title: WT-sorbitol-repeat1

status: Public on Nov 01 2020

city: Shanghai

first: Bo

last: Yu

address: Fenglin Road 300

department: Institute of Plant Physiology & Ecology

institute: SIBS, CAS

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
CK_SOBI.1

hyb_protocol: chip hybridization and washing were undertaken according to the manual of One-Color Microarray-Based Gene Expression Analysis from Agilent Technologies. Gene Expression Hybridization Kit，Agilent，5188-4242.Gene Expression Wash Pack,Agilent,5188-5327.

scan_protocol: Gene Chip array hybridization signals were scanned with Agilent scanner (G2505c) according to Expression Analysis Technical Manual.

data_processing: Background corrections, loess normalization within arrays. Quantile normalization across arrays

organism: Arabidopsis thaliana

source_name: CK Sor

label_protocol: cRNA were labelled according to LowInput Quick-Amp Labeling Kit，one-color(24×)，Agilent，5190-2305

growth_protocol: Seedlings were grown 1/2MS agar with  6% gulcose or 6% sorbitol plate at 22℃ under constant light 4 days after 3 days stratification

extract_protocol: The Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen, 74903).

treatment_protocol: The seedling growth on the 1/2MS agar plate with 6% glucose and 6% sorbitol

value: seedlings

tag: ecotype

value: Columbia (Col-0)

value: wild type

tag: treatment

value: sorbitol


title: anac060-glucose-repeat2

type: RNA

country: China

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
MUT_GLU.2

molecule: total RNA

source_name: MUT Glc

tag: tissue

tag: genotype

value: anac060 mutant

value: glucose


title: anac060-glucose-repeat1

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
MUT_GLU.1


title: WT-glucose-repeat2

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
CK_GLU.2

source_name: CK Glc


title: WT-glucose-repeat1

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
CK_GLU.1


title: WT-sorbitol-repeat2

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
CK_SOBI.2


title: K9-DMM-1

city: Sheffield

first: Heba

last: Ismail

address: Firth Court, University of Sheffield, Western Bank, Sheffield

department: Infection, Immunity and Cardiovascular disease.

country: United Kingdom

institute: University of Sheffield

description:
F1
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

label: biotin

organism: Mus musculus

source_name: Mouse total knee

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

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

tag: strain/background

tag: genotype/variation

value: MAPK9 KO

tag: age

value: 12 weeks

value: Total knee

tag: condition

value: 6 hr post knee cartilage injury


title: TGFBR2/SMAD4 cKO fibroblasts

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

country: USA

institute: MDACC

description: Gene expression was measured using a mouse-specific oligonucleotide microarray Gene 1.0 ST Array (Affymetrix) which interrogate transcripts from approximately 28,000 well-annotated genes (http://chip.dfci.harvard.edu). Each transcript was probed by approximately 25 probes from exons distributed across the gene. Transcript level, but not exon level, expression values can be generated from the data. Mismatch (MM)probes are not present on the array. In detail, 1 μg RNA was submitted to the Microarray Core facility at Dana Farber Cancer Institute. Double-stranded cDNA was synthesized from the RNA sample starting with T7 promoter-tailed random hexamers. Then, cRNA was synthesized in a T7 polymerase catalyzed reaction containing unmodified ribonucleoside triphosphates. Single-stranded cDNA was synthesized from the cRNA template using random primers and dUTP, dTTP, dATP, dCTP and dGTP. The remaining cRNA was hydrolyzed by RNase H, and the single-stranded cDNA was purified. Thereafter, Uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I were used to fragment the cDNA at Uracil-containing positions. The fragmented cDNA was end-labeled with a biotinylated nucleotide analog. The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to the Affymetrix mouse Gene 1.0 ST microarray chip overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cDNA that had not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

hyb_protocol: The fragmented and biotin-labeled cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to the Affymetrix mouse Gene 1.0 ST microarray chip overnight at 45°C.

scan_protocol: Scanner model: M10

data_processing:
Data were processed by the Microarray Core facility at Dana Farber Cancer Institute.
The relative gene expression in TGFBR2 cKO forestomach fibroblasts was assessed, compared to expression levels in wt and TGFBR2/SMAD4 cKO fibroblasts.

label: Biotin

source_name: Forestomach FSP1 positive fibroblasts

growth_protocol: Fibroblasts were grown in Dulbecco Minimal Essential Medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and 100 μg/ml of streptomycin (Cellgro). The cells were grown at 37˚C in 5% CO2 under sterile tissue culture conditions and passaged when they reached 80% confluency.

extract_protocol: Total RNA was extracted from the fibroblasts using the Qiagen RNeasy kit, as described in the product manual, followed by DNAse (Invitrogen) treatment. RNA concentration was measured using a NanoDrop spectrophotometer (Thermo Scientific), and submitted for gene expression analysis.

treatment_protocol: Fibroblasts were plated on 10 cm Petri dishes (Falcon), and grown in DMEM w/10% FBS until subconfluency. Thereafter the cells were washed with warm (37°C) PBS, before RNA was extracted. Fibroblast cell cultures at passages 4-6 were used for RNA extraction.

tag: sample type

value: Mix of C57BL6 and BALBc male or female mice, fibroblasts from normal forestomach


title: anac060-sorbitol-repeat1

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
MUT_SOBI.1

source_name: MUT Sor


title: anac060-sorbitol-repeat3

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
MUT_SOBI.3


title: anac060-glucose-repeat3

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
MUT_GLU.3


title: TGFBR2cKO fibroblasts

label_protocol: Uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I were used to fragment the cDNA at Uracil-containing positions. The fragmented cDNA was end-labeled with a biotinylated nucleotide analog.

value: Mix of C57BL6 and BALBc male or female mice, fibroblasts from forestomach squamous cell carcinoma


title: WT-DMM-3

description:
A3
Replicate 3

value: WT


title: WT-DMM-2

description:
C2
Replicate 2


title: K9-DMM-2

description:
D2
Replicate 2


title: WT-sorbitol-repeat3

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
CK_SOBI.3


title: anac060-sorbitol-repeat2

description:
The seedling growth on the 1/2MS agar plate with 6% sorbitol
MUT_SOBI.2


title: WT-glucose-repeat3

description:
The seedling growth on the 1/2MS agar plate with 6% glucose
CK_GLU.3


title: WT-4HR-3

description:
F2
Replicate 3

source_name: Mouse Hip Cartilage

value: 4-6 weeks

value: Hip cartilage

value: 4 hr post hip cartilage injury


title: K9-CTRL-3

description:
G2
Replicate 3

value: Control


title: K9-DMM-3

description:
B3
Replicate 3


title: K9-4HR-1

description:
D1
Replicate 1


title: wt fibroblasts_control


title: K9-4HR-3

description:
H2
Replicate 3


title: WT-4HR-2

description:
H1
Replicate 2


title: K9-4HR-2

description:
B2
Replicate 2


title: K9-CTRL-2

description:
A2
Replicate 2


title: WT-DMM-1

description:
E1
Replicate 1


title: K9-CTRL-1

description:
C1
Replicate 1


title: WT-4HR-1

description:
B1
Replicate 1


title: IgG_ChIPSeq_KSHV infected PBMCs_Hypoxia

type: SRA

city: Philadelphia

first: Rajnish

middle: Kumar

last: Singh

state: Pennsylvania

address: 202B Johnson Pavilion 3610 Hamilton walk

department: Otorhinolaryngology

institute: University of Pennsylvania

library_source: genomic

data_processing:
ChIP sequencing data analysis was performed using CLC Genomics workbench 12 software.
ChIP sequencing reads were aligned to Kaposi's sarcoma assoiated herpesvirus genome using CLC Genomics workbench 12 software.
specific enrichment on KSHV genome was compared against IgG control.
Histogram of specific enrichment on KSHV genome was generated and a comaprative study was perfomed on cells grown under normoxic or hypoxic conditions.
Significantly enriched regions on KSHV genome was extracted in the form of genomic co-ordinate on KSHV (HHV8) genome.
Genome_build: HHV8;NC_009333.1
Supplementary_files_format_and_content: File format: .xlsx file exported from CLC Genomics workbench; Content: Genomic co-ordinates of KSHV(HHV8)

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: KSHV positive BC3 cells were routinly grown in RPMI medium supplemented with 10%fetal bovine serum in a cell culture incubator at 37 degree centigrade and 5% CO2. PBMCs were also grown in RPMI medium supplemented with 10%fetal bovine serum at 37 degree centigrade, 5%CO2.

extract_protocol:
Cells were harvested by centrifugation and washed by resuspending them in PBS. Washed cells were lysed in hypotonic lysis buffer followed by passing through syringe and centrifugation to isolate nuclei. Isolated nuclei were resuspended in detergent containing buffer to lyse the membrane followed by sonication for fragmentation of chromatin. size of fragmented chromatin was estimated by runnig on agarose gel.
Libraries were prepared according to Illumina's instructions using ChIP sequencing sample preparation kit following the manufacturer's protocols.

treatment_protocol: Hypoxic induction was provided by growing the cells in hypoxic chamber with 1% oxygen setting. The culture medium composition remain same as that of cells grown under normoxic conditions.

tag: cell type

value: Peripheral blood mononuclear cells

tag: passage

value: Freshly isolated

tag: chip antibody

value: IgG


title: HIF1 alpha_ChIPSeq_KSHV infected PBMCs_Hypoxia

value: HIF 1 alpha


title: IgG_ChIPSeq_KSHV infected PBMCs_Normoxia


title: HIF1 alpha_ChIPSeq_KSHV infected PBMCs_Normoxia


title: HIF1 alpha_ChIPSeq_BC3_Hypoxia

source_name: BC3 cells

value: Blood derived B-cells


title: HIF1 alpha_ChIPSeq_BC3_Normoxia


title: WT-CTRL-2

description:
G1
Replicate 2


title: WT-CTRL-3

description:
E2
Replicate 3


title: WT-CTRL-1

description:
A1
Replicate 1


title: IgG_ChIPSeq_BC3_Hypoxia


title: IgG_ChIPSeq_BC3_Normoxia


title: 40

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Melanoma tumor biopsy

label_protocol: 300 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated from harvested tumors with RNeasy Plus Mini kits (Qiagen) with subsequent RNA quality assessment using an Agilent 2100 Bioanalyzer.

tag: timepoint

value: Pre-treatment

tag: previous ipilumimab

value: Yes

tag: response (pd = progressive disease; sd = stable disease; pr = partial response; cr = complete response)

value: PD

tag: gender

value: F


title: 106a

value: PR


title: 38

value: SD

value: M


title: 135

value: No

value: CR


title: HRT, Control, replicate 1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.44.0).

source_name: heart, control treatment, mouse 13

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Twenty-four male CD2F1 mice weighing approximately 20g (BALB/c x DBA/2, Charles River, The Netherlands) were individually housed in macrolon type 3 cages with sawdust and tissues as cage enrichment, in a climate-controlled room (21 °C ± 1 °C) with a 12:12 hour dark-light cycle. Mice had ad libitum access to chow and water. Upon arrival, mice were stratified on body weight and divided into groups of 6 animals (Control [C], Control + WBV [C+V], Tumour bearing [T] and Tumour bearing + WBV [T+V]). Subsequently, mice were allowed to acclimatize for 1 week prior to the start of the experiment.

