title: B16F0-RFP

city: New York

first: James

middle: C

last: Chen

state: NEW YORK

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: (Human: NCBI/build37.2; Mouse: UCSC/mm10)
Supplementary_files_format_and_content: tab-delimited TPM reads

source_name: B16f10 line (derived from B6 mice)

growth_protocol: Variable, human lines maintained according to recommendations by ATCC. B16F10 using standard DMEM 10% FBS protocols

extract_protocol:
Trizol RNA extraction, manufacturer protocols
Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: Transfected with viral particles of PLOC vectors and placed on 5-day blasticidin selection at manufacturer recommended protocols

tag: sample type

value: in vitro culture

tag: treatment

value: pLOC RFP, stable transfection


title: B16F0-DLX4

status: Public on Feb 27 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: pLOC DLX4 stable transfection


title: Participant ID and visit (v) number [phchp048v1]

type: RNA

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

description: Independent Test cohort blood gene expression data

hyb_protocol: Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.

scan_protocol: Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values

data_processing: The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis.  We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and  statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.

label: Biotin

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Sample Labeling:  Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps:     1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.    2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA.    3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.    4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step.    5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol:
We used three independent cohorts: discovery (major psychiatric disorders), validation (major psychiatric disorders with clinically severe pain disorders), and testing (an independent major psychiatric disorders cohort for predicting pain state, and for predicting future ED visits for pain) (Figure 1A).
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per Indiana University IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a visual analog scale (1-10) for assessing pain and the SF-36 quality of life scale, which has two pain related items (items 21 and 22), and the blood was drawn. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing. Whole-blood RNA was extracted for microarray gene expression studies from the PAXgene tubes, as detailed below.
Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

tag: gender

value: Male

tag: diagnosis

value: SZA

tag: test cohort first year emergency department visits with pain

value: Yes

tag: test cohort all future emergency department visits with pain


title: Participant ID and visit (v) number [phchp048v3]


title: Participant ID and visit (v) number [phchp048v2]


title: Participant ID and visit (v) number [phchp055v2]

value: Female

value: BP


title: Male_KO_D07_Rep2

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description:
Liver homogenate
DS057

data_processing:
RNA-seq reads were aligned to the Mouse mm9 genome assembly and transcriptome using TopHat version 2.0.13 with Bowtie version 1.1.2. Counts per gene were calculated using the Rsubreads R package and transformed in RPKM. Normalization was done via the edgeR R package using TMM. The cutoff for genes considered as non-transcribed was calculated according to the method described in https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-778.
Genome_build: UCSC Mm9
Supplementary_files_format_and_content: Matrix table with processed log2 FPKM for all samples

molecule: polyA RNA

source_name: Liver

growth_protocol: Females and littermate males were housed four to five per cage at 23°C, with a 12:12 hour light-dark cycle and ad libitum access to water and food. Tamoxifen treatment and all tissue collections were performed at ZT2–3 where ZT0 is the start of the light period

extract_protocol:
Liver tissue from 10-14 week old mice maintained on a breeder chow diet was harvested and freeze-clamped in liquid nitrogen.
Poly(A)-containing RNA from individual livers was used for RNA-seq. RNA was extracted with RNeasy kit (Qiagen cat. # 74104). The disruption and homogenization was done with TissueLyser II. Samples were quantified with MySpec machine and 200μg (in 100μl) of RNA sample was used for further analysis. Strand-specific libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina catalog # RS-122-9004DOC). The fragment ends (50 nucleotides) were sequenced with single-end sequencing technology from HiSeq 2500 (Illumina).

treatment_protocol: Control female Hcfc1 lox/+ and male Hcfc1 lox/Y, and test female Alb-Cre-ERT2tg ; Hcfc1 lox/+ and male Alb-Cre-ERT2tg ; Hcfc1 131 lox/Y mice (10 to 14 weeks old) were administered intraperitoneal injections of 1 mg/mouse tamoxifen [100 μl of 10 mg/ml (1:10 ethanol:corn oil); Sigma-Aldrich CAS # 10540-29-1] three times at 24 hr intervals from Day 0 to Day 2.

tag: Sex

tag: tissue

value: Liver

tag: genotype

value: Hcfc1 hepKO/Y

tag: age (weeks)

tag: time after tamoxifen injection, in days


title: Male_WT_D00_Rep1

description:
Liver homogenate
DS001


title: RFP-5

value: recovered xenografts

value: B6 mouse 10, RFP B16f10 xenograft


title: RFP-4

value: B6 mouse 9, RFP B16f10 xenograft


title: IKZF1-5

value: B6 mouse 5, IKFZ1 B16f10 xenograft


title: Participant ID and visit (v) number [phchp047v1]


title: B16F0-IKZF1

value: pLOC IKZF1, stable transfection


title: Participant ID and visit (v) number [phchp047v3]


title: Participant ID and visit (v) number [phchp047v2]


title: RFP-2

value: B6 mouse 7, RFP B16f10 xenograft


title: RFP-3

value: B6 mouse 8, RFP B16f10 xenograft


title: IKZF1-2

value: B6 mouse 2, IKFZ1 B16f10 xenograft


title: IKZF1-1

value: B6 mouse 1, IKFZ1 B16f10 xenograft


title: IKZF1-3

value: B6 mouse 3, IKFZ1 B16f10 xenograft


title: Participant ID and visit (v) number [phchp046v2]

value: Male


title: IKZF1-4

value: B6 mouse 4, IKFZ1 B16f10 xenograft


title: Participant ID and visit (v) number [phchp042v2]

value: SZA

value: Yes


title: Participant ID and visit (v) number [phchp046v3]


title: Participant ID and visit (v) number [phchp046v1]


title: Participant ID and visit (v) number [phchp041v1]

value: SZ


title: Participant ID and visit (v) number [phchp039v3]

value: BP


title: Participant ID and visit (v) number [phchp042v3]


title: Participant ID and visit (v) number [phchp039v1]


title: Participant ID and visit (v) number [phchp040v1]


title: Participant ID and visit (v) number [phchp040v2]


title: Participant ID and visit (v) number [phchp038v2]


title: White adipose tissue (WAT), LA2_30mpk, rep3

city: Boston

first: eric

last: muise

state: MA

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose WAT tissue was taken for RNA profiling.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Gene expression data were processed using the Robust Multiarray Average (RMA) pipeline and one-way ANOVA analysis was performed to obtain fold change, raw p values, and False Discovery Rate Benjamini & Hochberg (FDR_BH) corrected p values using the Array Studio Software (Omicsoft Corporation, Cary, NC). Probe sets had to pass a pre-filter of Affymetrix MAS5 present call p-value < 0.05 in > 50% of the samples, per treatment group, to qualify for further analysis. Average fold changes between 1) exercise and sedentary (vehicle treated) or 2) compound and vehicle treatment groups (both sedentary) were generated with the sedentary vehicle group serving as baseline.

label: biotin

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cDNA.

growth_protocol: Male lean C57BL/6 were purchased from Taconic (Hudson, NY) at 8 weeks of age and maintained on chow diet (Teklad 7012, Research Diets, Inc., New Brunswick, NJ) with free access to water in a 12 h light/12 h dark cycle.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

treatment_protocol: At 12 weeks of age, lean C57BL/6 mice were fasted by removing food at 7:30 am and then dosed with vehicle (0.25% MC, 5% Tween-80, 0.02% SDS) or AMPK activators by oral gavage at around 9:30 am, and kept sedentary for the remainder of the study period. For the exercise arm, mice were put on a treadmill (Columbus Instruments International, OH) for exercise with speed set at 10 meter/min. Mice exercised for 30 min followed by 30 min rest and the total running distance was 1300 meters.

value: IWAT

tag: strain

tag: age

value: 12 weeks


title: Participant ID and visit (v) number [phchp038v3]


title: Participant ID and visit (v) number [phchp031v3]


title: White adipose tissue (WAT), LA2_3mpk, rep5

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 3mpk and 6 hours post dose WAT tissue was taken for RNA profiling.


title: White adipose tissue (WAT), LA2_30mpk, rep4


title: Participant ID and visit (v) number [phchp040v3]


title: White adipose tissue (WAT), LA2_30mpk, rep1


title: White adipose tissue (WAT), LA2_30mpk, rep2


title: Participant ID and visit (v) number [phchp042v1]


title: White adipose tissue (WAT), LA2_3mpk, rep2


title: Participant ID and visit (v) number [phchp031v2]


title: White adipose tissue (WAT), LA2_3mpk, rep4


title: White adipose tissue (WAT), LA2_3mpk, rep3


title: White adipose tissue (WAT), LA2_3mpk, rep1


title: White adipose tissue (WAT), exercise, rep5

description: Mice underwent an acute bout of exercise consisting of 1300 m of treadmill running.


title: Participant ID and visit (v) number [phchp031v1]


title: Participant ID and visit (v) number [phchp033v1]


title: Participant ID and visit (v) number [phchp038v1]


title: White adipose tissue (WAT), exercise, rep4


title: Heart, Vehicle, rep4

description: Mice were treated with a single dose of Vehicle and 6 hours post dose Heart was taken for RNA profiling.

source_name: Heart, Vehicle, rep4

value: Heart


title: Participant ID and visit (v) number [phchp030v1]


title: Participant ID and visit (v) number [phchp027v1]


title: Heart, Vehicle, rep2

source_name: Heart, Vehicle, rep2


title: Participant ID and visit (v) number [phchp026v1]


title: White adipose tissue (WAT), exercise, rep2


title: Participant ID and visit (v) number [phchp030v3]


title: White adipose tissue (WAT), exercise, rep1


title: Participant ID and visit (v) number [phchp026v3]


title: Heart, Vehicle, rep1

source_name: Heart, Vehicle, rep1


title: Heart, Vehicle, rep5

source_name: Heart, Vehicle, rep5


title: White adipose tissue (WAT), exercise, rep3


title: Participant ID and visit (v) number [phchp026v2]


title: Participant ID and visit (v) number [phchp025v1]


title: Participant ID and visit (v) number [phchp021v3]


title: Participant ID and visit (v) number [phchp021v2]


title: Participant ID and visit (v) number [phchp024v1]


title: Heart, SA2_3mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 3mpk and 6 hours post dose Heart was taken for RNA profiling.

source_name: Heart, SA2_3mpk, rep5


title: Heart, SA2_20mpk, rep2

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 20mpk and 6 hours post dose Heart was taken for RNA profiling.

source_name: Heart, SA2_20mpk, rep2


title: Heart, SA2_3mpk, rep4

source_name: Heart, SA2_3mpk, rep4


title: Participant ID and visit (v) number [phchp022v2]


title: Participant ID and visit (v) number [phchp021v1]


title: Participant ID and visit (v) number [phchp020v1]


title: Participant ID and visit (v) number [phchp019v5]

tag: test cohort pain state


title: Heart, SA2_20mpk, rep4

source_name: Heart, SA2_20mpk, rep4


title: Heart, LA2_30mpk, rep4

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose Heart was taken for RNA profiling.

