: adult_ART_Donor_18


title: adult_ART_Donor_36


title: adult_ART_Donor_155


title: adult_ART_Donor_19


title: adult_ART_Donor_14


title: adult_ART_Donor_153


title: adult_ART_Donor_15


title: adult_ART_Donor_154


title: adult_ART_Donor_152


title: adult_ART_Donor_16


title: adult_ART_Donor_10


title: adult_ART_Donor_13


title: adult_ART_Donor_8


title: adult_ART_Donor_151


title: adult_ART_Donor_27


title: adult_ART_Donor_9


title: adult_ART_Donor_150


title: adult_ART_Donor_6


title: adult_ART_Donor_3


title: adult_ART_Donor_5


title: adult_ART_Donor_4


title: neonate_non-ART_Donor_58

description: guthrie blood spot from naturally (non-ART) conceived individual

value: Guthrie blood spot

value: birth


title: neonate_non-ART_Donor_57


title: neonate_non-ART_Donor_54


title: neonate_non-ART_Donor_56


title: neonate_non-ART_Donor_55


title: neonate_non-ART_Donor_53


title: neonate_non-ART_Donor_52


title: neonate_non-ART_Donor_51


title: adult_ART_Donor_11

value: Whole blood


title: neonate_non-ART_Donor_45


title: neonate_non-ART_Donor_50


title: neonate_non-ART_Donor_48


title: neonate_non-ART_Donor_46


title: neonate_non-ART_Donor_44


title: neonate_non-ART_Donor_47


title: neonate_non-ART_Donor_42


title: neonate_non-ART_Donor_49


title: neonate_non-ART_Donor_43


title: neonate_non-ART_Donor_39


title: neonate_non-ART_Donor_38


title: neonate_non-ART_Donor_37


title: neonate_non-ART_Donor_36


title: neonate_non-ART_Donor_41


title: neonate_non-ART_Donor_40


title: neonate_non-ART_Donor_32


title: neonate_non-ART_Donor_30


title: neonate_non-ART_Donor_33


title: neonate_non-ART_Donor_29


title: neonate_non-ART_Donor_34


title: neonate_non-ART_Donor_35


title: neonate_non-ART_Donor_31


title: neonate_non-ART_Donor_26


title: neonate_non-ART_Donor_28


title: neonate_non-ART_Donor_27


title: neonate_non-ART_Donor_24


title: neonate_non-ART_Donor_25


title: neonate_non-ART_Donor_23


title: neonate_non-ART_Donor_22


title: neonate_non-ART_Donor_21


title: neonate_non-ART_Donor_20


title: neonate_non-ART_Donor_19


title: neonate_non-ART_Donor_12


title: neonate_non-ART_Donor_18


title: neonate_non-ART_Donor_10


title: neonate_non-ART_Donor_17


title: neonate_non-ART_Donor_13


title: neonate_non-ART_Donor_7


title: neonate_non-ART_Donor_5


title: neonate_non-ART_Donor_6


title: neonate_non-ART_Donor_2


title: neonate_non-ART_Donor_3


title: neonate_non-ART_Donor_9


title: neonate_ART_Donor_148

description: guthrie blood spot from ART conceived individual


title: neonate_ART_Donor_149


title: neonate_non-ART_Donor_1


title: neonate_non-ART_Donor_8


title: neonate_ART_Donor_146


title: neonate_ART_Donor_144


title: neonate_non-ART_Donor_16


title: neonate_non-ART_Donor_15


title: neonate_non-ART_Donor_14


title: neonate_ART_Donor_141


title: neonate_ART_Donor_140


title: neonate_non-ART_Donor_11


title: neonate_ART_Donor_139


title: neonate_ART_Donor_137


title: neonate_ART_Donor_138


title: neonate_ART_Donor_136


title: neonate_ART_Donor_135


title: neonate_ART_Donor_134


title: neonate_non-ART_Donor_4


title: neonate_ART_Donor_133


title: neonate_ART_Donor_131


title: neonate_ART_Donor_130


title: neonate_ART_Donor_128


title: neonate_ART_Donor_129


title: neonate_ART_Donor_145


title: neonate_ART_Donor_147


title: neonate_ART_Donor_132


title: neonate_ART_Donor_126


title: neonate_ART_Donor_127


title: neonate_ART_Donor_123


title: neonate_ART_Donor_122


title: neonate_ART_Donor_121


title: neonate_ART_Donor_125


title: neonate_ART_Donor_143


title: neonate_ART_Donor_120


title: neonate_ART_Donor_118