extract_protocol: RNA from EDL, SOL and heart was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands). Subsequently, RNA was quantified (Nanodrop ND1000, Nanodrop technologies Wilmington, DE, USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK).

treatment_protocol: Murine C26 adenocarcinoma cells were cultured and suspended as described previously [PMID: 19259092]. Tumour cells (1x106 cells in 0.2 ml of Hank's balanced salt solution (HBSS)) were inoculated subcutaneously into the right inguinal flank of the mice under general anaesthesia (isoflurane/N2O/O2). HBSS was used as sham injection (0.2 ml). Starting on D1 mice were subjected to a whole-body vibration training (WBV) protocol with 15 min of vibration training for 7 days/week, with a frequency of 45 Hz and 1.0 g acceleration. The vibration platform used was an adjusted commercially available VG Professional power plate (VibroGym, Badhoevedorp, The Netherlands).

tag: Sex

value: male

tag: mouseid

value: heart (HRT)

tag: combined treatment group

tag: tumor bearing (yes/no)

value: no

tag: whole-body vibration training (wbv) (yes/no)

tag: body mass at day 19 (as % of mean of day 1 and day 0)

tag: carcass mass at day 19 (g)

tag: mass muscle sample (mg)


title: 19

tag: treatment

tag: age


title: HRT, Tumour bearing, replicate 2

source_name: heart, tumour bearing, mouse 23

tag: tissue

value: Tumour bearing

value: yes


title: 72


title: SOL, Tumour bearing, replicate 5

source_name: m. soleus, tumour bearing, mouse 23

value: m. soleus (SOL)


title: 43


title: 112


title: HRT, Tumour bearing + WBV, replicate 2

source_name: heart, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 16

value: Tumour bearing + WBV


title: HRT, Tumour bearing, replicate 1

source_name: heart, tumour bearing, mouse 20


title: HRT, Tumour bearing, replicate 3

source_name: heart, tumour bearing, mouse 7


title: HRT, Tumour bearing + WBV, replicate 1

source_name: heart, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 11


title: HRT, Control + WBV, replicate 1

source_name: heart, control treatment, subjected to whole-body-vibration-training (WBV), mouse 22

value: Control + WBV


title: SOL, Control, replicate 4

source_name: m. soleus, control treatment, mouse 24

value: Control


title: HRT, Control + WBV, replicate 2

source_name: heart, control treatment, subjected to whole-body-vibration-training (WBV), mouse 6


title: HRT, Control, replicate 2

source_name: heart, control treatment, mouse 19


title: 27

value: Pre-treatment

value: Yes


title: HRT, Control, replicate 3

source_name: heart, control treatment, mouse 4


title: SOL, Control, replicate 3

source_name: m. soleus, control treatment, mouse 19


title: SOL, Tumour bearing + WBV, replicate 3

source_name: m. soleus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 17


title: SOL, Control + WBV, replicate 3

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 22


title: HRT, Control + WBV, replicate 3

source_name: heart, control treatment, subjected to whole-body-vibration-training (WBV), mouse 9


title: HRT, Tumour bearing + WBV, replicate 3

source_name: heart, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 2


title: SOL, Control + WBV, replicate 2

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 18


title: SOL, Tumour bearing + WBV, replicate 5

source_name: m. soleus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 21


title: 108

source_name: Melanoma tumor biopsy

value: F


title: SOL, Tumour bearing, replicate 4

source_name: m. soleus, tumour bearing, mouse 20


title: SOL, Control, replicate 2

source_name: m. soleus, control treatment, mouse 13


title: SOL, Control + WBV, replicate 6

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 9


title: SOL, Control, replicate 5

source_name: m. soleus, control treatment, mouse 4


title: EDL, Control, replicate 4

source_name: m. extensor digitorum longus, control treatment, mouse 24

value: m. extensor digitorum longus (EDL)


title: SOL, Tumour bearing, replicate 3

source_name: m. soleus, tumour bearing, mouse 14


title: SOL, Tumour bearing + WBV, replicate 2

source_name: m. soleus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 16


title: SOL, Control + WBV, replicate 1

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 15


title: SOL, Tumour bearing, replicate 1

source_name: m. soleus, tumour bearing, mouse 1


title: EDL, Tumour bearing, replicate 4

source_name: m. extensor digitorum longus, tumour bearing, mouse 20


title: SOL, Control, replicate 6

source_name: m. soleus, control treatment, mouse 8


title: SOL, Tumour bearing + WBV, replicate 4

source_name: m. soleus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 2


title: SOL, Tumour bearing + WBV, replicate 1

source_name: m. soleus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 11


title: EDL, Tumour bearing + WBV, replicate 5

source_name: m. extensor digitorum longus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 21


title: SOL, Control + WBV, replicate 4

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 3


title: EDL, Control + WBV, replicate 2

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 18


title: SOL, Tumour bearing, replicate 2

source_name: m. soleus, tumour bearing, mouse 12


title: SOL, Tumour bearing, replicate 6

source_name: m. soleus, tumour bearing, mouse 7


title: EDL, Control + WBV, replicate 3

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 22


title: EDL, Tumour bearing, replicate 3

source_name: m. extensor digitorum longus, tumour bearing, mouse 14


title: EDL, Control, replicate 1

source_name: m. extensor digitorum longus, control treatment, mouse 10


title: EDL, Control + WBV, replicate 6

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 9


title: SOL, Control + WBV, replicate 5

source_name: m. soleus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 6


title: EDL, Tumour bearing, replicate 5

source_name: m. extensor digitorum longus, tumour bearing, mouse 23


title: SOL, Control, replicate 1

source_name: m. soleus, control treatment, mouse 10


title: EDL, Control, replicate 2

source_name: m. extensor digitorum longus, control treatment, mouse 13


title: EDL, Control, replicate 3

source_name: m. extensor digitorum longus, control treatment, mouse 19


title: EDL, Control + WBV, replicate 1

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 15


title: EDL, Tumour bearing + WBV, replicate 2

source_name: m. extensor digitorum longus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 16


title: EDL, Tumour bearing + WBV, replicate 1

source_name: m. extensor digitorum longus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 11


title: EDL, Tumour bearing, replicate 2

source_name: m. extensor digitorum longus, tumour bearing, mouse 12


title: EDL, Tumour bearing + WBV, replicate 3

source_name: m. extensor digitorum longus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 17


title: EDL, Tumour bearing, replicate 6

source_name: m. extensor digitorum longus, tumour bearing, mouse 7


title: EDL, Control, replicate 5

source_name: m. extensor digitorum longus,control treatment, mouse 4


title: Input_rep1

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

description: Input DNA of sall samples were mixed with the equal ratio and sequenced.

data_processing:
Full length reads were mapped to mm9 using Bowtie (v1.1.2)
PCR-duplicates were removed.
For conversion to bigwig files, reads were extended to a total length of 180 bases from the first sequenced base. Libraries were normalized to 1 million reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage after normalizing to 1 million reads.

growth_protocol: KDM1A WT mESCs were cultured in DMEM containing 15% FBS and 1,000 U/ml LIF. Differentiation was induced by replacing media with 20ng/mL Activin A (R&D Systems, #338-AC) and 10 ng/mL FGF2 (R&D Systems, #233-FB).

extract_protocol:
We made following modifications to the parental protocol. To shear chromatin, we treated chromatin with 2 ul MNase (NEB M0247) in 90 ul reaction for 30 min at 25°C, quenched the reactions by adding 5 ul of 100 mM EDTA, and then sonicated the samples with QSonica Q800R at 70% amplitude for total 30 min at 4°C. w Before IP, we spiked in cross-linked chromatin from 0.25 million Drosophila S2 cells in each ChIP reaction. We performed internal ChIP control by an in-house polyclonal rabbit antibody against H2Av (1.6 ug), the fly specific histone variant. The sequencing libraries were prepared using NEBNext Ultra™ II DNA Library Prep Kit for Illumina.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
Input DNA from all the  samples are mixed.

tag: cell type


title: KMT2D_ChIP-seq_24h_rep1

tag: antibody

value: 701869, Invitrogen


title: KMT2D_ChIP-seq_0h_rep1


title: KDM1A_ChIP-seq_24h_rep1

value: ab17721, Abcam


title: KDM1A_ChIP-seq_0h_rep1


title: H3K4me2_ChIP-seq_24h_rep1

value: ab7766, Abcam


title: EDL, Control + WBV, replicate 4

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 3


title: H3K4me2_ChIP-seq_0h_rep1


title: EDL, Control, replicate 6

source_name: m. extensor digitorum longus, control treatment, mouse 8


title: EDL, Control + WBV, replicate 5

source_name: m. extensor digitorum longus, control treatment, subjected to whole-body-vibration-training (WBV), mouse 6


title: CSD_H3K36me3_ChIP-Seq

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
FASTQ files were aligned to the mm9 genome (and hg19 to be used for normalization) using Bowtie aligner with default parameters
BAM and index files were generated using SAMtools with the “view” and “index” commands, respectively
Total reads aligning to the human genome, hg19 were quantified, and a Scaling Factor was determined such that the total human mapped reads would be the same across samples
ChIP samples were normalized by the Scaling Factor using Deeptools "bamCoverage" command (using default 50bp bins) to generate bigWig files
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file generated using Deeptools

source_name: V6.5 Mouse Embryonic Stem Cells

growth_protocol: Cells were maintained on irradiated mouse embryonic fibroblasts (MEFs) in ESC media (KnockOut DMEM, 15% fetal bovine serum (FBS), L-glutamine, Penicillin/Streptomycin, non-essential amino acids, 2-mercaptoethanol, and leukemia inhibitory factor)

extract_protocol:
ESCs were harvested and MEF-depleted. Chromatin was prepared by cross-linking cells with 1% formaldehyde for 5 min, followed by adding glycine to 0.125M for 5 min. Cells were washed and resuspended in ChIP Lysis Buffer (50mM Tris-HCl pH8.0, 20mM EDTA,1% SDS, protease inhibitor cocktail) and sonicated using Covaris S220 for 14 cycles of alternating 45s on/off with peak power = 170, duty factor = 5, cycles per burst = 200, 10-13x106 cells at a time. Soluble chromatin was collected by centrifuging at 12,000 x g for 10 min. 20ug of chromatin was used for each sample, together with a 0.4ug spike-in of human chromatin from 293T cells (50:1 of sample to spike-in chromatin ratio). The combined chromatin was diluted with 9 parts volume of Dilution Buffer (16.7mM Tris pH8.0, 0.01% SDS, 1.1% Triton-X-100, 1.2mM EDTA, 167mM NaCl), and incubated with 3ug of H3K36me3 antibody (Active Motif, 61101) overnight at 4°C. Equal portions of protein A and protein G magnetic beads (Thermo Fisher Scientific, 1002D and 1004D, respectively) were washed and added to each sample for 2 hrs at 4°C. Following IP, beads were washed twice with low salt buffer (50 mM HEPES, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 1 mM EDTA, and 140 mM NaCl), high salt buffer (50 mM HEPES, 0.1% SDS, 1% Triton X-100, 0.1% deoxy- cholate, 1 mM EDTA, and 500 mM NaCl), LiCl buffer (20 mM Tris, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA, and 250 mM LiCl), and TE. Elution of DNA was performed by incubating beads with elution buffer (50 mM Tris, 1 mM EDTA, and 0.1% SDS) followed by reverse cross-linking at 65°C overnight with 1% SDS. Samples were treated with RNase A for 30 min followed by 2 h of proteinase K digestion. Magnetic beads were removed, and DNA was purified by phenol:chloroform extraction followed by ethanol precipitation.
Libraries were prepared using the Ovation Ultralow System V2 (NuGen, 0344) according to manufacturer's protocol

treatment_protocol: Expression of rescue constructs were induced growing cells in ESC media containing 1ug/ml doxycyline for 72hrs.