source_name: Heart, LA2_30mpk, rep4


title: Participant ID and visit (v) number [phchp020v2]


title: Participant ID and visit (v) number [phchp020v3]


title: Heart, SA2_20mpk, rep1

source_name: Heart, SA2_20mpk, rep1


title: Heart, SA2_3mpk, rep2

source_name: Heart, SA2_3mpk, rep2


title: Participant ID and visit (v) number [phchp019v1]


title: Heart, SA2_3mpk, rep3

source_name: Heart, SA2_3mpk, rep3


title: Participant ID and visit (v) number [phchp019v3]


title: Heart, LA2_30mpk, rep5

source_name: Heart, LA2_30mpk, rep5


title: Participant ID and visit (v) number [phchp019v2]


title: Heart, LA2_30mpk, rep3

source_name: Heart, LA2_30mpk, rep3


title: Heart, LA2_30mpk, rep2

source_name: Heart, LA2_30mpk, rep2


title: Heart, Vehicle, rep3

source_name: Heart, Vehicle, rep3


title: Participant ID and visit (v) number [phchp017v3]

source_name: Whole Blood


title: Heart, SA2_3mpk, rep1

source_name: Heart, SA2_3mpk, rep1


title: Participant ID and visit (v) number [phchp017v2]


title: Participant ID and visit (v) number [phchp016v3]


title: Participant ID and visit (v) number [phchp016v2]


title: Participant ID and visit (v) number [phchp016v1]


title: Heart, LA2_30mpk, rep1

source_name: Heart, LA2_30mpk, rep1


title: Heart, LA2_3mpk, rep4

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 3mpk and 6 hours post dose Heart was taken for RNA profiling.

source_name: Heart, LA2_3mpk, rep4


title: Participant ID and visit (v) number [phchp014v1]

value: PSYCH


title: Heart, LA2_3mpk, rep5

source_name: Heart, LA2_3mpk, rep5


title: Heart, SA2_20mpk, rep3

source_name: Heart, SA2_20mpk, rep3


title: Heart, LA2_3mpk, rep3

source_name: Heart, LA2_3mpk, rep3


title: Heart, LA2_3mpk, rep1

source_name: Heart, LA2_3mpk, rep1


title: Participant ID and visit (v) number [phchp013v3]


title: Participant ID and visit (v) number [phchp013v1]


title: Heart, LA2_3mpk, rep2

source_name: Heart, LA2_3mpk, rep2


title: Heart, exercise, rep5

source_name: Heart, exercise, rep5


title: Heart, exercise, rep3

source_name: Heart, exercise, rep3


title: Participant ID and visit (v) number [phchp012v3]


title: Heart, exercise, rep4

source_name: Heart, exercise, rep4


title: Participant ID and visit (v) number [phchp010v3]


title: Participant ID and visit (v) number [phchp022v1]


title: Heart, exercise, rep2

source_name: Heart, exercise, rep2


title: Brown adipose tissue (BAT), Vehicle, rep5

description: Mice were treated with a single dose of Vehicle and 6 hours post dose BAT tissue was taken for RNA profiling.

value: BAT


title: Heart, exercise, rep1

source_name: Heart, exercise, rep1


title: Participant ID and visit (v) number [phchp010v1]


title: Brown adipose tissue (BAT), Vehicle, rep3


title: Participant ID and visit (v) number [phchp012v1]


title: Participant ID and visit (v) number [phchp009v3]


title: Participant ID and visit (v) number [phchp012v2]


title: Participant ID and visit (v) number [phchp010v2]


title: Participant ID and visit (v) number [phchp009v1]


title: Participant ID and visit (v) number [phchp008v1]


title: Participant ID and visit (v) number [phchp006v1]


title: Brown adipose tissue (BAT), Vehicle, rep2


title: Participant ID and visit (v) number [phchp006v2]


title: Participant ID and visit (v) number [phchp005v3]


title: Participant ID and visit (v) number [phchp003v5]


title: Brown adipose tissue (BAT), SA2_20mpk, rep4

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 20mpk and 6 hours post dose BAT tissue was taken for RNA profiling.


title: Brown adipose tissue (BAT), SA2_20mpk, rep5


title: Participant ID and visit (v) number [phchp005v2]


title: Brown adipose tissue (BAT), Vehicle, rep1


title: Brown adipose tissue (BAT), SA2_20mpk, rep1


title: Participant ID and visit (v) number [phchp003v4]


title: Brown adipose tissue (BAT), SA2_3mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 3mpk and 6 hours post dose BAT tissue was taken for RNA profiling.


title: Brown adipose tissue (BAT), SA2_20mpk, rep2


title: Participant ID and visit (v) number [phchp005v1]


title: Participant ID and visit (v) number [phchp003v3]


title: Brown adipose tissue (BAT), SA2_3mpk, rep4


title: Participant ID and visit (v) number [phchp003v2]


title: Brown adipose tissue (BAT), SA2_3mpk, rep3


title: Brown adipose tissue (BAT), SA2_3mpk, rep2


title: Participant ID and visit (v) number [phchp003v1]


title: Brown adipose tissue (BAT), SA2_3mpk, rep1


title: Brown adipose tissue (BAT), LA2_30mpk, rep3

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose BAT tissue was taken for RNA profiling.


title: Brown adipose tissue (BAT), LA2_30mpk, rep5


title: Participant ID and visit (v) number [phchp367v1]

description: Validation Cohort Blood Gene Expression

tag: pain scale(1-10)

tag: sf-36 pain (q21+ q22) severe>=10


title: Participant ID and visit (v) number [phchp355v2]

description: Validation Cohort Blood Gene Expression

value: Female

value: MDD


title: Brown adipose tissue (BAT), LA2_30mpk, rep1


title: Participant ID and visit (v) number [phchp346v1]

description: Validation Cohort Blood Gene Expression

value: PTSD


title: Brown adipose tissue (BAT), LA2_3mpk, rep4

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 3mpk and 6 hours post dose BAT tissue was taken for RNA profiling.


title: Brown adipose tissue (BAT), LA2_3mpk, rep5


title: Participant ID and visit (v) number [phchp340v3]

description: Validation Cohort Blood Gene Expression


title: Brown adipose tissue (BAT), LA2_30mpk, rep4


title: Participant ID and visit (v) number [phchp350v1]

description: Validation Cohort Blood Gene Expression


title: Brown adipose tissue (BAT), LA2_3mpk, rep3


title: GU-MNG-1_1

type: genomic

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchips using standard Illumina protocols.

scan_protocol: Standard Illumina protocol

data_processing: Raw methylation data was processed and normalized with Noob normalization using the statistical software R with the packages ChAMP and Minfi. Probes with single-nucleotide polymorphisms (SNP), aligning to multiple locations, located on the sex chromosomes and probes with missing values were removed leaving 763,043 CpG sites for analysis.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Meningioma_1_biopsy 1

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using the DNeasy Blood and Tissue Kit and TissueLyser (Qiagen) according to the manufacturer's instructions except lysis with Proteinase K was performed overnight.

treatment_protocol: Tissue specimen were fresh-frozen in liquid nitrogen.

value: Meningioma


title: Participant ID and visit (v) number [phchp338v3]

description: Validation Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp338v4]

description: Validation Cohort Blood Gene Expression


title: GU-MNG-3_2

source_name: Meningioma_3_biopsy 2


title: GU-MNG-2_2

source_name: Meningioma_2_biopsy 2


title: GU-HGG-287_3

source_name: High-grade glioma_287_biopsy 3

value: High-grade glioma


title: GU-MNG-3_1

source_name: Meningioma_3_biopsy 1


title: GU-HGG-287_2

source_name: High-grade glioma_287_biopsy 2


title: GU-MNG-3_3

source_name: Meningioma_3_biopsy 3


title: GU-HGG-271_3

source_name: High-grade glioma_271_biopsy 3


title: GU-HGG-287_4

source_name: High-grade glioma_287_biopsy 4


title: Brown adipose tissue (BAT), LA2_3mpk, rep2


title: GU-HGG-271_2

source_name: High-grade glioma_271_biopsy 2


title: GU-MNG-1_3

source_name: Meningioma_1_biopsy 3


title: Participant ID and visit (v) number [phchp338v2]

description: Validation Cohort Blood Gene Expression

source_name: Whole Blood


title: GU-MNG-2_3

source_name: Meningioma_2_biopsy 3


title: Brown adipose tissue (BAT), exercise, rep5


title: Brown adipose tissue (BAT), LA2_3mpk, rep1


title: GU-HGG-269_2

source_name: High-grade glioma_269_biopsy 2


title: GU-MNG-1_2

source_name: Meningioma_1_biopsy 2


title: GU-HGG-287_1

source_name: High-grade glioma_287_biopsy 1


title: GU-HGG-269_3

source_name: High-grade glioma_269_biopsy 3


title: GU-MNG-2_1

source_name: Meningioma_2_biopsy 1


title: GU-HGG-269_1

source_name: High-grade glioma_269_biopsy 1


title: GU-HGG-260_3

source_name: High-grade glioma_260_biopsy 3


title: Brown adipose tissue (BAT), exercise, rep4


title: GU-HGG-271_1

source_name: High-grade glioma_271_biopsy 1


title: Participant ID and visit (v) number [phchp311v1]

description: Validation Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp311v2]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-225_2

source_name: High-grade glioma_225_biopsy 2

value: high-grade glioma


title: Brown adipose tissue (BAT), exercise, rep2


title: Brown adipose tissue (BAT), exercise, rep3


title: GU-HGG-260_2

source_name: High-grade glioma_260_biopsy 2

value: Male


title: Brown adipose tissue (BAT), exercise, rep1


title: Participant ID and visit (v) number [phchp310v3]

description: Validation Cohort Blood Gene Expression

value: MOOD


title: GU-HGG-260_1

source_name: High-grade glioma_260_biopsy 1


title: Participant ID and visit (v) number [phchp336v2]

description: Validation Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp287v2]

description: Validation Cohort Blood Gene Expression

value: SZA


title: GU-HGG-225_3

source_name: High-grade glioma_225_biopsy 3


title: GU-HGG-225_1

source_name: High-grade glioma_225_biopsy 1


title: Muscle, Vehicle, rep5

description: Mice were treated with a single dose of Vehicle and 6 hours post dose Muscle (Vastus Lateralis) was taken for RNA profiling.

source_name: Muscle, Vehicle, rep5

value: Vastus


title: GU-HGG-224_2

source_name: High-grade glioma_224_biopsy 2


title: Muscle, Vehicle, rep4

source_name: Muscle, Vehicle, rep4


title: Participant ID and visit (v) number [phchp285v3]

description: Validation Cohort Blood Gene Expression

source_name: Whole Blood


title: Muscle, Vehicle, rep2

source_name: Muscle, Vehicle, rep2


title: Participant ID and visit (v) number [phchp282v1]

description: Validation Cohort Blood Gene Expression

value: SZ


title: Participant ID and visit (v) number [phchp282v2]

description: Validation Cohort Blood Gene Expression


title: Muscle, Vehicle, rep3

source_name: Muscle, Vehicle, rep3


title: GU-HGG-224_1

source_name: High-grade glioma_224_biopsy 1


title: GU-HGG-216_3

source_name: High-grade glioma_216_biopsy 3


title: mRNA_dcp2∆dhh1∆_replicate 2

city: Bethesda

first: Alan

last: Hinnebusch

state: MD

address: 6 Center Drive, Building 6, Room 233

department: NICHD

institute: NIH

description:
mRNA
Experiment 2
DESeq2_dcp2deltadhh1delta_vs_dcp2delta

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with Bowtie2-2.6.0
Transcriptome alignment with TopHat v2.1.1
Read quantitation using custom scripts
Analysis of reads using DESeq2
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed data (csv) files contain five sections of DESeq2 analysis, each with 5 columns of data, providing:  Fold changes in mutant versus WT (or double mutant versus single mutant) in translational efficiency (TE Change), ribosome occupancy  (Ribo Change) , or mRNA abundance (mRNA Change) all presented as ratios of mutant to WT values (sections 1-3); TE in WT (or single mutant) (section 4); TE in mutant (or double mutant) (section 5). In each section, there are five columns providing: systemmatic gene name, log2 values of the indicated parameter, p value, FDRpadj (or adjusted p value), and common gene name.  The last column in the file provides a "description" of each gene product.

