title: 60_SYVN1 DsiRNA + C18

city: Iowa City

first: Paul

middle: B

last: McCray

state: IA

address: 6320 PBDB

department: Pediatrics

institute: University of Iowa

description:
SYVN1 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were quantile normalized with background subtracted and missing data excluded using GenomeStudio and Partek Genomics Suite.

label: Biotin

source_name: CFBE_SYVN1 DsiRNA + C18

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

growth_protocol: CFBE cells were grown in MEM, 10% FBS, and 1µg/ml puromycin. For detailed protocols, see PMID: 23624792.

extract_protocol: mirVana isolation kit was used following manufacturer's recommended protocol to extract RNA.

treatment_protocol: Cells were transfected with oligonucleotides using lipofectamine RNAiMAX. Cells were treated with 6µM Corrector Compound C18 dissolved in DMSO. Cells were incubated at the noted temperatures. For detailed protocols, see PMID: 23624792.

tag: tag

value: Cell line:CFBE


title: test1

status: Public on Dec 01 2020

type: SRA

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

description: combined.testplus.results.csv.gz

library_source: genomic

data_processing:
The samples were processed and sequenced independently several times. The main analysis only considered the first sequencing of samples IVI1-IVI26.
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the GRCh38 human genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with less than 200 total mapped reads across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
In addition to the main analysis, a second analysis was performed to classify test samples into treatment groups. For this analysis, two additional sets of replicate analysis samples were processed and sequenced with independent MeDIP procedures. The two additional replicate sample sets were combined with the original samples to obtain a set of combined samples containing equal numbers of reads from each replicate set. Seven of the combined case samples showed high levels of correlation with each other, yet diverged considerably with the remaining samples. This appears most likely due to batch effects related to the MeDIP procedure. In this case, the batch effects were largely due to the third replicate analysis of these samples. These seven samples were removed from the analysis. DMR were then identified between the eight remaining combined case samples and the 13 combined control samples using identical methods to those used in the main DMR analysis presented previously. The sites identified as DMR in this analysis were then used to classify ten test samples into sample groups.
The test samples were processed and sequenced in four separate MeDIP-seq procedures. Equal reads from each of the four replicates for each sample were merged into a single combined sample. An additional eight technical replicates were also processed a single time. These technical replicates were selected from the original 26 samples and were used as an additional blinded test set.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values if applicable.

molecule: genomic DNA

organism: Homo sapiens

source_name: Sperm

growth_protocol: A single center (IVIRMA Valencia) performed the prospective and open clinical study. The IRB approval code protocol number is #1311-VLC-136-FC. The men included caucasians between 26 and 54 years of age with a total sperm concentration (concentration in millions/mL x volume in mL). Sperm samples were frozen with liquid nitrogen and stored (-20 C) for the subsequent epigenetic analysis.

extract_protocol:
Frozen human sperm samples were stored at -20 C and thawed for analysis. Genomic DNA from sperm was prepared as follows: A 400 μl of sperm suspension was used and centrifuged for 10 minutes at low speed to concentrate sperm. The supernatant was discarded, and the pellet resuspended in 100 ul PBS. Then 820 μl DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl 0.1 M Dithiothreitol (DTT) were added and the sample incubated at 65 C for 15 min. Proteinase K (20 mg/ml) (80 μl) was added, and the sample was incubated on a rotator at 55 C for at least 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A, Madison, WI) was added, the sample was mixed and incubated on ice for 15-30 min, then spun at 4 C at 13,000 rpm for 30 min. The supernatant was transferred to a fresh tube, then precipitated over night at -20 C with the same volume. 100% isopropanol and 2 μl glycoblue. The sample was then centrifuged, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). The freeze-thaw will destroy any contaminating somatic cells in the sperm collection.Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual sperm DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer. NGS was performed at WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 20-50 million reads per sample, and 6-7 sample libraries each were run in one lane.

treatment_protocol: We included two groups (sperm from father with offspring with autism (case) or without (control)).

tag: treatment

value: control

tag: sample

tag: combined sample id

tag: sequencing batch

value: B


title: 317_Doberman Pinscher_HC_

type: genomic

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

description:
317
Canis familiaris

hyb_protocol: SNP array genotyping was performed on samples using the Illumina CanineHD Whole-Genome Genotyping BeadChip arrays including 173,662 SNPs located on autosomes and sex chromosomes.

scan_protocol: Arrays were scanned.

data_processing: Genotype calling of SNPs as well as data visualization were performed with GenomeStudio v2.0 and exported to PLINK format using the CanFam3.1.75 genome assembly to retrieve chromosomal coordinates. SNP array data imputation was conducted using a phased genotype reference dataset of 365 dogs from multiple breeds genotyped by whole-genome sequencing. The reference dataset was filtered excluding sex chromosomes, removing insertion/deletions, non-PASS variants, and variants with more than two alleles. The SNP array dataset of all 241 dogs on our study (target dataset) was filtered excluding sex chromosomes and duplicate variants, including variants with: minor allele frequency (MAF) ≥ 0.005, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. The resulting dataset was subjected to principal component analysis (PCA) in PLINK v1.9 to identify outliers and dogs whose PCA clustering would differ from the owner-identified breed information. We computed the relatedness PIHAT metric using PLINK v1.9 for each pair of samples aiming to identify duplicated samples (PIHAT=1.0). Outliers, duplicated and misclassified samples were removed from the dataset. Reference and target datasets were compared using the Conform-gt software, keeping only variants shared between the target and the reference dataset. Finally, the genotypes were imputed with the software Beagle v5, using the recombination rate map reference, default settings and effective population size = 200. After imputation, variants were filtered with dosage R2 (DR2)< 0.4, ultimately including only with MAF ≥ 0.05, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. Gene annotation of SNPs was performed with R-BiomartTv2.40.4 using the dog genome reference CanFam3.1.

label: biotin/dinitrophenyl

organism: Canis lupus familiaris

source_name: Peripheral blood

label_protocol: Extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl-labeled. Signal amplification of the incorporated label further improves the overall signal-to-noise ratio of the assay.

extract_protocol: Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).

tag: breed

value: Doberman Pinscher

tag: status (hc = healthy control, gdv

value: gastric dilatation-volvulus:HC

tag: tissue

value: Peripheral blood


title: Lung_401_Control_Day3_rep6

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 6

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
Data were normalized by shift to 75.0 percentile and filtered by flags and by expression based on the signal intensity values (to remove very low signal values and those that have reached saturation)

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat, Lung, NM-401, Control, Day 3

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to two doses of NM-401 carbon nanotube.

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: female

tag: age

value: 13 weeks-old (at the onset of inhalation)

tag: dose

value: Control

tag: time

value: Day 3


title: 309_German Shepherd Dog_Acute_GDV_Male

description:
309
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV

tag: Sex

value: Male


title: 59_NEDD8 DsiRNA

description:
NEDD8 DsiRNA
Replicate 5

source_name: CFBE_NEDD8 DsiRNA

value: NEDD8 DsiRNA


title: 58_Scrambled

description:
Scrambled DsiRNA
Replicate 4

value: Scrambled DsiRNA


title: 57_No-Treatment

description:
No treatment
Replicate 4

value: Cell line:CFBE

value: No treatment


title: test2

description: combined.testplus.results.csv.gz

value: case

value: B


title: IVI25

description:
autism.results.csv.gz
combined.analysis.results.csv.gz

value: control

value: A


title: Lung_401_Control_Day3_rep5

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 5

value: Sprague Dawley


title: 56_SYVN1 DsiRNA + C18

description:
SYVN1 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 3


title: 307_Borzoi_Chronic_bloater_Female

description:
307
Canis familiaris

value: Borzoi

value: Female

value: Peripheral blood


title: Lung_401_Control_Day3_rep4

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 4

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Control


title: Lung_401_Control_Day3_rep3

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 3

value: Day 3


title: 306_Borzoi_Chronic_bloater_Male

description:
306
Canis familiaris

value: Male


title: IVI24


title: 54_SYVN1 DsiRNA + C18

description:
SYVN1 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 2


title: 55_SYVN1 DsiRNA

description:
SYVN1 DsiRNA
Replicate 5

source_name: CFBE_SYVN1 DsiRNA

value: SYVN1 DsiRNA


title: IVI23


title: 53_NEDD8 DsiRNA + C18

description:
NEDD8 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 4

source_name: CFBE_NEDD8 DsiRNA + C18

value: Cell line:CFBE


title: 305_Borzoi_Chronic_bloater_Male

description:
305
Canis familiaris


title: Lung_401_Control_Day3_rep2

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 2


title: 303_Borzoi_HC_Female

description:
303
Canis familiaris

value: gastric dilatation-volvulus:HC


title: 302_Borzoi_HC_Male

description:
302
Canis familiaris


title: IVI21


title: Lung_401_Control_Day3_rep1

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-401, Control, Day 3, replicate 1


title: 52_40C for 24hr

description:
40°C incubation for 24h
Replicate 4

source_name: CFBE_40C for 24hr

tag: temperature

value: 40°C incubation for 24h


title: 301_Borzoi_HC_Female

description:
301
Canis familiaris


title: IVI20


title: 300_Borzoi_HC_Female

description:
300
Canis familiaris


title: 51_27C for 24hr

description:
27°C incubation for 24h
Replicate 5

source_name: CFBE_27C for 24hr

value: 27°C incubation for 24h


title: IVI19

value: control


title: 50_NEDD8 DsiRNA + C18

description:
NEDD8 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 3


title: NASH model biopsy liver sample (CD7)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the  oligo Bioconductor environment in R.3.6.2