tag: genotype

value: HP1g CSD

value: Doxycycline (1ug/ml) for 72 hrs


title: HCSD_H3K36me3_ChIP-Seq

value: HP1g HCSD


title: EDL, Tumour bearing, replicate 1

source_name: m. extensor digitorum longus, tumour bearing, mouse 1

value: male

value: no


title: CD_H3K36me3_ChIP-Seq

value: HP1g CD


title: I165E_H3K36me3_ChIP-Seq

value: HP1g I165E


title: Full-length_H3K36me3_ChIP-Seq

value: HP1g Full length


title: Uninduced_H3K36me3_ChIP-Seq

value: uninduced-KO


title: HP1gKO_H3K36me3_ChIP-Seq

value: HP1g KO


title: Lung metastases 2 matched with Primary 6

city: Durham

first: David

last: Kirsch

state: NC

address: PO Box 96100

institute: Duke University

library_source: transcriptomic

data_processing:
Base-calling was done on the instrument using RTA
Demultiplexing was done using bcl2fatq
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to mouse mm10 genome using STAR v5.5.4b and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with read counts per feature

source_name: Mouse tumor tissues

extract_protocol:
RNA from tissues was extracted using Direct-zol RNA miniprep kit (Zymo Research).
20 stranded RNA seq with Ribozero Gold (Human/Mouse/Rat), Library was constructed using the kit RS-122-2301

value: Mixed background


title: WT_H3K36me3_ChIP-Seq

value: WT


title: Primary 5


title: Primary 6


title: V32M_H3K36me3_ChIP-Seq

value: HP1g V32M


title: Lung metastases matched with Primary 5


title: Lung metastases 1 matched with Primary 6


title: Lung metastases 1 matched with Primary 4


title: Lung metastases 1 matched with Primary 3


title: Lung metastases 3 matched with Primary 2


title: Primary 3


title: Lung metastases 2 matched with Primary 3


title: Lung metastases 4 matched with Primary 2


title: Lung metastases 1 matched with Primary 2


title: Lung metastases 3 matched with Primary 1


title: Primary 2


title: Lung metastases 4 matched with Primary 1


title: Primary 1


title: Lung metastases 1 matched with Primary 1


title: Lung metastases 2 matched with Primary 1


title: W174A_H3K36me3_ChIP-Seq

value: HP1g W174A


title: AIR42-2

city: Beijing

first: Xing

last: Chen

address: Yiheyuan Road

department: Chemical Biology

institute: Peking University

data_processing:
Base-calling was performed using CASAVA v2.19
Reads were filtered by TrimGalore v0.6.5 with Q30
Reads from sequencing were aligned to the genome using Hisat v2.1.0, with the index built from  ASM584v2 genome
The resulting SAM alignment files were converted to BAM formats and sorted using SAMtools v1.3
Reads aligned to genes were counted with featureCounts v1.6.3
FPKM of genes were analysed by stringtie v2.1.4
Differential analysis was performed with DESeq2 v1.20.0
Genome_build: ASM584v2
Supplementary_files_format_and_content: Excel file containing raw counts of sequencing reads generated by featureCounts. Excel file containing FPKMs of sequencing reads generated by stringtie v2.1.4.Excel file containing differential expression analysis by DESeq2 v1.20.0

organism: Escherichia coli

source_name: E.coli K12

growth_protocol: Escherichia coli strains K12 were grown in LB at 37℃ with shaking at 220 rpm. Overnight cultures were diluted 1:100 into nucleoside-free medium [M9+0.4% (wt/vol) glucose+ 10g/L tryptone ].

extract_protocol:
Total RNA was extracted using TRIzol Reagent. After DBCO-reaction, RNA was extracted through PCI (acidic phenol:chloroform:isoamyl alcohol, 25:24:1; Sigma).
A total amount of 3µg RNA per sample was used as input material for total-RNA seq sample preparations. A total amount of 20 ng RNA per sample was used as input material for  newly transcribed RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

treatment_protocol: Overnight cultured bacteria were diluted 1:100 into fresh media and grown to an OD600 of approximately 0.3. The bacteria were incubated with 100 μM AzG and separated into two groups. One of them was cultured at 37 ℃ as negative control, the other was cultured at 42 ℃ to imitate heat shock. After ten minutes, bacteria were centrifugated and treated with TRIzol and RNA was extracted following the manufacturer’s instructions.

tag: strain

tag: sample type

value: immunoprecipitated RNA

tag: temperature treatment

value: 42C for 10 minutes


title: AIR37-2


title: AIR42-1


title: Lung metastases 2 matched with Primary 2


title: AIR37-1


title: Primary 4


title: 10min-3

data_processing:
Base-calling was performed using CASAVA v2.19
Reads were filtered by TrimGalore v0.6.5 with Q > 30
Reads from sequencing were aligned to the  genome using Hisat v2.1.0, with the index built from  ASM584v2 genome
The resulting SAM alignment files were converted to BAM format sand sorted using SAMtools v1.3
FPKM of genes were analysed by stringtie v2.1.4
Genome_build: ASM584v2
Supplementary_files_format_and_content: Excel file containing FPKMs of sequencing reads generated by stringtie v2.1.4

growth_protocol: Escherichia coli strains K12 were grown in LB at 37℃ with shaking at 220rpm. Overnight cultures were diluted 1:100 into nucleoside-free medium [M9+0.4% (wt/vol) glucose+ 10g/L tryptone ].

extract_protocol:
Total RNA was extracted using TRIzol Reagent. After DBCO-reaction, RNA was extracted through PCI (acidic phenol:chloroform:isoamyl alcohol, 25:24:1; Sigma).
A total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional  RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

treatment_protocol: Overnight cultured bacteria were diluted 1:100 into fresh media and grown to an OD600 of approximately 0.3. The bacteria were incubated with 100 μM AzG for two hours. Bacteria were centrifugated at 4000 g for 10 minutes. The medium were thorough removed and the bacteria were resuspended by our nucleoside-free medium supplied with 100 μM Guanosine and separated into three groups. Those three groups of bacteria were chased for 0, 5, 10 minutes respectively.

tag: timepoint

value: 10 min


title: 10min-2


title: total37-2

value: total RNA


title: total42-2


title: 10min-1


title: 5min-1

value: 5 min


title: 5min-3


title: 5min-2


title: 0min-2

value: 0 min


title: total37-1


title: AzG-2

data_processing:
Base-calling was performed using CASAVA v2.19
Reads were filtered by TrimGalore v0.6.5 with Q>30
Reads from sequencing were aligned to the genome using Hisat v2.1.0, with the index built from  ASM584v2 genome
The resulting SAM alignment files were converted to BAM format sand sorted using SAMtools v1.3
Reads aligned to exons were counted with featureCounts v1.6.3
FPKM of genes were analysed by stringtie v2.1.4
Genome_build: ASM584v2
Supplementary_files_format_and_content: Excel file containing raw counts of sequencing reads generated by featureCounts.Excel file containing FPKMs of sequencing reads generated by stringtie v2.1.4.

growth_protocol: Escherichia coli strains K12 were grown in LB at 37℃ with shaking at 220rpm. Overnight cultures were diluted 1:100 into nucleoside-free medium [M9+0.4% (wt / vol) glucose+ 10 g / L tryptone ].

extract_protocol:
Total RNA was exracted using TRIzol Reagent
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

treatment_protocol: We treated E.coli with or without 100 μM AzG when it was grown to OD600=0.3 in nucleoside-free medium.


title: 0min-3


title: 0min-1


title: AzG-3


title: total42-1


title: Blank-3


title: Blank-1


title: Blank-2


title: EDL, Tumour bearing + WBV, replicate 4

source_name: m. extensor digitorum longus, tumour bearing, subjected to whole-body-vibration-training (WBV), mouse 2

tag: Sex

value: male

tag: mouseid

value: m. extensor digitorum longus (EDL)

value: Tumour bearing + WBV

value: yes


title: Rat-OH8-Emb3-M1-L-E15

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The quality control of the rna-seq reads were done by AfterQC, Trimmomatic , MultiQC and FastQC
The ribosomal rRNA were filtered out using SortMeRna
The reads where aligned to rat genome using STAR (1.5) with default parameters Rnor_6.0 (Ensembl release 101),
The gene expression was measured by counting the corresponding reads of the exons. This step was performed by htseq-count with parameters (-s reverse -t exon -i gene_id)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited gene expression count values of each samples

organism: Rattus norvegicus

source_name: Molar 1

growth_protocol: Tooth germs were dissected carefully under microscope from E15.5, or E17.5 DA/HanRj rat embryos.

extract_protocol:
The tooth germ was homogenised into TRI Reagent (Merck, Darmstadt, Germany) using Precellys 24 -homogenizer (Bertin Instruments, Montigny-le-Bretonneux, France). The RNA was extracted by guanidium thiocyanate-phenol-chloroform method and then further purified by RNeasy Plus micro kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's instructions.
The cDNA libraries were prepared with Ovation Rat RNAseq System (Tecan, Zürich, Schwitzerland).


title: Rat-OH8-Emb2-M1-L-E15


title: Rat-OH6-Emb4-M1-L-E17


title: Rat-OH8-Emb1-M1-R-E15


title: Rat-OH8-Emb5-M1-L-E15


title: Rat-OH6-Emb2-M1-R-E17


title: Rat-OH6-Emb2-M1-L-E17


title: AzG-1


title: esb1sgn3.3.1

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

data_processing:
Trimmomatic v0.36 was used to identify and discard reads containing the Illumina adaptor sequence.
We mapped the resulting high-quality filtered reads against the TAIR10 Arabidopsis reference genome using HISAT2 v.2.1.0 with default parameters
We applied the featureCounts function from the Subread package to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10 Arabidopsis reference genome
Supplementary_files_format_and_content: mRNA_counts_reyt_schengen_pathway.txt contains the count matrix

source_name: root tips

growth_protocol: The plants were grown for 6 days on ½ M/S plates. Seeds were sown in three parallel lines per square plates (12*12 cm) at high density

extract_protocol:
The samples were snap-frozen at harvest and ground into fine powder in a 2 mL centrifuge tube. Total RNA was extracted according to Logemann et al., 1987. Samples were homogenized in 400 µL of Z6-buffer containing 8 M guanidine-HCl, 20 mM MES, 20 mM EDTA pH 7.0 After the addition of 400 µl phenol:chloroform:isoamylalcohol, 25:24:1, samples were vortexed and centrifuged (15,000g 10 min.) for phase separation. The aqueous phase was transferred to a new 1.5 mL tube and 0.05 volumes of 1 N acetic acid qnd 0.7 volumes 96% ethanol was added. The RNA was precipitated at -20°C overnight. Following centrifugation (15,000g 10 min, 4°C), the pellet was washed with 200µL 3M sodium acetate at pH 5.2 and 70% ethanol. The RNA was dried and dissolved in 30 µL of ultrapure water and store at -80°C until use. DNase treatment (DNase I, Amplification Grade, 18068015, Invitrogen) was carried out on the samples to remove genomic DNA
The RNA Concentration and quality were determined using Qubit (Invitrogen; Q10210) and TapeStation (Agilent; G2991A) protocols. Librairies were generated using the Lexogen Quant Seq 3’ mRNA Seq (FWD) Library Prep Kit (Lexogen; 015) which employs polyA selection to enrich for mRNA. Library yield was measured by Qubit (Invitrogen; Q10210) and TapeStation (Agilent; G2991A) systems. protocols to determine concentration and library size, these are then pooled together in equimolar concentrations.
The concentration of the pool of libraries were confirmed using the Qubit and qPCR and then loaded onto an Illlumina NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina; 20024906), to generate approximately 5 million 75bp single-end reads per sample.