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were grown to an OD600 of 0.6-0.7 in YPD medium

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in a freezer mill.
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast" Martin Marcos et al. (2017) eLife 6:e31250

treatment_protocol: No treatment was applied to these cells

tag: strain/genotype

value: QZY128 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100) dcp2delta::HIS3 dhh1delta::KanMX4)


title: mRNA_dcp2∆dhh1∆_replicate 1


title: mRNA_dcp2∆two_replicate 1


title: mRNA_dcp2∆two_replicate 2


title: Muscle, Vehicle, rep1

source_name: Muscle, Vehicle, rep1


title: mRNA_dcp2∆scd6∆_replicate 2

description:
mRNA
Experiment 2
DESeq2_dcp2deltascd6delta_vs_dcp2delta

value: FZY843 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100) dcp2delta::HIS3 scd6delta::KanMX4)


title: mRNA_dcp2∆scd6∆_replicate 1


title: GU-HGG-204_3

source_name: High-grade glioma_204_biopsy 3


title: Participant ID and visit (v) number [phchp254v2]

description: Validation Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp215v1]

description: Validation Cohort Blood Gene Expression


title: mRNA_dcp2∆one_replicate 2


title: Muscle, SA2_20mpk, rep4

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 20mpk and 6 hours post dose Muscle (Vastus Lateralis) was taken for RNA profiling.

source_name: Muscle, SA2_20mpk, rep4

value: 12 weeks


title: mRNA_dcp2∆one_replicate 1


title: Participant ID and visit (v) number [phchp287v1]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-224_3

source_name: High-grade glioma_224_biopsy 3


title: Ribo_dcp2∆dhh1∆_replicate 2

description:
Ribosome-protected RNA
Experiment 2
DESeq2_dcp2deltadhh1delta_vs_dcp2delta


title: Muscle, SA2_20mpk, rep5

source_name: Muscle, SA2_20mpk, rep5


title: Participant ID and visit (v) number [phchp203v1]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-204_2

source_name: High-grade glioma_204_biopsy 2


title: Ribo_dcp2∆dhh1∆_replicate 1


title: Ribo_dcp2∆two_replicate 2


title: GU-HGG-204_1

source_name: High-grade glioma_204_biopsy 1


title: GU-HGG-200_3

source_name: High-grade glioma_200_biopsy 3


title: Muscle, SA2_20mpk, rep2

source_name: Muscle, SA2_20mpk, rep2


title: Muscle, SA2_20mpk, rep1

source_name: Muscle, SA2_20mpk, rep1


title: Participant ID and visit (v) number [phchp160v3]

description: Validation Cohort Blood Gene Expression


title: Ribo_dcp2∆one_replicate 2

description:
Ribosome-protected RNA
Experiment 2
DESeq2_dcp2deltascd6delta_vs_dcp2delta


title: GU-HGG-216_1

source_name: High-grade glioma_216_biopsy 1


title: Muscle, SA2_20mpk, rep3

source_name: Muscle, SA2_20mpk, rep3


title: GU-HGG-200_2

source_name: High-grade glioma_200_biopsy 2


title: Ribo_dcp2∆scd6∆_replicate 1


title: Participant ID and visit (v) number [phchp182v2]

description: Validation Cohort Blood Gene Expression

source_name: Whole Blood


title: GU-HGG-200_1

source_name: High-grade glioma_200_biopsy 1


title: GU-HGG-182_3

source_name: High-grade glioma_182_biopsy 3


title: Muscle, SA2_3mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 3mpk and 6 hours post dose Muscle (Vastus Lateralis) was taken for RNA profiling.

source_name: Muscle, SA2_3mpk, rep5


title: Ribo_dcp2∆one_replicate 1

source_name: Whole cells


title: mRNA_dhh1∆_replicate 1

description:
mRNA
Experiment 1
DESeq2_dhh1delta_vs_WT

value: QZY126 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100) dhh1delta::KanMX4)


title: GU-HGG-185_1

source_name: High-grade glioma_185_biopsy 1


title: mRNA_dhh1∆_replicate 2


title: Muscle, SA2_3mpk, rep4

source_name: Muscle, SA2_3mpk, rep4


title: GU-HGG-216_2

source_name: High-grade glioma_216_biopsy 2


title: mRNA_scd6∆_replicate 2

description:
mRNA
Experiment 1
DESeq2_scd6delta_vs_WT


title: GU-HGG-182_1

source_name: High-grade glioma_182_biopsy 1


title: Participant ID and visit (v) number [phchp155v1]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-185_2

source_name: High-grade glioma_185_biopsy 2


title: mRNA_scd6∆_replicate 1


title: mRNA_WT_replicate 2

description:
mRNA
Experiment 1
DESeq2_scd6delta_vs_WT and DESeq2_dhh1delta_vs_WT


title: mRNA_WT_replicate 1


title: Ribo_dhh1∆_replicate 1

description:
Ribosome-protected RNA
Experiment 1
DESeq2_dhh1delta_vs_WT


title: GU-HGG-185_3

source_name: High-grade glioma_185_biopsy 3


title: GU-HGG-154_1

source_name: High-grade glioma_154_biopsy 1


title: Ribo_scd6∆_replicate 2

description:
Ribosome-protected RNA
Experiment 1
DESeq2_scd6delta_vs_WT


title: Ribo_dhh1∆_replicate 2


title: Ribo_scd6∆_replicate 1


title: Ribo_WT_replicate 2

description:
Ribosome-protected RNA
Experiment 1
DESeq2_scd6delta_vs_WT and DESeq2_dhh1delta_vs_WT


title: Participant ID and visit (v) number [phchp141v1]

description: Validation Cohort Blood Gene Expression

value: BP


title: Participant ID and visit (v) number [phchp141v3]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-154_3

source_name: High-grade glioma_154_biopsy 3


title: Participant ID and visit (v) number [phchp133v1]

description: Validation Cohort Blood Gene Expression


title: Ribo_dcp2∆two_replicate 1


title: Muscle, SA2_3mpk, rep3

source_name: Muscle, SA2_3mpk, rep3


title: Participant ID and visit (v) number [phchp206v1]

description: Validation Cohort Blood Gene Expression


title: GU-HGG-154_2

source_name: High-grade glioma_154_biopsy 2


title: Ribo_WT_replicate 1


title: Muscle, SA2_3mpk, rep1

source_name: Muscle, SA2_3mpk, rep1


title: Ribo_dcp2∆scd6∆_replicate 2


title: SUP130

city: Seville

first: Belén

last: Gómez-González

email: gomezb@us.es, belen.gomez@cabimer.es

address: Cabimer/Avda Américo Vespucio, 24

country: Spain

institute: University of Seville

description: Whole genome sequencing

library_source: genomic

data_processing:
Library strategy: Whole genome sequencing
Paired-end reads were aligned to the yeast sacCer2 genome assembly using Novoalign 2.07.14 (http://novocraft.com), with the parameters for the mean and standard deviation of the expected size distribution set to 175 and 125, respectively. Alignments for 101bp paired-end reads were post-processed for removal of reads that could have arisen from PCR duplication (picard-tools 1.81; http://sourceforge.net/projects/picard/). Approximately 96% of paired reads were found to align concordantly to the reference genome resulting in a median coverage of 200x across all samples.
Base-level nucleotide counts were obtained using deepSNV 1.2.3 (Gerstung, et al. 2012) with a minimum base quality threshold of 30. SNV calling was performed simultaneously across the relevant sample groups per experiment using scripts written in Python. A minimum allele count of 5 and minimum allele frequency of 0.25 were applied for the rad53∆ chk1∆ exo1∆ (S64Bα vs W64Aα strain) and exo1∆ rad53∆ (YMS6 vs YGDP939 strain) genome sequencing experiments. These thresholds were increased to a minimum allele count of 20 and minimum allele frequency of 0.40 for the rad53∆ batch sequencing experiment (MMS-resistant, suppressor containing strains (SUP) vs YJT75 strain). Multiallelic loci and variants identified in any of the control samples with an allele frequency of 0.1 or above were discarded.
Variant annotation was performed with snpEff 3.0j (Cingolani, et al. 2012) using the sacCer2.61 ensembl genomic database provided by the package. SNVs that passed the above criteria were further filtered to only include those that were labelled as nonsynonymous mutations, and had a minimum allele frequency of 0.7.
Genome_build: sacCer2
Supplementary_files_format_and_content: Tab-delimited file for SNVs identified to be specific to suppressor samples.  Columns represent: "chrom" (chromosome), "pos" (genomic position), "ref" (sacCer2 reference nucleotide), "alt" (alternate allele identified in suppressor strain(s)), "maximum_allele_frequency" (maximum allele frequency across all suppressors), "num_suppressors_pass_0.7_allele_frequency" (number of suppressors with allele frequency equal or above 0.7), "upstream_gene" (closest upstream gene to SNV), "downstream_gene" (closest downstream gene to SNV), "overlapping_gene" (overlapping gene for SNV), "gene_effect" (snpEff derived effect type of SNV). The remainder of the columns in the file represent the allele frequency per sample strain.

source_name: (MATa sml1Δ::URA3 rad53Δ::LEU2) W303 derivative

growth_protocol: Cells were grown in YPD medium (1% yeast extract, 2% bacto peptone, 2% glucose) media at 30 °C, shaking at 300 RPM in incubators and recovered at exponential growth (OD600 ~0.6).