title: neonate_ART_Donor_117


title: neonate_ART_Donor_119


title: neonate_ART_Donor_115


title: neonate_ART_Donor_116


title: neonate_ART_Donor_114


title: neonate_ART_Donor_112


title: neonate_ART_Donor_113


title: neonate_ART_Donor_110


title: neonate_ART_Donor_111


title: neonate_ART_Donor_109


title: neonate_ART_Donor_108


title: neonate_ART_Donor_107


title: neonate_ART_Donor_124


title: neonate_ART_Donor_102


title: neonate_ART_Donor_101


title: neonate_ART_Donor_103


title: neonate_ART_Donor_99


title: neonate_ART_Donor_104


title: neonate_ART_Donor_100


title: neonate_ART_Donor_96


title: neonate_ART_Donor_97


title: neonate_ART_Donor_95


title: neonate_ART_Donor_94


title: neonate_ART_Donor_93


title: neonate_ART_Donor_92


title: neonate_ART_Donor_91


title: neonate_ART_Donor_90


title: neonate_ART_Donor_89


title: neonate_ART_Donor_87


title: neonate_ART_Donor_88


title: neonate_ART_Donor_85


title: neonate_ART_Donor_84


title: neonate_ART_Donor_83


title: neonate_ART_Donor_81


title: neonate_ART_Donor_79


title: neonate_ART_Donor_106


title: neonate_ART_Donor_105


title: neonate_ART_Donor_80


title: neonate_ART_Donor_98


title: neonate_ART_Donor_78


title: neonate_ART_Donor_77


title: neonate_ART_Donor_75


title: neonate_ART_Donor_74


title: neonate_ART_Donor_76


title: neonate_ART_Donor_73


title: neonate_ART_Donor_71


title: neonate_ART_Donor_69


title: neonate_ART_Donor_70


title: neonate_ART_Donor_68


title: neonate_ART_Donor_65


title: neonate_ART_Donor_66


title: neonate_ART_Donor_86


title: neonate_ART_Donor_67


title: neonate_ART_Donor_63


title: neonate_ART_Donor_64


title: neonate_ART_Donor_62


title: neonate_ART_Donor_61


title: neonate_ART_Donor_60


title: neonate_ART_Donor_82


title: neonate_ART_Donor_57


title: neonate_ART_Donor_54


title: neonate_ART_Donor_56


title: neonate_ART_Donor_55


title: neonate_ART_Donor_53


title: neonate_ART_Donor_72


title: neonate_ART_Donor_52


title: neonate_ART_Donor_51


title: neonate_ART_Donor_50


title: neonate_ART_Donor_49


title: neonate_ART_Donor_47


title: neonate_ART_Donor_46


title: neonate_ART_Donor_48


title: neonate_ART_Donor_45


title: neonate_ART_Donor_44


title: neonate_ART_Donor_43


title: neonate_ART_Donor_42


title: neonate_ART_Donor_41


title: neonate_ART_Donor_39


title: neonate_ART_Donor_40


title: neonate_ART_Donor_38


title: neonate_ART_Donor_59


title: neonate_ART_Donor_36


title: neonate_ART_Donor_58


title: neonate_ART_Donor_35


title: neonate_ART_Donor_34


title: neonate_ART_Donor_33


title: neonate_ART_Donor_37


title: neonate_ART_Donor_32


title: neonate_ART_Donor_28


title: neonate_ART_Donor_29


title: neonate_ART_Donor_26


title: neonate_ART_Donor_30


title: neonate_ART_Donor_24


title: neonate_ART_Donor_19


title: neonate_ART_Donor_23


title: neonate_ART_Donor_25


title: neonate_ART_Donor_21


title: neonate_ART_Donor_17


title: neonate_ART_Donor_20


title: neonate_ART_Donor_18


title: neonate_ART_Donor_15


title: neonate_ART_Donor_16


title: neonate_ART_Donor_14


title: neonate_ART_Donor_12


title: neonate_ART_Donor_13


title: neonate_ART_Donor_11


title: neonate_ART_Donor_9


title: neonate_ART_Donor_31


title: neonate_ART_Donor_7


title: neonate_ART_Donor_10


title: neonate_ART_Donor_8


title: neonate_ART_Donor_4


title: neonate_ART_Donor_27


title: neonate_ART_Donor_2


title: neonate_ART_Donor_1


title: neonate_ART_Donor_6


title: neonate_ART_Donor_3


title: neonate_ART_Donor_22


title: WT_act_rep3

status: Public on Jun 05 2019

city: Riverside

first: Fedor

last: Karginov

