title: 215025_45

description: CD45+ cells separated with anti-CD45 magnetic beads.

source_name: duodenum biopsy, leukocytes, celiac disease

tag: cell type

value: Leukocytes


title: 211086

status: Public on Feb 04 2019

type: genomic

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

description: Complete biopsy.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan with standard recommended Illumina scanner settings.

data_processing: GenomeStudio v2011.1 and R/Bioconductor packages

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: duodenum biopsy, complete, control

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Nucleic acids from all samples were isolated with AllPrep DNA/RNA microkit (Qiagen, Hilden, Germany, Cat No 80284).

treatment_protocol: Not applicable

tag: disease status

value: Non-celiac disease

tag: tissue

value: Duodenum

tag: sample type

value: Control

tag: individual identifier


title: iI44

type: SRA

city: Palo Alto

first: Wu

last: Wei

state: CA

address: 3165 Porter Dr.

country: USA

institute: Stanford Genome Technology Center

description:
FACS sorted
normExpression_YPD_NatMicro.tab.gz

library_source: transcriptomic

data_processing:
For 5’ cap sequencing reads, random barcodes were first extracted and added to the reads name. The reads were aligned to yeast genome  with Novoalign (http://www.novocraft.com) using default setting.
Reads with multiple alignments, or mapping quality <30, or carrying soft-clipped bases on the 5’ end were excluded from downstream analysis
5' end of reads passing quality filtering were extracted; total number of reads per genome location were calculated; total unique number of reads (or unique molecule, based on random barcode sequences) per genome location were calculated
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3), downloaded from SGD(http://www.yeastgenome.org/).
Supplementary_files_format_and_content: Table for normalized express value per gene per cell

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae single cell

growth_protocol: In short, BY4741 or YJM789 were pre-grown in rich media overnight. The next morning cells were diluted to OD(660) 0.05 and grown for at least two full divisions before sorting. Prior to sorting cells were diluted at a final OD of 0.01 and briefly sonicated for 3 pulses 0.5 seconds to remove aggregates (Sonicator Branson M1800).

extract_protocol:
Cell lysis buffer was added into each well and lysis was performed for 10 minutes at 37ºC followed by 3 minutes at 72ºC
Library preparation has performed using in-house protocol (explained details in the method section)
Single-cell RNA seq

tag: strain

tag: growth media

value: YPD

tag: external control

value: ERCC


title: 27028

description: Complete biopsy.

source_name: duodenum biopsy, complete, celiac disease

value: Celiac Disease


title: iI40


title: 28039

description: Complete biopsy.


title: iI45


title: 215021_326

description: CD326+ cells separated with anti-CD326 magnetic beads.

source_name: duodenum biopsy, epithelium, celiac disease

value: Epithelium


title: iI41


title: 215021_45


title: 214108_45


title: 211075

description: Complete biopsy.


title: iI38


title: 214113_45

source_name: duodenum biopsy, leukocytes, control


title: 214113_326

source_name: duodenum biopsy, epithelium, control


title: 214114_45


title: 214112_45


title: iI34


title: iI39


title: 214108_326


title: iI37


title: 214105_45


title: iI33


title: iI32


title: 215026_45


title: 214105_326


title: iI30


title: iI28


title: 214102_326


title: 214114_326


title: 214110_326


title: 214112_326


title: iI25


title: iI20


title: TUMOR_68052

city: Los Angeles

first: Julie

middle: E

last: Lang

address: 1510 San Pablo Street, Suite 412

department: Deparment of Surgery

institute: University of Southern California

data_processing:
Fastq files have been created using bcl2fastq-1.8.3 from Illumina
Trimmomatic ver. 0.36. was used to remove adaptor sequences and to trim the reads based on quality, using the following parameters: ILLUMINACLIP:my_TrueSeq_list.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 The file my_TrueSeq_list.fa contains the adaptor sequences, and it is different from the default file provided by Trimmomatic. Available upon request.
Reads were aligned to the human genome ver. GRCh38.p7 using STAR 2.5.0a, with the only additional option: --chimSegmentMin 20
Read counts for every feature in the genome were obtained by adding --quantMode GeneCounts to the STAR 2.5.0a command line, and using the gencode.v25.annotation.gtf file
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Text files with read counts for features as described above

source_name: formalin-fixed, paraffin embedded primary tumor

extract_protocol:
Blood: 200μL of PB was placed in 600μL of RNAlater then later RNA was extracted with the QIAamp RNA Blood Mini Kit (QIAGEN, Hilden, Germany), CTC were sorted into Prelude Direct Lysis Module (NuGEN, San Carlos, CA). Tumors: RNeasy FFPE kit (QIAGEN)
Blood: NuGEN Ovation RNA System V2, CTC: the Ovation Single Cell RNA-Seq System (NuGEN); Tumors: NuGEN Ultra Low Library System V2.
RNA-Seq with poly-A isolation

treatment_protocol: Not applicable. All samples were prior to treatment.

tag: individual id

tag: disease state

value: female Stage II-III breast cancer


title: 214089_45


title: iI27


title: iI26


title: iI22


title: TUMOR_78322

value: formalin-fixed, paraffin embedded primary tumor


title: TUMOR_78858


title: TUMOR_47934


title: 214103_326


title: 214107_45


title: iI18


title: TUMOR_37289


title: iI19


title: 214064_326


title: iI17


title: TUMOR_36828


title: iI16


title: TUMOR_36683


title: 214089_326


title: iI15


title: 214110_45


title: ovarian grafts at 20d, biological rep1

type: RNA

city: Tokyo

first: Kento

last: Miura

address: Yayoi 1-1-1, Bunkyo-ku

department: Veterinary Anatomy

country: Japan

institute: The University of Tokyo

description: Gene expression data from ovarian grafts at day 20 post-transplantation

hyb_protocol: 11mg of amplified biotin-RNA were fragmented and hybridized to each array 16 hours at 45°C in a rotating hybridization. Chips were washed and stained with streptavidin/phycoerythrin in Fluidics Station 450 (Affymetrix) following protocol FS450_0001.

scan_protocol: Chips were scanned using GeneChip scanner 3000 (Affymetrix).

data_processing: Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages.  the Robust Multi Array (RMA) method from the BioConductor software was used for background correction and normalization of the DNA microarray data.

label: biotin

organism: Mus musculus

source_name: ovarian grafted into male host mice at day 20 post-transplantation

label_protocol: 100ng of purified total RNA was amplified and labelled with biotin as directed in GeneChip 3’ IVT Express kit or GeneChip 3’ IVT PLUS Reagent kit manual (Affymetrix).

extract_protocol: Total RNA of all samples was purified by NucleoSpin RNA XS kit (Macherey-Nagel).

value: ovary

value: ICR

tag: trasnplantation period

value: 20 days


title: 214027_326


title: 214102_45


title: ovarian grafts at 20d, biological rep2


title: ovarian grafts at 15d

description: Gene expression data from ovarian grafts at day 15 post-transplantation

source_name: ovarian grafted into male host mice at day 15 post-transplantation

value: 15 days


title: ovarian grafts at 10d, biological rep2

description: Gene expression data from ovarian grafts at day 10 post-transplantation

source_name: ovarian grafted into male host mice at day 10 post-transplantation

value: 10 days


title: 214065_326


title: TUMOR_36581


title: 214107_326


title: ovarian grafts at 10d, biological rep1


title: 214064_45


title: SG063-0 root on sufficient N, biological rep 3

city: Seeland

first: Rhonda

middle: C

last: Meyer

address: Corrensstrasse 3

department: Molecular Genetics

country: Germany

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

hyb_protocol: Performed by Atlas Biolabs, Berlin, Germany, according to Affymetrix standard protocols. Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with wash protocol EukGEWS2v4_450

scan_protocol: Performed by Atlas Biolabs, Berlin, Germany, according to Affymetrix standard protocols. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with R/Bioconductor using the R packages affy, limma, simpleaffy, and affyPLM. Quality was controlled using fitPLM (affyPLM package) and qc (simpleaffy package). Data was normalized with GC-RMA algorithm (affy package). Differential expression was detected by fitting linear models using lmFit (limma package) to the contrasts between plus and minus nitrogen samples. Resulting p-values were controlled for multiple error correction using false discovery rate (FDR).

organism: Arabidopsis thaliana

source_name: Arabidopsis root after 21 days growth on 9 mM nitrate

label_protocol:
Performed by Atlas Biolabs, Berlin, Germany, according to Affymetrix standard protocols.
Biotinylated cRNA were prepared with the MessageAmpII-96 aRNA Kit (Ambion, Cat-No. 1819 / Manual Version: 0511) from 1 ug total RNA

growth_protocol: Plants were grown in vertical square petri dishes (120 x 120 x 17 mm). The medium was based on Estelle and Somerville mineral solutions (Molecular & General Genetics 1987, 206:200-206) supplemented with 8% agar and 1% sucrose. 6 seeds were regularly spaced 1 cm from the upper border of the dish. Seeds were stratified for 24 h at 4°C, then transferred to a growth cabinet set to 16 h light (100 µmol PAR m-2 s-1) / 8 h dark, 20° / 18 °C for 21 days.

extract_protocol: Total RNA was isolated using the adapted hot-borate method (Wan & Wilkins, Analytical Biochemistry 1994, 223:7-12)

treatment_protocol: The control medium (9 mM nitrate) contained 5 mM KNO3 and 2 mM Ca(NO3)2, the low nitrogen medium (0.4 mM nitrate) contained 0.2 mM Ca(NO3)2 and 5 mM KCl.

value: root

tag: treatment

value: 9 mM nitrate

tag: genotype

value: RIL SG063 (Sorbo x Gy-0)

tag: age

value: 21 days after sowing

tag: culture

value: synthetic agar medium with 1% sucrose


title: 214053_326

value: Duodenum


title: TUMOR_37232


title: iI13

value: YPD


title: TUMOR_36515


title: SG063-0 root on sufficient N, biological rep 2


title: 214053_45

value: Leukocytes


title: iI14

value: ERCC


title: 214103_45

value: Celiac Disease


title: 214027_45

value: Non-celiac disease

value: Control


title: TUMOR_36285

value: female Stage II-III breast cancer

value: formalin-fixed, paraffin embedded primary tumor


title: 214047_45


title: 214052_45

source_name: duodenum biopsy, leukocytes, potential celiac disease

value: Potential celiac disease


title: iI6


title: TUMOR_31176


title: 214047_326

value: Epithelium


title: 214032_45


title: CTC_78956

source_name: circulating tumor cells sorted from peripheral blood


title: 214032_326


title: SG063-0 root on sufficient N, biological rep 1


title: iI5


title: CTC_78858

value: circulating tumor cells sorted from peripheral blood


title: iI3


title: SCCOHT1_100

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
Sequencing reads were mapped to reference human genome sequence (hg19) downloaded from Illumina iGenomes using STAR57 (version 2.4.2. --quantMode)
The number of fragments was counted with HTSeq58 (version 0.6.1p1)  based on known gene from RefSeq database on UCSC Genome Browser.
Differentially expressed gene (DEG) analysis was performed using DESeq2 (v 1.16.1) bioconductor R package.
Genome_build: hg19
Supplementary_files_format_and_content: Comma seperated values including raw counts

source_name: SCCOHT Cell line

growth_protocol: BIN-67 and SCCOHT-1 cells were all cultured in RPMI with 7% fetal bovine serum (FBS), 1% penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For CDK6 knockdown, cells were infected with control vector pLKO and two shRNAs targeting CDK6 for 8 hours followed by puromycin selection for 2 days before harvesting. For palbociclib treatment, cells were cultured in the presence of 0 or 100 nM palbociclib for 24 hours before harvesting.