extract_protocol:
DNA for whole-genome sequencing was extracted by the CTAB protocol. Briefly, cells were treated with 1M sorbitol-10mM EDTA pH 8-0.1% β-mercaptoethanol-2 mg/mL Zimoliase 20T at 30ºC during one hour to get sferoplasts. Speroplasts were then broken with cold water and treated with 1.4M NaCl-100mM Tris-Cl pH 7.6-25mM EDTA pH 8-2% CTAB , and then with RNase and Proteinase K. After centrifugation, pellet and supernatant were treated separately. The supernatant was extracted with 24:1 Cloroform:Isoamyl Alcohol and DNA precipitated with two volumes of 50 mM Tris-Cl pH 7.6-0 mM EDTA pH 8-1% CTAB and further resuspended in 1.4M NaCl-1 mM EDTA pH 8-10 mM Tris-Cl pH 7.6. The pellet pellet was resuspended directly in 1.4M NaCl-1 mM EDTA pH 8-10 mM Tris-Cl pH 7.6 and incubated during one hour at 50ºC, extracted with 24:1 Cloroform:Isoamyl Alcohol and rejoined with the supernatant DNA. The whole sample was precipitated then with one volume room temperature isopropanol, centrifuged, washed with 70% ethanol and resuspended in 10mM Tris-Cl pH 8.
Total extracted DNA was sheared using the Covaris S2 to ~300bp. The sheared DNA samples were end repaired, poly-A tailed and Illumina Single End Adapters were ligated (Paired End protocol. Illumina San Diego, CA, USA). The standard protocol by Illumina was adjusted to fit our samples.  We used Agencourt AMPure XP beads (AMPure bead protocol. Beckman Coulter, Inc.)  at 0.8x ratio to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa).  Post PCR we used AMPure XP beads at a 1:1 ratio to maintain size integrity, which also helped us to optimise the pH and other salt concentrations to allow us to use the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol. Life Technologies Corporation).  Unlike for the Illumina Paired End sample preparation protocol we ran the PCR before the gel. This improved visualisation of the product and removal of the correct band.  To aid us to remove any gel residue that would cause issues in later quality control (QC) and cluster formation we purified with QAIquick gel extraction kit (Gel purification protocol. QIAGEN Ltd.). After a final QC using the DNA 1000 BioAnalyser 2100 chip (Agilent, Santa Clara, CA, USA), the libraries were ready for Flowcell cluster formation on a cluster station  followed by Illumina paired-end sequencing on either the Genome Analyzer IIx or HiSeq 2500 with a read length of 36bp, 72bp or 101bp. Due to the increased output of the HiSeq 2500 we were able to multiplex 17 samples per lane.

value: yeast strains in small batch culture


title: Participant ID and visit (v) number [phchp141v2]

description: Validation Cohort Blood Gene Expression

source_name: Whole Blood

value: Female


title: Muscle, SA2_3mpk, rep2

source_name: Muscle, SA2_3mpk, rep2


title: SUP128

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp088v5]

description: Validation Cohort Blood Gene Expression


title: SUP129

description: Whole genome sequencing


title: Muscle, LA2_30mpk, rep3

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose Muscle (Vastus Lateralis) was taken for RNA profiling.

source_name: Muscle, LA2_30mpk, rep3


title: Muscle, LA2_30mpk, rep4

source_name: Muscle, LA2_30mpk, rep4


title: GU-HGG-154_4

source_name: High-grade glioma_154_biopsy 4


title: zPer2 zCry1a zCry2a triple KO (TKO) zebrafish treated with 3-h light

city: Tokyo

first: Jun

last: Hirayama

address: 1-5-45 Yushima, Bunkyo-ku

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression in TKO zebrafish exposed to 3-h light

hyb_protocol: RNA quality assurance, cDNA synthesis, and cRNA labeling and hybridization were carried out by Takara Bio Inc. (Otsu, Japan) using a Zebrafish (V3) Gene Expression Microarray 4X44K, the Low Input Quick Amp Labeling Kit, the Gene Expression Hybridization Kit, and the Gene Expression Wash Buffers Pack (all from Agilent Technologies) according to the manufacturer’s protocols.

scan_protocol: Genechips scanned using an Agilent DNA Microarray Scanner (G2565CA)

data_processing: Microarray data were processed using GeneChip Operating Software (Feature Extraction)

organism: Danio rerio

source_name: TKO 3-h light

label_protocol: cDNAs were synthesized by the Low Input Quick Amp Labeling Kit. Cy3-labelled cRNA was synthesized by in vitro transcription with T7 RNA Polymerase.

extract_protocol: Total RNA was extracted from zebrafish treated as described in figure legends using Trizol Reagent (Invitrogen). The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and further by absorption spectrophotometry.

treatment_protocol: WT, zPer2 zCry1a double KO (DKO) , and zPer2 zCry1a zCry2a triple KO (TKO) zebrafish were  kept in constant darkness after fertilization. They were then treated with light for 3- or 12-h at 6 dpf, or kept in constant darkness.

value: 3h light

value: zPer2 zCry1a zCry2a triple KO

value: Whole body of larva

tag: developmental stage

value: 6 day post fertilization


title: GU-HGG-182_4

source_name: High-grade glioma_182_biopsy 4

value: high-grade glioma


title: Participant ID and visit (v) number [phchp341v5]

description: Discovery Cohort Blood Gene Expression

value: Male

value: MDD


title: Muscle, LA2_30mpk, rep1

source_name: Muscle, LA2_30mpk, rep1


title: SUP131

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp349v1]

description: Discovery Cohort Blood Gene Expression

value: PSYCH


title: Participant ID and visit (v) number [phchp349v2]

description: Discovery Cohort Blood Gene Expression


title: Muscle, LA2_3mpk, rep5

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 3mpk and 6 hours post dose Muscle (Vastus Lateralis) was taken for RNA profiling.

source_name: Muscle, LA2_3mpk, rep5

value: Vastus


title: zPer2 zCry1a double KO (DKO) zebrafish treated with 12-h light

description: Gene expression in DKO zebrafish exposed to 12-h light

source_name: DKO 12-h light

tag: treatment

value: 12h light

value: zPer2 zCry1a double KO


title: zPer2 zCry1a zCry2a triple KO (TKO) zebrafish kept in darkness

description: Gene expression in TKO zebrafish kept in darkness

source_name: TKO Dark

value: dark


title: Muscle, LA2_30mpk, rep5

source_name: Muscle, LA2_30mpk, rep5

value: 12 weeks


title: Participant ID and visit (v) number [phchp341v4]

description: Discovery Cohort Blood Gene Expression

tag: gender


title: SUP127

description: Whole genome sequencing


title: SUP126

description: Whole genome sequencing


title: zPer2 zCry1a zCry2a triple KO (TKO) zebrafish treated with 12-h light

description: Gene expression in TKO zebrafish exposed to 12-h light

source_name: TKO 12-h light


title: Muscle, LA2_30mpk, rep2

source_name: Muscle, LA2_30mpk, rep2


title: Participant ID and visit (v) number [phchp121v1]

description: Validation Cohort Blood Gene Expression

tag: diagnosis

value: MOOD


title: Participant ID and visit (v) number [phchp341v3]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp341v2]

description: Discovery Cohort Blood Gene Expression


title: zPer2 zCry1a double KO (DKO) zebrafish treated with 3-h light

description: Gene expression in DKO zebrafish exposed to 3-h light

source_name: DKO 3-h light


title: SUP124

description: Whole genome sequencing


title: SUP125

description: Whole genome sequencing


title: SUP122

description: Whole genome sequencing


title: Spt16-AA_Nospike_minusrap_TFIIB_YPD

first: Natalia

last: Petrenko

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: performed in YPD media

data_processing:
map using Bowtie in Galaxy (Penn State).  Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy
Bed-to-SGR for viewing with IGB
Bam-to-Bigwig to get read coverage over the genome, using Galaxy deepTools (Freiburg, Germany)
for plotting or viewing "Spikein" files, normalize to equal S.pombe reads.  **The "Spikein" files with "NP" at the end of the name have a different amount of S.pombe, as they were prepared by a different person.  Normalize the "Nospike" files by the # of mapped reads, as well as by the number of reads at non-transcribed regions (beginning of ChrV, HML, HMR loci)
Genome_build: sacCer3 (and S.pombe for normalization of "Spikein" files)
Supplementary_files_format_and_content: bigwig,sgr

extract_protocol:
as described in Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36, e125.
as described in Wong, K.-H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7, Unit 7.11.

tag: general transcription factor subunit anchor-away

tag: chip antibody

value: TFIIB antibody


title: Spt16-AA_Spikein_plusrap_TFIIB_YPD

description: performed in YPD media


title: Spt16-AA_Nospike_plusrap_Rpb1_YPD_2

description: performed in YPD media

value: 8wg16 antibody


title: Muscle, LA2_3mpk, rep2

source_name: Muscle, LA2_3mpk, rep2


title: Muscle, LA2_3mpk, rep3

source_name: Muscle, LA2_3mpk, rep3


title: SUP121

description: Whole genome sequencing

source_name: (MATa sml1Δ::URA3 rad53Δ::LEU2) W303 derivative

value: yeast strains in small batch culture


title: WT zebrafish treated with 12-h light

description: Gene expression in WT zebrafish exposed to 12-h light

source_name: WT 12-h light

value: wild type


title: zPer2 zCry1a double KO (DKO) zebrafish kept in darkness

description: Gene expression in DKO zebrafish kept in darkness

source_name: DKO Dark


title: Participant ID and visit (v) number [phchp334v3]

description: Discovery Cohort Blood Gene Expression

source_name: Whole Blood

value: Female

value: BP


title: SUP120

description: Whole genome sequencing


title: WT zebrafish treated with 3-h light

description: Gene expression in WT zebrafish exposed to 3-h light

source_name: WT 3-h light

value: 3h light

value: Whole body of larva

value: 6 day post fertilization


title: Muscle, exercise, rep5

description: Mice underwent an acute bout of exercise consisting of 1300 m of treadmill running.