address: 900 University Ave

department: MCSB

institute: UC Riverside

data_processing:
reads were reverse-complemented
reads were aligned by tophat/bowtie2 to the hg38 genome build with gencode27 annotations with the following parameters: -g 1 --segment-length 25 -i 30 --no-novel-juncs
reads were annotated by gencode27 annotations
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text, log2 fold changes and false discovery rate values for differentially expressed genes in KOrest vs WTrest, KOact vs WTact, and WTact vs WTrest comparisons at fold change of 4 and FDR of 0.05

source_name: WT Jurkat cells

growth_protocol: Cells were cultured in RPMI1640 media with 10% FBS and 1x penicillin/streptomycin at 37 °C with 5% CO2

extract_protocol:
Total RNA from cell pellets was collected with RiboZol.
RNAseq libraries were produced using the NEBnext Ultra Directional RNA library prep kit

treatment_protocol: Cells at a density of 0.5 x 10^6 cells/mL were activated with 20 ng/mL PMA + 500 ng/mL ionomycin or left untreated for 24 hours

tag: cell line

value: Jurkat

tag: genotype

value: WT

tag: activation state

value: act

tag: replicate


title: HuRKO_act_rep2

source_name: HuRKO Jurkat cells

value: HuRKO


title: WT_act_rep2


title: HuRKO_rest_rep2

value: rest


title: HuRKO_rest_rep3


title: WT_rest_rep1


title: HuRKO_act_rep1


title: WT_rest_rep2


title: WT_act_rep1


title: HuRKO_act_rep3


title: neonate_ART_Donor_5


title: HuRKO_rest_rep1


title: PQ12

status: Public on May 06 2019

source_name: Q fever seropositive controls (QS)_PBMCs

growth_protocol: Monocytes were isolated from PBMCs with Percoll

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared using the KAPA HyperPrep Kit with RiboZero rRNA removal.

tag: donor id

tag: subject status

value: Q fever seropositive controls (QS)

value: Adult Human Peripheral Blood

value: Monocytes


title: PQ21

tag: cell type


title: PQ14


title: PQ17


title: PQ20


title: PQ15


title: PQ9


title: PQ4


title: PQ6


title: QFS19

source_name: Q Fever Fatigue Syndrom (QFS)_PBMCs

value: Q Fever Fatigue Syndrom (QFS)


title: PQ8


title: QFS18


title: QFS16


title: WT_rest_rep3


title: QFS11


title: neonate_ART_Donor_142

value: F

value: ART

value: GIFT


title: QFS12


title: QFS15


title: QFS10


title: QFS6


title: QFS7


title: CSF15

source_name: Chronic Fatigue Syndrome (FCS)_PBMCs

value: Chronic Fatigue Syndrome (FCS)


title: CFS19


title: CFS11


title: CFS8


title: QFS2


title: CFS12


title: CFS10


title: CFS5


title: HC22

source_name: Healthy control_PBMCs

value: Healthy control


title: HC24


title: CSF4


title: HC39


title: HC7


title: HC20


title: HC13


title: HC25


title: CFS2


title: CFS13


title: HC16


title: HC41


title: PBMC-Control-6

status: Public on May 01 2019

hyb_protocol: 750ng of labelled cRNA was hybridized overnight to Illumina Human HT-12 BeadChip arrays (Illumina Inc, San Diego, CA, USA), which contain more than 48,000 probes.

scan_protocol: The arrays were then washed, blocked, stained and scanned on an Illumina BeadStation 500 following the manufacturer's protocols. Illumina GenomeStudio software (Illumina Inc, San Diego, CA, USA) was used to generate signal intensity values from the scans.

data_processing: Differential gene expression analysis was performed using linear modeling with the Limma package. Gene set analysis was conducted using the QuSAGE algorithm, which tests whether the average log2-fold change of a gene set is different from 0 and takes into account the correlations of the genes by incorporating an estimate of the variance inflation factor of the gene set.