label: biotin

organism: Mus musculus

source_name: NASH model biopsy liver sample

label_protocol: Standard Affymetrix protocol

extract_protocol: Isolation of total RNA was performed using the TRIzol reagent (MRC, Cincinnati, OH). RNA concentration was assessed in a NanoDrop-1000 spectrophotometer (NanoDrop Technologies), and its integrity was tested on a 6000 LabChip in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

tag: strain background

tag: mouse model

value: NASH model

value: liver


title: IVI22

value: A


title: 49_miR-138 mimic

description:
miR-138 mimic
Replicate 4

source_name: CFBE_miR-138 mimic

tag: tag

value: miR-138 mimic


title: 299_Borzoi_HC_Female

description:
299
Canis familiaris

value: Borzoi

value: Female

value: Peripheral blood


title: NASH model biopsy liver sample (CD5)


title: 46_SIN3A DsiRNA

description:
SIN3A DsiRNA
Replicate 3

source_name: CFBE_SIN3A DsiRNA

tag: treatment

value: SIN3A DsiRNA


title: 47_SIN3A DsiRNA

description:
SIN3A DsiRNA
Replicate 4


title: NASH model biopsy liver sample (CD6)


title: 48_Corrector compound C18

description:
6µM Corrector Compound C18 treatment for 24h
Replicate 5

source_name: CFBE_Corrector compound C18


title: NASH model biopsy liver sample (CD3)


title: IVI18

tag: sample


title: NASH model biopsy liver sample (CD4)


title: IVI17

tag: combined sample id


title: 298_Borzoi_HC_Male

description:
298
Canis familiaris


title: 297_Borzoi_Acute_GDV_Male

description:
297
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: NASH model biopsy liver sample (CD2)


title: 45_37C

description:
37°C incubation for 24h
Replicate 4

value: 37°C incubation for 24h


title: IVI15

tag: sequencing batch


title: IVI16


title: 296_Borzoi_HC_Female

description:
296
Canis familiaris

tag: breed


title: IVI14


title: NASH model biopsy liver sample (CD1b)


title: 294_Borzoi_Acute_GDV_Male

description:
294
Canis familiaris

tag: status (hc = healthy control, gdv

value: Male


title: 293_Borzoi_HC_Female

description:
293
Canis familiaris

tag: tissue


title: IVI12

value: case


title: SUDHL6 iEZH D4 R2

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

library_source: transcriptomic

data_processing:
Sequencing was performed on the HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold.  Samples with fewer than 10 reads FPKM are replaced with  the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19

source_name: Diffuse large B cell lymphoma

growth_protocol: HT and SUDHL6 cell lines were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: RNA-seq

treatment_protocol: 96 hours of treatment with iEZH

tag: cell line

value: iEZH


title: 44_40C (24hr) + 27C (24hr

description:
40°C incubation for 24h followed by 27°C incubation for 24h
Replicate 4

value: Cell line:CFBE


title: 292_German Shepherd Dog_Acute_GDV_Male

description:
292
Canis familiaris

value: German Shepherd Dog


title: 43_DMSO

description:
DMSO treatment for 24h
Replicate 4

value: DMSO for 24h


title: IVI11


title: Control biopsy liver sample (C10)

source_name: Control biopsy liver sample

value: Control


title: 41_SIN3A DsiRNA

description:
SIN3A DsiRNA
Replicate 2


title: Control biopsy liver sample (C9)


title: 42_Corrector compound C18

description:
6µM Corrector Compound C18 treatment for 24h
Replicate 4


title: 40_27C for 24hr

description:
27°C incubation for 24h
Replicate 4

value: 27°C incubation for 24h


title: Control biopsy liver sample (C5)

value: liver


title: Control biopsy liver sample (C7)


title: NASH model biopsy liver sample (CD1a)

value: NASH model


title: 39_40C (24hr) + 27C (24hr

description:
40°C incubation for 24h followed by 27°C incubation for 24h
Replicate 3


title: 38_miR-138 mimic

description:
miR-138 mimic
Replicate 3

value: miR-138 mimic


title: 295_Borzoi_HC_Female

description:
295
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC


title: 290_German Shepherd Dog_HC_Male

description:
290
Canis familiaris

value: Peripheral blood


title: Control biopsy liver sample (C4)


title: Control biopsy liver sample (C6)


title: 37_37C

description:
37°C incubation for 24h
Replicate 3


title: IVI10

value: A


title: 289_German Shepherd Dog_Acute_GDV_Male

description:
289
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: IVI8


title: IVI13


title: FT237shRBN1

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

description: FT237 cells stably expressing shRB1 (replicate 1)

hyb_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)

data_processing: For CNV analysis, processed data was analyzed using CNV partition according to the default parameters.

label: Cy3, Cy5

source_name: Fallopian tube immortalized cells

growth_protocol: FTSECs were cultured in a 1:1 ratio of DMEM and Ham’s F12 media (Corning) supplemented with L-glutamine, 15mM HEPES, 10% FBS (v/v) (Denville Scientific), and 0.6% Penicillin/Streptomycin (v/v) (Corning).

extract_protocol: Total genomc DNA was extracted using DNAesay kit (Qiagen)

value: Fallopian tube immortalized cells

tag: genotype/variation

value: stably expressing shRB1


title: FT237shRBN2

description: FT237 cells stably expressing shRB1 (replicate 2)

scan_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)


title: 288_German Shepherd Dog_Acute_GDV_Male

description:
288
Canis familiaris

value: Male


title: IVI7

description:
autism.results.csv.gz
combined.testplus.results.csv.gz

value: case


title: 36_NEDD8 DsiRNA

description:
NEDD8 DsiRNA
Replicate 4

value: Cell line:CFBE

value: NEDD8 DsiRNA


title: Control biopsy liver sample (C3)


title: 287_Briard_HC_Female

description:
287
Canis familiaris

value: Briard

value: Female


title: Control biopsy liver sample (C1)

value: Control


title: 35_Corrector compound C18

description:
6µM Corrector Compound C18 treatment for 24h
Replicate 3


title: FT237p181aN2

description: FT237 cells stably expressing miR-181a (replicate 2)

label_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)

value: stably expressing miR-181a


title: IVI6


title: FT237p181aN1

description: FT237 cells stably expressing miR-181a (replicate 1)


title: IVI5


title: 285_Briard_HC_Male

description:
285
Canis familiaris


title: 284_Briard_HC_Male

description:
284
Canis familiaris


title: FT237p181a-hmiRN1

description: FT237 cells stably expressing miR181a & miR181a antigomer (replicate 1)


title: IVI4


title: 283_Briard_HC_Male

description:
283
Canis familiaris


title: FT237p181a-hmiRN2

description: FT237 cells stably expressing miR181a & miR181a antigomer (replicate 2)


title: 34_NEDD8 DsiRNA + C18

description:
NEDD8 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 2


title: 33_40C for 24hr

description:
40°C incubation for 24h
Replicate 3

value: 40°C incubation for 24h


title: FT237p000N2

description: FT237 cells stably expressing empty vector control (replicate 1)

value: stably expressing empty vector control


title: 282_Briard_HC_Male

description:
282
Canis familiaris


title: IVI3


title: FT237p000N1

description: FT237 cells stably expressing empty vector control (replicate 2)


title: 32_No-Treatment

description:
No treatment
Replicate 3

value: No treatment


title: IVI1


title: 286_Briard_HC_Female

description:
286
Canis familiaris

value: gastric dilatation-volvulus:HC


title: 280_Briard_HC_Male

description:
280
Canis familiaris

value: Peripheral blood


title: 281_Briard_HC_Male

description:
281
Canis familiaris


title: 30_miR-138 mimic

description:
miR-138 mimic
Replicate 2

value: miR-138 mimic


title: 279_Briard_HC_Female

description:
279
Canis familiaris


title: shMETTL3_RNC_2

city: Wuhan

first: Hanyang

last: Hu

state: Please Select

address: School of Basic Medical Sciences, Wuhan University

country: China

institute: Wuhan University

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to the hg19 build of the human genome using Subread aligner v2.0.0.
featureCounts v2.0.0 was used to count the reads numbers mapped to each gene
Genome_build: hg19

extract_protocol:
For RNC-seq, RNC isolation was performed in accordance with a previously reported procedure. Briefly, cells were cultured in 10 cm dishes and incubated with 100 mg/ml cycloheximide (APExBIO) for 15 min, washed with pre-chilled PBS and add 2 ml cell lysis buffer (1% Triton X-100 in ribosome buffer (RB buffer) (20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200 mM KCl, 100 mg/ml cycloheximide and 2 mM dithiothreitol). After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 2 ml tubes. Cell debris was removed by centrifuging at 16200 g for 10 min at 4 °C. Supernatants were transferred on the surface of 12 ml of sucrose buffer (30% sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185,000 g for 5 h at 4 °C. The RNC-RNA was isolated by using TRIzol.
RNC-seq libraries were constructed usinig NEBNext UltraTM RNA Library Prep Kit