treatment_protocol: The first 5 mm of root tips were collected. One plate was used as a biological replicate.

tag: biorep

tag: techrep


title: esb1sgn3.3


title: esb1sgn3.3.3


title: sm.5.3


title: sm.5


title: sm.5.1


title: esb1sgn3.3.2


title: Wtcif.4.3

value: Wtcif


title: WT.2.2


title: WT.2.3


title: WT.2.1


title: Wtcif.4.2


title: sm.5.2


title: WT.2


title: Wtcif.4


title: Rat-OH8-Emb4-M1-R-E15


title: Rat-OH6-Emb6-M1-L-E17


title: Rat-OH6-Emb7-M1-R-E17


title: sm.2.1


title: sm.2.2


title: Organoid lineage tracing - previous

city: Vienna

first: Christopher

last: Esk

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

data_processing:
demultiplexing
LID error correction & filtering
lineage size determination
Supplementary_files_format_and_content: tab separeted text file with reads per lineage

source_name: mouse

extract_protocol:
Phenol/Chloroform
PCR introducing adaptors

tag: target tissue

value: mouse


title: sm.2.3


title: mESCH3.3 ChIP-seq

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
H33_ES_S1
processed data file: ESC_H33_bin100.bw

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin.
RNA-seq reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore!.
After the reads were aligned, the reads correspond to rRNA were removed. featureCounts was then used to assign the mapped reads to a transcriptional model file.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: mESCH3.3 ChIP-seq

growth_protocol: Early embryos were cultured in KSOM. Male mouse embryonic stem cells were cultured with the medium that consists of GMEM (Sigma-Aldrich) containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates.

extract_protocol:
MNase-digested chromatin was used for ULI-N-ChIP-seq. Total RNA in cell lysates was directly used for RNA-seq sample preparation according to the manufacturer's  instructions (SMART-seq stranded kit, TAKARA).
ULI-N-ChIP-seq protocol was used for ChIP-seq. For RNA-seq, SMART-seq stranded kit was used.

value: hybrid C57BL/6/129

tag: tissue/cell type

value: Embryonic stem cell

tag: chip antibody


title: 4-cell H3.3 ChIP-seq rep2

description:
H33_4C_rep2_S3
processed data file: 4C_H33_bin100.bw

source_name: 4-cell H3.3 ChIP-seq

value: hybrid C57BL/6/JF-1

value: Embryo


title: Wtcif.4.1


title: sm.2


title: mESC input

description:
input_ES_S2
processed data file: ESC_H33_bin100.bw

source_name: mESC input


title: 2-cell H3.3 ChIP-seq rep2

description:
H33_2C_rep2_S2
processed data file: 2C_H33_bin100.bw

source_name: 2-cell H3.3 ChIP-seq


title: 8-cell input rep1

description:
input_8C_rep1_S8
processed data file: 8C_H33_bin100.bw

source_name: 8-cell input


title: 8-cell H3.3 ChIP-seq rep1

description:
H33_8C_rep1_S4
processed data file: 8C_H33_bin100.bw

source_name: 8-cell H3.3 ChIP-seq


title: 4-cell H3.3 ChIP-seq rep1

description:
H33_4C_rep1_S3
processed data file: 4C_H33_bin100.bw


title: esb1sgn3.2.3


title: esb1sgn3.2.2


title: 2-cell input rep2

description:
input_2C_rep2_S6
processed data file: 2C_H33_bin100.bw

source_name: 2-cell input


title: 4-cell input rep2

description:
input_4C_rep2_S7
processed data file: 4C_H33_bin100.bw

source_name: 4-cell input


title: esb1sgn3.2


title: esb1sgn3.2.1


title: 2-cell input rep1

description:
input_2C_rep1_S6
processed data file: 2C_H33_bin100.bw


title: Samp22-Mature-Control

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

description: Second of two control replicates of differentiated/mature 3T3-L1 adipocyte cells in culture.

hyb_protocol: Samples were combined with a hybridization mix, injected into Mouse ClariomTM S arrays, and placed in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C and 60 RPM for 16.5 hours overnight.

scan_protocol: Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450 and scanned with the 7G Affymetrix® GeneChip® Scanner 3000. Raw image analysis was performed with Affymetrix® Expression ConsoleTM software. The raw data images produced from the scanner were processed into .CEL files, which contain measure intensities for each probe on the array.

data_processing: The .CEL files were imported into Partek® Genomics SuiteTM (GS) version 6.6 (Partek Inc., St. Louis, MO, USA, www.partek.com). Background correction, quantile normalization, log2 transformation, and probe set summarization were performed using default settings for the Robust Multichip Average (RMA) procedure (see Bolstad et al. Bioinformatics 19(2):185; Irizarry et al. Biostatistics 4(2):249; Nucleic Acids Res. 31:e15). A two-way Analysis of Variance (ANOVA) with factors matrix type and subject (paired design) was performed on the RMA-normalized probesets to assess differential expression.

source_name: Adipose 3T3-L1 cell culture after 7 days of adipogenic differentiation and no exposure to myeloma MM1S cells

label_protocol: Approximately 5.5µg of single-stranded cDNA was fragmented using UDG (10U/µL) and APE1 (1000U/µL), provided in the GeneChip® WT PLUS Reagent Kit. Samples were then labeled with biotin using TdT (30U/µL), also provided in the GeneChip® WT PLUS Reagent Kit. Efficiency of the fragmentation and labeling reactions were verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

growth_protocol: Preadipocytes were cultured in basal growth media (DMEM supplemented with 10% FBS and 1% penicillin/streptomycin) for 4 days and then switched to an adipogenic differentiation media (basal supplemented with 0.5 mM IBMX, 1 µM Dex, 5 µg/mL insulin) for 4 days, and then a second adipogenic media (basal supplemented with 5 µg/mL insulin) for 2 days and then maintained in basal media for an additional day to ensure terminal differentiation into adipocytes.

extract_protocol: After differentiation and myeloma exposure periods, total RNA was isolated from 10 samples using the Qiazol and miRNeasy isolation mini-kit (Qiagen) according to the manufacturer’s protocol. 50ng of RNA was used to synthesize cDNA through a first-strand reverse transcription reaction and second-strand RNA degradation reaction, using reagents from the GeneChip® WT PLUS Reagent Kit. cRNA was then synthesized through an overnight (16-hour) in-vitro transcription reaction, which utilizes a T7 RNA polymerase. The cRNA was purified using an Affymetrix® magnetic bead protocol. Sample concentrations were determined using a 40µg/mL/A260 constant on a Nanodrop 1000 spectrophotometer.

treatment_protocol: For the pre-exposure experiment, after two days in basal growth media pre-adipocytes reached confluency and were switched to RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin either alone, or with MM.1S myeloma cells for 48 hours. At this time, myeloma cells were removed, pre-adipocytes were washed, and then differentiated as outlined above. For the mature adipocyte experiment, 3T3-L1 pre-adipocytes were cultured exactly as outlined above. After differentiation, adipocytes were changed to RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin either alone, or with MM.1S myeloma cells for 72 hours. In both experiments myeloma cells were co-cultured with 3T3-L1 cells indirectly utilizing a 0.4 µm transwell membrane.

tag: experiment

value: Experiment 2

tag: cell line

value: Pre-adipocyte Cell Line

tag: adipocyte developmental stage

value: Mature

tag: exposure to mm1s myeloma cell line


title: Zygote input rep2

description:
input_zyg_rep2_S5
processed data file: Zyg_H33_bin100.bw

source_name: Zygote input


title: Wtcif.1.3


title: Samp8-Mature-Myeloma

description: First of three experimental replicates of differentiated/mature 3T3-L1 adipocyte cells in culture exposed to myeloma MM1S cells.

source_name: Adipose 3T3-L1 cell culture after 7 days of adipogenic differentiation followed by exposure to myeloma MM1S cells

tag: cell type

value: Mature exposure


title: Samp14-Mature-Control

description: First of two control replicates of differentiated/mature 3T3-L1 adipocyte cells in culture.


title: 2-cell H3.3 ChIP-seq rep1

description:
H33_2C_rep1_S2
processed data file: 2C_H33_bin100.bw


title: Samp16-Mature-Myeloma

description: Second of three experimental replicates of differentiated/mature 3T3-L1 adipocyte cells in culture exposed to myeloma MM1S cells.


title: Wtcif.1.2

tag: genotype


title: Zygote H3.3 ChIP-seq rep1

description:
H33_zyg_rep1_S1
processed data file: Zyg_H33_bin100.bw

source_name: Zygote H3.3 ChIP-seq

tag: strain


title: Zygote input rep1

description:
input_zyg_rep1_S5
processed data file: Zyg_H33_bin100.bw


title: Wtcif.1.1


title: Zygote H3.3 ChIP-seq rep2

description:
H33_zyg_rep2_S1
processed data file: Zyg_H33_bin100.bw


title: Samp24-Mature-Myeloma

description: Third of three experimental replicates of differentiated/mature 3T3-L1 adipocyte cells in culture exposed to myeloma MM1S cells.


title: 4-cell input rep1

description:
input_4C_rep1_S7
processed data file: 4C_H33_bin100.bw


title: failure1_ip

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

data_processing:
alignment of fastq files using hisat2 v2.2.0 with default settings
count matricies formed using htseq v2.0 with default settings
input differential expression calculation using DESeq2, FC set to 1.5 and p-val set to 0.05.
m6a peak calling using exomePeak v1.6, FDR set to 0.05
Genome_build: hg19
Supplementary_files_format_and_content: hisat2 alignment file (.bam), htseq count matrix (.txt), DEseq2 analysis (.csv), m6A exomePeak (.bed)

source_name: human heart tissue

extract_protocol:
Total RNA was purified with TRIzol reagents from human heart samples. Polyadenylated RNA was then isolated from total RNA with two rounds of polyA tail purification using Dynabeads® mRNA DIRECT™ kit (Thermo Scientific). rRNA was further removed from polyadenylated RNA using RiboMinus Eukaryote kit (Thermo Scientific). 50 ng polyadenylated RNA after rRNA depletion was digested by nuclease P1 (Sigma, N8630), respectively, in 20 μl of buffer containing 25 mM NaCl and 2.5 mM ZnCl2 for 1 h at 42 °C. 1 ug polyadenylated RNA was adjusted to 10 ng/μl in 100 μl and fragmented using a BioRuptor ultrasonicator (Diagenode) with 30 s on/off for 30 cycles. After fragmentation, 5% of the fragmented RNA was saved as input. m6A marked fragments were enriched using EpiMark N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer’s protocols and collected as IP. Both input and IP samples were subjected to library preparation using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocols
Both input and IP samples were subjected to library preparation using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocols.