source_name: Muscle, exercise, rep5


title: Participant ID and visit (v) number [phchp341v1]

description: Discovery Cohort Blood Gene Expression

value: Male

value: MDD


title: Spt16-AA_Nospike_minusrap_Rpb1_YPD_2

description: performed in YPD media


title: Muscle, LA2_3mpk, rep1

source_name: Muscle, LA2_3mpk, rep1

value: Vastus


title: Participant ID and visit (v) number [phchp332v3]

description: Discovery Cohort Blood Gene Expression

value: SZA


title: Participant ID and visit (v) number [phchp334v1]

description: Discovery Cohort Blood Gene Expression


title: Muscle, exercise, rep4

source_name: Muscle, exercise, rep4


title: Muscle, exercise, rep3

source_name: Muscle, exercise, rep3


title: SUP119

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp323v2]

description: Discovery Cohort Blood Gene Expression

value: PTSD


title: Muscle, exercise, rep2

source_name: Muscle, exercise, rep2


title: Participant ID and visit (v) number [phchp332v2]

description: Discovery Cohort Blood Gene Expression


title: Spt16-AA_Nospike_plusrap_Rpb1_YPD

description: performed in YPD media


title: Spt16-AA_Nospike_minusrap_Rpb1_YPD

description: performed in YPD media


title: Participant ID and visit (v) number [phchp323v1]

description: Discovery Cohort Blood Gene Expression


title: WT zebrafish kept in darkness

description: Gene expression in WT zebrafish kept in darkness

source_name: WT Dark

value: dark


title: Toa2_Nospike_plusrap_Rpb1

description: Chip-seq of sonicated sample with 8wg16 antibody

tag: antibody


title: SUP116

description: Whole genome sequencing

tag: tissue


title: Muscle, exercise, rep1

source_name: Muscle, exercise, rep1

value: 12 weeks


title: SUP117

description: Whole genome sequencing


title: Toa2_Nospike_minusrap_Rpb1


title: Toa1_Nospike_plusrap_Rpb1


title: SUP115

description: Whole genome sequencing


title: SUP114

description: Whole genome sequencing


title: SUP118

description: Whole genome sequencing


title: Tfg1_Nospike_plusrap_Rpb1


title: Participant ID and visit (v) number [phchp302v1]

description: Discovery Cohort Blood Gene Expression


title: SUP112

description: Whole genome sequencing


title: Tfg1_Nospike_minusrap_Rpb1


title: Tfa2_Nospike_plusrap_Rpb1


title: Liver, Vehicle, rep3

description: Mice were treated with a single dose of Vehicle and 6 hours post dose Liver was taken for RNA profiling.

source_name: Liver, Vehicle, rep3

value: Liver


title: Liver, Vehicle, rep1

source_name: Liver, Vehicle, rep1


title: Participant ID and visit (v) number [phchp291v2]

description: Discovery Cohort Blood Gene Expression

value: SZ


title: Participant ID and visit (v) number [phchp291v5]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp243v4]

description: Discovery Cohort Blood Gene Expression

tag: diagnosis:


title: Toa1_Nospike_minusrap_Rpb1


title: SUP113

description: Whole genome sequencing


title: SUP106

description: Whole genome sequencing


title: Liver, Vehicle, rep2

source_name: Liver, Vehicle, rep2


title: Liver, Vehicle, rep4

source_name: Liver, Vehicle, rep4


title: Liver, Vehicle, rep5

source_name: Liver, Vehicle, rep5


title: Liver, SA2_20mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 20mpk and 6 hours post dose Liver was taken for RNA profiling.

source_name: Liver, SA2_20mpk, rep5


title: Participant ID and visit (v) number [phchp243v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp223v3]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp291v1]

description: Discovery Cohort Blood Gene Expression


title: Liver, SA2_3mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 3mpk and 6 hours post dose Liver was taken for RNA profiling.

source_name: Liver, SA2_3mpk, rep5


title: Liver, SA2_20mpk, rep1

source_name: Liver, SA2_20mpk, rep1


title: SUP105

description: Whole genome sequencing

source_name: (MATa sml1Δ::URA3 rad53Δ::LEU2) W303 derivative


title: SUP111

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp223v1]

description: Discovery Cohort Blood Gene Expression

source_name: Whole Blood


title: Liver, SA2_3mpk, rep3

source_name: Liver, SA2_3mpk, rep3


title: Tfa1_Nospike_plusrap_Rpb1


title: Liver, SA2_3mpk, rep4

source_name: Liver, SA2_3mpk, rep4


title: Tfa2_Nospike_minusrap_Rpb1


title: SUP104

description: Whole genome sequencing


title: SUP103

description: Whole genome sequencing


title: Tfa1_Nospike_minusrap_Rpb1


title: Tbp_Nospike_plusrap_Rpb1

value: TBP


title: Tbp_Nospike_minusrap_Rpb1


title: Taf1_Nospike_plusrap_Rpb1


title: SUP100

description: Whole genome sequencing

value: yeast strains in small batch culture


title: Taf1_Nospike_minusrap_Rpb1


title: SUP96

description: Whole genome sequencing


title: SUP94

description: Whole genome sequencing


title: Sua7_Nospike_plusrap_Rpb1


title: Participant ID and visit (v) number [phchp223v2]

description: Discovery Cohort Blood Gene Expression


title: Liver, SA2_3mpk, rep2

source_name: Liver, SA2_3mpk, rep2


title: SUP93

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp214v3]

description: Discovery Cohort Blood Gene Expression


title: SUP102

description: Whole genome sequencing


title: SUP92

description: Whole genome sequencing


title: Muscle, LA2_3mpk, rep4

source_name: Muscle, LA2_3mpk, rep4


title: Liver, SA2_3mpk, rep1

source_name: Liver, SA2_3mpk, rep1


title: Liver, LA2_30mpk, rep3

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose Liver was taken for RNA profiling.

source_name: Liver, LA2_30mpk, rep3


title: Liver, LA2_30mpk, rep5

source_name: Liver, LA2_30mpk, rep5


title: Liver, LA2_30mpk, rep2

source_name: Liver, LA2_30mpk, rep2


title: Participant ID and visit (v) number [phchp221v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp221v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp221v3]

description: Discovery Cohort Blood Gene Expression


title: Liver, LA2_30mpk, rep1

source_name: Liver, LA2_30mpk, rep1


title: Participant ID and visit (v) number [phchp210v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp214v1]

description: Discovery Cohort Blood Gene Expression


title: Ssl2_Nospike_plusrap_Rpb1


title: Participant ID and visit (v) number [phchp210v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp209v3]

description: Discovery Cohort Blood Gene Expression


title: Liver, LA2_3mpk, rep4

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 3mpk and 6 hours post dose Liver was taken for RNA profiling.

source_name: Liver, LA2_3mpk, rep4


title: SUP91

description: Whole genome sequencing


title: Ssl2_Nospike_minusrap_Rpb1


title: SUP90

description: Whole genome sequencing


title: Sua7_Nospike_minusrap_Rpb1


title: Ssl1_Nospike_plusrap_Rpb1


title: SUP89

description: Whole genome sequencing


title: Liver, LA2_3mpk, rep5

source_name: Liver, LA2_3mpk, rep5


title: Ssl1_Nospike_minusrap_Rpb1


title: SUP88

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp209v2]

description: Discovery Cohort Blood Gene Expression


title: Liver, LA2_3mpk, rep1

source_name: Liver, LA2_3mpk, rep1


title: HHY168_Nospike_plusrap_Rpb1_2

value: WT


title: Liver, LA2_3mpk, rep2

source_name: Liver, LA2_3mpk, rep2


title: SUP85

description: Whole genome sequencing


title: HHY168_Nospike_minusrap_Rpb1_2


title: HHY168_Nospike_plusrap_Rpb1


title: SUP84

description: Whole genome sequencing


title: SUP83

description: Whole genome sequencing


title: HHY168_Nospike_minusrap_Rpb1


title: Participant ID and visit (v) number [phchp209v1]

description: Discovery Cohort Blood Gene Expression


title: Toa2-AA_Spikein_plusrap_Rpb1

description: Chip-seq of sonicated sample with 8wg16 antibody, S. pombe spike-in added


title: Liver, exercise, rep4

source_name: Liver, exercise, rep4


title: Liver, LA2_3mpk, rep3

source_name: Liver, LA2_3mpk, rep3


title: SUP86

description: Whole genome sequencing

source_name: (MATa sml1Δ::URA3 rad53Δ::LEU2) W303 derivative


title: Liver, exercise, rep5

source_name: Liver, exercise, rep5


title: Participant ID and visit (v) number [phchp205v1]

description: Discovery Cohort Blood Gene Expression

source_name: Whole Blood

value: Female


title: Participant ID and visit (v) number [phchp192v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp205v2]

description: Discovery Cohort Blood Gene Expression


title: Toa2-AA_Spikein_minusrap_Rpb1


title: SUP82

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp192v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp191v3]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp205v3]

description: Discovery Cohort Blood Gene Expression


title: Liver, exercise, rep3

source_name: Liver, exercise, rep3


title: SUP81

description: Whole genome sequencing


title: Toa1-AA_Spikein_plusrap_Rpb1


title: SUP80

description: Whole genome sequencing


title: Toa1-AA_Spikein_minusrap_Rpb1


title: SUP79

description: Whole genome sequencing


title: White adipose tissue (WAT), Vehicle, rep5

description: Mice were treated with a single dose of Vehicle and 6 hours post dose WAT tissue was taken for RNA profiling.

value: IWAT


title: Liver, exercise, rep2

source_name: Liver, exercise, rep2


title: Tfg1-AA_Spikein_plusrap_Rpb1


title: Participant ID and visit (v) number [phchp191v1]

description: Discovery Cohort Blood Gene Expression


title: White adipose tissue (WAT), Vehicle, rep3


title: Tfg1-AA_Spikein_minusrap_Rpb1


title: Tfa2-AA_Spikein_plusrap_Rpb1


title: White adipose tissue (WAT), Vehicle, rep4


title: Tfa2-AA_Spikein_minusrap_Rpb1


title: SUP78

description: Whole genome sequencing


title: SUP77

description: Whole genome sequencing


title: SUP76

description: Whole genome sequencing


title: White adipose tissue (WAT), Vehicle, rep2


title: White adipose tissue (WAT), Vehicle, rep1


title: Participant ID and visit (v) number [phchp185v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp185v3]

description: Discovery Cohort Blood Gene Expression


title: SUP75

description: Whole genome sequencing


title: Tfa1-AA_Spikein_plusrap_Rpb1


title: SUP74

description: Whole genome sequencing


title: Tfa1-AA_Spikein_minusrap_Rpb1


title: SUP73

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp185v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp164v3]

description: Discovery Cohort Blood Gene Expression


title: White adipose tissue (WAT), SA2_20mpk, rep5

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 20mpk and 6 hours post dose WAT tissue was taken for RNA profiling.


title: White adipose tissue (WAT), SA2_20mpk, rep3


title: Participant ID and visit (v) number [phchp164v1]

description: Discovery Cohort Blood Gene Expression


title: SUP71

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp154v2]

description: Discovery Cohort Blood Gene Expression

value: PSYCH


title: Tbp-AA_Spikein_minusrap_Rpb1


title: SUP72

description: Whole genome sequencing


title: Tbp-AA_Spikein_plusrap_Rpb1


title: White adipose tissue (WAT), SA2_20mpk, rep1


title: White adipose tissue (WAT), SA2_20mpk, rep4


title: Participant ID and visit (v) number [phchp191v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp154v3]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp153v6]

description: Discovery Cohort Blood Gene Expression

value: BP


title: White adipose tissue (WAT), SA2_3mpk, rep3

description: Mice were treated with a single dose of the short acting AMPK activator, SA2, at 3mpk and 6 hours post dose WAT tissue was taken for RNA profiling.