value: Cancer cells

value: 100 nM palbociclib


title: CTC_78486


title: iI2


title: SCCOHT1_0

value: 0 nM palbociclib


title: iI9


title: iH91


title: CTC_68052


title: SG063-0 root on low N, biological rep 3

source_name: Arabidopsis root after 21 days growth on 0.4 mM nitrate

value: root

value: 0.4 mM nitrate

value: RIL SG063 (Sorbo x Gy-0)

value: 21 days after sowing


title: BIN67_0


title: CTC_78322


title: iI1

value: YPD


title: CTC_37289


title: SG063-0 root on low N, biological rep 1

value: synthetic agar medium with 1% sucrose


title: SG063-0 root on low N, biological rep 2


title: iH81

value: ERCC


title: 214065_45

value: Celiac Disease

value: Duodenum

value: Leukocytes


title: ovarian grafts at 4d

description: Gene expression data from ovarian grafts at day 4 post-transplantation

source_name: ovaries grafted into male host mice at day 4 post-transplantation

value: ovary

value: ICR

value: 4 days


title: SG063-0 shoot on sufficient N, biological rep 2

source_name: Arabidopsis shoot after 21 days growth on 9 mM nitrate

value: shoot

value: 9 mM nitrate


title: ovarian grafts at 7d

description: Gene expression data from ovarian grafts at day 7 post-transplantation

source_name: ovarian grafted into male host mice at day 7 post-transplantation

value: 7 days


title: CTC_36515

value: female Stage II-III breast cancer

value: circulating tumor cells sorted from peripheral blood


title: CTC_37232


title: iH76

source_name: Saccharomyces cerevisiae single cell


title: SG063-0 shoot on sufficient N, biological rep 3


title: E13.0 ovaries at 0d, biological rep2

description: Gene expression data from E13.0 ovaries before transplantation

source_name: E13.0 ovaries before transplantation (at day 0 post-transplantation)

value: before transplantation (0 day)


title: CTC_36285


title: iH74


title: CTC_31176


title: iH70


title: BIN67_pLKO

value: Cancer cells

value: pLKO


title: CTC_68172


title: iH77

value: YPD


title: E13.0 ovaries at 0d, biological rep1


title: SG063-0 shoot on low N, biological rep 3

source_name: Arabidopsis shoot after 21 days growth on 0.4 mM nitrate

value: 0.4 mM nitrate

value: RIL SG063 (Sorbo x Gy-0)

value: 21 days after sowing

value: synthetic agar medium with 1% sucrose


title: SG063-0 shoot on low N, biological rep 1


title: NG087-0 root on sufficient N, biological rep 3

value: root

value: RIL NG087 (Nok-3 x Ga-0)


title: NG087-0 root on sufficient N, biological rep 2


title: CTC_58029


title: CTC_47934


title: iH65

value: ERCC


title: High dose (0.2mg/kg) DXR treated

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

library_source: genomic

data_processing:
Sequence data were mapped on the mouse genome (mm10) using CLC Genomics Workbench v8.
Methylation region report calculated with Strand NGS software (Strand Life Sciences) and region list was annotated to near genes (within 2kbp).
Genome_build: mm10
Supplementary_files_format_and_content: A tabbular file containing information about methylation score (Vehicle control: "Control", Low dose (0.02mg/kg) DXR treated: "Low", High dose (0.2mg/kg) DXR treated: "High" )

source_name: Sperm

growth_protocol: The cauda epididymides were collected from each group of mice and sperms were purified to extract genomic DNA for MBD2 mediated enrichment.

extract_protocol:
Genomic DNA was extracted using phenol/chloroform method. Extracted DNA was sonicated with Picoruptor (Diagenode, Seraing, Belgium) to obtain ~300 bp fragments. MBD2-mediated enrichment of methylated DNA was performed using the methylated DNA enrichment kit, EpiXplore (TAKARA, Japan) according to the manufacturer’s instructions.
MBD-Seq libraries were prepared using QIAseq Ultralow Input Library Kit (Qiagen) according to the manufacturer’s instructions and validated for an average size of about 300-700 bp using a TapeStation and the Agilent High Sensitivity D1000 ScreenTape kit.

treatment_protocol: From 8 to 13 weeks of age, doxorubicin and saline were intraperitoneally administered twice weekly for 5 weeks. Four days after the final dose, animals were anesthetized, sacrificed, and used subsequent experiments.

value: Sperm

value: 14 weeks old

value: High dose (0.2mg/kg) DXR


title: iH66


title: NG087-0 root on sufficient N, biological rep 1

value: 9 mM nitrate


title: NG087-0 root on low N, biological rep 3


title: CTC_36828

value: female Stage II-III breast cancer


title: iH64


title: Vehicle control

value: vehicle control


title: NG087-0 root on low N, biological rep 2


title: iH67


title: CTC_36683

value: circulating tumor cells sorted from peripheral blood


title: iH63


title: BLOOD_68172

source_name: peripheral blood

value: healthy female

value: peripheral blood


title: 214052_326

source_name: duodenum biopsy, epithelium, potential celiac disease

value: Potential celiac disease

value: Duodenum

value: Epithelium


title: NG087-0 shoot on sufficient N, biological rep 3

value: shoot

value: 21 days after sowing


title: NG087-0 root on low N, biological rep 1

value: root

value: 0.4 mM nitrate

value: synthetic agar medium with 1% sucrose


title: Low dose (0.02mg/kg) DXR treated

value: Sperm

value: Low dose (0.02mg/kg) DXR


title: iH60

value: YPD

value: ERCC


title: BLOOD_47934


title: iH61


title: BLOOD_36828


title: BLOOD_58029


title: iH58


title: iH59


title: BLOOD_36683


title: iH62


title: BLOOD_36581


title: NG087-0 shoot on sufficient N, biological rep 1

value: 9 mM nitrate

value: RIL NG087 (Nok-3 x Ga-0)


title: iH57


title: NG087-0 shoot on low N, biological rep 3


title: iH55


title: SG063-0 shoot on sufficient N, biological rep 1

value: RIL SG063 (Sorbo x Gy-0)


title: CTC_36581

value: female Stage II-III breast cancer

value: circulating tumor cells sorted from peripheral blood


title: NG087-0 shoot on sufficient N, biological rep 2


title: iH54


title: NG087-0 shoot on low N, biological rep 2


title: NG064-0 root on sufficient N, biological rep 3

value: RIL NG064 (Nok-3 x Ga-0)


title: iH53


title: 3-022-01

city: Stanford

first: Purvesh

last: Khatri

address: 279 Campus Dr., Beckman B235A

department: Medicine

institute: Stanford University

description: Dengue score was calcluated by subtracting the geometric mean of the underexpressed genes from the geometric mean of the overexpressed genes

data_processing: For the normalization the housekeeping gene ACTB was used

source_name: whole blood from healthy control

label_protocol: Biomark microfluidic qRT-PCR array

extract_protocol: Total RNA was extracted with a Paxgene RNA extraction kit

value: whole blood from healthy control

tag: donor

value: healthy

tag: sample

tag: pos

tag: neg

tag: score


title: 3-021-01

tag: tissue


title: 3-023-01


title: iH52


title: 3-020-01


title: iH51


title: NG064-0 root on sufficient N, biological rep 1


title: iH50


title: 3-019-01


title: iH49


title: 3-018-01


title: 3-024-01


title: NG064-0 root on low N, biological rep 2


title: NG064-0 root on low N, biological rep 1


title: NG064-0 root on low N, biological rep 3


title: NG064-0 shoot on sufficient N, biological rep 2

value: shoot


title: iH48


title: 3-016-01


title: 3-017-01


title: iH43


title: iH42


title: NG064-0 shoot on sufficient N, biological rep 3

value: 21 days after sowing


title: NG087-0 shoot on low N, biological rep 1


title: 3-015-01


title: 3-012-01


title: 3-011-01


title: iH40


title: NG064-0 root on sufficient N, biological rep 2

value: root


title: NG064-0 shoot on low N, biological rep 1

value: 0.4 mM nitrate


title: NG064-0 shoot on low N, biological rep 2

value: synthetic agar medium with 1% sucrose


title: 3-013-01


title: iH47


title: KB006-0 root on sufficient N, biological rep 3

value: RIL KB006 (Kondara x Br-0)


title: 3-010-01


title: NG064-0 shoot on low N, biological rep 3


title: iH44


title: 3-014-01


title: 3-009-01


title: KB006-0 root on low N, biological rep 3


title: NG064-0 shoot on sufficient N, biological rep 1


title: iH36


title: 3-008-01


title: KB006-0 root on low N, biological rep 2


title: KB006-0 root on sufficient N, biological rep 2


title: iH35


title: 3-007-01


title: KB006-0 root on sufficient N, biological rep 1


title: KB006-0 root on low N, biological rep 1


title: iH32


title: SG063-0 shoot on low N, biological rep 2


title: iH38


title: 3-005-01


title: KB006-0 shoot on sufficient N, biological rep 3


title: iH34


title: iH30


title: iH29


title: 1-041-1

source_name: whole blood from dengue infected patient

value: D

value: DF


title: 3-004-01


title: iH37

value: YPD

value: ERCC


title: KB006-0 shoot on sufficient N, biological rep 1

value: 9 mM nitrate


title: KB006-0 shoot on sufficient N, biological rep 2


title: KB006-0 shoot on low N, biological rep 3


title: 1-039-1

value: whole blood from dengue infected patient

value: DWS


title: 1-040-1


title: 3-006-01


title: iH27


title: iH31


title: 1-038-1


title: iH24


title: iH25


title: 14SC_B_lane 1

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Samples were analyzed on 2 lanes of Illumina HiSeq 2500 in rapid run mode.
The reads were mapped to the mouse transcriptome (mm10) using STAR and the influenza genome using Bowtie and samples were run on Basespace (Illumina).
Mapped reads were analyzed using DeSeq2 in R. First, technical duplicates across lanes were collapsed by summing them together.
The library was then normalized using the DeSeq2 function and fold-change and Wald test p-values were calculated and corrected using the Benjamini-Hochberg procedure for sample comparisons.
Supplementary_files_format_and_content: Mapped reads, normalized reads

molecule: polyA RNA

source_name: 14SC_whole lung

extract_protocol:
Cells were sorted by a FACS DIVA and RNA collected using Rneasy Mini kit (74104). Samples were then prepped using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E74905).
NEBNext Ultra II RNA Library Prep Kit (E7770S) was used to prep libraries with NEBNext Multiplex Oligos for Illumina (E7335S, E7500S) for adaptor ligation and enrichment of libraries

treatment_protocol: Mice were infected at the indicated timepoints and collected

value: C57BL/6 transgenic line; 'tdTomato transgenic mice' (Jax catalog # 007914)

tag: infected with

value: influenza B virus

tag: time point

value: direct viral infection (14 DPI Survivor Cell)

value: whole lung

tag: cell type

value: lung ciliated cells


title: 2DPI_B_lane 2

source_name: 2DPI_whole lung

tag: strain

value: during active infection (2 DPI)


title: 14DPI_B_lane 2

source_name: 14DPI_whole lung

value: at 14 days post-infection that had never been infected (14 DPI).