tag: disease state

value: failing heart

tag: tissue

value: heart

tag: isolation method

value: m6A-IP RNA


title: failure5_ip


title: esb1.2.3


title: failure4_ip


title: failure2_ip


title: failure3_ip


title: esb1.2.2


title: Wtcif.1


title: healthy5_ip

value: healthy heart


title: healthy3_ip


title: healthy4_ip


title: esb1.2


title: healthy1_ip


title: esb1.2.1


title: failure5_input

value: input


title: failure3_input


title: WT.6.3

value: WT


title: failure2_input


title: failure4_input


title: healthy5_input


title: failure1_input


title: WT.6.1


title: healthy4_input


title: WT.6


title: healthy3_input


title: healthy2_input


title: healthy1_input


title: esb1sgn3.6.3


title: TP53TNKS1/2TKO rep3

first: Litong

last: Nie

address: 6565 MD Anderson Blvd Unit, Desk Z6.2026

department: ERO

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data were processed with FastQC to filter data. Genome mapping was carried out using Star software.The mapped reads were assembled into transcripts and genes with the human genome annotation file (genecode.v28.annotation.gtf) using HTseq software (v0.11.0).
DESeq2 (v 1.28.1) was used to analysis the fold change and adjusted p value of transcripts or genes.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 293A cells

extract_protocol:
The whole mRNA of four cells were extracted with RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: genotype/variation


title: TP53TNKS1/2TKO rep1


title: esb1sgn3.6.2


title: TP53TNKS1/2TKO rep2


title: TP53KO rep1


title: RNF146KO rep3


title: healthy2_ip


title: esb1sgn3.6


title: 293A wt rep3


title: WT.6.2


title: TP53KO rep2


title: RNF146KO rep1


title: esb1sgn3.6.1


title: sgn3cif.5.3


title: TP53KO rep3


title: sgn3cif.5.2


title: sgn3cif.5.1


title: 293A wt rep1


title: sgn3cif.5


title: V_Treated_10_KCBG

city: Aurora

first: Stanca

last: Birlea

state: CO

department: Dermatology

institute: University of Colorado, Anschutz Medical Campus

data_processing:
Using a customized pipeline from our group (PMID: 24600007), RNA-Seq reads from each library were aligned using GSNAP.
Transcripts were assembled and normalized gene expression levels (FPKM) were estimated using Cufflinks software and normalized read count.
Genome_build: GRCh37/hg19

source_name: Keratinocytes

extract_protocol:
Frozen tissue sections were immunostained using a rapid immunostaining protocol (<30 minutes) and F-LCM was performed using an NKI-Beteb antibody using established methods (PMID: 27193292).  Total RNA was extracted using the ARCTURUS® PicoPure® RNA Isolation Kit (ThermoFisher Scientific, #KIT0204).  Total RNA was amplified and cDNA was transcribed using the Ovation® RNA-Seq System V2 kit (NuGEN Technologies, #7102-32)
After amplification and purification, the cDNA was fragmented in ~ 350 bp fragments and ligated into a sequencing library (NuGEN Technologies; Ovation Ultralow Library System). Illumina adapters were ligated to cDNA (Promega, LigaFast Kit). cDNA was purified via Am Pure magnetic bead and subjected to PCR amplification. The final libraries were sequenced with Illumina HiSeq 2000 with 4 samples/lane using a 1x50 bp format.

treatment_protocol: Patient biopsies were embedded in OCT and flash frozen in liquid nitrogen within 30 minutes after collection.

tag: condition

value: vitiligo

tag: treatment

value: NBUVB-Treated for 3-6 months

tag: biopsy

value: Full-thickness, repigmented skin

tag: location in tissue

value: Hair follicle bulge outer root sheath

tag: cell status

value: Putative precursor keratinocyte cells

tag: number of cells

value: 100 pooled

tag: antibody used

value: PMEL (Clone NKI-Beteb) (neg)

tag: method of isolation

value: F-LCM


title: V_Treated_2_KCBG


title: 293A wt rep2

tag: cell line


title: WT.3.3

source_name: root tips

tag: biorep

tag: techrep


title: V_Treated_1_KCBG


title: V_Treated_8_KCBG


title: V_Untreated_4_KCBG

value: Untreated


title: WT.3.2

tag: genotype


title: WT.3.1


title: RNF146KO rep2


title: esb1.1.3


title: V_Untreated_3_KCBG


title: WT.3


title: V_Untreated_2_KCBG


title: V_Untreated_7_KCBG


title: esb1.1.2


title: esb1.1.1


title: V_Treated_2_MCBG

source_name: Melanocytes

value: Putative precursor melanocytic cells

value: PMEL (Clone NKI-Beteb) (+)


title: V_Treated_1_MCBG


title: V_Treated_8_MCBG


title: V_Untreated_1_KCBG


title: esb1.1


title: V_Treated_7_KCBG


title: V_Treated_10_MCBG


title: V_Untreated_8_KCBG


title: V_Treated_9_KCBG


title: V_Treated_7_MCBG


title: V_Treated_9_MCBG


title: V_Untreated_3_MCBG


title: V_Untreated_2_MCBG


title: V_Untreated_8_MCBG


title: V_Untreated_7_MCBG


title: V_Untreated_1_MCBG


title: Wtcif.3.1

value: Wtcif


title: 105C - Ovarian Clear Cell Carcinoma (OCCC) cell-line

city: London

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

data_processing:
Amplicon locations: Exonic, Splice sites, 5′ UTR, 3′ UTR;
Nucleotide variant (MNV), Single nucleotide variant (SNV), Insertion or deletion (InDel) and Copy number variant (CNV);
Variant effects: frameshift insertion, non-frameshift insertion, frame shift deletion, non-frameshift deletion, stopless, missense, nonsense;
UCSC Common SNPs: filtered out;
1000 Genomes-Minor Allele Frequency (MAF): >0.01 filtered out;
5000 Exomes Global MAF: >0.01 filtered out;
CNV Confidence Range: >10;
p-value (data quality): >0.01 filtered out.
# of sequence reads mutated < 30% of total reads obtained filtered out
Genome_build: hg19

growth_protocol: Cell lines were cultured in Dulbecco’s modified Eagle medium/Ham’s F12 (Wisent) and supplemented with 10% FBS (Wisent). Cells were maintained in at 37 °C and a CO2 concentration of 5%. Cells were allowed to reach ~90% confluency at which point the media was aspirated and cells were washed with phosphate buffered saline (PBS) and exposed to 2 mL of trypsin/EDTA until cells detached from plate. Cells were resuspended in 10 mL of media and then split onto new plates at a minimum of a 1:3 dilution.

extract_protocol:
Genomic DNA obtained from 105C cell line was sent to the Sunnybrook Research Institute Genomics Core Facility in Toronto, Ontario, Canada where the assay was performed according to the manufacturer’s protocol.
AmpliSeq DNA

tag: cell type

value: Ovarian Clear Cell Carcinoma


title: WT.4.3


title: V_Untreated_4_MCBG


title: Wtcif.3


title: Wtcif.3.3


title: WT.4


title: WT.4.2


title: myb36.4.2


title: WT.4.1


title: Wtcif.3.2


title: myb36.4.1


title: myb36.4


title: Cam3II_R539T_24h_rep3

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were retained. Local background correction (normexp) and lowess normalization across all features was applied to generate the normalized log2 gene expression ratios.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum blood stage

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: Parasites were grown in RPMI1640 media (Gibco, Invitrogen) supplemented with 5% albumax II,  0.2% sodium bicarbonate and 150uM hypoxanthine, and human red blood cells at 3% hematocrit. Cultures were maintained in 3% oxygen and 5% carbon dioxide and kept at 37 degrees celsius.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211. Amplification of target DNA was carried out as  described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211, to generate sufficient material for hybridizations against a common RNA reference pool of 3D7 strain using a microarray platform.

treatment_protocol: 0-3 hpi ring stage parasites were treated with 700nM dihydroartemsinin (DHA) or 0.1% DMSO vehicle control for 6h at the start of the experiment and sampled thereafter.