value: HTR8/SVneo cells

tag: cell type

value: immortalized first-trimester invasive trophoblast cell line

tag: genotype

value: METTL3 knockdown


title: IVI2

value: A


title: 31_Scrambled

description:
Scrambled DsiRNA
Replicate 3

value: Scrambled DsiRNA


title: 29_Scrambled

description:
Scrambled DsiRNA
Replicate 2

value: Cell line:CFBE


title: 27_NEDD8 DsiRNA

description:
NEDD8 DsiRNA
Replicate 3

value: NEDD8 DsiRNA


title: 28_37C

description:
37°C incubation for 24h
Replicate 2

value: 37°C incubation for 24h


title: 278_Briard_HC_Male

description:
278
Canis familiaris

value: Briard

value: Male


title: 277_Briard_HC_Female

description:
277
Canis familiaris

value: Female


title: shMETTL3_RNC_1


title: IVI26

description:
autism.results.csv.gz
combined.analysis.results.csv.gz

value: control


title: 276_Borzoi_HC_Male

description:
276
Canis familiaris

value: Borzoi


title: shNC_RNC_2


title: shNC_RNC_3


title: 275_German Shepherd Pointer_Acute_GDV_Female

description:
275
Canis familiaris

value: German Shepherd Pointer

value: gastric dilatation-volvulus:Acute_GDV


title: 273_Great Dane_HC_Female

description:
273
Canis familiaris

value: Great Dane

value: gastric dilatation-volvulus:HC

value: Peripheral blood


title: shNC_RNC_1

value: HTR8/SVneo cells

value: immortalized first-trimester invasive trophoblast cell line


title: shMETTL3_M6a_Input_1

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to the hg19 build of the human genome using Subread aligner v2.0.0.
MACS2 was used to find m6A peaks with parameters '-q 0.05-nomodel-keep-dup all'
Genome_build: hg19

growth_protocol: HTR8/SVneo cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin

extract_protocol:
For m6A-seq, total RNA was extracted using TRIZOL Reagent (Life technologies), and was fragmented and mixed with anti-m6A antibody (Millipore, cat# ABE572 ) in 1× IP buffer and incubated with head-to-tail mixing at 4 °C for 2 h. The mixture was supplemented with 25 m L Protein A/G magnetic beads pre-washed two times with 1× IP buffer and incubated with head-to-tail mixing at 4 °C for another 2 h. The beads were then separated and washed with 1x IP buffer three times before eluted with m6A elution buffer for two times. The eluates were combined and puriﬁed with RNA Clean and Concentrator
m6A-seq libraries were constructed using SMARTer Stranded Total RNA-Seq Kit version 2

treatment_protocol: Cells were treated with 30 mM glucose for 24 hour

value: METTL3 knockdown


title: shNC_M6a_Input_2


title: 22_No-Treatment

description:
No treatment
Replicate 2

value: No treatment


title: 26_NEDD8 DsiRNA

description:
NEDD8 DsiRNA
Replicate 2

value: Cell line:CFBE


title: 23_27C for 24hr

description:
27°C incubation for 24h
Replicate 2

value: 27°C incubation for 24h


title: 21_SYVN1 DsiRNA

description:
SYVN1 DsiRNA
Replicate 4

value: SYVN1 DsiRNA


title: 24_27C for 24hr

description:
27°C incubation for 24h
Replicate 3


title: 272_Great Dane_HC_Female

description:
272
Canis familiaris


title: 271_Great Dane_HC_Female

description:
271
Canis familiaris


title: 20_DMSO

description:
DMSO treatment for 24h
Replicate 2

value: DMSO for 24h


title: shNC_M6a_Input_1


title: 269_Great Dane_HC_Male

description:
269
Canis familiaris

value: Male


title: 25_DMSO

description:
DMSO treatment for 24h
Replicate 3


title: prefrontal cortex_nrf2 knockout_3

city: Shijiazhuang

first: Lei

last: Wang

address: Hebei Medical University, No. 361, Zhongshan East Road, Chang'an District

institute: Heibei Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.
Compared to the wild-type mice, a total of 197 differentially expressed circRNAs (103 up- and 94 down-regulated), 685 differentially expressed lncRNAs (281 up- and 404 down-regulated), and 356 differentially expressed mRNAs (87 up- and 269 down-regulated) were detected in the prefrontal cortex of Nrf2 knockout mice with p-value < 0.05 and FC > 1.5.

source_name: Mouse prefrontal cortex

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: strain

value: ICR

tag: age

value: 3-4 months

value: Nrf2 gene knockout

value: prefrontal cortex


title: prefrontal cortex_wild_2

tag: Sex

value: Wild type


title: 267_Great Dane_Acute_GDV_Female

description:
267
Canis familiaris

value: Great Dane

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: shMETTL3_M6a_Input_2

value: HTR8/SVneo cells


title: shMETTL3_RNC_3

value: immortalized first-trimester invasive trophoblast cell line


title: prefrontal cortex_wild_3


title: 18_NEDD8 DsiRNA

description:
NEDD8 DsiRNA
Replicate 1

value: NEDD8 DsiRNA


title: prefrontal cortex_nrf2 knockout_2


title: shMETTL3_M6a_IP_2

value: METTL3 knockdown


title: IVI9

value: case

value: A


title: shMETTL3_M6a_IP_1


title: prefrontal cortex_nrf2 knockout_1


title: shNC_M6a_IP_2

value: control


title: 17_40C for 24hr

description:
40°C incubation for 24h
Replicate 2

value: Cell line:CFBE

tag: temperature

value: 40°C incubation for 24h


title: prefrontal cortex_wild_1

value: ICR

value: Male


title: 263_Poodle Standard_Acute_GDV_Male

description:
263
Canis familiaris

value: Poodle Standard

value: Peripheral blood


title: shNC_M6a_IP_1


title: 16_40C for 24hr

description:
40°C incubation for 24h
Replicate 1


title: 262_Poodle Standard_Acute_GDV_Female

description:
262
Canis familiaris


title: 265_Collie Smooth_Acute_GDV_Female

description:
265
Canis familiaris

value: Collie Smooth


title: patient tumor sample, S9IDC

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
76 nt paired-end sequencing using Illumina HiSeq2500 platform
Illumina Casava1.7 software used for basecalling.
Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
Datasets were aligned to the human reference GRCh37 genome & ensembl annotation file using the STAR RNA-Seq aligner
TPM counts were calculated using RSEM package
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: RNA-Seq: csv file of TPM counts

source_name: breast IDC

extract_protocol:
Patient samples were macro-dissected into stromal and epithelial fractions from FFPE tissue-slides. RNA was extracted from epithelial fractions using AllPrep DNA/RNA FFPE Kit (Qiagen)
cDNA library was constructed using Illumina’s TruSeq RNA Access Library Prep kit and hybridized to a set of DNA oligonucleotide probes to enrich the library for mRNA transcript fragments

tag: patient id

value: IDC (stromal)


title: patient tumor sample, S9DCIS

source_name: breast DCIS

value: DCIS (stromal)


title: 264_Poodle Standard_Acute_GDV_Female

description:
264
Canis familiaris

source_name: Peripheral blood

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: 19_SYVN1 DsiRNA

description:
SYVN1 DsiRNA
Replicate 3

tag: tag

value: SYVN1 DsiRNA


title: 15_SYVN1 DsiRNA + C18

description:
SYVN1 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 1

source_name: CFBE_SYVN1 DsiRNA + C18

tag: treatment


title: patient tumor sample, S8IDC


title: 14_miR-138 mimic

description:
miR-138 mimic
Replicate 1

value: miR-138 mimic


title: 260_Borzoi_HC_Male

description:
260
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC


title: patient tumor sample, S8DCIS


title: 13_Corrector compound C18

description:
6µM Corrector Compound C18 treatment for 24h
Replicate 2


title: 258_Borzoi_HC_Female

description:
258
Canis familiaris


title: 257_Borzoi_HC_Female

description:
257
Canis familiaris


title: patient tumor sample, 9DCIS

value: DCIS (epithelial)


title: 256_Borzoi_HC_Female

description:
256
Canis familiaris


title: 11_No Treatment

description:
No treatment
Replicate 1

source_name: CFBE_No Treatment

value: No treatment


title: patient tumor sample, 8IDC

value: IDC (epithelial)


title: 10_Corrector Compound C18

description:
6µM Corrector Compound C18 treatment for 24h
Replicate 1

source_name: CFBE_Corrector Compound C18

value: Cell line:CFBE


title: 255_Borzoi_HC_Male

description:
255
Canis familiaris


title: 254_Labrador Retriever_Acute_GDV_Male

description:
254
Canis familiaris

value: Labrador Retriever


title: patient tumor sample, 8DCIS


title: 253_German Shepherd Dog_Acute_GDV_Female

description:
253
Canis familiaris

value: German Shepherd Dog


title: 259_Borzoi_HC_Female

description:
259
Canis familiaris


title: 12_SYVN1 DsiRNA

description:
SYVN1 DsiRNA
Replicate 2

source_name: CFBE_SYVN1 DsiRNA


title: 09_SYVN1 DsiRNA

description:
SYVN1 DsiRNA
Replicate 1


title: 08_37C

description:
37°C incubation for 24h
Replicate 1

value: 37°C incubation for 24h


title: 06_27C_24hr

description:
27°C incubation for 24h
Replicate 1

value: 27°C incubation for 24h


title: 07_SIN3A DsiRNA

description:
SIN3A DsiRNA
Replicate 1

value: SIN3A DsiRNA


title: 05_40C_24hr_27C_24hr

description:
40°C incubation for 24h followed by 27°C incubation for 24h
Replicate 2


title: patient tumor sample, 9IDC


title: 251_German Shepherd Dog_Acute_GDV_Male

description:
251
Canis familiaris

value: Male

value: Peripheral blood


title: 249_Borzoi_HC_Female

description:
249
Canis familiaris


title: 04_Scrambled

description:
Scrambled DsiRNA
Replicate 1

value: Scrambled DsiRNA


title: 248_German Shepherd Dog_Acute_GDV_Female

description:
248
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: PHH_C

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

country: Germany

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the hg19 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition

source_name: hepatocytes

extract_protocol:
Total RNA from total liver was extracted using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: phh donor

value: C

value: hepatocytes


title: 244_Great Dane_Acute_GDV_Male

description:
244
Canis familiaris

value: Great Dane


title: PHH_B

value: B


title: patient tumor sample, 2IDC


title: 241_Labrador Retriever_Acute_GDV_Female

description:
241
Canis familiaris


title: patient tumor sample, 3IDC


title: Huh7.5 cells, mCd302_DCPT_3

description: Deletion of cytoplasmic tail of Cd302

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were initially mapped against the murine Cd302 and/or Cr1l coding sequences to remove exogenously introduced reads prior hg19 mapping.
Mouse gene-depleted cellular transcriptomes were saved.
Mouse gene-depleted fastq files were mapped against the hg19 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition

source_name: hepatocellular carcinoma (Huh7.5)

extract_protocol:
Total RNA from cells was extracted using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: replicate no.