title: Taf1-AA_Spikein_plusrap_Rpb1


title: White adipose tissue (WAT), SA2_3mpk, rep4


title: Participant ID and visit (v) number [phchp154v1]

description: Discovery Cohort Blood Gene Expression


title: SUP70

description: Whole genome sequencing


title: White adipose tissue (WAT), SA2_3mpk, rep5


title: Taf1-AA_Spikein_minusrap_Rpb1


title: Participant ID and visit (v) number [phchp153v4]

description: Discovery Cohort Blood Gene Expression


title: SUP69

description: Whole genome sequencing


title: Sua7-AA_Spikein_plusrap_Rpb1_2_NP


title: Sua7-AA_Spikein_minusrap_Rpb1_2_NP


title: GATA3 transfected, Lesion [L31256_Track-63644]

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

data_processing:
The FastQ files were aligned to human genome (GRCh38/hg19) using gsnap (2016-0923) with default options. The read counts for each gene were calculated using featureCounts (V1.5.3) and GTF file from ensemble genome browser (Homo_sapiens.GRCh38.90.gtf).
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: The processed data file contains read counts calculated by featureCounts. The first 6 columns contain information about the gene (Geneid, Chr, Start, End, Strand, Length), and the remaining columns countain read counts of each gene in each sample. The colnames have not been changed and contain Raw Files names with additional suffix ".gz.sam"

source_name: Primary Human Astrocytes

growth_protocol: The cells were seeded in 0.75 ml complete medium/well and kept in a cell culture incubator at 37 °C, 5% CO2. The complete cell culture medium consisted of astrocyte medium supplemented with 2% fetal bovine serum, 1% astrocyte growth supplement and 1% penicillin/streptomycin solution.

extract_protocol:
Total RNA was isolated by Norgen Total RNA isolation Kit.
Complete cDNA was synthesized from the obtained mRNA with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75bp single-end sequencing on the Illumina HiSeq2000 platform providing on average 31 million reads per sample.

treatment_protocol: Primary human astrocytes (pHAs) transduced with GATA3 or GFP were encapsulated in 20 ul of StarPEG-Heparin hydrogels at 40,000 cells/gel and maintained in 24-well plates in 0.75 ml complete medium/well. The stab lesions were created 2 weeks post-encapsulation using a 1 ml pipette tip, and the medium was replenished. The plates were returned to the cell culture incubator at 37 °C, 5% CO2 for another 1 week until RNA isolation.

value: GATA3 transfected, Lesion

tag: cell type

value: Primary Human Astrocytes


title: SUP67

description: Whole genome sequencing


title: SUP68

description: Whole genome sequencing


title: White adipose tissue (WAT), SA2_3mpk, rep1


title: GATA3 transfected, Lesion [L31256_Track-63615]


title: GATA3 transfected, Lesion [L31255_Track-63289]


title: SUP65

description: Whole genome sequencing


title: SUP63

description: Whole genome sequencing


title: Sua7-AA_Spikein_minusrap_Rpb1


title: GATA3 transfected, Lesion [L31254_Track-63288]


title: Participant ID and visit (v) number [phchp153v3]

description: Discovery Cohort Blood Gene Expression

value: Male


title: GATA3 transfected, No Lesion [L31253_Track-63287]

value: GATA3 transfected, No Lesion


title: White adipose tissue (WAT), SA2_3mpk, rep2


title: Participant ID and visit (v) number [phchp153v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp142v6]

description: Discovery Cohort Blood Gene Expression


title: Ssl2-AA_Spikein_minusrap_Rpb1_NP


title: Participant ID and visit (v) number [phchp142v5]

description: Discovery Cohort Blood Gene Expression


title: SUP62

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp142v3]

description: Discovery Cohort Blood Gene Expression


title: SUP61

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp302v2]

description: Discovery Cohort Blood Gene Expression


title: Ssl1-AA_Spikein_plusrap_Rpb1_NP


title: Participant ID and visit (v) number [phchp142v1]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp142v2]

description: Discovery Cohort Blood Gene Expression


title: Sua7-AA_Spikein_plusrap_Rpb1


title: Ssl1-AA_Spikein_minusrap_Rpb1_NP


title: GATA3 transfected, No Lesion [L31252_Track-63286]


title: GFP transfected, Lesion [L31250_Track-63643]

value: GFP transfected, Lesion


title: Ssl2-AA_Spikein_plusrap_Rpb1_NP


title: SUP59

description: Whole genome sequencing


title: SUP58

description: Whole genome sequencing


title: Rpb1-AA_Spikein_plusrap_Rpb1


title: GATA3 transfected, No Lesion [L31251_Track-63285]


title: SUP57

description: Whole genome sequencing


title: GFP transfected, Lesion [L31250_Track-63614]


title: Participant ID and visit (v) number [phchp140v2]

description: Discovery Cohort Blood Gene Expression


title: SUP54

description: Whole genome sequencing


title: Rpb1-AA_Spikein_minusrap_Rpb1


title: HHY168_Spikein_plusrap_Rpb1


title: GFP transfected, Lesion [L31249_Track-63613]


title: SUP53

description: Whole genome sequencing


title: GFP transfected, Lesion [L31249_Track-63642]


title: Participant ID and visit (v) number [phchp140v1]

description: Discovery Cohort Blood Gene Expression


title: GFP transfected, Lesion [L31248_Track-63641]


title: SUP52

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp136v3]

description: Discovery Cohort Blood Gene Expression


title: MUT_NTR_37

city: Rosario

first: Pablo

middle: Emiliano

last: Tomatis

address: Ocampo y Esmeralda

country: Argentina

institute: IBR-CONICET

data_processing:
Illumina CASAVA-1.8.2 software used for base calling
Reads were trimmed (5 based on left, 10 based on right). Trimmed reads were aligned to E. coli K12 DH10B using bowtie2.
Mapped reads were counted for annotated genes using countOverlaps in the Bioconductor package GenomicRanges
Differential expression analysis was performed using the Bioconductor package edger, with TMM as the normalization method.
Genome_build: Escherichia_coli_K12, ASM1942v1 (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-15/embl/escherichia_shigella_collection/e_coli_dh10b/) and plasmid gene rNTR1 (see fasta file)
Supplementary_files_format_and_content: tab-delimited text files of raw counts

organism: Escherichia coli

source_name: bacteria

growth_protocol: E. coli cells were grown in 2×YT medium supplemented with 0.2% (w/v) glucose and 100 μg/ml ampicillin at 37°C until the culture reached OD600 = 0.5. At this cell density, protein expression was induced by addition of 250 μM IPTG and the cells were cultivated at 20°C or 37 °C for 4 hours.

extract_protocol:
Total RNA was extracted from approximately 5 × 108 E. coli cells using the RNeasy Mini kit (Qiagen, Cat. No. 74104). Briefly, bacterial cell cultures were directly mixed with twice the volume of RNA-protect Bacteria Reagent (Qiagen, Cat. No. 76506) and the recommended protocol of lysozyme-mediated lysis and digestion with Proteinase K was followed. The RNase-Free DNase Set (Qiagen, Cat. No. 79254) was used for an on-column DNase digestion for 30 min prior to RNA elution.
The TruSeq RNA Sample Prep kit v2 (Illumina, Cat. No. RS-122-2001) was used.  Total RNA samples (1000 ng) were ribosomal-RNA-depleted using the Ribo-Zero™ Magnetic kit for bacteria (Epicentre, Cat. No. MRZMB126) and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the barcode index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched by PCR.  The quality and quantity of the enriched libraries were validated using the 2200 TapeStation system (Agilent) and quantitative PCR.  The products were a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10 nM in 10 mM Tris-Cl, pH 8.5 at 25ºC supplemented with 0.1% (v/v) Tween-20.  Samples were pooled to equimolar amounts and sequenced in a single lane. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Cat. No. GD-401-3001) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT.  Sequencing was performed on the Illumina HiSeq 2500 single end 126 bp using the TruSeq SBS Kit v4-HS (Illumina, Cat. No.  FC-401-3001).

tag: genotype

value: rpoD E575V mutant

tag: exogenous gpcr

value: NTR

tag: temperature c during protein induction


title: GFP transfected, Lesion [L31248_Track-63612]


title: GFP transfected, No Lesion [L31247_Track-63611]

value: GFP transfected, No Lesion


title: SUP47

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp134v6]

description: Discovery Cohort Blood Gene Expression


title: SUP46

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp136v2]

description: Discovery Cohort Blood Gene Expression


title: MUT_NTR_20

tag: strain


title: WT_NTR_37

value: wild type


title: SUP45

description: Whole genome sequencing


title: GFP transfected, No Lesion [L31246_Track-63610]


title: WT_NTR_20


title: GFP transfected, No Lesion [L31245_Track-63640]


title: HHY168_Spikein_minusrap_Rpb1


title: MUT_20


title: SUP39

description: Whole genome sequencing


title: MM at diagnosis, sample 30 [miRNA-Seq]

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

data_processing:
base-calling Casava 1.9
read adapter trimming with FastxToolkit v0.0.13
reads longer than 30nt and with average quality less than 30 (Phred) were discarded
read alignment to genome and precursor sequences with Bowtie v1.1.0
read count was performed with custom scripts on miRBase v21 annotation and small RNAs predicted by the miR&moRe pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_data.txt
Supplementary_files_format_and_content: raw_variants.txt

source_name: Highly purified PCs from MM patient

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
Small RNA cDNA libraries (for transcripts <30nt) were built following standard Illumina Truseq® Small RNA protocol, starting from 2 micrograms of total RNA for each sample. BluePippin system was used for fragments selection within the range of 145-160 bp. RNA-seq was performed on Illumina HiSeq platform. A 50-cycle single-reads sequencing was run to generate the tags corresponding to small-RNAs

value: Bone marrow plasma cells

tag: molecular alteration


title: WT_20


title: SUP38

description: Whole genome sequencing


title: MM at diagnosis, sample 29 [miRNA-Seq]


title: White adipose tissue (WAT), LA2_30mpk, rep5

description: Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose WAT tissue was taken for RNA profiling.