tag: culture

value: in vitro

tag: Stage

value: asexual blood stage

tag: strain

tag: genetic modification

value: ZFN-edited for K13 mutation

tag: k13 allele

tag: sampling timepoint

tag: treatment protocol

tag: experimental replicate

source_name: Plasmodium falciparum reference RNA pool

value: laboratory strain 3D7

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: Cam3II_R539T_16h_rep3


title: Cam3II_R539T_24h_DHA_rep1

value: 700nM DHA added to 0-3 hpi rings for 6h at start of experiment


title: Cam3II_R539T_32h_rep3


title: Cam3II_R539T_32h_DHA_rep1


title: Cam3II_R539T_32h_rep2


title: Cam3II_R539T_40h_DHA_rep1


title: Cam3II_R539T_48h_rep3


title: Cam3II_R539T_48h_DHA_rep1


title: Cam3II_R539T_0h_rep3


title: myb36.4.3


title: Cam3II_R539T_40h_rep3


title: Cam3II_R539T_24h_rep2


title: Cam3II_R539T_8h_DHA_rep1


title: Cam3II_R539T_48h_rep2


title: esb1.4.3


title: Cam3II_R539T_16h_rep2


title: Cam3II_R539T_8h_rep3


title: Cam3II_R539T_16h_DHA_rep1


title: Cam3II_R539T_40h_rep2


title: Cam3II_R539T_0h_rep2


title: Cam3II_R539T_8h_rep2


title: Cam3II_R539T_48h_rep1

value: 0.1% DMSO vehicle added to 0-3 hpi rings for 6h at start of experiment


title: esb1.4


title: Cam3II_R539T_40h_rep1


title: Cam3II_R539T_32h_rep1


title: sgn3.2.3


title: Cam3II_R539T_24h_rep1


title: sgn3.2.2


title: esb1.4.1


title: sgn3.3.3


title: sgn3.2.1


title: sgn3.2


title: Cam3II_R539T_8h_rep1


title: sgn3.3.2


title: Cam3II_R539T_0h_rep1


title: esb1.4.2


title: Cam3II_revWT_48h_DHA_rep1

value: ZFN-edited for silent binding site mutation

value: wild-type


title: sgn3.3.1


title: Cam3II_revWT_32h_DHA_rep1


title: Cam3II_revWT_24h_rep3


title: sgn3.3


title: Cam3II_revWT_24h_DHA_rep1


title: Cam3II_revWT_48h_rep3


title: Cam3II_revWT_40h_rep3


title: Cam3II_revWT_16h_DHA_rep1


title: esb1.3.3


title: Cam3II_revWT_8h_DHA_rep1


title: Cam3II_revWT_16h_rep3


title: esb1.3.1


title: Cam3II_revWT_8h_rep3


title: esb1.3.2


title: Cam3II_revWT_0h_rep3


title: Cam3II_revWT_32h_rep3


title: esb1.3


title: Cam3II_revWT_32h_rep2


title: Cam3II_revWT_40h_DHA_rep1


title: Cam3II_revWT_24h_rep2


title: Cam3II_R539T_16h_rep1


title: Wtcif.2.3


title: Wtcif.2.2


title: Cam3II_revWT_40h_rep2


title: Wtcif.2


title: Cam3II_revWT_48h_rep2


title: Cam3II_revWT_32h_rep1


title: Cam3II_revWT_40h_rep1


title: Cam3II_revWT_48h_rep1


title: Cam3II_revWT_24h_rep1


title: sgn3cif.2.2


title: sgn3cif.2.3


title: sgn3cif.2.1


title: Wtcif.2.1


title: sgn3cif.2


title: Cam3II_revWT_16h_rep1


title: Dd2_C580Y_32h_DHA_rep2


title: Dd2_C580Y_24h_DHA_rep2


title: Dd2_C580Y_48h_DHA_rep3


title: Dd2_C580Y_6h_DHA_rep2


title: Dd2_C580Y_48h_DHA_rep2


title: WT.5.3

value: WT


title: Cam3II_revWT_8h_rep2


title: Cam3II_revWT_0h_rep2


title: Dd2_C580Y_3h_DHA_rep3


title: Cam3II_revWT_16h_rep2


title: Cam3II_revWT_8h_rep1


title: Dd2_C580Y_3h_DHA_rep2


title: Dd2_C580Y_6h_DHA_rep3


title: Dd2_C580Y_32h_DHA_rep3


title: Dd2_C580Y_24h_DHA_rep3


title: WT.5.2


title: WT.5.1


title: Dd2_C580Y_6h_DHA_rep1


title: sm.4.2


title: sm.4.3


title: WT.5


title: Dd2_C580Y_32h_DHA_rep1


title: Cam3II_revWT_0h_rep1


title: Dd2_C580Y_48h_rep3


title: Dd2_C580Y_24h_rep3


title: Dd2_C580Y_48h_DHA_rep1


title: Dd2_C580Y_32h_rep3


title: Dd2_C580Y_24h_DHA_rep1


title: sm.4


title: sm.4.1


title: esb1.6.2


title: esb1.6.3


title: Dd2_C580Y_24h_rep2


title: Dd2_C580Y_32h_rep2


title: Dd2_C580Y_48h_rep2


title: Dd2_C580Y_0h_rep2


title: Dd2_C580Y_3h_DHA_rep1


title: Dd2_C580Y_6h_rep2


title: Dd2_C580Y_48h_rep1


title: esb1.6


title: esb1.6.1


title: esb1sgn3.4.3


title: esb1sgn3.4.2


title: Dd2_C580Y_32h_rep1


title: Dd2_C580Y_3h_rep3


title: Dd2_C580Y_24h_rep1


title: Dd2_C580Y_6h_rep3


title: Dd2_C580Y_0h_rep3


title: Dd2_C580Y_6h_rep1


title: esb1sgn3.4.1


title: Dd2_R539T_6h_DHA_rep3


title: Dd2_C580Y_3h_rep1


title: Dd2_R539T_48h_DHA_rep3


title: Dd2_C580Y_3h_rep2


title: Dd2_C580Y_0h_rep1


title: Dd2_R539T_24h_DHA_rep3


title: Dd2_R539T_32h_DHA_rep3


title: Dd2_R539T_3h_DHA_rep3


title: Dd2_R539T_48h_DHA_rep2


title: Dd2_C580Y_16h_rep1


title: Dd2_R539T_32h_DHA_rep2


title: esb1sgn3.4


title: Dd2_R539T_24h_DHA_rep2


title: sgn3cif.4.3


title: Dd2_R539T_6h_DHA_rep2


title: sgn3cif.4.2


title: Dd2_R539T_3h_DHA_rep2


title: Dd2_R539T_48h_DHA_rep1


title: Dd2_R539T_32h_DHA_rep1


title: sgn3cif.4.1


title: sm.1.3


title: sgn3cif.4


title: Dd2_R539T_3h_DHA_rep1


title: sm.1.2


title: sm.1


title: Dd2_R539T_48h_rep3


title: Dd2_R539T_24h_rep3


title: Dd2_R539T_24h_DHA_rep1


title: Dd2_R539T_32h_rep3


title: sm.1.1


title: esb1sgn3.1.2


title: esb1sgn3.1.3


title: Dd2_R539T_6h_rep2


title: Dd2_R539T_48h_rep2


title: esb1sgn3.1.1


title: Dd2_R539T_24h_rep2


title: Dd2_R539T_3h_rep3


title: esb1sgn3.1


title: Dd2_R539T_48h_rep1


title: Dd2_R539T_3h_rep2


title: Dd2_R539T_0h_rep3


title: Dd2_R539T_6h_DHA_rep1


title: Dd2_R539T_32h_rep2


title: Dd2_R539T_6h_rep3


title: sgn3.6.2


title: sgn3.6.1


title: Dd2_R539T_32h_rep1


title: Dd2_R539T_0h_rep2


title: Dd2_R539T_24h_rep1


title: sgn3.4.3


title: sgn3.4.1


title: sgn3.6.3


title: sgn3.4.2


title: Dd2_WT_32h_DHA_rep3


title: Dd2_WT_48h_DHA_rep3


title: Dd2_R539T_0h_rep1


title: Dd2_WT_24h_DHA_rep3


title: Dd2_R539T_3h_rep1


title: Dd2_WT_3h_DHA_rep3


title: Dd2_R539T_16h_rep1


title: Dd2_WT_32h_DHA_rep1


title: Dd2_WT_6h_DHA_rep3


title: Dd2_R539T_6h_rep1


title: Dd2_WT_48h_DHA_rep1


title: Dd2_WT_32h_DHA_rep2


title: Dd2_WT_24h_DHA_rep2


title: sgn3.4


title: sgn3.6


title: Dd2_WT_3h_DHA_rep2


title: sgn3cif.6.3


title: Dd2_WT_6h_DHA_rep2


title: Dd2_WT_48h_DHA_rep2


title: Dd2_WT_3h_DHA_rep1


title: Dd2_WT_24h_DHA_rep1


title: sgn3cif.6.2


title: Dd2_WT_32h_rep3


title: Dd2_WT_48h_rep3


title: Dd2_WT_6h_DHA_rep1


title: sgn3cif.6.1


title: sgn3cif.6


title: Dd2_WT_24h_rep3


title: Dd2_WT_6h_rep3


title: sgn3.1.2


title: sgn3.1.3


title: sgn3.1.1


title: Dd2_WT_0h_rep3


title: Dd2_WT_32h_rep2


title: Dd2_WT_48h_rep2


title: Dd2_WT_6h_rep2


title: sgn3.1


title: Dd2_WT_24h_rep2


title: sgn3.5.1


title: sgn3.5.2


title: HeLa mRNA; FTO -; 100 ng total RNA; up probe + down probe; 5x Bst polymerase

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

data_processing:
de-duplication with BBMap v38.26
trimming UMI and cutting adapter using the cutadapt command. When trimming the adapter sequence, the option ‘-q 20 -m 12’ was applied to select for reads with quality scores higher than 20 and lengths longer than 12 nt
Alignment to human genome assembly GRCh38/hg38
converting sam files to bam files using samtools v0.1.18
sorting bam files using samtools v0.1.18
Acquiring information about the position on the reference sequence of the 5’ end of the query sequence and the associated read counts with an in-house R script.
Supplementary_files_format_and_content: .csv; position, sample name, read counts

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa cells were cultured with complete DMEM medium under standard conditions. Briefly, HeLa cells were grown in high glucose DMEM medium (Thermo Fisher Scientific, 11995) with 10% FBS and 1% Pen-Strep (Penicillin-Streptomycin) to 80% confluency and passaged. Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency.

extract_protocol:
Total RNA was isolated from HeLa cells using Trizol reagent (Life Technologies). Poly-A RNA was purified from total RNA using Dynabeads mRNA DIRECT kit (Life Technologies).
Purified DNA was ligated to an adapter on the 3' end. PCR was performed to add on other components for illumina sequencing.

treatment_protocol: poly-A RNA was annealed with DNA probes.The annealing product was subjected to cDNA extension reaction mediated by the Bst DNA polymerase. RNA was digested and DNA was purified using DNA oligo clean and concentrator (Zymo research).

value: HeLa

tag: enzyme treatment


title: HeLa mRNA; FTO -; 1 μg total RNA; up probe + down probe; 5x Bst polymerase


title: HeLa mRNA; FTO -; 100 ng total RNA; up probe + down probe; 1x Bst polymerase


title: sgn3.5.3


title: HeLa mRNA; FTO -; 10 ng total RNA; up probe + down probe; 5x Bst polymerase


title: Dd2_WT_24h_rep1


title: Dd2_WT_32h_rep1


title: Dd2_WT_16h_rep1


title: Dd2_WT_3h_rep2


title: Dd2_WT_0h_rep1


title: Dd2_WT_3h_rep3


title: Dd2_WT_6h_rep1


title: Dd2_WT_0h_rep2


title: Dd2_WT_48h_rep1


title: HeLa mRNA; FTO -; 1 μg total RNA; up probe + down probe; 1x Bst polymerase


title: sgn3.5


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe; 1x Bst polymerase; bio rep 2


title: Dd2_WT_3h_rep1


title: sm.6.3


title: HeLa mRNA; FTO -; 10 ng total RNA; up probe + down probe; 1x Bst polymerase


title: sm.6.2


title: HeLa mRNA; FTO +; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 2


title: HeLa mRNA; FTO +; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 3


title: HeLa mRNA; FTO +; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 1


title: sm.6.1


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 2x Bst polymerase; bio rep 3


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 2x Bst polymerase; bio rep 2


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 2x Bst polymerase; bio rep 1


title: sm.6


title: myb36.1.3


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 2


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 1


title: myb36.1.2


title: myb36.2.3


title: myb36.2.2


title: myb36.2.1


title: LNbs1 replicate 3

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

data_processing:
Fastq files were mapped to reference using STAR/v2.5.3a and gencode gtf(v19)
Gene counts were calculated using featureCounts (subread/v1.4.6)
Normalized read counts and differentially expressed genes found using edgeR/v3.2.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with raw gene counts per sample

source_name: cell line derived from LNCaP treated with IL-1 beta for 4 months

extract_protocol:
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 75bp single-end reads.

treatment_protocol: LNCaP cells were treated with 0.5 ng/ml IL-1 alpha (in DMEM + 10% FBS) for 3 months or treated with 0.5 ng/ml IL-1 beta (in DMEM + 10% FBS) for 4 months. IL-1 is cytotoxic, so the viable, proliferating colonies that emerged after 3 months in IL-1a or 4 months in IL-1b were expanded to generate the IL-1a subline (LNas1) and the IL-1b subline (LNbs1).  LNCaP, LNas1, and LNbs1 cells were plated and cultured in DMEM + 10% FBS for 7 days and RNA isolated for RNA sequencing.