source_name: PBMC

label_protocol: Biotinylated, amplified antisense complementary RNA targets (cRNA) were then prepared from 200 - 250ng of the globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion, Austin, TX, USA).

extract_protocol: 3mls of whole blood was collected into Tempus tubes (Applied Biosystems, Foster City, CA, USA), vigorously mixed immediately after collection, and stored between −20°C and −80°C before RNA extraction. RNA was isolated from Training Set samples using 1.5mls whole blood and the PerfectPure RNA Blood kit (5 PRIME Inc, Gaithersburg, MD, USA). Test and Validation (SA) Set samples were extracted from 1ml of whole blood using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions. 2.5mg of isolated total RNA was then globin reduced using the GLOBINclear™ 96-well format kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer showing a quality of RIN of 7 – 9.5 (Agilent Technologies, Santa Clara, CA, USA). RNA yield was assessed using a Nanodrop 1000 spectrophotometer (NanoDrop Products, The rmo Fisher Scientific Inc, Wilmington, DE, USA).

tag: age

tag: condition

value: Control


title: PBMC-SLE-31

tag: ethnicity (country of origin if outside us)

value: Spanish (mother) and latin american (father)

value: SLE


title: PBMC-Control-1

value: Persian


title: PBMC-SLE-30

tag: race

value: Caucasian

value: Australia

tag: kindrec id


title: PBMC-Control-4


title: PBMC-Control-8

value: Middle Eastern / Iraqi


title: PBMC-Control-2

value: Australian (Anglo-Celtic)


title: PBMC-SLE-21

value: M


title: PBMC-SLE-22


title: PBMC-Control-7

value: White Australian / Anglo-Celtic


title: PBMC-SLE-20


title: PBMC-SLE-18

value: born in India - ethinicity unknown


title: PBMC-Control-3

value: Australian / UK


title: PBMC-SLE-27

value: F


title: PBMC-SLE-25


title: PBMC-SLE-28

value: Caucasian/Japanese

value: Father is Japanese, mother is Australian


title: PBMC-SLE-16


title: PBMC-SLE-14


title: PBMC-Control-5

value: Indian


title: PBMC-SLE-29


title: PBMC-Control-9

value: Australian (Irish / Scottish decent)


title: PBMC-SLE-26


title: PBMC-SLE-23


title: PBMC-SLE-17


title: PBMC-SLE-24


title: PBMC-SLE-13


title: PBMC-SLE-15

value: England


title: PBMC-SLE-19

value: Causcasian

value: England/Australia


title: THESCs-NTsi-2

status: Public on Apr 22 2019

description: THESC control siRNA exp.2

data_processing:
The pair-ended reads were mapped to the human genome using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference. STAR generated read count for each gene.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt file; 10 columns: 6 columns with counts (JY12130.Control.siRNA_1; JY12131.EGR1.siRNA_1; JY12132.Control.siRNA_2; JY12136.EGR1.siRNA_2; JY12134.Control.siRNA_3; JY12135.EGR1.siRNA_3) and 4 columns with gene descriptors (EntrezGene; symbol; Description; Description2)

source_name: T HESCs (ATCC CRL-4003)

growth_protocol: Plated 1x10^5 cells per well in 6-well format. 48 hours allowed for growth before siRNA transfection

extract_protocol:
RNeasy Plus kit (Qiagen Inc., Germantown, MD)
Libraries for mRNA sequencing were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) from 250 ng of RNA. Quality analysis of libraries was performed using Agilent 4200 TapeStation with D1000 ScreenTape assays (Agilent Technologies). Libraries were pooled and then quantified by two methods: 1) on a 2100 Bioanalyzer with DNA chips using High Sensitivity DNA Kit (Agilent Technologies); and 2) with KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: nontargeting vs. EGR1 siRNA transfection for 48 hours; cells were collected following 48h siRNA transfection

tag: sirna

value: nontargeting siRNA

tag: experiment number

value: experiment 2


title: THESCs-EGR1si-3

description: THESC EGR1 siRNA exp.3

value: EGR1 siRNA

value: experiment 3


title: THESCs-NTsi-3

description: THESC control siRNA exp.3


title: THESCs-EGR1si-1

description: THESC EGR1 siRNA exp.1

value: experiment 1


title: THESCs-NTsi-1

description: THESC control siRNA exp.1


title: THESCs-EGR1si-2

description: THESC EGR1 siRNA exp.2


title: whole_blood-SLE_P_NC_5-rep9

status: Public on Mar 22 2019

description:
9269325057_B
Early version of manifest, only 47,231 probes

scan_protocol: Scanned on an Illumina Beadstation 500

data_processing: Data was normalized using GenomeStudio's Global Average Normalization. Sample name is included in 'description' field. Two samples (whole blood_SLE+_<16 weeks_3 [9269325029_K], whole blood_SLE+_PP_8 [9269325029_J]) were processed separately and raw and processed data for these samples were included in separate files.