tag: overexpression


title: 239_Great Dane_Acute_GDV_Male

description:
239
Canis familiaris

tag: breed


title: 02_40C_24hr_27C_24hr

description:
40°C incubation for 24h followed by 27°C incubation for 24h
Replicate 1


title: Huh7.5 cells, mCd302_DCPT_2

description: Deletion of cytoplasmic tail of Cd302


title: Huh7.5 cells, mCd302_DCPT_1

description: Deletion of cytoplasmic tail of Cd302


title: 238_Golden Retriever_Acute_GDV_Female

description:
238
Canis familiaris

value: Golden Retriever

tag: status (hc = healthy control, gdv


title: Huh7.5 cells, mCd302-mCr1l_3


title: PHH_A

value: A


title: 01_DMSO

description:
DMSO treatment for 24h
Replicate 1

value: Cell line:CFBE

value: DMSO for 24h


title: Huh7.5 cells, mCd302-mCr1l_2


title: 03_NEDD8 DsiRNA_C18

description:
NEDD8 DsiRNA + 6µM Corrector Compound C18 treatment for 24h
Replicate 1

source_name: CFBE_NEDD8 DsiRNA_C18


title: Huh7.5 cells, mCd302-mCr1l_1


title: astrocyte_alfaD11_24h 4

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description:
alfaD11
mouse astrocyte cells from primary cultures

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 10.7  software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09 for FE ver 10.7 ).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using R, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale.  Differentially expressed genes were selected by a combination of fold change and moderated T-test thresholds (with FDR Pvalue correction) by the R-Bioconductor  tool Limma (FDR<0.05; |Log2 fold-change ratio| >1.0 equivalent to 2.0 fold in linear scale). The final differentially expressed gene list was  selected as the intersection between the comaparisons against the two controls: alfaD11 vs anti-V5 and alfaD11 va Naive.

source_name: primary astrocyte cells

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Primary astrocyte cells were derived from the brains of B6129 mice (male and female) at postnatal day 3-4. Cells were maintained in Dulbecco's modified Eagle's medium (DMEM/F12) containing 1% penicillin/streptomycin, 1% Glutamax and 10% FBS, in 5% CO2 pH 7.4. After 2 weeks in colture, the astrocytes were detached with soft tripsinisation and re-plated in 12 multiwell plates onto small glasses for the tratmenents within 1 week.

extract_protocol: Total RNA was extracted at 24h from alfaD11 treated (test samples), anti-V5 treated (controls type 1) and untreated naive cells (controls type 2). Total RNA was extracted  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: Primary astrocyte culture cells were treated with 100 ng/ml alfaD11 anti-NGF antibody for 24 hours. Control samples are time-matched anti-V5 antibody treated (100 ng/ml) and untreated naive cells.

tag: tissue

value: astrocytes

tag: transgenic

value: pooled male and female

value: anti-NGF alfaD11 antibody

tag: time post transfection

value: Postnatal day 3-4


title: 232_Borzoi_HC_Female

description:
232
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC


title: 231_Borzoi_HC_Female

description:
231
Canis familiaris

value: Peripheral blood


title: 233_Borzoi_HC_Female

description:
233
Canis familiaris


title: Huh7.5 cells, mCr1l_3

tag: cell line


title: astrocyte_CTR_antiV5_24h 2

description:
control2
mouse astrocyte cells from primary cultures

value: anti-V5 antibody


title: 230_Borzoi_HC_Female

description:
230
Canis familiaris

value: Female


title: SUDHL6 H3K4me3

data_processing:
The 36-nt sequence reads from Illumina's Genome Analyzer 2 were mapped to the genome using the ELAND algorithm.  Only tags that mapped uniquely, had no more than 2 mismatches, and passed quality control filtering were used in the subsequent analysis.
Mapped reads were extended in silico at their 3' ends to a length of 140 bp, reflecting the average fragment length in the size selected library.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the output of applying SICER to each sample.  WIG and TDF files were generating using IGVTools' count function on aligned sequence reads, assuming a fragment length of 200, and using a bin size of 25 nt for WIG and 10 nt for TDF files.

treatment_protocol: No treatment -- baseline measurement of methylation / occupancy without perturbation.

tag: chip antibody manufacturer

value: Cell Signaling

tag: chip antibody catalog #

tag: chip antibody


title: Huh7.5 cells, mCr1l_2


title: 229_Borzoi_HC_Female

description:
229
Canis familiaris

tag: Sex


title: Huh7.5 cells, mCr1l_1


title: HT H3K4me3

extract_protocol: baseline measurement of methylation / occupancy without perturbation

value: HT


title: 228_Borzoi_HC_Male

description:
228
Canis familiaris

value: Male


title: 226_Borzoi_HC_Female

description:
226
Canis familiaris


title: astrocyte_alfaD11_24h 3

tag: strain

tag: age


title: Huh7.5 cells, mCd302_2


title: 237_Collie Smooth_Acute_GDV_Female

description:
237
Canis familiaris

value: Collie Smooth

value: gastric dilatation-volvulus:Acute_GDV


title: astrocyte_CTR_Naive_24h 1

description:
control1
mouse astrocyte cells from primary cultures

value: untreated  cells


title: astrocyte_CTR_Naive_24h 2


title: astrocyte_CTR_antiV5_24h 1


title: 225_Borzoi_HC_Female

description:
225
Canis familiaris


title: Huh7.5 cells, mCd302_1


title: HT Input


title: astrocyte_alfaD11_24h 2


title: astrocyte_alfaD11_24h 1


title: pEXP35sHSrCTXPMiDONORCd20191001dapi2

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

data_processing:
Bcl2fastq & Demultiplex by sample: 'mkfastq' Cell Ranger 3.1.0
Alignment/Counts: 'count' Cell Ranger 3.1.0
Aggregate: 'Aggr' Cell Ranger 3.1.0 (normalize = none)
Analysis: LIGER & Seurat
Genome_build: 10X Default 3.1 (GRCh38 (hg38); Annotation: Filtered Ensembl v93 premRNA modified)
Supplementary_files_format_and_content: 10X Cell Ranger Count Output (.tsv & .mtx)

source_name: brain

extract_protocol: 10X Genomics 3' Version 3 Single Cell Kit

tag: tissue preparation

value: Fresh frozen

tag: donor

value: C

tag: batch

value: Batch 2

value: brain

tag: brain region

value: Cortex


title: Huh7.5 cells, mCd302_3

tag: replicate no.

tag: overexpression


title: SUDHL6 EZH2


title: 216_Borzoi_HC_Female

description:
216
Canis familiaris

tag: breed

tag: status (hc = healthy control, gdv


title: n4mBid+MIILL_S2

description: S2 (GE); S2 RNA-Seq un-mapped reads (GE)

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the hg19 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Unmapped reads were mapped against the mm9 mouse reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition

source_name: hepatocellular carcinoma

extract_protocol:
Total RNA from cells was extracted using TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: passage


title: Enriched BM: patient 7370

city: Saint Louis

first: Sanjay

last: Jain

state: MO

address: 660 S. Euclid Ave.

department: Division of Nephrology

institute: Washington University in Saint Louis

description: 10X Genomics Single Cell Library

data_processing:
Demultiplexing of the raw base calls by cellranger mkfastq
Alignment, filtering, barcode counting, and UMI counting by cellranger count
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix

source_name: bone marrow aspirate

extract_protocol:
10x Genomics Single Cell Library
10x Genomics Single Cell Library
10X genomics single cell RNA

tag: disease state

value: advanced stage breast cancer

tag: cell type

value: tumor cell enriched bone marrow


title: SUDHL6 Input

source_name: Diffuse large B cell lymphoma

tag: cell line


title: pEXP35sHSrCTXPMiDONORBd20191001dapi2

value: B

tag: tissue


title: n4mBid+MIILL_S0_Sample

description: Sample_S0 (GE); Sample_S0 RNA-Seq un-mapped reads (GE)


title: HT EZH2

tag: chip antibody manufacturer

tag: chip antibody catalog #

tag: chip antibody


title: SUDHL6 H3K27me3


title: pEXP27sHSrCTXPMiDONORCd20191001dapi

value: Batch 1


title: 214_Borzoi_Acute_GDV_Female

description:
214
Canis familiaris

value: Borzoi

tag: Sex

value: Peripheral blood


title: pEXP35sHSrCTXPMiDONORAd20191001dapi2

tag: tissue preparation

value: A


title: 217_Borzoi_HC_Male

description:
217
Canis familiaris

value: gastric dilatation-volvulus:HC


title: 212_Borzoi_HC_Female

description:
212
Canis familiaris

value: Female


title: n4mBid+MIILL_S0

description: S0 (GE); S0 RNA-Seq un-mapped reads [S0] (GE)


title: HT H3K27me3

value: HT

value: Cell Signaling


title: pEXP27sHSrCTXPMiDONORBd20191001dapi

tag: donor


title: HepG2 input DNA 2

city: Buffalo

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description: input

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie.
Peaks were called using macs2 with the following setting: p-value threshold (1e-3 for H3K27ac ChIP-seq, and 1e-4 for ΔNp63 ChIP-seq).
Blacklist coordinates were removed from above called peaks.
ΔNp63 bound sites were obtained after excluding ΔNp63α(R304W) peaks from ΔNp63α peaks.