title: 1-037-1

value: exclude


title: KB006-0 shoot on low N, biological rep 2

value: shoot

value: 0.4 mM nitrate

value: 21 days after sowing

value: synthetic agar medium with 1% sucrose


title: iH28

tag: growth media

value: YPD

tag: external control


title: 1-036-3

value: SD

value: DF


title: 1-036-2

value: whole blood from dengue infected patient


title: iH22

value: ERCC


title: 2DPI_B_lane 1

value: C57BL/6 transgenic line; 'tdTomato transgenic mice' (Jax catalog # 007914)


title: Fei-0 root on sufficient N, biological rep 2

source_name: Arabidopsis root after 21 days growth on 9 mM nitrate

value: root

value: 9 mM nitrate

value: accession Fei-0 CS76412


title: Fei-0 root on sufficient N, biological rep 1


title: Fei-0 root on low N, biological rep 3


title: 1-035-2

value: D


title: 14DPI_B_lane 1

value: influenza B virus

value: whole lung

value: lung ciliated cells


title: Mock_B_lane 2

source_name: Mock_whole lung

value: mock


title: iH19


title: Mock_B_lane 1


title: 14SC_B_lane 2

value: direct viral infection (14 DPI Survivor Cell)


title: KB006-0 shoot on low N, biological rep 1

value: shoot

value: 0.4 mM nitrate

value: RIL KB006 (Kondara x Br-0)

value: 21 days after sowing


title: Fei-0 root on sufficient N, biological rep 3

value: synthetic agar medium with 1% sucrose


title: Fei-0 root on low N, biological rep 2

source_name: Arabidopsis root after 21 days growth on 0.4 mM nitrate


title: Fei-0 shoot on sufficient N, biological rep 3


title: Fei-0 root on low N, biological rep 1


title: 1-035-1

value: whole blood from dengue infected patient

value: DF


title: 14DPI_A_lane 2

value: C57BL/6 transgenic line; 'tdTomato transgenic mice' (Jax catalog # 007914)

value: at 14 days post-infection that had never been infected (14 DPI).


title: 1-034-1


title: iH17

value: YPD

value: ERCC


title: 14DPI_A_lane 1


title: 14SC_A_lane 2


title: iH16


title: iH20


title: 1-033-1

value: D


title: 1-033-2


title: iH18


title: iH15


title: 1-032-1


title: iH14


title: 2DPI_A_lane 2

value: influenza B virus

value: during active infection (2 DPI)


title: 1-031-1

value: DWS


title: iH13


title: 2DPI_A_lane 1

value: whole lung

value: lung ciliated cells


title: Fei-0 shoot on low N, biological rep 3

value: shoot

value: accession Fei-0 CS76412


title: 1-030-3


title: Fei-0 shoot on sufficient N, biological rep 1

value: 9 mM nitrate


title: iH12


title: Fei-0 shoot on sufficient N, biological rep 2

value: 21 days after sowing


title: Mock_A_lane 2

value: mock


title: Fei-0 shoot on low N, biological rep 2

value: 0.4 mM nitrate

value: synthetic agar medium with 1% sucrose


title: 1-030-2

value: whole blood from dengue infected patient

value: DF


title: Fei-0 shoot on low N, biological rep 1


title: 14SC_A_lane 1

value: C57BL/6 transgenic line; 'tdTomato transgenic mice' (Jax catalog # 007914)

value: direct viral infection (14 DPI Survivor Cell)


title: El-0 root on sufficient N, biological rep 2

value: root

value: accession El-0 N1134


title: 1-029-2

value: SD

value: DSS


title: El-0 root on sufficient N, biological rep 3


title: Sko1-MT.HA (+NaCl) Rep 2

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

institute: York University

data_processing:
Trimmed sequencing read alignment to the sacCer3 reference genome was performed using Bowtie2 (version 2.3.3).
Peak calling of paired-end alignments was performed using MACS2 (2.1.1).
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: *_peaks.txt: Tab-delimited peaks files include fold enrichment and statistical analysis values (p and q).

source_name: Budding yeast culture

growth_protocol: 200 mL cultures were grown in YPD to a density (O.D. at 595 nm) within the range 0.5 - 0.8.

extract_protocol:
Extracts were prepared by bead-beating formaldehyde cross-linked and sonicated samples, followed by centrifugation.
Libraries were constructed at The Centre for Applied Genomics at the Hospital for Sick Children in Toronto using the NEBNExt Ultra II DNA library prep kit (New England Biolabs).

treatment_protocol: For +NaCl samples, cultures were treated with 0.4 M NaCl (final concentration) for 5 min prior to cross-linking.

tag: strain/background

tag: genotype/variation

tag: medium

value: YPD + 0.4 M NaCl for 5 min

tag: chip antibody

value: Novus Rabbit anti-HA NB600-363


title: Mock_A_lane 1

value: whole lung

value: lung ciliated cells


title: Sko1-WT.HA (+NaCl) Rep 2


title: 1-030-1

value: DWS


title: Sko1-MT.HA (No treatment) Rep 2

value: YPD


title: Sko1-WT.HA (No treatment) Rep 2


title: Sko1-MT.HA (+NaCl) Input

description: Derived from Rep 1


title: 1-027-1


title: Sko1-WT.HA (+NaCl) Input

description: Derived from Rep 1


title: 1-026-4


title: Sko1-MT.HA (No treatment) Input

description: Derived from Rep 1


title: 1-026-3


title: Sko1-WT.HA (No treatment) Input

description: Derived from Rep 1


title: 1-029-1


title: El-0 shoot on sufficient N, biological rep 2

source_name: Arabidopsis shoot after 21 days growth on 9 mM nitrate

value: shoot

tag: treatment

value: 9 mM nitrate

tag: genotype

tag: age

value: 21 days after sowing

tag: culture


title: 1-026-1

value: whole blood from dengue infected patient

tag: donor

tag: sample

tag: pos

tag: neg


title: El-0 root on low N, biological rep 1

tag: tissue

value: 0.4 mM nitrate

value: synthetic agar medium with 1% sucrose


title: 1-026-2

tag: score


title: 1-025-2

value: exclude


title: 1-028-1

value: DF


title: 1-025-1


title: Sko1-MT.HA (+NaCl) Rep 1


title: Sko1-MT.HA (No treatment) Rep 1


title: OXID_m20h30-5

city: Saint Paul

first: Kristin

middle: L

last: Sikkink

state: MN

address: 1987 Upper Buford Circle

department: Ecology, Evolution, and Behavior

institute: University of Minnesota

data_processing:
Base-calls were performed using Illumina software
Initial processing was performed using the process_shortreads component of Stacks. In short, reads were demultiplexed, and the barcodes were removed simultaneously. Reads with ambiguous barcodes were rescued if there were fewer than 2 mismatches, and discarded otherwise. Reads failing the Illumina chastity filter were also removed.
Filtered reads were aligned to the C. remanei genome using GSNAP version 2013-03-31 with parameters -N 1 -s -w 10000 --pairmax-RNA 10000
Reads aligning to genes were counted using htseq-count with parameters -m union -s no
Genome_build: C_remanei-15.0.1
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene

organism: Caenorhabditis remanei

source_name: pooled L1 tissue

growth_protocol: Worms were maintained on NGM-lite seeded with E. coli strain OP50 at 20°C

extract_protocol:
Approximately 100,000 individuals per replicate were flash frozen in Trizol. Total RNA was extracted using a standard Trizol extraction protocol. Poly-A mRNA was isolated from total RNA using the Dynabeads mRNA purification kit (Ambion).
mRNA was sheared to 200-600nt fragments using a buffered zinc solution (RNA fragmentation kit; Ambion). cDNA was synthesized from fragments using Superscript III, and sequencing adaptors with in-line barcodes were added to enable multiplexing of samples.

treatment_protocol: Populations were age-synchronized during the embryonic stage via a standard bleaching procedure. Embryos were incubated at either 20°C or 30°C (rearing temperature) in liquid buffer without food for 20 hours. Pooled L1 larvae were passed through a 20 micron filter immediately prior to tissue collection.

tag: strain

value: Oxidative stress selected, derived from PX443

tag: developmental stage

tag: rearing temperature (degree c)

tag: batch

value: G


title: OXID_m20h30-6


title: Sko1-WT.HA (+NaCl) Rep 1

tag: strain/background

tag: genotype/variation


title: El-0 root on low N, biological rep 2

value: root

value: accession El-0 N1134


title: Sko1-WT.HA (No treatment) Rep 1

tag: medium

tag: chip antibody

value: Novus Rabbit anti-HA NB600-363


title: 1-024-2


title: El-0 shoot on sufficient N, biological rep 3

tag: treatment

tag: genotype


title: OXID_m20h30-4


title: El-0 root on sufficient N, biological rep 1

tag: age

tag: culture


title: El-0 shoot on sufficient N, biological rep 1


title: El-0 shoot on low N, biological rep 2


title: T4d_rep2

city: Kansas City

first: Shui

middle: Q

last: Ye

state: MO

address: 2411 Holmes Street

department: Departmetn of Biomedical and Health Informatics

institute: University of Missouri Kansas City School of Medicine

data_processing:
The sequence reads were demultiplexed and converted to fastQ with BCL2FastQ v2.17
The fastq files were trimmed in cutadapt 1.7.1 (with Python 2.7.6) to include only the 20bp sgRNA using the 5’ sequence GTGGAAAGGACGAAACACCG and the 3’ sequence GTTTTAGAGCTAGA
Trimmed reads were aligned to the index in Bowtie2 v2.1 with a 1bp mismatch allowance
Raw read counts were calculated in unix and combined across the 4 technical replicates per sample
Read counts were normalized to the median with T0 as control and analyzed using sgRNA and gene-level RRA (Robust Rank Aggregation) in MaGeCK v0.5.6
Genome_build: GeKOv2 sgRNA library index
Supplementary_files_format_and_content: tab-delimited text file of a matrix table of raw read counts.

source_name: HuH7 human hepatocarcinoma cell line

growth_protocol: HuH7 cells were maintained in DMEM (Thermo Fisher cat. 111885092) supplemented with 100 U/ml penicillin and streptomycin (Thermo Fisher cat. 15140122), non-essential amino acids (Thermo Fisher cat. 11140050), and 10% fetal bovine serum (Atlanta Biologicals cat. S11150) as previously described, with the addition of 2mM L-glutamine (Thermo Fisher cat. 25030081) and 1mM sodium pyruvate (Thermo Fisher)67. Cells were detached with trypsin-EDTA (Thermo Fisher cat. 25200056). All incubations were performed at 37°C and 5% CO2.

extract_protocol:
Genomic DNA was isolated from samples of a minimum of 2E7 cells using the Blood and Cell Culture Midi Kit (Qiagen cat. 13343, Valencia, CA)
5µl amplicon or 1µl diluted plasmid library was used as template in 13 50µl Herculase II DNA polymerase reactions per sample to attach pooled variable-length spacers and Illumina indexes (custom primers, see manuscript). 24 cycles were used to amplify DNA in the first and second PCR, respectively. The amplicon fragments after PCR 2 comprise a 354-362bp library with variable 20bp sgRNA sequence in the middle. DNA was pooled by sample and purified using the Nucleospin Gel and PCR Clean-up kit (Clontech cat. 740609.250, Mountain View, CA). DNA was quantified using a Qubit high-sensitivity DNA quantification assay (Thermo Fisher cat. Q32851) and Take3 microspot plate reader (BioTek). DNA quality was analyzed by Experion CHIP assay (BioRad cat. 7007-163, Hercules, CA). Clusters were generated on the flow cell using the HiSeq Rapid Duo CBot Sample Loading Kit (Illumina CT- cat. 403-2001, San Diego, CA).
A single-read rapid run of 75 cycles was performed on a HiSeq 1500 (Illumina cat. GD-402-4002) using the HiSeq Rapid SBS kit (Illumina cat. FC-402-4022) with 10% PhiX.