tag: age

value: 12 weeks


title: Participant ID and visit (v) number [phchp134v3]

description: Discovery Cohort Blood Gene Expression

tag: pain scale(1-10)


title: Participant ID and visit (v) number [phchp134v4]

description: Discovery Cohort Blood Gene Expression


title: MM at diagnosis, sample 27 [miRNA-Seq]


title: SUP36

description: Whole genome sequencing

value: yeast strains in small batch culture


title: Participant ID and visit (v) number [phchp134v2]

description: Discovery Cohort Blood Gene Expression


title: SUP40

description: Whole genome sequencing


title: SUP35

description: Whole genome sequencing


title: MM at diagnosis, sample 26 [miRNA-Seq]

value: MAF translocation


title: Participant ID and visit (v) number [phchp131v1]

description: Discovery Cohort Blood Gene Expression

value: Female

value: SZ


title: MM at diagnosis, sample 28 [miRNA-Seq]

value: hyperdiploid karyotype


title: SUP30

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp131v2]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp106v3]

description: Discovery Cohort Blood Gene Expression

value: BP


title: Participant ID and visit (v) number [phchp134v5]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp131v3]

description: Discovery Cohort Blood Gene Expression


title: MM at diagnosis, sample 25 [miRNA-Seq]


title: SUP27

description: Whole genome sequencing


title: SUP26

description: Whole genome sequencing


title: MM at diagnosis, sample 24 [miRNA-Seq]


title: MM at diagnosis, sample 23 [miRNA-Seq]


title: SUP23

description: Whole genome sequencing


title: MM at diagnosis, sample 22 [miRNA-Seq]

value: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: SUP22

description: Whole genome sequencing


title: MM at diagnosis, sample 21 [miRNA-Seq]


title: Participant ID and visit (v) number [phchp052v3]

description: Discovery Cohort Blood Gene Expression


title: SUP20

description: Whole genome sequencing


title: MM at diagnosis, sample 19 [miRNA-Seq]


title: SUP19

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp140v3]

description: Discovery Cohort Blood Gene Expression


title: Participant ID and visit (v) number [phchp052v2]

description: Discovery Cohort Blood Gene Expression


title: UMSCC_110 HNSCC Cell Line

city: Ann Arbor

first: Chad

last: Brenner

state: Michigan

address: 1500 E Medical Center Drive / Cancer Center 6430

institute: University of Michigan

hyb_protocol: Affymetrix Oncoscan Array Protocol

scan_protocol: Affymetrix Oncoscan Array Protocol

data_processing: Raw CEL files were converted to OSCHP files using OncoScan Console (v1.3). The TuScan algorithm provided by the Nexus Express for OncoScan software was used to calculate copy numbers.

source_name: Genomic DNA isolated from cell line in log phase growth

label_protocol: Affymetrix Oncoscan Array Protocol

growth_protocol: Cell lines were in log phase growth

extract_protocol: Qiagen Allprep Kit

treatment_protocol: 10% fetal bovine serum, 7µg/mL penicillin/streptomycin and 1% Non-essential amino acids in 5% CO2 incubator

tag: cell line

tag: Sex

value: male


title: Participant ID and visit (v) number [phchp106v1]

description: Discovery Cohort Blood Gene Expression

tag: gender


title: UMSCC_118 HNSCC Cell Line

value: female


title: SUP21

description: Whole genome sequencing


title: MM at diagnosis, sample 18 [miRNA-Seq]


title: MM at diagnosis, sample 20 [miRNA-Seq]


title: UMSCC_105 HNSCC Cell Line


title: Participant ID and visit (v) number [phchp004v2]

description: Discovery Cohort Blood Gene Expression

value: Male

tag: diagnosis

value: SZA


title: Participant ID and visit (v) number [phchp004v4]

description: Discovery Cohort Blood Gene Expression


title: SUP18

description: Whole genome sequencing


title: Participant ID and visit (v) number [phchp004v3]

description: Discovery Cohort Blood Gene Expression


title: MM at diagnosis, sample 17 [miRNA-Seq]


title: UMSCC_108 HNSCC Cell Line


title: Participant ID and visit (v) number [phchp052v1]

description: Discovery Cohort Blood Gene Expression


title: UMSCC_104 HNSCC Cell Line


title: MM at diagnosis, sample 16 [miRNA-Seq]


title: UMSCC_103 HNSCC Cell Line


title: MM at diagnosis, sample 15 [miRNA-Seq]


title: SUP15

description: Whole genome sequencing


title: SUP14

description: Whole genome sequencing


title: MM at diagnosis, sample 14 [miRNA-Seq]


title: SUP13

description: Whole genome sequencing


title: UMSCC_92 HNSCC Cell Line


title: MM at diagnosis, sample 13 [miRNA-Seq]


title: SUP17

description: Whole genome sequencing


title: SUP10

description: Whole genome sequencing


title: UMSCC_97 HNSCC Cell Line


title: MM at diagnosis, sample 12 [miRNA-Seq]


title: UMSCC_81B HNSCC Cell Line


title: MM at diagnosis, sample 11 [miRNA-Seq]


title: SUP9

description: Whole genome sequencing


title: 10x_osk_d8

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

country: China

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

data_processing:
The cellranger-2.1.1 was used for mapping of the 10x single cell RNA-seq data.
The read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bp. The next 10 bp were recorded as unique molecular identifiers (UMIs). Read2 with 75 bp were aligned to the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include UMI counts for each cell.

source_name: mouse embryonic fibroblasts(MEFs)

growth_protocol: Mouse ESCs (mESCs) and iPS cell lines were cultured on feeder layers with mESC medium (high glucose DMEM, 15%FBS, NEAA, GlutaMAX, LIF) plus 2i (1 m PD0325901, 3 m CHIR99021). MEF cells were maintained in 10% FBS medium (high glucose DMEM supplemented with 10% FBS, GlutaMAX and NEAA).  The reprogramming cells at different days were cultured in iCD1 medium.

extract_protocol:
Cells in each day were isolated using 10x Genomics
The libraries were constructed using Chromium™ Single Cell 3' Reagent Kits v2; R2 is biological. R1 includes cell barcode and UMI sequence. In R1, the first 16bp is cell barcode while the last 10bp is UMI.

tag: strain background

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: time point


title: UMSCC_85 HNSCC Cell Line


title: SUP8

description: Whole genome sequencing


title: 10x_osk_d7


title: 10x_osk_d6


title: SUP7

description: Whole genome sequencing


title: 10x_osk_d5


title: MM at diagnosis, sample 9 [miRNA-Seq]

value: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: UMSCC_81A HNSCC Cell Line


title: UMSCC_59 HNSCC Cell Line


title: MM at diagnosis, sample 10 [miRNA-Seq]


title: 10x_osk_d3


title: MM at diagnosis, sample 8 [miRNA-Seq]


title: SUP6

description: Whole genome sequencing


title: SUP5

description: Whole genome sequencing


title: UMSCC_57 HNSCC Cell Line


title: 10x_osk_d0


title: SUP4

description: Whole genome sequencing


title: UMSCC_55 HNSCC Cell Line


title: MM at diagnosis, sample 7 [miRNA-Seq]


title: MM at diagnosis, sample 6 [miRNA-Seq]


title: SUP3

description: Whole genome sequencing


title: UMSCC_49 HNSCC Cell Line


title: 10x_osk_d1


title: SUP2

description: Whole genome sequencing


title: UMSCC_69 HNSCC Cell Line


title: UMSCC_47 HNSCC Cell Line


title: 10x_osk_esc

source_name: mouse embryonic stem cells(ESCs)

value: OG2 transgenic mouse embryonic stem cells(OG2-mESCs)


title: MM at diagnosis, sample 5 [miRNA-Seq]


title: 10x_osk_mef


title: MM at diagnosis, sample 4 [miRNA-Seq]


title: SUP1

description: Whole genome sequencing


title: UMSCC_46 HNSCC Cell Line


title: Control_infection_stage3_F2

city: Townsville

first: David

middle: John

last: Miller

state: Queensland

address: 1 James Cook Drive, Douglas

department: Molecular and Cell Biology

country: Australia

institute: James Cook University

description:
sample name in processed data file:
F2R3

data_processing:
Illumina read were mapped onto Ricordea yuma transcriptome (PRJNA313487) using BOWTIE v2.1.0.
Differential gene expression was inferred by mapping counts using the EdgeR package
Gene ontology analysis was conducted by using GOseq v1.16.1
Genome_build: TSA: Ricordea yuma, transcriptome shotgun assembly (GenBank: GELN00000000.1)
Supplementary_files_format_and_content: text file with counts.

organism: Ricordea yuma

source_name: corallimorph tissue

extract_protocol:
Total RNA was extracted using TRIZOL reagent
cDNA libraries were prepared using NEBNext Ultra RNA Directional Library Prep Kit for Illumina

value: corallimorph tissue

tag: infection status

tag: developmental stage

value: adult

tag: group

value: control


title: MM at diagnosis, sample 3 [miRNA-Seq]

tag: tissue

value: Bone marrow plasma cells


title: UMSCC_43 HNSCC Cell Line


title: MM at diagnosis, sample 2 [miRNA-Seq]

value: MAF translocation


title: Control_infection_stage2_F2

description:
sample name in processed data file:
F2R2


title: 2612

description: Whole genome sequencing

source_name: YMS6 (MAt a ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ) W303 derivative

value: yeast strains in small batch culture


title: C

description: Whole genome sequencing

source_name: YJT75 (MATa sml1Δ::URA3 rad53Δ::LEU2) W303 derivative


title: MM at diagnosis, sample 1 [miRNA-Seq]


title: UMSCC_29 HNSCC Cell Line


title: Control_infection_stage1_F2

description:
sample name in processed data file:
F2R1


title: GroupD_infection_stage3_F1

description:
sample name in processed data file:
F1R3

value: groupD


title: GATA3 transfected, Unscratched rep3

treatment_protocol: Primary human astrocytes (pHAs) transduced with GATA3 or GFP were seeded at 10,000 cells/well in 24-well plates in 0.75 ml complete medium/well at passage 3. The scratch assay was performed 6 days post seeding, when the cells were 100 % confluent. Each well except for the control (unscratched) wells was scratched with a 1 ml pipette tip according to a preset cross shape to remove about 30% of the total cells. The wells were immediately washed with 0.2 ml of complete medium twice and then the medium was replenished. The plates were returned to the cell culture incubator at 37 °C, 5% CO2 for another 3 days until RNA isolation.

tag: treatment

value: GATA3 transfected, Unscratched


title: UMSCC_28 HNSCC Cell Line


title: SW620-3

city: Guangzhou，China

first: jide

last: Wang

state: Guangdong ，China

address: 1838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

description: replicate 3

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

source_name: colon cancer cells

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: DMEM supplemented with 10% FBS，37℃，5% CO2

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: no treatment


title: NT-OFF 3

city: Huddinge

first: Martin

last: Lord

address: Alfred Nobels Alle 8

department: Institutionen för Laboratoriemedicin Avdelningen för patologi

institute: KI

hyb_protocol: The samples were hybridized to an array GeneChip® Mouse Transcriptome Array 1.0 according to standard protocol   GeneChip® Mouse Transcriptome Array 1.0  according to standard protocol.