extract_protocol: Blood was collected in PAXgene tubes (Qiagen), immediately placed on ice and stored within 2-4 hours at -20°C until further analyses in batches. RNA was extracted, amplified, quantified and globin reduced according to manufacturer’s instructions.

tag: tissue

value: whole blood

value: PP

tag: gender

value: Female

value: As

tag: ethnicity

value: Not Hispanic or Latino

tag: sle

tag: apl

tag: lac

tag: tp

tag: pe

tag: fd

tag: nnd

tag: iugr

tag: sga

tag: batch


title: whole_blood-SLE_P_NC_5-rep2

description:
9269325029_D
Early version of manifest, only 47,231 probes

tag: age

tag: race

value: C


title: whole_blood-SLE_P_NC_5-rep6

description:
9269325035_E
Early version of manifest, only 47,231 probes

value: H


title: whole_blood-SLE_P_NC_5-rep22

description:
9339657017_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep18

description:
9339657010_G
Early version of manifest, only 47,231 probes


title: PBMC-SLE-1

value: F

value: Filipino

tag: ethnicity (country of origin if outside us)

value: Philipines

tag: kindrec id

tag: condition

value: SLE


title: whole_blood-SLE_P_NC_5-rep14

description:
9270006096_D
Early version of manifest, only 47,231 probes

tag: tissue

tag: gender


title: whole_blood-SLE_P_NC_5-rep24

description:
9339657019_J
Early version of manifest, only 47,231 probes

tag: ethnicity

tag: sle


title: whole_blood-SLE_P_NC_5-rep17

description:
9339657006_A
Early version of manifest, only 47,231 probes

tag: apl

tag: lac


title: whole_blood-SLE_P_NC_5-rep8

description:
9269325036_B
Early version of manifest, only 47,231 probes

value: Hispanic or Latino

tag: tp

tag: pe


title: PBMC-SLE-6

value: M

value: Caucasian

value: Egypt


title: PBMC-SLE-10

value: Australia


title: PBMC-SLE-11


title: PBMC-SLE-7


title: PBMC-SLE-5


title: PBMC-SLE-2


title: PBMC-SLE-8


title: PBMC-SLE-3

value: mat grandparents Filipino


title: PBMC-SLE-12


title: whole_blood-SLE_P_NC_5-rep13

description:
9270006084_I
Early version of manifest, only 47,231 probes

value: whole blood

tag: fd

tag: nnd


title: whole_blood-SLE_P_NC_5-rep4

description:
9269325031_B
Early version of manifest, only 47,231 probes

value: PP

tag: iugr

tag: sga


title: PBMC-SLE-9

tag: age


title: whole_blood-SLE_P_NC_5-rep15

description:
9271668036_D
Early version of manifest, only 47,231 probes

value: Female

tag: race

value: AA

tag: batch


title: whole_blood-SLE_P_NC_5-rep11

description:
9269325078_K
Early version of manifest, only 47,231 probes

value: Not Hispanic or Latino


title: whole_blood-SLE_P_NC_5-rep7

description:
9269325035_G
Early version of manifest, only 47,231 probes

value: C


title: whole_blood-SLE_P_NC_5-rep23

description:
9339657019_B
Early version of manifest, only 47,231 probes

value: As


title: whole_blood-SLE_P_NC_5-rep25

description:
9339657020_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep21

description:
9339657015_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep16

description:
9339657003_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep1

description:
9269325025_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep10

description:
9269325078_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep20

description:
9339657015_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep19

description:
9339657015_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep12

description:
9269325097_E
Early version of manifest, only 47,231 probes

value: 8.6 WPP


title: whole_blood-SLE_P_NC_5-rep5

description:
9269325031_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_5-rep3