source_name: ΔNp63α(R304W)-expressing HepG2 cells

extract_protocol:
Lysates were clarified from sonicated cell pellets,  ΔNp63-DNA and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). After adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq??? following the manufacturer's protocols.

treatment_protocol: ΔNp63 expression was induced by 300 ng/ml DOX  for 16 hours.

value: HepG2 cells

tag: passages


title: n4mBid+MIILL_S2_Sample

description: Sample_S2 (GE); Sample_S2 RNA-Seq un-mapped reads (GE)


title: HepG2 input DNA 1

description: input

source_name: ΔNp63α-expressing HepG2 cells


title: 209_Labrador Retriever_HC_Male

description:
209
Canis familiaris

data_processing: Genotype calling of SNPs as well as data visualization were performed with GenomeStudio v2.0 and exported to PLINK format using the CanFam3.1.75 genome assembly to retrieve chromosomal coordinates. SNP array data imputation was conducted using a phased genotype reference dataset of 365 dogs from multiple breeds genotyped by whole-genome sequencing. The reference dataset was filtered excluding sex chromosomes, removing insertion/deletions, non-PASS variants, and variants with more than two alleles. The SNP array dataset of all 241 dogs on our study (target dataset) was filtered excluding sex chromosomes and duplicate variants, including variants with: minor allele frequency (MAF) ≥ 0.005, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. The resulting dataset was subjected to principal component analysis (PCA) in PLINK v1.9 to identify outliers and dogs whose PCA clustering would differ from the owner-identified breed information. We computed the relatedness PIHAT metric using PLINK v1.9 for each pair of samples aiming to identify duplicated samples (PIHAT=1.0). Outliers, duplicated and misclassified samples were removed from the dataset. Reference and target datasets were compared using the Conform-gt software, keeping only variants shared between the target and the reference dataset. Finally, the genotypes were imputed with the software Beagle v5, using the recombination rate map reference, default settings and effective population size = 200. After imputation, variants were filtered with dosage R2 (DR2)< 0.4, ultimately including only with MAF ≥ 0.05, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. Gene annotation of SNPs was performed with R-BiomartTv2.40.4 using the dog genome reference CanFam3.1.

extract_protocol: Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).

value: Labrador Retriever

value: Male


title: K562 input DNA 4

description: input

source_name: ΔNp63α(R304W)-expressing K562 cells

value: K562 cells


title: siTP53 2

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

data_processing:
The adapter segment at the 3’ end of the sequenced reads was removed using the FASTX program (version 0.0.14) (-l 1 -c).
The remaining reads were mapped to the human genome (version hg38) using the HISAT program (version 0.1.6) (--no-unal --rna-strandness FR --fr) and the gene expression level was determined by the StringTie program (version 1.3.5).
The gene expression fold change upon siRNA treatment was calculated by comparing the gene expression levels in sample transfected with a shRNA targeting TP53, LMNA or an empty vector.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HEK293 cell lines

growth_protocol: Lenti-X 293T (Clontech, Mountain View, CA, USA) cells were grown in Dulbecco’s modified Eagle’s medium (Clontech, Mountain View, CA, USA) with 10% fetal bovine serum (Gibco, Chagrin Falls, OH, USA)

extract_protocol: library construction were conducted according to NEB E7420 RNA library prep kit

treatment_protocol: For production of the lentiviruses, Lenti-X 293T cells were transfected with a virus vector encoding an AGO protein as well as the VSVG and ΔR8.91 plasmids by using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). Lentiviruses were harvested 48 hr post-transfection. AGO-expressing Lenti-X 293T stable cell lines were generated by transduction with lentiviruses in the presence of 8 μg/ml polybrene (Sigma-Aldrich, St. Louis, MO, USA) overnight, followed by selection with 1 μg/ml puromycin (BBI, Shanghai, China) for 1 week. For induction of AGO protein expression, 1 ng/ml Dox (BBI, Shanghai, China) was added to the cell culture medium.

tag: transfection


title: 210_Labrador Retriever_HC_Male

description:
210
Canis familiaris

source_name: Peripheral blood


title: siTP53 1


title: pEXP27sHSrCTXPMiDONORAd20191001dapi

value: Fresh frozen

tag: batch

value: brain

tag: brain region


title: 206_German Shepherd Dog_Acute_GDV_Male

description:
206
Canis familiaris

tag: breed

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV


title: siLMNA 2

value: shLMNA


title: 588 WT V::3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from WT uterus, vehicle, 6hr

hyb_protocol: For each sample, 1.65 ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: WT uterus, vehicle, 6hr, replicate 3

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Animals were maintained on a NIH-31 regular diet.

extract_protocol: Frozen uteri were homogenized and total RNA was extracted using TRIzol (Invitrogen). The quality of extracted RNA was checked by agarose gel electrophoresis.

treatment_protocol: OVX 12-wk-old AF2ERKI or WT littermate female mice (three animals per group) were injected intraperitoneally with 2 mg/kg fulvestrant/ICI182780 (ICI) dissolved in DMSO or 10 µg/kg estradiol (E2) dissolved in DMSO. 50 µl DMSO was injected as vehicle (Veh). After 6h injection, animals were euthanized with carbon dioxide, then uterus was collected. Collected tissues were stored at -70 ˚C until processed.

tag: gender

value: female

tag: organ

value: uterus


title: K562 input DNA 1

description: input

source_name: ΔNp63α-expressing K562 cells


title: K562 input DNA 2

description: input


title: siLMNA 1


title: 202_German Shepherd Dog_Acute_GDV_Male

description:
202
Canis familiaris

tag: status (hc = healthy control, gdv

value: Peripheral blood


title: siCtr 2

value: empty vector


title: 207_German Shepherd Dog_HC_Female

description:
207
Canis familiaris

value: gastric dilatation-volvulus:HC


title: 205_German Shepherd Dog_Acute_GDV_Male

description:
205
Canis familiaris


title: 588 WT V::2

source_name: WT uterus, vehicle, 6hr, replicate 2


title: 211_Borzoi_HC_Female

description:
211
Canis familiaris

value: Borzoi

value: Female


title: H3K27ac K562 ChIPSeq 4

tag: cell type

value: H3K27ac (Diagenode:C15410174)


title: siCtr 1

tag: cell line


title: H3K27ac K562 ChIPSeq 3


title: 198_Collie Smooth_Acute_GDV_Female

description:
198
Canis familiaris

value: Collie Smooth

tag: tissue


title: 588 WT V::1

source_name: WT uterus, vehicle, 6hr, replicate 1


title: K562 input DNA 3

description: input


title: 197_Collie Smooth_HC_Male

description:
197
Canis familiaris


title: 588 KI V::2

description: Gene expression from AF2ERKI uterus, vehicle, 6hr

source_name: AF2ERKI uterus, vehicle, 6hr, replicate 2


title: 588 WT E::2

description: Gene expression from WT uterus, E2, 6hr

source_name: WT uterus, E2, 6hr, replicate 2


title: 588 WT E::1

description: Gene expression from WT uterus, E2, 6hr

source_name: WT uterus, E2, 6hr, replicate 1


title: THP-1 cells-TM3 [RNA-seq]

city: Nanning

first: Yueqi

last: Li

state: Guangxi

address: NO.22 Shuangyong Road

institute: Guangxi Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then use Trinity for assembly  with default parameters
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using RSEM software with  with default parameters .
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: THP-1 cells

growth_protocol: RPMI 1640 medium containing 10% FBS, 100 U / mL penicillin and 100 μg / mL streptomycin was prepared for THP-1 cells, and cultured in a 37 ° C and 5% CO 2 incubator.

extract_protocol: Total RNA from the samples was isolated using Trizol reagent according to the manufacturer's instructions (Invitrogen, CA, USA). RNA integrity was detected using an RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA purity and concentration was measured using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The 260/280 ratio for all samples was approximately 2.0 and the RNA integrity number (RIN) ≥ 8.0.

treatment_protocol: After 72h of stimulation with 50 ng / ml PMA, THP-1 differentiated into macrophages.THP-1 differentiated macrophages were maintained in 10% heat-inactivated FBS in DMEM containing 100 U/mL penicillin and 100 μg/mL streptomycin for further processing.