scan_protocol: The arrays  were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the SST-RMA method

source_name: Ba/F3 cell line

label_protocol: 150 ng of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: 0.5x10^6 Ba/F3 cells/ml were plated and cultured in medium containing IL-3

extract_protocol: RNA was extracted from cells using RNeasy Plus mini kit (Qiagen) according to standard protocol

treatment_protocol: 80x10^-6 g/ml doxycycline ("Doxyferm", Nordic Drugs AB)

tag: cell type

value: pro-B cells

tag: phenotype

value: NT-OFF


title: GroupD_infection_stage2_F1

description:
sample name in processed data file:
F1R2


title: SW620-2

description: replicate 2


title: GATA3 transfected, Unscratched rep2


title: UMSCC_25 HNSCC Cell Line

value: male


title: GroupD_infection_stage1_F1

description:
sample name in processed data file:
F1R1


title: NT-OFF 2


title: NT-ON 4

value: NT-ON


title: UMSCC_23 HNSCC Cell Line

value: female


title: SW620-1

description: replicate 1


title: LOVO-3

description: replicate 3

value: LoVo


title: GroupD_infection_stage3_E2

description:
sample name in processed data file:
E2R3


title: Sox11-OFF 4

description: Affymetrix’s MTA-1 mouse array (genome version mm10, NetAffx Build 34


title: GATA3 transfected, Scratched rep3

value: GATA3 transfected, Scratched


title: UMSCC_19 HNSCC Cell Line


title: NT-ON 1


title: GroupD_infection_stage2_E2

description:
sample name in processed data file:
E2R2


title: GATA3 transfected, Scratched rep2


title: GATA3 transfected, Unscratched rep1


title: GroupD_infection_stage1_E2

description:
sample name in processed data file:
E2R1


title: NT-ON 3


title: NT-OFF 4


title: LOVO-2

description: replicate 2


title: GATA3 transfected, Scratched rep1


title: NT-OFF 1


title: UMSCC_41 HNSCC Cell Line


title: UMSCC_14A HNSCC Cell Line


title: GFP transfected, Unscratched rep3

value: GFP transfected, Unscratched


title: FHC-3

description: replicate 3

source_name: normal colorectal mucosa cells

value: FHC


title: LOVO-1

description: replicate 1


title: UMSCC_12 HNSCC Cell Line


title: Sox11-OFF 2


title: Sox11-OFF 3


title: GFP transfected, Unscratched rep2


title: GFP transfected, Unscratched rep1


title: GroupC_infection_stage2_E1

description:
sample name in processed data file:
E1R2

value: corallimorph tissue

value: groupC


title: GroupC_infection_stage3_D2

description:
sample name in processed data file:
D2R3

value: adult


title: UMSCC_10A HNSCC Cell Line


title: FHC-2

description: replicate 2


title: GFP transfected, Scratched rep3

value: GFP transfected, Scratched


title: Sox11-ON 2


title: GroupC_infection_stage2_D2

description:
sample name in processed data file:
D2R2


title: UMSCC_11A HNSCC Cell Line


title: FHC-1

description: replicate 1


title: UMSCC_17B HNSCC Cell Line


title: UMSCC_8 HNSCC Cell Line


title: NT-ON 2


title: UMSCC_10B HNSCC Cell Line


title: GroupC_infection_stage1_E1

description:
sample name in processed data file:
E1R1


title: GFP transfected, Scratched rep2


title: Sox11-ON 4


title: GFP transfected, Scratched rep1


title: GroupC_infection_stage1_D2

description:
sample name in processed data file:
D2R1


title: Sox11-OFF 1


title: UMSCC_1 HNSCC Cell Line


title: Control_infection_stage3_C2

description:
sample name in processed data file:
C2R3

value: control


title: PC3_RNA-Seq_siOC2_Hypoxia_siRNA2

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description:
PC3_RNA-Seq_siOC2_Hypoxia_siRNA2
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
H-SIOC2-2

data_processing:
The trimmed reads were aligned to human genome hg19 with STAR (version 2.4.2a) and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method by Cufflinks (version 2.1.1) with GENCODE v24 GRCh37 GTF file
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the gene expression matrices

source_name: PC3 cells

growth_protocol: LNCaP and PC3 cell lines were obtained from the American Type Culture Collection (ATCC). All prostate cancer cell lines were cultured as recommended by ATCC. No mycoplasma contamination was detected in these cell lines using MycoAlert™ Mycoplasma Detection Kit (LT07-118, Lonza).

extract_protocol:
Total RNA of PC3 and LNCaP cells was extracted using RNeasy Mini Kit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: For hypoxia treatment, cells were incubated in hypoxia chamber at 0.2% O2.

tag: tumor type

value: prostate cancer

tag: protocol


title: Sox11-ON 1


title: Sox11-ON 3


title: Control_infection_stage2_C2

description:
sample name in processed data file:
C2R2


title: UDSCC_2 HNSCC Cell Line


title: Control_infection_stage1_C2

description:
sample name in processed data file:
C2R1


title: PC3_RNA-Seq_siCtrl_Hypoxia_rep2

description:
PC3_RNA-Seq_siCtrl_Hypoxia_rep2
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
H-siCtrl-2


title: GroupD_infection_stage3_C1

description:
sample name in processed data file:
C1R3

value: groupD


title: PC3_RNA-Seq_siCtrl_Hypoxia_rep1

description:
PC3_RNA-Seq_siCtrl_Hypoxia_rep1
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
H-siCtrl-1


title: GroupD_infection_stage2_C1

description:
sample name in processed data file:
C1R2


title: PC3_RNA-Seq_siOC2_Normoxia_siRNA2

description:
PC3_RNA-Seq_siOC2_Normoxia_siRNA2
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
N-SIOC2-2


title: 28_NoH2O-H63-Seedling-6dat-1

city: Morgantown

first: Nik

last: Kovinich

state: WV

address: 1194 Evansdale Drive

department: Plant and Soil Sciences

institute: West Virginia University

data_processing:
FastQC software was used to assess quality before further analysis
The reads were then mapped/aligned to Glycine max reference genome (Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html) using STAR
The number of reads per gene was calculated using featureCounts counting only reads which mapped concordantly and —ignore-dup set
Differentially expressed genes (DEGs) were identified using a Negative Binomial Distribution in DESeq2
Genome_build: Wm82.a2 (Glyma 2.0)
Supplementary_files_format_and_content: count data

organism: Glycine max

growth_protocol: Harosoy 63 seeds (16 per batch) were sterilized in 30 mL of 70% ethanol, 0.2% triton X (v/v) for 5 min on a mixer wheel, rinsed thrice with sterile water, and imbibed overnight. The imbibate was then discarded to remove growth inhibitors and seeds were transferred to water soaked sterile vermiculite (250 mL in volume) in 500 mL beakers. Beakers were covered with a ring of sterile cheese cloth to permit the passage of light and covered with plastic wrap to ensure aseptic growth. Seedlings were grown at 22 °C under a 16 h photoperiod using cool white T5 fluorescent lights (500 μE m−2 s−1). At the first trifoliate leaf stage (~8 day old), seedling roots were gently wrapped with filter paper saturated with half-strength Murashige and Skoog (MS) medium (pH 5.8) containing vitamins and 1% (w/v) sucrose, and were transferred to their respective abiotic stress treatments.

extract_protocol:
After 9 d of treatment (pH 3.0 medium and control) or 6 d treatment (dehydration and control), seedlings were flash-frozen in liquid nitrogen, lyophilized to dryness, ground to a fine powder and stored at – 80˚C for extraction of metabolites and RNA. Tissue powder was freeze dried again for 1 h, then weighed prior to extractions. Lyophilized tissue was pulverized for 3 min using 5 mm stainless steel grinding balls in a MM400 mixer mill (Retsch, Newtown, CT, USA) at frequency of 30/s. Total RNAs were extracted the using the Spectrum Plant Total RNA Kit.
The mRNA stranded library prep kit from KAPA Biosystems was used to build the libraries

treatment_protocol: Five seedlings per treatment were transferred to a 100 mL beaker containing 50 mL of fresh medium (pH 5.8) for control. Each of the beakers were then placed inside a sterile 500 mL beaker and wrapped with sterile mesh overlaid with plastic wrap to maintain ventilation and aseptic growth conditions. For acidic conditions, seedlings were transferred to beakers containing pH 3.0 medium. For dehydration, the medium-saturated germination paper was allowed to dry gradually in the 100 mL beaker containing no medium.

tag: cultivar

value: Harosoy 63

tag: medium ph

tag: days after treatment

tag: dehydration

value: Yes

tag: glyceollins elicitation

value: Suppressed

value: Whole seedling


title: 30_NoH2O-H63-Seedling-6dat-3


title: GroupD_infection_stage1_C1

description:
sample name in processed data file:
C1R1


title: 29_NoH2O-H63-Seedling-6dat-2


title: HEKa HNSCC Cell Line

tag: cell line

value: HEKa

tag: Sex


title: GroupD_infection_stage3_B2

description:
sample name in processed data file:
B2R3


title: PC3_RNA-Seq_siCtrl_Normoxia_rep2

description:
PC3_RNA-Seq_siCtrl_Normoxia_rep2
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
N-siCtrl-2


title: Dolly_primary_tumor

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: new canine model of melanoma

hyb_protocol: Scanned on an Agilent G2505C scanner and Agilent-022060_D_F_20111015 whole canine genome microarrays 4x180K (Probe Name version).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.   Normalized log10 ratios in sample data tables were obtained with the FE default protocol.

organism: Canis lupus familiaris

label_protocol: probe labeling used Agilent Technologies Genomic DNA Enzymatic Labeling Kit. Labelling was performed following manufacturer's instructions.CA).

growth_protocol: RPMI 1640 glutamax growth medium supplemented with 10% heat inactivated fetal calf serum (FCS) and antibiotics (Penicillin 100 U/ mL and Streptomycin 0.1 mg/ mL)

extract_protocol: DNA extraction was performed using the Qiagen DNeasy Kit according to the manufacturer's instructions

treatment_protocol: Surgically removed oral CMM tissue sample were digested mechanically and enzymatically using 2mg/ mL type II collagenase (Gibco®) for two hours at 37°C

tag: sample type

value: primary tumor

value: oral malignant melanoma

tag: patient id

value: Dolly

source_name: self blood DNA

value: blood


title: Dolly_first_passage

description: new canine model of melanoma

value: first passage


title: Tania_xenograft

description: new canine model of melanoma

value: xenograft

value: Tania


title: Tania_primary_tumor

description: new canine model of melanoma


title: 26_Cont-H63-Seedling-6dat-2

value: No


title: Dolly_xenograft

description: new canine model of melanoma


title: Tania_first_passage

description: new canine model of melanoma


title: PC3_RNA-Seq_siCtrl_Normoxia_rep1

description:
PC3_RNA-Seq_siCtrl_Normoxia_rep1
PC3_RNA-seq_RPKM_OC2_Knockdown.txt
N-siCtrl-1


title: GroupD_infection_stage2_B2

description:
sample name in processed data file:
B2R2

value: corallimorph tissue

tag: infection status

tag: developmental stage

value: adult