description:
9269325030_G
Early version of manifest, only 47,231 probes


title: PBMC-SLE-4

value: Filipino

tag: ethnicity (country of origin if outside us)

tag: kindrec id


title: whole_blood-SLE_P_NC_4-rep19

description:
9270006067_K
Early version of manifest, only 47,231 probes

tag: tissue

value: 32-40 weeks


title: whole_blood-SLE_P_NC_4-rep9

description:
9269325057_K
Early version of manifest, only 47,231 probes

tag: gender


title: whole_blood-SLE_P_NC_4-rep39

description:
9339657017_E
Early version of manifest, only 47,231 probes

tag: ethnicity


title: whole_blood-SLE_P_NC_4-rep20

description:
9270006067_L
Early version of manifest, only 47,231 probes

value: H

tag: sle


title: whole_blood-SLE_P_NC_4-rep12

description:
9269325078_E
Early version of manifest, only 47,231 probes

tag: apl


title: whole_blood-SLE_P_NC_4-rep4

description:
9269325034_C
Early version of manifest, only 47,231 probes

tag: lac


title: whole_blood-SLE_P_NC_4-rep31

description:
9339657010_D
Early version of manifest, only 47,231 probes

tag: tp


title: whole_blood-SLE_P_NC_4-rep6

description:
9269325036_L
Early version of manifest, only 47,231 probes

tag: pe


title: whole_blood-SLE_P_NC_4-rep5

description:
9269325034_K
Early version of manifest, only 47,231 probes

tag: fd


title: whole_blood-SLE_P_NC_4-rep36

description:
9339657013_G
Early version of manifest, only 47,231 probes

tag: nnd


title: whole_blood-SLE_P_NC_4-rep2

description:
9269325025_G
Early version of manifest, only 47,231 probes

tag: iugr


title: HC19

tag: donor id

tag: subject status

value: Healthy control

value: Adult Human Peripheral Blood

tag: cell type

value: Monocytes


title: whole_blood-SLE_P_NC_4-rep8

description:
9269325057_I
Early version of manifest, only 47,231 probes

tag: age

tag: race

value: Hispanic or Latino

tag: sga

tag: batch


title: whole_blood-SLE_P_NC_4-rep41

description:
9339657018_G
Early version of manifest, only 47,231 probes

tag: tissue

tag: gender


title: whole_blood-SLE_P_NC_4-rep18

description:
9270006067_E
Early version of manifest, only 47,231 probes

tag: ethnicity

tag: sle


title: whole_blood-SLE_P_NC_4-rep38

description:
9339657016_B
Early version of manifest, only 47,231 probes

tag: apl

tag: lac


title: whole_blood-SLE_P_NC_4-rep13

description:
9269325082_L
Early version of manifest, only 47,231 probes

tag: tp

tag: pe


title: whole_blood-SLE_P_NC_4-rep25

description:
9339657002_F
Early version of manifest, only 47,231 probes

tag: fd

tag: nnd


title: whole_blood-SLE_P_NC_4-rep33

description:
9339657012_I
Early version of manifest, only 47,231 probes

tag: iugr


title: whole_blood-SLE_P_NC_4-rep15

description:
9270006058_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep1

description:
9269325021_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep42

description:
9339657019_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep34

description:
9339657013_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep37

description:
9339657015_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep14

description:
9269325097_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep28

description:
9339657009_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep7

description:
9269325038_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep26

description:
9339657002_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep21

description:
9270006076_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep40

description:
9339657018_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep3

description:
9269325031_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep29

description:
9339657009_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep11

description:
9269325067_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep27

description:
9339657006_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep10

description:
9269325057_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep22

description:
9270006096_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep16

description:
9270006058_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep35

description:
9339657013_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep30

description:
9339657010_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep23

description:
9270006096_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep17

description:
9270006063_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep32

description:
9339657012_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep21

description:
9269325048_B
Early version of manifest, only 47,231 probes

value: 24-31 weeks


title: whole_blood-SLE_P_NC_3-rep32

description:
9270006084_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep36

description:
9339657008_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep15

description:
9269325039_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep34

description:
9270006096_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep38

description:
9339657010_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep11

description:
9269325036_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep19

description:
9269325041_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep5

description:
9269325029_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep25

description:
9269325082_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep42

description:
9339657017_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep7

description:
9269325031_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep29