value: monocyte

tag: co-culture

value: T. marneffei L0


title: 588 WT E::3

description: Gene expression from WT uterus, E2, 6hr

source_name: WT uterus, E2, 6hr, replicate 3


title: H3K27ac K562 ChIPSeq 2

value: K562 cells


title: THP-1 cells-TM2 [RNA-seq]


title: 195_Collie Smooth_HC_Female

description:
195
Canis familiaris


title: THP-1 cells-TM1 [RNA-seq]


title: THP-1 cells-3 [RNA-seq]


title: 188_Collie Smooth_HC_Female

description:
188
Canis familiaris


title: ΔNp63 HepG2 ChIPSeq 1

value: HepG2 cells

value: HA


title: THP-1 cells-1 [RNA-seq]


title: 189_Collie Smooth_HC_Female

description:
189
Canis familiaris


title: Input AthDNAa_rep2

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Sample 6
Input DNA for samples 1-4

data_processing:
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

organism: Arabidopsis thaliana

source_name: 10 days-old seedlings

growth_protocol: 10 days-old seedlings grown in MS medium

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

tag: protein

value: Input DNA for samples 1-4

tag: gene id

value: Input DNA

tag: protein expression


title: 588 KI V::1

source_name: AF2ERKI uterus, vehicle, 6hr, replicate 1


title: THP-1 cells-2 [RNA-seq]


title: H3K27ac K562 ChIPSeq 1

first: Michael

tag: chip antibody


title: 588 KI I::2

description: Gene expression from AF2ERKI uterus, ICI, 6hr

source_name: AF2ERKI uterus, ICI, 6hr, replicate 2


title: 588 KI I::1

source_name: AF2ERKI uterus, ICI, 6hr, replicate 1


title: 588 KI V::3

source_name: AF2ERKI uterus, vehicle, 6hr, replicate 3


title: ΔNp63 K562 ChIPSeq 3

source_name: ΔNp63α(R304W)-expressing K562 cells


title: 588 KI I::3

source_name: AF2ERKI uterus, ICI, 6hr, replicate 3


title: 187_German Shepherd Dog_HC_Male

first: Ignazio

last: Piras

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

description:
187
Canis familiaris

source_name: Peripheral blood

value: German Shepherd Dog

tag: Sex

value: Male


title: DAP-MYC3_rep2

description:
Sample 4
Protein-DNA interaction

value: E.coli expressed


title: 196_Collie Smooth_HC_Male

description:
196
Canis familiaris

value: Peripheral blood


title: 183_Borzoi_HC_Male

description:
183
Canis familiaris


title: DAP-MYC3_rep1

description:
Sample 3
Protein-DNA interaction


title: ΔNp63 K562 ChIPSeq 2

tag: passages


title: THP-1 cells-TM3 [miRNA-seq]

data_processing:
SOAPnuke software was used to filter fastq files
Clean Tag was compared to the genome by Bowtie2, and the ratio of Clean Tag and its distribution on the genome were calculated
For miRNA information of this species in the miRBase database, we first compared the Clean Tag with the miRNA precursor /miRNA mature sequence of this species known in miRBase, and the result will show the details of the matching small RNA
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .


title: THP-1 cells-TM2 [miRNA-seq]


title: ΔNp63 K562 ChIPSeq 1


title: CAL-27, hZ2

city: Liaocheng

first: Haiying

last: Chen

state: Shandong

address: Dongchang West Road 67#

institute: Liaocheng People's Hospital

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
Raw data were filtered into clean data, and single-end clean reads were aligned to the reference genome (Feb. 2009, GRCh37/hg19) using TopHat v2.0.9.
Data were expressed as reads per kilobase per million mapped reads (RPKM). Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: readcounts, RPKMs

source_name: Oral

growth_protocol: Oral squamous cell cancer (OSCC) cell line CAL-27 cells (1 × 10^6 cells into a T25 flask) were grown in Dulbecco’s modified Eagle’s medium (DMEM) media supplemented with 10% FBS, 1% penicillin/streptomycin

extract_protocol:
Total RNA extraction from each groups was performed using the RNeasy Mini Kit on a fully automated QIAcube® DNA extraction device (Qiagen, Hilden, Germany). The NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) were used for the quantification and qualification of the RNA sample
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were randomly divided into two groups: Vector groups (mRNA_C groups, infected with pLVX-PGK-Puro lentivirus) and ZNF750 groups (mRNA_Z groups, infected with pLVX-hZNF750-PGK-Puro lentivirus)

value: oral squamous cell carcinoma

tag: group

value: mRNA_Z (overexpressed ZNF750 gene)

tag: genotype

value: ZNF750 overexpression


title: ΔNp63 HepG2 ChIPSeq 2

source_name: ΔNp63α(R304W)-expressing HepG2 cells


title: THP-1 cells-TM1 [miRNA-seq]


title: THP-1 cells-3 [miRNA-seq]


title: 177_German Shepherd Dog_Acute_GDV_Male

city: Phoenix

description:
177
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: DAP-MYC2_rep2

description:
Sample 2
Protein-DNA interaction


title: DAP-MYC2_rep1

description:
Sample 1
Protein-DNA interaction


title: CAL-27, hZ1


title: Input AthDNAa_rep1

description:
Sample 5
Input DNA for samples 1-4


title: THP-1 cells-2 [miRNA-seq]


title: 175_Borzoi_HC_Male

description:
175
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC


title: CAL-27, hC2

value: mRNA_C (Vector)

value: control


title: 178_German Shepherd Dog_Acute_GDV_Male

description:
178
Canis familiaris


title: CAL-27, hC1


title: 169_Golden Retriever_Acute_GDV_Male

description:
169
Canis familiaris

value: Golden Retriever


title: K562_H3K14cr_rep2 ChIP-seq

city: Beijing

first: fan

last: feng

address: Tsinghua West Road

institute: Tsinghua University

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited bed files including number of reads (not input-normalized) in 100bp bin in the genome for each ChIP-seq sample

source_name: K562 cell line

growth_protocol: K562 cells were cultured in RPMI1640 medium(Gibco ) with 10% FBS(Gibco) accoring to ATCC

extract_protocol:
Cells were fixed by 1% final concentration formaldehyde,and lysed using lysis buffer.Then lysis were sonicated and added H3K14cr antibody(PTM 535) to supernatant. Next day, beads were added to lysis and washed by lysis buffer, high salt lysis buffer, Tris-LiCl buffer and Tris-EDTA buffer.Beads were reversed cross-link in 65℃ overnight.The last day, DNA was purificated with phenol chloroform method.
5μg DNA were used to construct the library with NEBNext Ultra DNA Library Prep Kit for Illumina (E7645s)

tag: chip-antibody

value: WT


title: 171_Borzoi_HC_Female

description:
171
Canis familiaris

tag: breed

value: Female


title: GT92_W8_T

city: Manchester

first: Ardeshir

last: Bayat

address: Oxford Road

country: United Kingdom

institute: University of Manchester

data_processing:
Raw image data file from high-throughput sequencing (Illumina PE150 Nova-Seq) was transformed to Sequenced Reads by CASAVA v1.8 base recognition (Base Calling)
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR v2.5) software.
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.  The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
For samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package providing statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genome_build: Ensembl version Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: Processed data is in Excel format including differential expression analysis data

source_name: Human skin

extract_protocol:
Tissue biopsies were homogenised in 300μL of RLT buffer (Qiagen, GmbH, Helden, Germany) mixed with β-mercaptoethanol (Sigma-Aldrich, St Louis, MO) (10μl β-mercaptoethanol/ml RLT buffer) using 5-mm stainless steel beads and a Qiagen TissueLyser II (Qiagen GmbH) at 30 oscillations/second for 10 minutes. RNA was extracted using RNeasy Tissue Mini Kits (Qiagen GmbH). Eluted RNA quantity and purity was assessed using NanoDrop ND-100 v3.0.1 spectrophotometer (NanoDrop Technologies, Wilmington, DE), Agarose gel electrophoresis and Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human skin

tag: wound/scar time point and group

value: Week 8

tag: egcg treated/placebo

value: Treatment

tag: group allocation


title: 163_Great Dane_Acute_GDV_Male

description:
163
Canis familiaris

value: Great Dane

tag: status (hc = healthy control, gdv

value: Male


title: GT92_W8_P

value: Placebo


title: K562_H3K14cr_rep1 ChIP-seq

tag: cell line


title: K562_DPF2_rep2 ChIP-seq

extract_protocol:
Cells were fixed by 1% final concentration formaldehyde,and lysed using lysis buffer.Then lysis were sonicated and added DPF2 antibody(Abcam 134942) to supernatant. Next day, beads were added to lysis and washed by lysis buffer, high salt lysis buffer, Tris-LiCl buffer and Tris-EDTA buffer.Beads were reversed cross-link in 65℃ overnight.The last day, DNA was purificated with phenol chloroform method.
5μg DNA were used to construct the library with NEBNext Ultra DNA Library Prep Kit for Illumina (E7645s)


title: GT92_W4_T

tag: tissue

value: Week 4


title: 151_Great Dane_Acute_GDV_Male

description:
151
Canis familiaris

value: Peripheral blood


title: 176_Borzoi_HC_Female

description:
176
Canis familiaris


title: GT92_W4_P


title: K562_DPF2_rep1 ChIP-seq

growth_protocol: K562 cells were cultured in RPMI1640 medium(Gibco,11875093 ) with 10% FBS(Gibco)

extract_protocol:
Cells were fixed by 1% final concentration formaldehyde and lysed using lysis buffer.Then lysis were sonicated and added DPF2 antibody(Abcam 134942) to supernatant. Nextday, beads were added to lysis and washed by lysis buffer, high salt lysis buffer, Tris-LiCl buffer and Tris-EDTA buffer.Beads were reversed cross-link in 65℃overnight.The last day, DNA was purificated with phenol chloroform method.
5μg DNA were used to construct the library with NEBNext Ultra DNA Library Prep Kit for Illumina (E7645s)


title: H3K27ac_WT

first: Catherine

address: 450 Brookline Avenue

data_processing:
RNA-seq
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1).
TPM (Transcripts Per Kilobase Million) value was used to measure gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for all samples
ChIP-Seq
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to the mouse reference genome using using Bowtie2 (v2.3.4.1).
Peak detection was performed with MACS2 (v2.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for each sample

source_name: B cell

growth_protocol: Chromatin immunoprecipitation (ChIP) was performed on splenic B cells (80x106) from 2-3 months old Ikzf3 wild-type and homozygous mutant mice.