tag: tissue

value: prostate cancer


title: myb36.1.1


title: myb36.1


title: LNas1 replicate 2

source_name: cell line derived from LNCaP treated with IL-1 alpha for 3 months


title: LNbs1 replicate 2


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe; 1x Bst polymerase; bio rep 1


title: LNas1 replicate 1


title: LNas1 replicate 3


title: LNbs1 replicate 1


title: LNCaP replicate 3

source_name: parental cell line

value: LNCaP


title: LNCaP replicate 2


title: myb36.2


title: LNCaP replicate 1


title: HeLa mRNA; FTO -; 100 ng poly-A RNA; up probe + down probe; 1x Bst polymerase; bio rep 3


title: myb36.3.3


title: IS31C: HCAEC 20 dyne/cm2-BVS+Drug

city: Pisa

first: Federico

last: Vozzi

state: Tuscany

address: Via Moruzzi 1

department: Institute of Clinical Physiology

country: Italy

institute: CNR

data_processing:
Raw data were processed for basecalling and demultiplexing conversion and de-multiplexing by Bcl2Fastq 2.0.2 version of the Illumina pipeline
Removing lower quality bases and adapters by ERNE and Cutadapt software.
Reads were deduplicated based on unique molecular identifier (UMI) composed of 8 random bases for unambiguous identification of unique library molecules by IGATech proprietary script
Reads were aligned on reference GRCh38 genome/transcriptome with STAR (default parameters)
Assembling and quantification of full-length transcripts representing multiple spliced variants for each gene locus were performed by Stringtie (default parameters)
Htseq-count was used to preprocess RNA-Seq data for differential expression analysis by counting the overlap of reads with genes
DESeq2 is used to perform comparisons between expression levels of genes and transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, a tab-delimited text file containing gene expression data used for differential expression analysis, a tab-delimited test file containing results data from DESeq2 analysis

source_name: Primary Human Coronary Artery

growth_protocol: Primary human coronary artery endothelial cells (HCAECs) were purchased from Promocell GmbH (Heidelberg, Germany) and cultured in the manufacturer’s recommended medium, designated as Endothelial Cell Growth Basal Medium MV 2 supplemented with Growth Medium MV 2 Supplement Pack, constituted by a mix of Fetal Calf Serum (FCS), Epidermal Growth Factor, Basic Fibroblast Growth Factor, Insulin-like Growth Factor, Vascular Endothelial Growth Factor 165, Ascorbic Acid and Hydrocortisone. Every 2 days media culture was changed, until the confluence. Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from Thermo Scientific (Waltham, MA, USA) and cultured in the manufacturer’s recommended medium, designated as Medium 231 supplemented with Smooth Muscle Growth Supplement, constituted by a mix of Fetal bovine serum, Human basic fibroblast growth factor, Human epidermal growth factor, Heparin, Recombinant human insulin-like growth factor-I, BSA.

extract_protocol:
For molecular biology analysis, cells were washed with PBS and trypsinised with 200 μl/system. Once cells were detached, 1 ml of medium was added to block trypsin action and centrifuged. The pellet was washed once again with 1 ml of PBS, centrifuged and the final pellet was cryopreserved at -80°C.   Total RNA was extracted from on HCAECs and HCASMCs by a dedicated kit (RNeasy Plus Micro Kit, Qiagen SpA, Milano, Italy) accurately modified to purify total RNA (including miRNA) from small amounts of cells (<5*10^5); after re-suspension and lysis of the cells in a highly denaturing guanidine-isothiocyanate–containing buffer, which immediately inactivates RNases to ensure isolation of intact RNA, samples were selective passed through a gDNA Eliminator spin column. This column, in combination with the optimized high-salt buffer, efficiently removes genomic DNA.  Ethanol was added to the flow-through to provide appropriate binding conditions for RNA, and the samples were then applied to a silica-based membrane (RNeasy MinElute spin column), speeded on a microspin centrifuge; specific buffers allowed RNA to bind to the RNeasy silica membrane and contaminants were efficiently washed away. High-quality RNA was then eluted in 14 μl of RNAse free water without the need for additional DNase digestion.   The total RNA concentration was determined in all samples by measuring the spectrophotometer absorbance at 260 and 280 nm (NanoDrop Thermofisher) and calculated using the Beer-Lambert law, with expected values between 1.8-2.1. The RNA samples were stored at -80 °C for use in gene expression studies.
Ovation SoLo RNA-seq Library Preparation kit (NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-second strand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on single-end 75 bp mode on NextSeq 500 (Illumina, San Diego, CA).

value: Human Coronary Artery Endothelial Cells

tag: passages

tag: bvs+drug presence

value: Y


title: IS27E: HCAEC 20 dyne/cm2-BVS+Drug


title: myb36.3.1

tag: biorep


title: myb36.3.2

tag: techrep


title: IS24G: HCAEC 20 dyne/cm2-BVS+Drug


title: IS24C: HCAEC 1 dyne/cm2-BVS+Drug


title: myb36.3

tag: genotype


title: IS24D: HCAEC 0 dyne/cm2-BVS+Drug

tag: cell type


title: IS23C: HCAEC 1 dyne/cm2-BVS+Drug


title: myb36.6.3


title: IS23L: HCAEC 0 dyne/cm2-BVS+Drug


title: IS23D: HCAEC 0 dyne/cm2-BVS+Drug


title: myb36.6.2


title: IS20B: HCAEC 20 dyne/cm2

value: N


title: IS20A: HCAEC 20 dyne/cm2


title: myb36.6.1


title: IS19G: HCAEC 1 dyne/cm2


title: myb36.6


title: IS20F: HCAEC 1 dyne/cm2


title: sgn3cif.1.3


title: IS19I: HCAEC 0 dyne/cm2


title: sgn3cif.1.2


title: ID18E: HCAEC 0 dyne/cm2


title: IS18D: HCAEC 0 dyne/cm2


title: input DNA Glc Col-0

city: Shanghai

first: Bo

last: Yu

address: Fenglin Road 300

institute: SIBS, CAS

description:
Chromatin IP against GFP transcription factor (input control)
Glc_vs_input._nolambda_peaks.bed

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using BWA 0.7.15-r1140 with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
MACS1.4 was used to identify read enriched regions (peaks)
Genome_build: TAIR10
Supplementary_files_format_and_content: peak files

source_name: wild type whole seedlings

growth_protocol: Seedlings were grown 1/2MS with or without 6% glucose agar plate at 22℃ under constant light 10 days after 3 days stratification

extract_protocol:
Lysates were clarified from sonicated nuclei and ANAC060-DNA complexes were isolated with antibody.
Sequencing libraries were constructed according to the Illumina’s instructions.

tag: ecotype

value: Columbia (Col-0)

value: wild type

tag: developmental stage

value: seedlings

tag: treatment

value: glucose

tag: chip antibody


title: IS30A: HCAEC 1 dyne/cm2-BVS+Drug


title: ANAC060_ChIPSeq

description:
Chromatin IP against GFP transcription factor
YB60GF_vs_ctrl.nolambda_peaks.bed

source_name: 35S:ANAC060-GFP whole seedlings

value: 35S:ANAC060-GFP/anac060 transgenic line

value: without glucose

value: Polyclonal anti-GFP antibodies (Abcam, ab290)


title: sgn3cif.1.1


title: ANAC060_ChIPSeq Glc

description:
Chromatin IP against GFP transcription factor
Glc_vs_input._nolambda_peaks.bed


title: sgn3cif.1


title: sgn3cif.3.3


title: IS40C: HCASMC 20 dyne/cm2-BVS+Drug

value: Human Coronary Artery Smooth Muscle Cells


title: input DNA Col-0

description:
Chromatin IP against GFP transcription factor (input control)
YB60GF_vs_ctrl.nolambda_peaks.bed


title: IS32E: HCASMC 20 dyne/cm2-BVS+Drug


title: sgn3cif.3.2


title: IS19C: HCAEC 20 dyne/cm2


title: sgn3cif.3.1


title: IS18G: HCAEC 1 dyne/cm2


title: sgn3cif.3


title: IS33C: HCASMC 1 dyne/cm2-BVS+Drug


title: IS33B: HCASMC 1 dyne/cm2-BVS+Drug


title: IS32B: HCASMC 1 dyne/cm2-BVS+Drug


title: WT.1.3


title: IS44M: HCASMC 0 dyne/cm2-BVS+Drug


title: IS33D: HCASMC 20 dyne/cm2-BVS+Drug


title: IS44L: HCASMC 0 dyne/cm2-BVS+Drug


title: WT.1.1


title: sm.3.3


title: IS44H: HCASMC 0 dyne/cm2-BVS+Drug


title: sm.3.2


title: WT.1


title: IS15B: HCASMC 20 dyne/cm2


title: sm.3.1


title: WT.1.2


title: sm.3


title: IS17C: HCASMC 20 dyne/cm2


title: IS2B: HCASMC 1 dyne/cm2


title: IS4B: HCASMC 1 dyne/cm2


title: myb36.5.3


title: myb36.5.2


title: Subject10_24h_HO_muscle

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.2).

source_name: Muscle tissue isolated from subject 10, 24h after treatment with a High Meal Frequency (t=24)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Subjects were recruited by advertisements at local educational institutions and newspapers. Subjects with IGT were included according to the World Health Organization when glucose levels were lower than 7.0 mmol/L at fasting and 2 hours postload >7.8 mmol/L and <11.1 mmol/L. Glucose tolerance was determined with an Oral Glucose Tolerance Test (OGTT). Insulin sensitivity (IS) was assessed using the oral glucose insulin sensitivity (OGIS)-index. Additional inclusion criteria; weight stable over the past 3 months, no excess alcohol intake (28 drinks weekly), no major organ dysfunction, and no use of medication that could influence the results. For homogeneity reasons as well as to avoid menstrual cycle effects on energy expenditure, only Caucasian males were included. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Muscle biopsies were taken in the fasting state (T24). Total RNA was extracted using TRIzol reagent (Invitrogen, Breda, the Netherlands) and puriﬁed on columns using the Qiagen RNeasy Micro Kit (Qiagen, Venlo, Netherlands). RNA quantity was measured with the ND-100 spectrophotometer (Isogen Life Science, IJsselstein, the Netherlands), and RNA integrity was analysed on an Agilent 2100 BioAnalyzer (Agilent Technologies, Amsterdam, The Netherlands) using nanochips according to manufacturer's instructions

treatment_protocol: The study had randomized, 2-way cross-over design with a wash-out period of at least two weeks. Each intervention lasted for 36 hours in a respiration chamber. All subjects randomly received the same iso-energetic diet with a Low meal Frequency (3x-LFr) or a High meal Frequency (14x-HFr). The diet consisted of 15 energy% (En%) dairy protein, 30 En% fat, and 55 En% carbohydrates. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on T0 (fasting state), T13 (21.30h) and T24 (next morning at 08.00h in fasting state). A muscle biopsy was taken from the vastus lateralis muscle was taken after each respiration chamber stay in the fasting state (T24).