description:
9270006076_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_4-rep24

description:
9271668036_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep6

description:
9269325030_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep17

description:
9269325041_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep44

description:
9339657021_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep40

description:
9339657016_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep9

description:
9269325035_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep33

description:
9270006096_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep23

description:
9269325078_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep1

description:
9269325023_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep22

description:
9269325061_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep8

description:
9269325034_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep20

description:
9269325043_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep35

description:
9339657006_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep37

description:
9339657009_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep4

description:
9269325025_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep12

description:
9269325037_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep10

description:
9269325036_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep24

description:
9269325082_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep28

description:
9270006067_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep41

description:
9339657016_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep39

description:
9339657010_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep43

description:
9339657020_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep13

description:
9269325037_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep16

description:
9269325041_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep14

description:
9269325039_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep3

description:
9269325023_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep27

description:
9270006058_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep26

description:
9269325091_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep30

description:
9270006076_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep31

description:
9270006076_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep24

description:
9339657002_D
Early version of manifest, only 47,231 probes

value: 16-23 weeks


title: whole_blood-SLE_P_NC_2-rep4

description:
9269325023_E
Early version of manifest, only 47,231 probes

value: whole blood


title: whole_blood-SLE_P_NC_2-rep34

description:
9339657012_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep18

description:
9269325041_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep3

description:
9269325021_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep38

description:
9339657021_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep27

description:
9339657006_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep8

description:
9269325038_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_3-rep2

description:
9269325023_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep6

description:
9269325030_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep26

description:
9339657003_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep13

description:
9269325091_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep29

description:
9339657008_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep16

description:
9270006063_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep25

description:
9339657002_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep35

description:
9339657019_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep2

description:
9269325021_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep32

description:
9339657012_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep33

description:
9339657012_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep28

description:
9339657006_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep9

description:
9269325039_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep37

description:
9339657020_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep39

description:
9339657021_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep1

description:
9269325021_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep20

description:
9270006084_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep17

description:
9270006063_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep15

description:
9270006058_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep18

description:
9270006067_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep14

description:
9269325097_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep36

description:
9339657019_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep11

description:
9269325067_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep19

description:
9270006076_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep21

description:
9270006096_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep7

description:
9269325033_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep12

description:
9269325091_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep5

description:
9269325029_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep11

description:
9269325038_L
Early version of manifest, only 47,231 probes

value: <16 weeks


title: whole_blood-SLE_P_NC_1-rep2

description:
9269325025_B
Early version of manifest, only 47,231 probes

value: Female


title: whole_blood-SLE_P_NC_1-rep15

description:
9269325067_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep5

description:
9269325033_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep18

description:
9269325082_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep23

description:
9339657002_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep10

description:
9269325044_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep22

description:
9271668022_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep31

description:
9339657009_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep28

description:
9339657003_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep7

description:
9269325034_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep24

description:
9270006076_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep19

description:
9269325082_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep22

description:
9270006058_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep14

description:
9269325043_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep39

description:
9339657018_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep35

description:
9339657014_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep26

description:
9339657002_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep6

description:
9269325034_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep45

description:
9339657021_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep3

description:
9269325030_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep12

description:
9269325039_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_2-rep30

description:
9339657009_I
Early version of manifest, only 47,231 probes

value: AA


title: whole_blood-SLE_P_NC_1-rep8

description:
9269325035_C
Early version of manifest, only 47,231 probes

value: Not Hispanic or Latino


title: whole_blood-SLE_P_NC_1-rep36

description:
9339657014_H
Early version of manifest, only 47,231 probes

value: C


title: whole_blood-SLE_P_NC_1-rep31

description:
9339657008_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep43

description:
9339657021_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep33

description:
9339657012_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep44

description:
9339657021_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep34

description:
9339657013_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep10

description:
9269325037_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep38

description:
9339657017_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep25

description:
9271668022_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep9

description:
9269325035_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep23

description:
9270006067_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep27

description:
9339657003_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep30

description:
9339657006_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep13

description:
9269325039_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep37

description:
9339657017_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep17

description:
9269325078_L
Early version of manifest, only 47,231 probes