extract_protocol:
1 µl of 10mg/ml RNAse for 30 min at 37°C and 5µl of 20mg/ml Proteinase K at 65°C overnight.  The immunoprecipitated chromatin was cleaned up using the Qiagen PCR purification Kit.
Input and ChIP Libraries were prepared with the Rubicon ThruPLEX FD kit (ref. R400429, Takara Bio USA) and sequenced on Illumina NextSeq instrument to generate 75bp single-end sequencing reads.

treatment_protocol: Cells were washed in cold PBS, fixed in 1% formaldehyde at room temperature for 10 min and the fixation reaction was quenched with 0.125M glycine for 5 min at room temperature. The nuclei were resuspended and lysed in 500µl of shearing buffer containing 0.5% SDS, 10mM EDTA pH8, 50mM Tris-HCl pH8, 5mM sodium butyrate and protease inhibitor. The chromatin was sheared on the Covaris E220 sonifiyer, according to the following program: PIP70, 5% duty factor, 200 cycles per burst, 25min.

tag: cell type

value: Splenic B cell

tag: strain

value: Ikzf3 fl/+

tag: age

value: 15-18 months


title: GT92_DO_T

value: Day 0

value: Untreated (T)


title: 148_Doberman Pinscher_Acute_GDV_Male

description:
148
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:Acute_GDV


title: THP-1 cells-1 [miRNA-seq]

value: monocyte

tag: co-culture


title: H3K27ac_Homo

value: Ikzf3 fl/fl


title: GT92_DO_P

value: Human skin

value: Untreated (P)


title: 145_Borzoi_HC_Male

description:
145
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC


title: GT91_W8_P

value: Week 8


title: H3K4me3_WT


title: GT91_W8_T

value: Treatment


title: ΔNp63 K562 ChIPSeq 4

value: K562 cells

tag: chip antibody

value: HA


title: 161_Great Dane_Acute_GDV_Female

description:
161
Canis familiaris

value: Great Dane

tag: Sex

value: Female

value: Peripheral blood


title: cultured U87MG ATCC-HTB14 cell line_rep1

city: Amman

first: Deema

middle: Adnan

last: Ali

address: queen Rania street

department: cell therapy center

country: Jordan

institute: The University of Jordan

description: Gene expression data for cultured U87MG ATCC-HTB14 cell line (without any treatment)

hyb_protocol: Following fragmentation and labeling, 5.2 ug of ss-DNA were hybridized for 16 hr at 45C on Human Transcriptome Analysis 2 (HTA 2) chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix® GeneChip Scanner 3000.

data_processing:
The data were analyzed with Affymetrix® Transcriptome Analysis Console (TAC®) Software V4.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0
program_name = q_probeset_summarize.exe

source_name: cultured U87MG ATCC-HTB14 cell line

label_protocol: The fragmented cDNA was biotin labelled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent ( Manual target preperation for GeneChip whole trascript expression array, 2013, Affymetrix).

growth_protocol: Glioma stem cells were isolated from U87MG ATCC-HTB14 cell line by using FACS and were expanded in neuromedia {Dulbecco’s Modified Eagle Medium/F12 (Gibco),supplemented with N2 (Gibco), EGF (20 ng/mL, Invitrogen), bFGF (20 ng/mL, Gibco), leukemia inhibitory factor 10 ng/μL (LIF; Chemicon), and B27 (1:50; Life Technologies)}, in 6-well Ultrlow plates ( Corning) to enrich for glioma stem cells (gliospheres)}.

extract_protocol: RNA was extracted using the mixed Trizol- Qiagen® RNeasy Mini kit (Qiagen, USA) , according to the manufacturer's instructions.

treatment_protocol: Actively growing gliospheres at N13 were treated with conditioned media from six biological samples of mesenchymal stem cells ( BM and WJ) for 7 days and the effect was evaluated by morphological changes, viability and invasion assays  and molecular assays.

value: U87MG ATCC-HTB14 cell line

tag: tissue source

value: brain


title: 143_Borzoi_HC_Female

description:
143
Canis familiaris


title: cultured U87MG ATCC-HTB14 cell line_rep3

value: cultured U87MG ATCC-HTB14 cell line (without any treatment)


title: 142_Borzoi_HC_Female

description:
142
Canis familiaris


title: ATACseq_WT

growth_protocol: ATAC-seq was performed on splenic B cells (80x106) from 2-3 months old Ikzf3 wild-type and homozygous mutant mice.

extract_protocol:
After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at maximum speed ina pre-chilled (4 C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL of transposition mix (25 ul 2x TD buffer, 2.5 uL transposase (100 nM final), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, and 5 uL water) bypipetting.
Samples were transposed for 30 min at 37 C, purified with Qiagen columns, and libraries were prepared as previously described (Buenrostro et al., 2015)

treatment_protocol: 100,000 cells were resuspended in 1 mL of cold756ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2757in water). Cells were centrifuged at maximum speed for 5 min in a pre-chilled (4 C) fixed-angle758centrifuge and supernatant was carefully aspirated. Cell pellets were then resuspended in 50 uL759of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times and incubated on ice for 3 min.

value: Splenic B cell

value: Ikzf3 fl/+

value: 15-18 months


title: 144_Borzoi_HC_Female

description:
144
Canis familiaris


title: cultured U87MG ATCC-HTB14 cell line_rep2


title: H3K4me3_Homo

value: Ikzf3 fl/fl


title: Negative spheres, biological rep 2

description: Gene expression data for actively growing glioma cells as spheroids (not-stem cells)

source_name: Negative spheres


title: positive spheres treated with wharton jelly-MSCs conditioning media biological rep 2

description: Gene expression data for actively growing glioma stem cells as spheroids treated with WJ-MSCs conditioning medis


title: positive spheres treated with wharton jelly-MSCs conditioning media biological rep 3

value: actively growing glioma stem cells as spheroids treated with WJ-MSCs conditioning medis


title: GT91_W4_T

value: Human skin

value: Week 4


title: positive spheres treated with bone marrow-MSCs conditioning media biological rep 3

description: Gene expression data for actively growing glioma stem cells as spheroids treated with BM-MSCs conditioning medis


title: Negative spheres, biological rep 1

value: actively growing glioma cells as spheroids (not-stem cells)


title: 141_Borzoi_Acute_GDV_Male

description:
141
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: positive spheres treated with wharton jelly-MSCs conditioning media biological rep 1


title: GT91_DO_P

value: Day 0

value: Untreated (P)


title: 135_Great Dane_Acute_GDV_Female

description:
135
Canis familiaris

value: Great Dane

value: Female

value: Peripheral blood


title: GT91_DO_T

value: Untreated (T)


title: 128_Great Dane_Acute_GDV_Female

description:
128
Canis familiaris


title: B_cell6_Homo

description:
CLL expression tpm.txt
B_cell6_Homo

growth_protocol: RNA-seq was performed on purified splenic B cells (1x106) from 15-18 months old Ikzf3 wild-type, heterozygous and homozygous mutant mice as well as FACS sorted B220+CD5+ CLL cells from leukemic mice.

extract_protocol:
Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were euthanized in a CO2 chamber and the harvested spleens or femurs were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells were immunomagnetically selected from the resulting cell suspension using the MACS B cell Isolation Kit for mouse (Miltenyi Biotec, Bergish Gladbach, Germany). Post-sort B cell purity was confirmed on a FACS Canto I using the flow cytometry staining procedures described above, and were at least 85% pure, but typically >90%.

value: Splenic B cell


title: H1_genome_hmC-seq_Rep2

city: Baltimore

first: Heng

last: Zhu

state: Maryland

address: MRB 340, 733 N. Broadway

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins School of Medicine

description:
enriched genome fragments with hmC modification
hmC-specific chemical labeling method: PMID: 29790956

data_processing:
Peaks were called using  MACS version 2.2.7.1 with the following setting:-q 0.01. Then using idr to evaluate the peak consistency between two replicates.
Supplementary_files_format_and_content: peak .xls files
Genome build: hg19

source_name: Homo sapiens

extract_protocol: The cell pellet of two million H1 cells was suspended in 500 µL digestion buffer (100 mM Tris-HCl at pH 8.5 with 5 mM EDTA, 1% SDS, 200 mM NaCl) on ice and then treated with Proteinase K at 55° C overnight. After phenol/chloroform (25:24:1 saturated with 10 mM Tris, pH 8.0, and 1 mM EDTA) extraction the aqueous phase was transferred to a test tube, mixed with same volume of isopropanol, and stored at -80° C overnight to precipitate the genomic DNA. After spinning at 12,000 rpm for 10 min at 4° C, the DNA pellet was washed with 75% ethanol, air-dried and dissolved in Nuclease-free Water. To perform the hmC-seq, hmC-specific chemical labeling and enrichment of DNA fragments with hmC were performed using a previously described method. DNA libraries were prepared following the Illumina protocol of ‘Preparing Samples for ChIP Sequencing of DNA’ (Illumina) using genomic DNA or hmC-captured DNA.