treatment_protocol: HuH7 were transduced with a Cas9 LLV and subsequently with control or sgRNA library LLV to produce gene knockouts. The pooled, transduced cells were selected with 1.5µg/ml puromycin (Invitrogen cat. Ant-pr-1) for 3 days alongside cells transduced with the empty vector lentiGuidePuro, positive fluorescent control PLJM1-EGFP. After 8 days of transduction a T0 sample was collected (N=2) and the remaining library-transduced cells were treated with 15mM APAP for 30 minutes up to 4 days (2 biological replicates for T0, 24 hour, and 4 day samples).  Samples that underwent 4 days of APAP treatment were outgrown for 21 days prior to collection.

tag: donor sex

value: Male

tag: donor age

value: 57 years

tag: donor cancer type

value: hepatocellular carcinoma, liver tumor

tag: treatment dosage

value: 15mM APAP for 4 days

value: APAP treated


title: L4440_rep1

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

data_processing:
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence with TrimGalore default parameters
Clean reads were mapped to c.elegans whole genome (WBcel235.85) with Tophat2 (v2.1.1 & default parameters). Then, resulting .bam file was sorted by position and indexed with Samtools.
Bam files were processed with FeatureCounts tool (Liao et al., 2014) in order to obtain raw counts on exonic features, provided by the GTF file.
Quantitative differential expression analysis between conditions was performed both by DESeq2 (Love et al., 2014) and edgeR (Robinson et al., 2010) implementations, to compare all groups in pairs to analyze the effect of the two variables of this study: food sources (E. coli diet vs B. subtilis diet) and growth temperatures (15ºC vs 20ºC vs 25ºC). Both of them, implemented as R Bioconductor packages, perform read-count normalization by following a negative binomial distribution model. In order to automate this process and facilitate all group combination analysis, the SARTools pipeline (Varet et al., 2016) was used.
Resulting charts, containing raw and normalized data were annotated with additional data from Biomart, WormBase and the org.Ce.eg.db databases.
Gene Ontology enrichment analysis was performed for common up/down regulated genes by using clusterProfiler package (Yu et al., 2012) through its enrichGO tool.
The regularized log2 transformation (rlog) data was represented into a 2-dimension Principal Component Analysis (PCA) plot, by tacking DESeq2 expression values
Sample-to-sample Euclidean distances were calculated from the rld data and represented in a heatmap, showing the adjacent clustering information
Genome_build: WBcel235.85
Supplementary_files_format_and_content: The tab delimited files with extension .counts contain raw counts data, generated with FeatureCounts software

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Wild-type nematodes were obtained from the Caenorhabditis Genetic Center (CGC, University of Minesota). Worm populations were synchronized by “bleaching” with hypochlorite solution, maintained in M9 medium during 20 hours to allow hatching eggs and synchronization at the first larval stage (L1). Then, worms were grown in plates seeded with the corresponding RNAi clones and they were kept at 15ºC during six days.

extract_protocol:
mirVana (miRNA Isolation Kit, Ambion), and treated with DNase I (Qiagen) following manufacturer’s instructions.
Sequencing libraries were prepared by following the TruSeq RNA Library (LS) Preparation Kit v2 (Illumina Inc., San Diego, CA) from 1 ug of totalRNA (after rRNA depletion with RiboZero H/M/R protocol).

treatment_protocol: Synchronization worms at the first larval stage were silenced by feeding for genes of the different components of integrator complex

tag: growth

value: grown at 15 C during six days

tag: diet

value: E.coli feeding


title: El-0 root on low N, biological rep 3

tag: tissue

value: 21 days after sowing


title: El-0 shoot on low N, biological rep 1

source_name: Arabidopsis shoot after 21 days growth on 0.4 mM nitrate

value: shoot

value: 0.4 mM nitrate


title: 1-024-1

value: whole blood from dengue infected patient

tag: donor

value: DWS

tag: sample

tag: pos

tag: neg

tag: score


title: OXID_m20h30-3

tag: strain

value: Oxidative stress selected, derived from PX443

tag: developmental stage

tag: rearing temperature (degree c)

tag: batch


title: 1-023-1

value: DF


title: Ints-11_rep1


title: OXID_m20h30-2

value: G


title: T4d_rep1

tag: treatment


title: T24h_rep2

tag: donor sex

value: 15mM APAP for 24 hours


title: OXID_m20h30-1


title: 1-022-2

value: DHF


title: Ints-9_rep1


title: Ints-7_rep1


title: T24h_rep1

value: Male

tag: donor age


title: El-0 shoot on low N, biological rep 3

tag: genotype

value: accession El-0 N1134

tag: age

tag: culture

value: synthetic agar medium with 1% sucrose


title: 1-022-1


title: Ints-6_rep1

tag: growth

tag: diet


title: OXID_m20h20-6


title: T12h

value: 57 years

tag: donor cancer type

value: hepatocellular carcinoma, liver tumor

tag: treatment dosage

value: 15mM APAP for 12 hours


title: OXID_m20h20-5


title: T6h

value: 15mM APAP for 6 hours

value: APAP treated


title: OXID_m20h20-4


title: 1-020-3

tag: tissue

tag: donor

value: D

tag: sample

tag: pos


title: Ints-3_rep1

value: grown at 15 C during six days

value: E.coli feeding


title: Ints-4_rep1


title: Ints-2_rep1


title: 1-021-1

value: whole blood from dengue infected patient

value: DWS

tag: neg

tag: score


title: T3h

value: 15mM APAP for 3 hours


title: OXID_m20h20-2

tag: strain

value: Oxidative stress selected, derived from PX443

tag: developmental stage

tag: rearing temperature (degree c)

tag: batch

value: G


title: 1-020-1

value: DF


title: OXID_m20h20-1


title: T30min

tag: donor sex

value: Male

tag: donor age

value: 15mM APAP for 30 minutes

tag: treatment


title: T0_rep1

value: no APAP treatment

value: untreated


title: HEAT_m20h30-6

value: Heat selected, derived from PX443

value: F


title: 1-019-3


title: 1-019-2


title: 1-019-1


title: L4440_rep3

tag: growth


title: HEAT_m20h30-5


title: L4440_rep2

tag: diet


title: HEAT_m20h30-4


title: iH41

source_name: Saccharomyces cerevisiae single cell

tag: growth media

value: YPD

tag: external control

value: ERCC


title: 1-018-1

tag: tissue


title: ints-14_rep3


title: 1-017-2

tag: donor

value: SD


title: HEAT_m20h30-3


title: OXID_m20h20-3


title: HEAT_m20h30-2

value: E


title: 1-020-2

value: D

tag: sample


title: T0_rep2

value: 57 years

tag: donor cancer type

value: hepatocellular carcinoma, liver tumor

tag: treatment dosage


title: 1-016-1

value: whole blood from dengue infected patient

value: DWS

tag: pos

tag: neg

tag: score


title: Ints-14_rep1

value: grown at 15 C during six days

value: E.coli feeding


title: Ints-13_rep3


title: 1-015-1

value: exclude


title: 1-014-3

value: DHF


title: Ints-14_rep2


title: HEAT_m20h30-1

tag: strain

tag: developmental stage

tag: rearing temperature (degree c)


title: HEAT_m20h20-5

tag: batch


title: HEAT_m20h20-6


title: HEAT_m20h20-4


title: Ints-13_rep2


title: Ints-12_rep3


title: HEAT_m20h20-3


title: 1-014-2


title: 1-014-1


title: 1-017-1

value: DF


title: Ints-12_rep2


title: HEAT_m20h20-2


title: 1-013-3

value: DSS


title: Ints-12_rep1


title: Ints-13_rep1


title: 1-013-2


title: HEAT_m20h20-1

value: Heat selected, derived from PX443


title: Ints-11_rep3


title: 1-013-1


title: CTRL_m20h30-6

value: Control selected, derived from PX443


title: Ints-11_rep2


title: 1-012-4


title: CTRL_m20h30-5


title: Ints-10_rep3


title: 1-012-3


title: Ints-10_rep2


title: 1-012-2


title: CTRL_m20h30-3


title: CTRL_m20h30-4


title: 1-012-1


title: CTRL_m20h30-2

value: C


title: CTRL_m20h30-1


title: Ints-10_rep1


title: DNA_214077

hyb_protocol: The samples were processed using Illumina's HumanImmuno_v1 DNA Analysis Kit and Immuno_BeadChip_11419691_B.bpm.

scan_protocol: The protocol Infinium® HD Assay was followed using BeadArray Reader.

data_processing: Genotyping report is based on GenomeStudio software.

label: C, G: biotin; A, T: dinitrophenyl

source_name: duodenum biopsy, control

label_protocol: The protocol Infinium® HD Assay was followed.

growth_protocol: Not applicable.

treatment_protocol: Not applicable.

tag: disease status

value: Non-celiac disease

value: Lamina propria of duodenum

tag: sample type

value: Control

tag: individual identifier


title: CTRL_m20h20-6

value: D


title: 1-011-5


title: Ints-9_rep2

tag: growth

tag: diet


title: DNA_211084

tag: tissue


title: Ints-8_rep3


title: DNA_211075


title: 1-011-3

tag: donor


title: DNA_211086


title: DNA_27028

source_name: duodenum biopsy, celiac disease

value: Celiac disease


title: DNA_27036


title: Ints-9_rep3


title: DNA_211073


title: Ints-8_rep2


title: CTRL_m20h20-5


title: DNA_214058


title: DNA_214051

source_name: duodenum biopsy, potential celiac disease

value: Potential celiac disease


title: CTRL_m20h20-3


title: DNA_215025


title: 1-011-1

source_name: whole blood from dengue infected patient

tag: sample


title: 1-010-1

value: whole blood from dengue infected patient

value: SD


title: DNA_214108


title: CTRL_m20h20-2


title: Ints-7_rep3

value: grown at 15 C during six days


title: Ints-7_rep2

value: E.coli feeding


title: CTRL_m20h20-1


title: DNA_214103


title: DNA_27017


title: DNA_215021


title: Ints-6_rep3


title: DNA_28039


title: 1-009-2

value: exclude


title: DNA_214096


title: CTRL_m20h20-4


title: DNA_214048


title: 1-009-1


title: ANC_m20h30-6

value: A


title: DNA_214092


title: Ints-6_rep2


title: 1-008-2

value: DF


title: Ints-5_rep3


title: 1-008-1


title: ANC_m20h30-4

value: B


title: 1-007-1

value: DWS


title: Ints-5_rep2


title: DNA_214055


title: Ints-5_rep1


title: ANC_m20h30-2


title: 1-006-1


title: Ints-4_rep3


title: ANC_m20h30-3


title: ANC_m20h30-1


title: 1-005-4


title: DNA_214071


title: DNA_214063


title: DNA_214089


title: DNA_214041


title: 1-005-1


title: ANC_m20h20-5


title: DNA_214065


title: Ints-4_rep2


title: Ints-3_rep2


title: 1-005-2


title: 1-004-3


title: ANC_m20h20-4


title: DNA_215018


title: 1-004-2


title: ANC_m20h20-3


title: Ints-2_rep3


title: Ints-3_rep3


title: Ints-8_rep1


title: ANC_m20h20-6


title: 1-004-1


title: ANC_m20h20-2


title: DNA_215010


title: ANC_m20h30-5


title: 1-003-3


title: Ints-2_rep2


title: ANC_m20h20-1


title: Ints-1rep2


title: LNCaP_DHT_ABBV-744 rep2

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned using the OmicSoft aligner and gene expression quantified based on UCSC gene model.
Differentially expressed genes between treatment conditions detected by DESeq2 with a statistical cut-off (FC>2, p<0.01)
Genome_build: B37
Supplementary_files_format_and_content: FPKMs

growth_protocol: LNCaP-FGC cells were grown for 72 hrs in charcoal stripped (steroid free) serum,

extract_protocol:
RNA was prepared by Qiazol extraction followed by RNeasy mini column (QIAGEN)
10 ug of total RNA was submitted to poly-A selection to remove ribosomal RNA and reverse transcribed to double-stranded cDNA. The cDNA was eblunt ended, adenylated, and ligated with Illumina indexes.