value: muscle

tag: subject number

tag: diet

value: high meal frequency

tag: Sex

value: Male

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

value: 6.1 mmol/L

tag: fasting insulin


title: IS15C: HCASMC 20 dyne/cm2

tag: passages

tag: bvs+drug presence


title: Subject11_24h_LA_muscle

source_name: Muscle tissue isolated from subject 11, 24h after treatment with a Low Meal Frequency (t=24)

tag: tissue

value: low meal frequency

value: 6.9 mmol/L


title: Subject10_24h_LA_muscle

source_name: Muscle tissue isolated from subject 10, 24h after treatment with a Low Meal Frequency (t=24)


title: Subject11_24h_HO_muscle

source_name: Muscle tissue isolated from subject 11, 24h after treatment with a High Meal Frequency (t=24)


title: Subject6_24h_LA_muscle

source_name: Muscle tissue isolated from subject 6, 24h after treatment with a Low Meal Frequency (t=24)

value: 4.8 mmol/L


title: Subject6_24h_HO_muscle

source_name: Muscle tissue isolated from subject 6, 24h after treatment with a High Meal Frequency (t=24)


title: Subject5_24h_LA_muscle

source_name: Muscle tissue isolated from subject 5, 24h after treatment with a Low Meal Frequency (t=24)

value: 6.2 mmol/L


title: Subject5_24h_HO_muscle

source_name: Muscle tissue isolated from subject 5, 24h after treatment with a High Meal Frequency (t=24)


title: Subject3_24h_LA_muscle

source_name: Muscle tissue isolated from subject 3, 24h after treatment with a Low Meal Frequency (t=24)

value: 5.4 mmol/L


title: Subject3_24h_HO_muscle

source_name: Muscle tissue isolated from subject 3, 24h after treatment with a High Meal Frequency (t=24)


title: myb36.5.1

source_name: root tips

tag: genotype

tag: biorep

tag: techrep


title: IS39B: HCASMC 0 dyne/cm2

tag: cell type

value: N


title: esb1.5.3


title: IS13H: HCASMC 0 dyne/cm2


title: Subject4_24h_LA_muscle

source_name: Muscle tissue isolated from subject 4, 24h after treatment with a Low Meal Frequency (t=24)


title: Subject2_24h_HO_muscle

source_name: Muscle tissue isolated from subject 2, 24h after treatment with a High Meal Frequency (t=24)


title: Subject1_24h_HO_muscle

source_name: Muscle tissue isolated from subject 1, 24h after treatment with a High Meal Frequency (t=24)

value: 6.4 mmol/L


title: Subject2_24h_LA_muscle

source_name: Muscle tissue isolated from subject 2, 24h after treatment with a Low Meal Frequency (t=24)


title: esb1.5.2


title: IS15D: HCASMC 0 dyne/cm2

source_name: Primary Human Coronary Artery


title: Subject1_24h_LA_muscle

source_name: Muscle tissue isolated from subject 1, 24h after treatment with a Low Meal Frequency (t=24)


title: Subject4_24h_HO_muscle

source_name: Muscle tissue isolated from subject 4, 24h after treatment with a High Meal Frequency (t=24)


title: P88

city: rome

first: simona

last: giglio

state: rome

address: via di grottarossa

department: clinical and molecolar medicine

institute: Sapienza university

description: small-RNA

data_processing:
Basecalls performed using bcl2fastq version 2.20
Raw sequence files (.fastq files) underwent quality control analysis using FastQC of Babraham Bioinformatics group (version v0.11.5)
Small RNA-Seq data were analyzed using iSmaRT tool with standard parameters, using miRBase v21 as reference track
Only miRNA showing a raw expression value > 50 raw-reads in at least one sample were considered for further analysis
Differentially expressed miRNAs were identified using DESeq2 package, available on Bioconductor. A cutoff of |FC| ≥ 2 and FDR ≤ 0.001 were used to select differentially expressed miRNAs between ADK vs Prostatitis samples
Differentially expressed Analysis was performed considering, also, Gleason Score classification and using DESeq2 package. Therefore only those samples with the present gleason score were considered (32 ADK samples).
To investigate the independence of samples from PSA-value, Age and BMI, the Chi-Square (Pearson's Chi-squared test) and Differentially expressed Analysis wer performed considering only the  ADK samples with the PSA-value, Age and BMI classification.
Genome_build: hg19
Supplementary_files_format_and_content: excel file include normalized count and Differentially expressed Analysis results

source_name: Prostatitis

extract_protocol:
Plasma was isolated whit miRNeasy Serum / Plasma kit according to the manufacturer's protocol (Qiagen).  Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the SmallRNA sample preparation kit

value: plasma

tag: patient diagnosis

value: Prostatitis

tag: patient age

tag: gleason score

value: Not Available (NA)

tag: cancer size

tag: psa-value

tag: bmi


title: myb36.5


title: P694

description: small-RNA


title: P737

description: small-RNA


title: Subject11_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11, 24h after treatment with a Low Meal Frequency diet (t=24h)

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturers’ instructions. Total RNA was extracted using TRIzol reagent (Invitrogen, Breda, the Netherlands) and puriﬁed on columns using the Qiagen RNeasy Micro Kit (Qiagen, Venlo, Netherlands). RNA quantity was measured with the ND-100 spectrophotometer (Isogen Life Science, Ijsselstein, the Netherlands), and RNA integrity was analysed on an Agilent 2100 BioAnalyzer (Agilent Technologies, Amsterdam, The Netherlands) using nanochips according to manufacturer's instructions

value: PBMC

tag: subject number

tag: diet

tag: Sex

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)


title: esb1sgn3.5.2


title: esb1sgn3.5.3


title: esb1sgn3.5.1


title: P676

description: small-RNA

tag: tissue


title: Subject11_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11 treated with a Low Meal Frequency diet for 13h

tag: blood pressure (bp)

tag: fasting glucose

tag: fasting insulin


title: P638

description: small-RNA


title: esb1sgn3.5

tag: genotype

tag: biorep

tag: techrep


title: P627

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: Wtcif.5.2

value: Wtcif


title: Wtcif.5.3


title: Subject11_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11, before treatment with a High Meal Frequency diet (t=0h)


title: Subject10_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10, 24h after treatment with a Low Meal Frequency diet (t=24h)


title: esb1.5.1


title: esb1.5


title: Wtcif.5.1


title: P680

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: P597

description: small-RNA


title: Wtcif.5


title: Subject11_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11 treated with a High Meal Frequency diet for 13h

tag: subject number

tag: diet

value: after treatment with a High Meal Frequency diet (t=13h)

tag: Sex


title: Wtcif.6.3


title: P587

description: small-RNA


title: P554

description: small-RNA


title: Wtcif.6.2


title: P606

description: small-RNA


title: Subject10_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10, before treatment with a Low Meal Frequency diet (t=0h)

tag: age(years)

tag: body mass index (bmi)

tag: body fat percentage (fm)


title: Subject10_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10, 24h after treatment with a High Meal Frequency diet (t=24h)

tag: tissue

tag: blood pressure (bp)

tag: fasting glucose


title: Subject11_0h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11, before treatment with a Low Meal Frequency diet (t=0h)

tag: fasting insulin


title: Subject10_13h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10 treated with a High Meal Frequency diet for 13h


title: Subject11_24h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 11, 24h after treatment with a High Meal Frequency diet (t=24h)


title: P551

description: small-RNA


title: Wtcif.6.1

source_name: root tips

tag: genotype

tag: biorep

tag: techrep


title: P546

description: small-RNA

tag: patient diagnosis

tag: patient age

tag: gleason score


title: Wtcif.6


title: Subject9_24h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 9, 24h after treatment with a Low Meal Frequency diet (t=24h)

value: 6.3 mmol/L


title: P536

description: small-RNA

tag: cancer size

tag: psa-value

tag: bmi


title: P540

description: small-RNA


title: S_95.3: Col-0_SynCom_BioRep2_S95TechRep4

city: Loughborough

last: Castrillo

address: Nr Loughborough

department: School of Biosciences

institute: University of Nottingham

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC v0.11.8. (Babraham Bioinformatics, Cambridge, UK).
Trimmomatic v0.36  was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 v2.1.0 with default parameters
The featureCounts function from the Subread package (Liao et al., 2013) was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes.
Genome_build: TAIR 10

source_name: root

growth_protocol: Sterilised Col-0 seeds were germinated on agar plate containing 0.5x MS medium solidified with 1% bacto-agar for a week. Ten seedlings of the different genotypes were then transferred to 0.5x MS agar plates inoculated with the 41-member synthetic community. In parallel 10 seedlings were also transferred to no bacteria control (agar plates inoculated with only 10 mM MgCl2). Plates were manually randomised and placed in a growth chambers and grown under a 16-h light/8-h dark regime at 21°C day/19°C night for another 7 days.

extract_protocol:
RNA was extracted from A. thaliana roots according to Logemann et al. We used three independent biological replicas per treatment and we repeated this experiment twice. Briefly, approximately 10 roots from 14-day-old seedlings were harvested from each sample and flash frozen using liquid N2. Frozen roots were pulverized using a TissueLyzer II (Qiagen), 2 cycles of 30 seconds, frequency 30 s-1, and 400 μL of Z6-buffer; 8 M guanidine HCl, 20 mM MES, 20 mM EDTA at pH 7.0 was added to the samples. Following the addition of 400 μL phenol:chloroform:isoamylalcohol; 25:24:1, samples were vortexed and centrifuged (20,000 g, 10 min) for phase separation. The aqueous phase was then transferred to a new 1.5 mL tube and 0.05 volumes of 1 N acetic acid and 0.7 volumes 96% ethanol were added. The RNA was precipitated at −20 °C overnight. Following centrifugation, (20,000 g, 10 min, 4 °C) the pellet was washed with 200 μL sodium-acetate (pH 5.2) and 70% ethanol. The RNA was dried and dissolved in 30 μL of ultrapure water and stored at −80 °C until use.
Before sequencing, RNA samples were quantified using the Qubit RNA BR Assay Kit (Invitrogen; Q10210) and quality was assessed using RNA Screen Tape (Agilent; 5067-5576) on the Agilent 4200 TapeStation System (Agilent; G2991A). Although TapeStation results showed RNA with high RNA integrity numbers (RINs > 8), indicative of good quality RNA, we detected the presence of high molecular weight nucleic acids typical of genomic DNA, therefore DNase treatment was carried out on the samples. TURBO DNase (Ambion; AM2238) was used to remove DNA from RNA samples. Briefly, 22.5 µL of RNA was combined with 2.5 µL of 10x TURBO DNase Buffer and 1 µL (2 Units) of TURBO DNAse and incubated at 37°C for 30 min. The RNA was then dissolved with 75 µL of nuclease free water and purified using the Qiagen RNeasy MinElute Cleanup Kit (Qiagen; 74204). The final elution was carried out with 15 µL of nuclease free water. For library construction, 200 ng of high-quality RNA was used as input into Lexogen Quant Seq 3’ mRNA Seq (FWD) Library Prep Kit (Lexogen; 015) and the standard protocol was followed. At the PCR stage 13 cycles of PCR were used. Library yield was measured by Qubit dsDNA HS (Invitrogen; Q32851) and library size was assessed using the High Sensitivity D1000 ScreenTape (Agilent; 5067- 5584) on the Agilent 4200 TapeStation System (Agilent; G2991A). Libraries were normalised to each other based on size and Qubit dsDNA HS concentration and pooled together. The pool was quantified by qPCR using the KAPA Library Quantification Kit for Illumina Platforms (KAPA Biosystems; KK4873)
The library pool was denatured and diluted according to the Illumina NextSeq System protocol (Illumina Document #15048776v09) and then sequenced on the Illumina NextSeq 500 on a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina; 20024906), to generate ~5 million 75bp single-end reads per sample

treatment_protocol: We used 5 replicas of each treatment and this experiment was repeated twice.

tag: bacteria

value: SynCom


title: S_95.2: Col-0_SynCom_BioRep2_S95TechRep3


title: P531

description: small-RNA


title: Subject10_13h_LA_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10 treated with a Low Meal Frequency diet for 13h

tag: subject number

tag: diet

tag: Sex

value: Male

tag: age(years)


title: P524

description: small-RNA

tag: tissue


title: Subject10_0h_HO_pbmc

source_name: Peripheral blood mononuclear cells isolated from subject 10, before treatment with a High Meal Frequency diet (t=0h)

tag: body mass index (bmi)

tag: body fat percentage (fm)

tag: blood pressure (bp)

tag: fasting glucose

value: 6.1 mmol/L


title: P520

description: small-RNA