tag: sample type

value: Human embryonic stem cell


title: B_cell5_Het

description:
CLL expression tpm.txt
B_cell5_Het

tag: genotype

value: Ikzf3 fl/+

value: 15-18 months


title: GT82_W8_P

value: Week 8

value: Placebo


title: B_cell4_Het

description:
CLL expression tpm.txt
B_cell4_Het


title: positive spheres treated with bone marrow-MSCs conditioning media biological rep 1

value: U87MG ATCC-HTB14 cell line

value: brain

value: actively growing glioma stem cells as spheroids treated with BM-MSCs conditioning medis


title: H1_genome_hmC-seq_Rep1

extract_protocol: The cell pellet of two million H1 cells was suspended in 500 µL digestion buffer (100 mM Tris-HCl at pH 8.5 with 5 mM EDTA, 1% SDS, 200 mM NaCl) on ice and then treated with Proteinase K at 55° C overnight. After phenol/chloroform (25:24:1 saturated with 10 mM Tris, pH 8.0, and 1 mM EDTA) extraction the aqueous phase was transferred to a test tube, mixed with same volume of isopropanol, and stored at -80° C overnight to precipitate the genomic DNA. After spinning at 12,000 rpm for 10 min at 4° C, the DNA pellet was washed with 75% ethanol, air-dried and dissolved in Nuclease-free Water. To perform the hmC-seq, hmC-specific chemical labeling and enrichment of DNA fragments with hmC were performed using a previously described method66. DNA libraries were prepared following the Illumina protocol of ‘Preparing Samples for ChIP Sequencing of DNA’ (Illumina) using genomic DNA or hmC-captured DNA.


title: 127_German Shepherd Dog_Acute_GDV_Male

description:
127
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV


title: 126_German Shepherd Dog_Acute_GDV_Female

description:
126
Canis familiaris


title: GT82_W8_T

value: Human skin

value: Treatment


title: B_cell2_Het

description:
CLL expression tpm.txt
B_cell2_Het


title: iNeuron.rna_seq.ATOH1.day6.rep3

city: Durham

first: Charles

last: Gersbach

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest human reference genome (GRCh38) using the aligner STAR (Langmead et al., 2009)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 running on R.
Genome_build: hg38
Supplementary_files_format_and_content: Comma separated value file with TPM gene counts

source_name: TUBB3-2A-mCherry iPSC

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and 100 ng of RNA was used to develop RNA-seq libraries.
RNA-sequencing libraries were prepared using the Truseq Stranded mRNA kit (Illumina) according to the manufacturer’s protocol.

value: induced pluripotent stem cell

tag: treatment


title: ATACseq_Homo

institute: Dana-Farber Cancer Institute

value: Ikzf3 fl/fl


title: positive spheres, biological rep 2

description: Gene expression data for actively growing glioma stem cells as spheroids

source_name: positive spheres


title: IKZF3_WT3

description:
CLL expression tpm.txt
IKZF3_WT3

value: wild type


title: 123_Great Dane_Acute_GDV_Female

description:
123
Canis familiaris

extract_protocol: Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).

tag: breed

value: Great Dane

value: Female

value: Peripheral blood


title: positive spheres, biological rep 1

value: actively growing glioma stem cells as spheroids


title: iNeuron.rna_seq.ATOH1.day6.rep2


title: iNeuron.rna_seq.ATOH1.day6.rep1


title: positive spheres, biological rep 3


title: IKZF3_WT2

description:
CLL expression tpm.txt
IKZF3_WT2

value: Splenic B cell

value: 15-18 months


title: GT82_W4_T

tag: wound/scar time point and group

value: Week 4


title: 122_Poodle Standard_Acute_GDV_Female

description:
122
Canis familiaris

value: Poodle Standard


title: 118_Golden Retriever_Acute_GDV_Female

description:
118
Canis familiaris

value: Golden Retriever


title: iNeuron.rna_seq.NGN3.day7.rep3


title: IKZF3_WT1

description:
CLL expression tpm.txt
IKZF3_WT1


title: 117_Poodle Standard_Acute_GDV_Male

description:
117
Canis familiaris

value: Male


title: GT82_DO_T

value: Day 0

tag: egcg treated/placebo

value: Untreated (T)


title: iNeuron.rna_seq.NGN3.day7.rep1


title: CLL5_Het

description:
CLL expression tpm.txt
CLL5_Het

source_name: CLL-like cells

value: Ikzf3 fl/+


title: positive spheres treated with bone marrow-MSCs conditioning media biological rep 2

value: U87MG ATCC-HTB14 cell line

value: brain

value: actively growing glioma stem cells as spheroids treated with BM-MSCs conditioning medis


title: 109_Poodle Standard_Acute_GDV_Male

description:
109
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: GT79_W8_T

value: Human skin

value: Week 8

value: Treatment

tag: group allocation


title: CLL4_Het

description:
CLL expression tpm.txt
CLL4_Het


title: iNeuron.rna_seq.NGN3.day7.rep2

value: induced pluripotent stem cell


title: GT79_W8_P

value: Placebo


title: CLL6_Homo

description:
CLL expression tpm.txt
CLL6_Homo

value: Splenic B cell

value: Ikzf3 fl/fl

value: 15-18 months


title: GT79_W4_P

value: Week 4


title: iPSC.rna_seq.Ctrl.day7.rep3

value: Untreated


title: 124_Great Dane_Acute_GDV_Male

description:
124
Canis familiaris

value: Great Dane

tag: status (hc = healthy control, gdv

value: Male

value: Peripheral blood


title: CLL2_Het

description:
CLL expression tpm.txt
CLL2_Het

value: Ikzf3 fl/+


title: 105_Golden Retriever_Acute_GDV_Male

description:
105
Canis familiaris

value: Golden Retriever


title: GT79_W4_T


title: 108_Doberman Pinscher_Acute_GDV_Female

description:
108
Canis familiaris

value: Doberman Pinscher

value: Female


title: CLL1_Het

description:
CLL expression tpm.txt
CLL1_Het


title: GT79_DO_P

value: Human skin

value: Day 0

value: Untreated (P)


title: iPSC.rna_seq.Ctrl.day7.rep1

value: induced pluripotent stem cell


title: 103_Doberman Pinscher_Acute_GDV_Male

description:
103
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: GT79_DO_T

value: Untreated (T)


title: iNeuron.rna_seq.E2F7_NGN3.day6.rep3

value: TetO-NGN3 + TetO-E2F7


title: GT77_W8_T

value: Week 8

value: Treatment


title: GT77_W8_P

value: Placebo


title: 101_Golden Retriever_Acute_GDV_Male

description:
101
Canis familiaris


title: iNeuron.rna_seq.RUNX3_NGN3.day6.rep1

value: TetO-NGN3 + TetO-RUNX3


title: iNeuron.rna_seq.RUNX3_NGN3.day6.rep2


title: GT77_W4_P

value: Week 4


title: iNeuron.rna_seq.E2F7_NGN3.day6.rep2


title: SUDHL6

city: Cambridge

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

hyb_protocol: GL.SOP.LAB.131 version b from Almac Diagnostics (diagnostics@almacgroup.com)

data_processing: Standard RMA background correction, quantile normalizsation and median polish summarization (Bolstad et al 2003) on the exon and transcript core probes, resulting in log2 expression estimates.  Affymetrix' Expression Console software was used, with default settings.

source_name: Diffuse large B cell lymphoma

extract_protocol: GL.SOP.LAB.017 version b from Almac Diagnostics (diagnostics@almacgroup.com)

treatment_protocol: No treatment -- baseline measurement of gene expression without perturbation.

tag: cell line


title: iPSC.rna_seq.Ctrl.day7.rep2

value: Untreated


title: HT

scan_protocol: GL.SOP.LAB.131 version b from Almac Diagnostics (diagnostics@almacgroup.com)

value: HT


title: GT77_W4_T

tag: tissue


title: GT77_DO_P


title: 85_Great Dane_Acute_GDV_Male

description:
85
Canis familiaris

value: Great Dane

value: Male

value: Peripheral blood


title: iNeuron.rna_seq.RUNX3_NGN3.day6.rep3

tag: cell type


title: 102_Poodle Standard_Acute_GDV_Male

description:
102
Canis familiaris

value: Poodle Standard


title: MSC from healthy bone marrow donor 29

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by using the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).  Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

source_name: MSC from healthy bone marrow donor

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: BM-MSCs were obtained as previously described (Guilloton F, Blood 2012).

extract_protocol: RNA extraction was  performed using RNEasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: MSC were expanded from bone marrow mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

tag: status

value: Healthy donor

value: Bone marrow

value: In vitro expanded bone marrow mesenchymal stroma cells


title: 92_German Shepherd Dog_Acute_GDV_Male

description:
92
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV


title: GT77_DO_T

value: Human skin

value: Day 0

value: Untreated (T)


title: iNeuron.rna_seq.LHX8_NGN3.day6.rep3

value: induced pluripotent stem cell

value: TetO-NGN3 + TetO-LHX8