treatment_protocol: Cells were pretreated with indicated inhibitors for 45 minutes followed by 24 hr stimulation with 5 nM DHT or EtOH.

tag: cell line

value: LNCaP-FGC prostate adenocarcinoma cancer cell line

tag: treatment


title: Ints-1_rep1


title: 1-003-1

tag: pos


title: LNCaP_DHT_ABBV-744 rep1


title: Adult astrocytes-GFAP-mCAT-animal 4

city: Salamanca

first: Juan P

last: Bolanos

state: SALAMANCA

address: C/Zacarías Gonzalez, 2

institute: University of Salamanca

description: Gene expression data from ACSA+ cells

hyb_protocol: Unidad de Genómica protocols. Centro de Investigación del Cancer, University of Salamanca.

data_processing: The data were processed by Affymetrix Transcriptome Analysis Console (TAC) Software with default setting of Gene + Exon-SST-RMA summarization method to calculate the expression level for each probeset of the array.

source_name: Freshly isolated adult astrocytes (ACSA+ cells)

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 5.5 µg ssDNA previously analyzed by Agilent 2100 Bioanalyzer.

growth_protocol: See in Nature Metabolism Vicente-Gutierrez et al. To achieve down-modulation of mitochondrial ROS in astrocytes in vivo, mCATLoxP/+ mice was mated with mice, under the C57BL/6-J background, harboring the estrogen receptor (ERT2)-inducible (tamoxifen-dependent) Cre recombinase (CreERT2) governed by the astrocyte-specific glial fibrillary acidic protein (GFAP) promoter (GFAP-CreERT2/+).

extract_protocol: RNeasy Mini Kit extraction of total RNA was performed according to the manufacturer's instructions (QIAGEN).

treatment_protocol: The progeny, namely GFAP-CreERT2/+; mCATLoxP/+, and +/+; mCATLoxP/+ littermates, at the age of 8 weeks were intraperitoneally injected with tamoxifen to activate Cre recombinase activity in astrocytes in vivo. The resulting mice, namely GFAP-CreERT2/+; mCAT/+ (henceforth GFAP-mCAT) and +/+; mCATLoxP/+ littermates (henceforth Control) were analyzed during adulthood (14 months old).

value: brain

tag: cell type

value: astrocytes

tag: genotype

value: GFAP-mCAT littermate

tag: background strain

tag: age

value: 14 months


title: 1-011-4

tag: neg

tag: score


title: 1-002-4

value: DSS


title: LNCaP_DHT_ABBV-075 rep2


title: DNA_214110

tag: disease status

value: Non-celiac disease

value: Lamina propria of duodenum

value: Control


title: DNA_214101

tag: sample type


title: DNA_215005

tag: individual identifier


title: DNA_214024

value: Celiac disease


title: DNA_214097


title: Adult astrocytes-GFAP-mCAT-animal 3

description: Gene expression data from ACSA+ cells

scan_protocol: Unidad de Genómica protocols. Centro de Investigación del Cancer, University of Salamanca.


title: LNCaP_DHT_ABBV-075 rep1


title: 1-011-2

value: whole blood from dengue infected patient


title: Adult astrocytes-GFAP-mCAT-animal 2

description: Gene expression data from ACSA+ cells


title: 1-002-2

value: SD


title: DNA_214064


title: 1-002-1


title: LNCaP_DHT ENZ rep2

source_name: LNCaP_DHT ENZ


title: 1-003-2

value: D


title: DNA_214032


title: DNA_214114


title: DNA_214059


title: Adult astrocytes-GFAP-mCAT-animal 1

description: Gene expression data from ACSA+ cells


title: 1-001-4


title: Adult astrocytes-control-animal 4

description: Gene expression data from ACSA+ cells

value: Control littermate


title: LNCaP_DHT_ENZ rep1


title: 1-001-3


title: LNCaP_DHT_DMSO rep2


title: Adult astrocytes-control-animal 3

description: Gene expression data from ACSA+ cells


title: LNCaP_DHT_DMSO rep1


title: 1-001-2


title: DNA_214105


title: DNA_214102


title: Adult astrocytes-control-animal 2

description: Gene expression data from ACSA+ cells


title: 1-001-1


title: Adult astrocytes-control-animal 1

description: Gene expression data from ACSA+ cells


title: DNA_214027


title: LNCaP_EtOH_DMSO rep2


title: Negative sample_rep2

status: Public on Feb 03 2019

city: Seoul

first: Phil Jun

last: Kang

address: 1, 5-Ka, Anam-Dong, Sungbuk-ku

department: Department of Biotechnology

country: South Korea

institute: Korea University

description: urine derived cells

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: urine derived cells

growth_protocol: neural stem cells (H9 embryonic stem cells derived neural stem cells and induced neural stem cells) were cultured in NSC growth medium incluing DMEM/F12+Neurobasal, N2, B27, LIF, SB431542 and CHIR99021 on Matrigel coated dishes. Urine derived cells were cultured in urine cell growth medium including DMEM+REGM, FGF2 and EGF on gelatin coated dishes.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). rRNA was removed using Lexogen RIBO COP rRNA depletion kit from each 1ug of total RNA.
RNA libraries were prepared for sequencing using  Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

value: urine derived cells

tag: donor information

value: Male, 32-year-old

value: WT


title: Negative sample_rep1

description: urine derived cells


title: LNCaP_EtOH_DMSO rep1

value: LNCaP-FGC prostate adenocarcinoma cancer cell line


title: Sample_rep2

description: induced neural stem cells derived from urine cells by synthetic mRNA

source_name: induced neural stem cells

value: induced neural stem cells


title: Positive sample_rep2

description: H9 embryonic stem cells derived neural stem cells

source_name: neural stem cells


title: Positive sample_rep1

value: H9 embryonic stem cells derived neural stem cells


title: PHB20_Rep02

city: Brisbane

first: Renato

last: de Souza Pinto Lemgruber

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd

country: Australia

institute: University of Queensland

description:
Expression changes1.txt
Expression changes2.txt

data_processing:
Basecalling was done using Illumina CASAVA 1.8.2 software.
Sequencing reads were aligned to the genome using Rsubread (Liao et al., 2013) and ribosomal RNA genes were moved prior further analysis.
Transcript abundances (RPKMs) were estimated using the RPKM function of edgeR (Robinson et al., 2009) using normalisation across all samples.
Significant transcript expression changes between EP and PHB-type or PHB-type between the two gases analysed were determined using limma (Ritchie et al., 2015), only for transcripts with >10 reads per million mapped reads in at least two samples, by a -value<0.05 after false discovery rate correction (Benjamini and Hochberg, 1995).
Genome_build: CP006763.1
Supplementary_files_format_and_content: Tab-delimited text file "Expression changes1.txt" includes log2 fold change with q-values for the signficantly differently expressed transcripts comparing EP and PHB-type
Supplementary_files_format_and_content: Tab-delimited text file "Expression changes2.txt" includes log2 fold change with q-values for the signficantly differently expressed transcripts comparing PHB-type between steel mill off gas and syngas growth
Supplementary_files_format_and_content: Tab-delimited text file "Empty_vs_PHB.rpkm.txt" includes RPKM values for each sample identified by sample title.

organism: Clostridium autoethanogenum

source_name: bacterial cell

growth_protocol: Clostridium autoethanogenum (EP and PHB type) was grown on steel mill off gas or syngas in chemically defined medium anaerobically at 37C and a pH of 5 (or 5.5) in chemostats at dilution rate ~1 1/day.

extract_protocol:
Frozen pellets were thawed and total RNA extracted using two cycles of cellular lysis in RNase-free zirconia beads (Ambion). RNA was purified using the RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Next, ribosomal RNA was removed using the Ribo-Zero rRNA removal kit (Illumina).
mRNA libraries were prepared using standard TruSeq library preparation protocols (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

tag: strain

tag: physiological state

value: PHB type grown on syngas (with 20% hydrogen) chemostat

tag: biological replicate


title: PHB20_Rep01


title: Sample_rep1


title: Tumor tissue from HCD mice,number 2

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

country: China

institute: Eastern Hepatobiliary Surgery Hospital

description: Tumor tissue from HCD mice were harvested and total RNA were extracted

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat(version:2.0.9)
Gene abundance measurements were generationed and normalized  using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed  using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: hepatocellular carcinoma

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

tag: culture condition

value: Hep1-6 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with high cholesterol diet.

tag: diet

value: high cholesterol diet (HCD)


title: Tumor tissue from HCD mice,number 3


title: PHB2_Rep02

value: PHB type grown on steel mill off gas (with 2% hydrogen) chemostat


title: Tumor tissue from HCD mice,number 1


title: PHB2_Rep01


title: DNA_214053

city: Leioa

first: Jose Ramon

last: Bilbao

address: Bº Sarriena

institute: University of the Basque Country (UPV/EHU)

extract_protocol: Nucleic acids from all samples were isolated with AllPrep DNA/RNA microkit (Qiagen, Hilden, Germany, Cat No 80284).

tag: tissue

value: Lamina propria of duodenum


title: EP20_rep01

description: Expression changes1.txt

value: Empty plasmid type grown on syngas (with 20% hydrogen) chemostat


title: Tumor tissue from ND mice,number 2

description: Tumor tissue from ND mice were harvested and total RNA were extracted

value: Hep1-6 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with normal diet.

value: normal diet (ND)


title: Tumor tissue from ND mice,number 3


title: EP2_rep02

description: Expression changes1.txt

value: Empty plasmid type grown on steel mill off gas (with 2% hydrogen) chemostat


title: Tumor tissue from ND mice,number 1


title: DNA_214023

value: Celiac disease


title: EP2_rep01

description: Expression changes1.txt


title: Ints-1_rep3

tag: growth

value: grown at 15 C during six days

value: E.coli feeding


title: EP20_Rep02

description: Expression changes1.txt


title: DNA_214046


title: Olig2cre/cre;p53fl/fl;hEGFRvIII #2

status: Public on Feb 02 2019

city: San Francisco

first: David

middle: H

last: Rowitch

address: 35 Medical Center Way

department: Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine

institute: UCSF

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Brain tumor

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: SCID

tag: cell type

value: 50 days

value: brain


title: DNA_214113

value: Non-celiac disease

value: Control


title: Olig2cre/+;p53fl/fl;hEGFRvIII #3

description: SAMPLE 5

value: 47 days


title: Olig2cre/cre;p53fl/fl;hEGFRvIII #1

description: SAMPLE 2

value: 45 days


title: DNA_214112


title: DNA_214047


title: Olig2cre/cre;p53fl/fl;hEGFRvIII #3

description: SAMPLE 6


title: Olig2cre/+;p53fl/fl;hEGFRvIII #1

description: SAMPLE 1


title: Olig2cre/+;p53fl/fl;hEGFRvIII #2

description: SAMPLE 3


title: DNA_214107


title: DNA_214028


title: genomic DNA from sperm cells 54

first: Dafna

middle: D

last: Gladman

state: Ontario

address: 60 Leonard Ave

department: Rheumatology Research

institute: Toronto Western Research Institute

description: psoriatic arthritis sperm

hyb_protocol: bisulphite converted DNA was amplified using the Illumina Infinium HD Methylation protocol, fragmented and hybridised to Illumina Infinium Human Methylation450k v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan system using standard recommended Illumina scanner settings

data_processing: GenomeStudio version 2011.1 using HumanMethylation450_15017482_v.1.2 annotation file

label: Cy5 and Cy56

source_name: semen sample 54

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted and purified from motile spermatozoa by phenol-chloroform extraction

tag: gender

value: Male

value: sperm cells

tag: disease state

value: Psoriatic arthritis


title: genomic DNA from sperm cells 43

description: psoriatic arthritis sperm

label: Cy5 and Cy45

source_name: semen sample 43


title: genomic DNA from sperm cells 51

description: psoriatic arthritis sperm

label: Cy5 and Cy53

source_name: semen sample 51


title: genomic DNA from sperm cells 52

description: psoriatic arthritis sperm

label: Cy5 and Cy54

source_name: semen sample 52


title: genomic DNA from sperm cells 46

description: psoriatic arthritis sperm

label: Cy5 and Cy48

source_name: semen sample 46


title: genomic DNA from sperm cells 48

description: psoriatic arthritis sperm

label: Cy5 and Cy50

source_name: semen sample 48


title: genomic DNA from sperm cells 53

description: psoriatic arthritis sperm

label: Cy5 and Cy55

source_name: semen sample 53


title: genomic DNA from sperm cells 50

description: psoriatic arthritis sperm

label: Cy5 and Cy52

source_name: semen sample 50


title: genomic DNA from sperm cells 44

description: psoriatic arthritis sperm

label: Cy5 and Cy46

source_name: semen sample 44


title: genomic DNA from sperm cells 49

description: psoriatic arthritis sperm

label: Cy5 and Cy51

source_name: semen sample 49


title: genomic DNA from sperm cells 42

description: psoriatic arthritis sperm

label: Cy5 and Cy44

source_name: semen sample 42


title: genomic DNA from sperm cells 38

description: psoriasis sperm

label: Cy5 and Cy40

source_name: semen sample 38

value: Psoriasis without arthritis


title: genomic DNA from sperm cells 36

description: psoriasis sperm

label: Cy5 and Cy38

source_name: semen sample 36


title: genomic DNA from sperm cells 29

description: psoriasis sperm

label: Cy5 and Cy31

source_name: semen sample 29


title: genomic DNA from sperm cells 37

description: psoriasis sperm

label: Cy5 and Cy39

source_name: semen sample 37


title: genomic DNA from sperm cells 30

description: psoriasis sperm

label: Cy5 and Cy32

source_name: semen sample 30


title: genomic DNA from sperm cells 31

description: psoriasis sperm

label: Cy5 and Cy33

source_name: semen sample 31


title: genomic DNA from sperm cells 33

description: psoriasis sperm

label: Cy5 and Cy35

source_name: semen sample 33


title: genomic DNA from sperm cells 47

description: psoriatic arthritis sperm

label: Cy5 and Cy49

source_name: semen sample 47


title: DNA_214026

department: Genetics, Physical Anthropology and Animal Physiology

label: C, G: biotin; A, T: dinitrophenyl

source_name: duodenum biopsy, control

value: Lamina propria of duodenum


title: PTex_15 [HU_BB_038_S22_L002]

city: Berlin

first: Benedikt

middle: M

last: Beckmann

address: Philippstrasse 13

department: IRI Life Sciences

institute: Humboldt University

data_processing:
Basecaller: Illumina bcl2fastq v2.17.1.14
Alignment: bowtie2 (v2.2.6) to map rRNA and tRNA reads and STAR (v020201) to map against full genome annotation (gencode.v28.chr_patch_hapl_scaff.annotation.gtf)
Genome_build: GENCODE (GRCh38.p12)
Supplementary_files_format_and_content: Summary table (tab-delimited) of raw counts from transcripts in RNA classes

growth_protocol: Human embryonic kidney cells (HEK293) were grown to 80% confluency.

extract_protocol:
RNA was extracted using the single step protocol (aka Trizol) as described by Chomczynski and Sacchi (1987) Analytical biochemistry
Libraries were constructed using the "TruSeq Stranded Total RNA LT" Kit from Illumina following the manufacturers instructions

treatment_protocol: Cells in monolayer were washed once with cold phosphate buffer saline and placed on ice. Then, PBS was removed completely and cells were irradiated with 0.015 - 1.5 J/cm2 UV light  (lambda= 254 nm), collected and pelleted by centrifugation (1000 x g, 3 min, 4 °C), aliquoted and stored at -20/-80°C. Non-irradiated cells were used as non-cross-link control (noCL).

tag: cell line

value: Human embryonic kidney cells

tag: uv-cross-linking intensity

value: RNA purified in complexes (PTex samples)


title: genomic DNA from sperm cells 45

description: psoriatic arthritis sperm

label: Cy5 and Cy47

source_name: semen sample 45


title: genomic DNA from sperm cells 28

description: psoriasis sperm

label: Cy5 and Cy30

source_name: semen sample 28


title: genomic DNA from sperm cells 27

description: psoriasis sperm

label: Cy5 and Cy29

source_name: semen sample 27


title: genomic DNA from sperm cells 32

description: psoriasis sperm

label: Cy5 and Cy34

source_name: semen sample 32


title: genomic DNA from sperm cells 26

description: psoriasis sperm

label: Cy5 and Cy28

source_name: semen sample 26


title: genomic DNA from sperm cells 35

description: psoriasis sperm

label: Cy5 and Cy37

source_name: semen sample 35


title: genomic DNA from sperm cells 39

description: psoriasis sperm

label: Cy5 and Cy41

source_name: semen sample 39


title: PTex_15 [HU_BB_039_S23_L002]


title: PTex_15 [HU_BB_037_S21_L002]


title: DNA_214052

source_name: duodenum biopsy, potential celiac disease

value: Potential celiac disease


title: genomic DNA from sperm cells 34

description: psoriasis sperm

label: Cy5 and Cy36

source_name: semen sample 34


title: genomic DNA from sperm cells 22

description: psoriasis sperm

label: Cy5 and Cy24

source_name: semen sample 22


title: genomic DNA from sperm cells 40

description: psoriasis sperm

label: Cy5 and Cy42

source_name: semen sample 40


title: genomic DNA from sperm cells 41

description: psoriasis sperm

label: Cy5 and Cy43

source_name: semen sample 41


title: PTex_015 [HU_BB_036_S20_L002]


title: genomic DNA from sperm cells 25

description: psoriasis sperm

label: Cy5 and Cy27

source_name: semen sample 25


title: PTex_015 [HU_BB_035_S19_L002]


title: PTex_015 [HU_BB_034_S18_L002]


title: genomic DNA from sperm cells 23

description: psoriasis sperm

label: Cy5 and Cy25

source_name: semen sample 23


title: PTex_0015 [HU_BB_033_S17_L002]


title: PTex_0015 [HU_BB_032_S16_L002]


title: genomic DNA from sperm cells 19

description: psoriasis sperm

label: Cy5 and Cy21

source_name: semen sample 19


title: PTex_0015 [HU_BB_031_S15_L002]


title: genomic DNA from sperm cells 21

description: psoriasis sperm

label: Cy5 and Cy23

source_name: semen sample 21


title: genomic DNA from sperm cells 24

description: psoriasis sperm

label: Cy5 and Cy26

source_name: semen sample 24


title: CdSe dark 2

city: Boulder

first: Thomas

last: Aunins

state: CO

address: 3460 Colorado Ave, B5

institute: University of Colorado Boulder

description:
bacterial mRNA
sample name in processed data file:
S10

data_processing:
Demultiplexing using fastq-multx in ea-utils v1.1.2
Trimmed low quality bases and Illumina adapters using Trimmomatic v0.32, settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
FASTQ files aligned to E. coli MG1655 genome (NCBI Reference Sequence NC_000913.3) using Bowtie2 v2.2.3 with "sensitive" settings
BAM files generated using Samtools v0.1.18
Count tables generated using HTSeq v0.6.1
Differential expression calculated using DESeq v3.4 using pooled replicates
Genome_build: NCBI genome assembly NC_000913/RefSeq Assembly GCF_000005845.2
Supplementary_files_format_and_content: Count tables for each condition, scaled to size factors generated by DESeq

organism: Escherichia coli

source_name: exponential phase bacteria culture

growth_protocol: Escherichia coli MG1655 (ATCC700926) was plated streaked from freezer stock onto lysogeny broth, agar plates (2% LB, 1.5% agar). Two individual colonies were selected and grown overnight in M9 minimal medium (1x M9 minimal media salts solution (MP Biomedicals), 2.0 mM MgSO4, 0.1 mM CaCl2, and 0.4% glucose). Cells were then diluted 1:100 into fresh M9 with respective treatment/illumination.

extract_protocol:
1 mL of culture was pelleted by centrifugation at 4,000 rpm for 10 min. Cell pellets described above we treated with Qiagen RNAprotect and flash frozen in a dry ice, ethanol bath for storage at -80C. RNA was then extracted using Thermo Scientific GeneJET RNA Purification Kit.
The RNA was then treated with Thermo Scientific TURBO DNA-free kit following the rigorous digestion protocol. Library preparation of the 10 samples (two biological replicates of five conditions) was done according to Shishkin et al (Shishkin et al., 2015). Sequencing was performed as 1x50, stranded, on three lanes in an Illumina HiSeq at the BioFrontiers Next Generation Sequencing facility at the University of Colorado Boulder. The three lanes generated an average of 126.7 million reads with a mean quality score of 35.7.

treatment_protocol: Nanoparticle concentration was held at 10 nM for both CdSe-2.4 and CdTe-2.4. The conditions, collected in biological duplicates, were as follows: no treatment, 10 nM CdTe-2.4 in light, 10 nM CdTe-2.4 in dark, 10 nM CdSe-2.4 in light, and 10 nM CdSe-2.4 in dark. The cells were treated for 5 hours.

tag: media

value: M9 minimal medium

tag: growth phase

value: exponential

tag: treatment

value: 10 nM CdSe-2.4 quantum dot, no LED illumination


title: PTex_noCL [HU_BB_030_S14_L002]

value: no cross-link (noCL)

tag: sample type


title: PTex_noCL [HU_BB_029_S13_L002]


title: PTex_noCL [HU_BB_028_S12_L002]


title: genomic DNA from sperm cells 18

description: normal sperm sample

label: Cy5 and Cy20

source_name: semen sample 18

value: Healthy control


title: CdSe light 1

description:
bacterial mRNA
sample name in processed data file:
S7

value: 10 nM CdSe-2.4 quantum dot, LED illumination


title: genomic DNA from sperm cells 16

description: normal sperm sample

label: Cy5 and Cy18

source_name: semen sample 16


title: CdSe dark 1

description:
bacterial mRNA
sample name in processed data file:
S9


title: CdSe light 2

description:
bacterial mRNA
sample name in processed data file:
S8


title: CdTe dark 2

description:
bacterial mRNA
sample name in processed data file:
S6

value: 10 nM CdTe-2.4 quantum dot, no LED illumination


title: Input_15 [HU_BB_027_S11_L001]

value: input total RNA control


title: Input_15 [HU_BB_025_S9_L001]


title: Input_015 [HU_BB_024_S8_L001]


title: Input_15 [HU_BB_026_S10_L001]


title: CdTe light 2

description:
bacterial mRNA
sample name in processed data file:
S4

value: 10 nM CdTe-2.4 quantum dot, LED illumination


title: CdTe dark 1

description:
bacterial mRNA
sample name in processed data file:
S5


title: Input_015 [HU_BB_023_S7_L001]


title: CdTe light 1

description:
bacterial mRNA
sample name in processed data file:
S3


title: genomic DNA from sperm cells 14

description: normal sperm sample

label: Cy5 and Cy16

source_name: semen sample 14

value: Male


title: genomic DNA from sperm cells 12

description: normal sperm sample

label: Cy5 and Cy14

source_name: semen sample 12

value: sperm cells


title: No treatment 1

description:
bacterial mRNA
sample name in processed data file:
S1


title: genomic DNA from sperm cells 13

description: normal sperm sample

label: Cy5 and Cy15

source_name: semen sample 13


title: VS_3

city: La Jolla

first: Jorge

middle: Silvio

last: Gutkind

state: CALIFORNIA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

data_processing:
RNA sequencing produce paired-end FASTQ files, which store short cDNA sequences sequenced.
Kallisto (https://pachterlab.github.io/kallisto/) map these sequences to human references transcriptome (ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz) and compute transcript per million (TPM) for the reference transcripts. A gene's expression value is the maximum of the TPMs of its transcripts.
This workflow is publicly available at https://github.com/KwatME/find_differential_expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv file of gene level data per sample

source_name: 92.1 cell line

growth_protocol: 92.1 cells were cultured in RPMI-1640+10% FBS.

extract_protocol:
Cells were lysed in Trizol RNA was collected using Qiagen Rneasy Plus Mini Kit (#74134) and sent to Novogene for library prep and sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown to 70% confluency and treated with 1uM VS-4718 or DMSO vehicle for 2hrs and then total RNA was collected for sequencing.


title: Input_0015 [HU_BB_019_S4_L001]


title: Input_015 [HU_BB_022_S6_L001]


title: Input_0015 [HU_BB_020_S5_L001]


title: HuR_pCLIP_R1

description: HuR_pCLIP rep1

data_processing:
Basecaller: Illumina bcl2fastq v2.17.1.14
Alignment: bowtie version 1.1.2 Mapping paramerters:  -v 1 -m 10 --best --strata
Genome_build: GRCh37 hg19 Gencode v19 annotation
Supplementary_files_format_and_content: comma-delimited files contain annotated clusters from transcripts bound to HuR; analysed by the PARpipe pipeline (https://github.com/ohlerlab/PARpipe)

growth_protocol: HEK293 cells stably expressing FLAG-tagged HuR (ELAVL1), were grown until ~90% confluence.

extract_protocol:
1. Classical PAR-CLIP as described by Hafner et al. (2010); 2. a variant using on-bead ligation of adapters as described in Benhalevy et al. (2017), and 3. a variant in which all gel or membrane excision steps were replaced py phenolic extraction to remove non-cross-linked RNA (pCLIP: Urdaneta et al.).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The last 16 h of incubation, 200 mM 4SU was added. Living cells were irradiated with 0.15 J/cm^2 365 nm UV light, snap-frozen on dry ice and stored at -80°C until use.

tag: genotype/variation

value: stably expressing HuR-FLAG

tag: method

value: phenolic extraction to remove non-cross-linked RNA (pCLIP)


title: VS_2


title: Input_noCL [HU_BB_018_S3_L001]


title: HuR_pCLIP_R2

description: HuR_pCLIP rep2


title: genomic DNA from sperm cells 10

description: normal sperm sample

label: Cy5 and Cy12

source_name: semen sample 10


title: zmlrl5 knock out root RNA-seq, rep2

city: Beijing

first: qi

middle: chuang

last: ye

state: Beijing

address: Yuanmingyuan West Road

department: national maize improvement center

institute: china agriculture university

data_processing:
Sequenced RNA-seq reads were trimmed to remove adaptor sequence and low-quality sequence ,then using Tophat2 and DESeq to identify differentially expressed genes.
Genome_build: B73 reference genome version 3
Supplementary_files_format_and_content: read count file was generated by HTSeq.

organism: Zea mays

source_name: root

growth_protocol: seeds of the maize inbred line B73 were germinated in moist germination paper

extract_protocol:
Total RNA was extracted using TRIzol reagenet(Invotrogen)
RNA-seq library construction was performed with NEB Next® mRNA Library Prep Master Mix Set (NEB, Ipswich, MA, USA) following manufacturer’s instructions

treatment_protocol: 3-day old uniform seedlings were dipped into liquid N and root hairs were scraped off and collected. The remaining root hair less roots and aerial seedling were collected

tag: cultivar

value: B73 inbred line

tag: developmental stage

value: 3-day old uniform

value: root

tag: genotype

value: zmlrl5 knock out


title: VS_1


title: genomic DNA from sperm cells 11

description: normal sperm sample

label: Cy5 and Cy13

source_name: semen sample 11


title: genomic DNA from sperm cells 17

description: normal sperm sample

label: Cy5 and Cy19

source_name: semen sample 17


title: HuR_PAR-CLIP_onbeads_R2

description: HuR_PConBeads rep2

value: using on-bead ligation of adapters


title: Input_noCL [HU_BB_017_S2_L001]

value: Human embryonic kidney cells


title: genomic DNA from sperm cells 8

description: normal sperm sample

label: Cy5 and Cy10

source_name: semen sample 8


title: C_3

value: control


title: genomic DNA from sperm cells 4

description: normal sperm sample

label: Cy5 and Cy6

source_name: semen sample 4


title: genomic DNA from sperm cells 2

description: normal sperm sample

label: Cy5 and Cy4

source_name: semen sample 2


title: C_2


title: HuR_PAR-CLIP_classic_R2

description: HuR_PC rep2

value: Classical PAR-CLIP


title: genomic DNA from sperm cells 9

description: normal sperm sample

label: Cy5 and Cy11

source_name: semen sample 9

value: Healthy control


title: Input_noCL [HU_BB_016_S1_L001]

value: no cross-link (noCL)


title: wild type root (root hairs were scrapped off) RNA-seq, rep1

value: WT


title: Si-1727-10%-input

city: Shanghai

first: Lei

last: Chen

address: Changhai Road 225, YangPu district

department: International Cooperation Laboratory on Signal Transduction,

institute: Eastern Hepatobiliary Surgery Institute, Second Military Medical University

data_processing:
Raw sequence files were subjected to quality control analysis using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Tophat v2.0.9  to map the cleaned reads to the human reference genome ensemble GRCh38 (hg38) with two mismatches. After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using Cuffdiff . The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM in each sample.
The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2 in hepatocellular carcinoma cell lines.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and reads counts values for all Samples

source_name: liver cancer cells

extract_protocol:
RNA from hepatocellular carcinoma cell lines was purified with RNeasy Micro Kit according to manufacturer’s instructions (Qiagen, Hilden, Germany).
TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions. Both RNA samples and final libraries were quantified by using the Qubit 2.0 Fluorometer(Invitrogen, Carlsbad, CA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies,Santa Clara, CA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on 150 bp pair-ends mode at the on HiSeq2500 (Illumina, San Diego, CA).

value: hepatocellular carcinoma cell

tag: passage

tag: cell lines

tag: antibody

tag: group

value: 10% of total RNA extracted from si-1727 group


title: wild type root (root hairs were scrapped off) RNA-seq, rep2

tag: tissue


title: HuR_PAR-CLIP_onbeads_R1

description: HuR_PConBeads rep1


title: HuR_PAR-CLIP_classic_R1

description: HuR_PC rep1


title: Si-NC-10%-input

tag: cell type

value: 10% of total RNA extracted from si-NC group


title: zmlrl5 knock down roothair RNA-seq, rep2

source_name: roothair

value: W22 inbred line

value: roothair

value: zmlrl5 knock down


title: genomic DNA from sperm cells 3

description: normal sperm sample

label: Cy5 and Cy5

source_name: semen sample 3

tag: gender

value: Male

value: sperm cells

tag: disease state


title: genomic DNA from sperm cells 15

description: normal sperm sample

label: Cy5 and Cy17

source_name: semen sample 15


title: genomic DNA from sperm cells 6

description: normal sperm sample

label: Cy5 and Cy8

source_name: semen sample 6


title: wt3

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

institute: University of British Columbia

description: ribosomally depleted RNA

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the NCTC8325 genome using bowtie2
Bam-sam file conversion/sorting was conducted using samtools
read count tables were generated using htseq-count v.2.5
Genome_build: Staphylococcus aureus subsp. aureus NCTC8325 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: bacteria

extract_protocol:
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

value: Wild-type

tag: strain


title: C_1


title: zmlrl5 knock down roothair RNA-seq, rep1

value: 3-day old uniform


title: genomic DNA from sperm cells 7

city: Toronto

description: normal sperm sample

label: Cy5 and Cy9

source_name: semen sample 7


title: genomic DNA from sperm cells 1

description: normal sperm sample

label: Cy5 and Cy3

source_name: semen sample 1


title: wild type roothair RNA-seq, rep2


title: genomic DNA from sperm cells 20

description: psoriasis sperm

label: Cy5 and Cy22

source_name: semen sample 20

value: Psoriasis without arthritis


title: Lv-1727-IgG-IP

value: IgG

value: lentivirus-mediated circZKSCAN1 overexpression group


title: wild type roothair RNA-seq, rep1


title: aerial seedling RNA-seq, rep2

source_name: aerial seedling

value: B73 inbred line

value: aerial seedling


title: wt_mup3

description: ribosomally depleted RNA

value: mupirocin


title: wt1

description: ribosomally depleted RNA

value: control


title: Lv-GFP-IgG-IP

value: hepatocellular carcinoma cell

value: lentivirus-mediated control group


title: Si-NC- FMRP-IP

value: FMRP

value: small interfering RNA-mediated control group


title: wt2

description: ribosomally depleted RNA


title: wt_mup2

description: ribosomally depleted RNA


title: Lv-1727- FMRP IP


title: aerial seedling RNA-seq, rep1

value: WT


title: 3D midbrain organoids

city: Jung-gu

first: BYOUNGGOOK

last: CHO

state: Seoul

address: 30, Pildong-ro 1-gil

institute: Dongguk Univ

description: Gene expression data in Midbrain organoids derived from human iPSCs.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: The hiPSCs were treated with Accutase to induce dissociation into single cells, and EBs were maintained in human embryonic stem cell growth medium without a ROCK inhibitor for 3 days. To generate 3D organoids, EBs were embedded in a Matrigel matrix (Corning) containing 60% laminin, 30% collagen IV, and 8% entactin to contribute to structural organization. EBs embedded in Matrigel were maintained in an incubator at 37 °C and 5% CO2. Human embryonic stem cell growth medium was replaced with neural stem cell medium (Advanced DMEM/F12 and neurobasal medium, 1x N2, 1x B27, 5% Albumax-I, 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, 3 µM CHIR99021, 0.5 µM A83-01, and 10 ng/ml LIF). Additionally, for neural induction, fibroblast growth factor-2 (20 ng/ml) and epidermal growth factor (20 ng/ml) were included in the neural stem cell medium.

extract_protocol: Total RNA was isolated from organoid samples using an RNeasy RNA isolation kit (QIAGEN).

treatment_protocol: 3D midbrain organoids with or without a G2019S mutation in LRRK2

value: midbrain organoids


title: LRRK2-G2019S 2D cultures

description: Gene expression data in DA neurons derived from LRRK2-G2019S iPSCs.

value: DA neurons


title: wt_mup1

description: ribosomally depleted RNA


title: LRRK2-G2019S 3D midbrain organoids

description: Gene expression data in Midbrain organoids derived from LRRK2-G2019S iPSCs.


title: Lv-GFP- FMRP -IP


title: Si-1727- FMRP-IP

value: small interfering RNA-mediated transient circZKSCAN1 knockdown


title: mut3

description: ribosomally depleted RNA

value: RSH synthase mutant


title: root RNA-seq, rep1

source_name: root

value: 3-day old uniform

value: root


title: roothair RNA-seq, rep2

value: roothair


title: mut_mup3

description: ribosomally depleted RNA


title: roothair RNA-seq, rep1


title: Wildtype 2D cultures

description: Gene expression data in neurons derived from human iPSCs.

source_name: DA neurons derived from human iPSCs


title: mut_mup2

description: ribosomally depleted RNA


title: genomic DNA from sperm cells 5

description: normal sperm sample

label: Cy5 and Cy7

source_name: semen sample 5

value: Male

value: sperm cells

value: Healthy control


title: mut_mup1

description: ribosomally depleted RNA

value: mupirocin


title: root RNA-seq, rep2

value: B73 inbred line


title: mut2

description: ribosomally depleted RNA

value: control


title: miR-122-Tet-On_with doxycycline

city: Guangzhou

first: Hui

last: Xu

address: 135#, Xingangxi Road

department: School of Life Sciences

institute: Sun Yat-Sen University

description: Gene expression data from  miR-122-Tet-On cells treated with doxycycline

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software (AGCC) and RMA method were used to identify differentially expressed genes.

source_name: miR-122-Tet-On, with doxycycline

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA with MessageAmp™ Premier RNA Amplification Kit (Ambion #1792) according to the manufacturer's instructions.

growth_protocol: HepG2 and miR-122-Tet-On HepG2 cells were maintained in MEM supplemented with 10% fetal bovine serum and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin).

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

treatment_protocol: HepG2 cells were transfected with 50nM control (NC) or miR-122 mimics and cells were harvested 72 hours after transfection. 1000ng/ml doxycycline was added into the culture medium of miR-122-Tet-On HepG2 cells for 72 hours to induce miR-122 expression; Cells without doxycycline served as control.

tag: tumor cell line


title: zmlrl5 knock out root RNA-seq, rep1

value: zmlrl5 knock out


title: miR-122-Tet-On_untreated

description: Gene expression data from untreated miR-122-Tet-On cells

source_name: miR-122-Tet-On, untreated


title: No treatment 2

description:
bacterial mRNA
sample name in processed data file:
S2

source_name: exponential phase bacteria culture

tag: media

value: M9 minimal medium

tag: growth phase

value: exponential

tag: treatment


title: 1012-00005.Psoriasis.LS.Week12.Etanercept

status: Public on Feb 01 2019

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: Lesional tissue of psoriasis patient

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subjectid

tag: condition

value: Psoriasis

value: Lesional

tag: timepoint

value: Week 12

value: Etanercept

tag: pasi75 response at week 12

value: R

tag: pasi

tag: technique

value: Vivo

tag: amplification cycles


title: 2015-00001.Psoriasis.LS.Week12.Etanercept


title: 1016-00003.Psoriasis.LS.Week12.Etanercept


title: 1022-00009.Psoriasis.LS.Week12.Etanercept


title: 1025-00008.Psoriasis.LS.Week12.Etanercept


title: 2012-00038.Psoriasis.LS.Week12.Etanercept

value: NR


title: 1006-00004.Psoriasis.LS.Week12.Etanercept


title: 2015-00012.Psoriasis.LS.Week12.Etanercept


title: M68_vs_WT_1

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Comparison of S1H and M68 strain

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 (Smyth 2005) as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50 (Ritchie et al. 2007). Data were normalized within each array using the printing-tip loess normalization algorithm (Smyth and Speed 2003). The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package (Smyth 2005). The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method (Smyth 2004). P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg 1995).

organism: Rhodospirillum rubrum

source_name: S1H, wildtype

label_protocol: Ten micrograms of RNA were reverse transcribed using Pronto kit (Promega, United States) following manufacturer’s instructions. Two color labeling, green for solvent control samples and red for condition (Triclosan challenge) samples, was performed using respectively Cy3-dCTP and Cy5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: R. rubrum cultures of S1H and M68 were grown to mid-log phase (ca. OD680 2).

extract_protocol: Twenty ml of cultures were mixed with RNAprotect® Bacteria Reagent (Qiagen) for total RNA stabilization following manufacturer’s instructions and stored as pellets at -80 °C until further use. Bacterial lysis was done following the protocol for Gram-negative bacteria of the SV Total RNA Isolation System kit (Promega). Briefly, stabilized bacterial pellets were resuspended in 100 μl of freshly prepared TE (Tris 10 mM, EDTA 1 mM) containing lysozyme 3 mg/ml and incubated for 10 minutes at room temperature. Total RNA isolation was performed using SV total RNA Isolation system (Promega). RNA quality/integrity was assessed using a BioAnalyzer 2100 (Agilent) where samples with a RNA Integrity Number (RIN) value above 8 were used for microarray experiment. RNA quantity was measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop technologies).

treatment_protocol: All strains were grown in normal conditions, as the aim of this study was to compare the general gene expression of two different strains.

source_name: M68, QS-deficient mutant


title: 1025-00002.Psoriasis.LS.Week12.Etanercept


title: 1016-00017.Psoriasis.LS.Week12.Etanercept


title: 1019-00003.Psoriasis.LS.Week12.Etanercept


title: 1025-00006.Psoriasis.LS.Week12.Etanercept


title: HepG2_miR-122 mimic

description: Gene expression data from HepG2 cells transfected with miR-122 mimic

source_name: HepG2 transfected with miR-122 mimic


title: M68_vs_WT_2

description: Comparison of S1H and M68 strain


title: M68_vs_WT_3

description: Comparison of S1H and M68 strain


title: 1016-00008.Psoriasis.LS.Week12.Etanercept


title: 2015-00005.Psoriasis.LS.Week12.Etanercept


title: 1019-00004.Psoriasis.LS.Week12.Etanercept


title: 1019-00016.Psoriasis.LS.Week12.Etanercept


title: M68_vs_WT_4

description: Comparison of S1H and M68 strain


title: 2016-00006.Psoriasis.LS.Week12.Etanercept


title: 1012-00002.Psoriasis.LS.Week12.Etanercept


title: 1019-00014.Psoriasis.LS.Week12.Etanercept


title: 1022-00006.Psoriasis.LS.Week12.Etanercept


title: 2016-00027.Psoriasis.LS.Week12.Etanercept


title: 1006-00002.Psoriasis.LS.Week12.Etanercept


title: 1022-00012.Psoriasis.LS.Week12.Etanercept


title: 2012-00036.Psoriasis.LS.Week12.Etanercept


title: HepG2_NC mimic

description: Gene expression data from HepG2 cells transfected with NC mimic

source_name: HepG2 transfected with NC mimic


title: 2016-00035.Psoriasis.LS.Week12.Etanercept


title: 2016-00001.Psoriasis.LS.Week12.Ustekinumab45mg

value: Ustekinumab 45 mg


title: 2012-00019.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1012-00004.Psoriasis.LS.Week12.Etanercept


title: 1016-00011.Psoriasis.LS.Week12.Ustekinumab45mg


title: 2016-00031.Psoriasis.LS.Week12.Etanercept


title: 1022-00016.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1019-00013.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1022-00020.Psoriasis.LS.Week12.Ustekinumab45mg


title: 2016-00020.Psoriasis.LS.Week12.Etanercept


title: 1022-00027.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1025-00004.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1022-00017.Psoriasis.LS.Week12.Etanercept


title: 1012-00007.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1022-00003.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1022-00005.Psoriasis.LS.Week12.Etanercept


title: 1006-00005.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1019-00015.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1016-00010.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1016-00019.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1012-00006.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1022-00024.Psoriasis.LS.Week12.Ustekinumab45mg


title: 2016-00018.Psoriasis.LS.Week12.Ustekinumab45mg


title: 2012-00023.Psoriasis.LS.Week12.Ustekinumab90mg

value: Ustekinumab 90 mg


title: 1019-00010.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1019-00007.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00002.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00021.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2016-00025.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1016-00014.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2015-00007.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00004.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2012-00008.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2012-00031.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00001.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00025.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00014.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00019.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1019-00001.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2015-00014.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1016-00001.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1012-00008.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2012-00042.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2016-00037.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1019-00008.Psoriasis.LS.Week12.Ustekinumab90mg


title: 2016-00013.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1012-00003.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00012.Psoriasis.LS.Week1.Etanercept

value: Week 1


title: 2016-00009.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1016-00008.Psoriasis.LS.Week1.Etanercept


title: 2016-00007.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1022-00017.Psoriasis.LS.Week1.Etanercept


title: 1019-00003.Psoriasis.LS.Week1.Etanercept


title: 2015-00012.Psoriasis.LS.Week1.Etanercept


title: 2015-00001.Psoriasis.LS.Week1.Etanercept


title: 1019-00009.Psoriasis.LS.Week1.Etanercept


title: 1019-00014.Psoriasis.LS.Week1.Etanercept


title: 1022-00008.Psoriasis.LS.Week1.Etanercept


title: 1022-00005.Psoriasis.LS.Week1.Etanercept


title: 2016-00035.Psoriasis.LS.Week1.Etanercept


title: 2016-00019.Psoriasis.LS.Week1.Etanercept


title: 1012-00001.Psoriasis.LS.Week12.Ustekinumab90mg


title: 1019-00005.Psoriasis.LS.Week12.Ustekinumab45mg


title: 1025-00008.Psoriasis.LS.Week1.Etanercept


title: 1019-00004.Psoriasis.LS.Week1.Etanercept


title: 1025-00002.Psoriasis.LS.Week1.Etanercept


title: 2016-00020.Psoriasis.LS.Week1.Etanercept


title: 1022-00006.Psoriasis.LS.Week1.Etanercept


title: 1016-00003.Psoriasis.LS.Week1.Etanercept


title: 2016-00006.Psoriasis.LS.Week1.Etanercept


title: 1005-00009.Psoriasis.LS.Week1.Etanercept


title: 1012-00002.Psoriasis.LS.Week1.Etanercept


title: 1012-00005.Psoriasis.LS.Week1.Etanercept


title: 1019-00016.Psoriasis.LS.Week1.Etanercept


title: 2016-00031.Psoriasis.LS.Week1.Etanercept


title: 1025-00006.Psoriasis.LS.Week1.Etanercept


title: 1006-00002.Psoriasis.LS.Week1.Etanercept


title: 1012-00004.Psoriasis.LS.Week1.Etanercept


title: 1022-00009.Psoriasis.LS.Week1.Etanercept


title: 1006-00004.Psoriasis.LS.Week1.Etanercept


title: 2015-00005.Psoriasis.LS.Week1.Etanercept


title: 2012-00038.Psoriasis.LS.Week1.Etanercept


title: 1019-00005.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1019-00015.Psoriasis.LS.Week1.Ustekinumab45mg


title: 2016-00008.Psoriasis.LS.Week1.Ustekinumab45mg


title: 2016-00018.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1019-00013.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1022-00016.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1016-00010.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1016-00017.Psoriasis.LS.Week1.Etanercept


title: 2016-00027.Psoriasis.LS.Week1.Etanercept


title: 1016-00011.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1022-00024.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1016-00019.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1016-00001.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00027.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1012-00001.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1012-00006.Psoriasis.LS.Week1.Ustekinumab45mg


title: 2015-00007.Psoriasis.LS.Week1.Ustekinumab90mg