title: invasive RB, biological rep2

city: Chennai

first: Sailaja

middle: V

last: Elchuri

state: Tamil Nadu

address: No18, College Road, Nungambakkam

department: Nanobiotechnology

institute: Vision Research Foundation

description: Gene expression data from RB primary tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console™ Software 1.3.1  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: RB primary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
tissue collection: the Retina and Tumor tissues were collected and stored in -80°C
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: invasive retinoblastoma

tag: age

value: 2 years


title: H1_EDECs_100nM_inhib

status: Public on Jun 30 2018

type: RNA

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array

data_processing: The data were normalized using RMA normalization from R/Bioconductor

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: endoderm derived epithelial cells (EDECs) treated with gamma-secretase inhibitor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: H1 ESC were differentiated intohepatocyte like cells (HLCs) as described previously (Graffmann et al. 2016). To induce endoderm derived epithelial cells (EDEC) differentiation, hepatic endoderm cells were split and plated at a low density 25,000/cm² onto matrigel coated plates on day 9 of the differentiation.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: In order to dissect the role of Notch signalling for EDEC development, cells were treated with 100 nM y-secretase inhibitor 1 after splitting into low density

tag: cell type

value: EDECs

tag: treatment

value: gamma-secretase inhibitor


title: Heart3

city: Chicago

first: Michael

last: Carrithers

state: IL

address: 912 S Wood

department: Neurology

country: USA

institute: University of Illinois

hyb_protocol: Sample were hybridized to the human transcriptome array (HTA 2.0; Affymetrix) and scanned at the University of Wisconsin Biotechnology Center (Molecular biology and microarray core facility)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: NetAffx and Transcription Array Console (Affymetrix)

source_name: pooled donor RNA

label_protocol: cRNA was synthesized and labeled according to the manufacturer's instruction (Affymetrix) at the University of Wisconsin Biotechnology Center

growth_protocol: Human macrophages were differentiated in m-CSF containing media; human DRG and heart RNA from Clontech

extract_protocol: Qiagen Rneasy column purification

treatment_protocol: plus minus veratrdine (2 hrs), DMSO vehicle, or cytosolic poly I:C

tag: sample type

value: pooled donor RNA


title: 54_Treg

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

hyb_protocol: Affymetrix® GeneChip® Hybridization Oven 645 at 45° C and 60 RPM for 16.5 hours overnight. Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: Scanned with the 7G Affymetrix® GeneChip® Scanner 3000.

data_processing:
Raw intensity CEL files were imported into Expression Console software (Affymetrix, USA), and CHP files were generated for gene-level analysis. CHP files were imported into Transcriptome Analysis Console software (Affymetrix, USA).
CHP files include log2 GC-RMA signals.

label: Biotin

organism: Mus musculus

source_name: spleen

label_protocol: Samples were then labeled with biotin using TdT (30U/µL), provided in the GeneChip® WT PLUS Reagent Kit.

growth_protocol: VitD high and low diet.

extract_protocol: RNeasy Qiagen mini kit.

treatment_protocol: Spleen cell isolation and sorting.

value: CD4 Treg

tag: strain/background

value: PWD

tag: Sex

value: Female

tag: diet

value: VitD low


title: invasive RB, biological rep1

country: India

tag: tissue

value: 18 months


title: 51_Treg

value: VitD high


title: invasive RB, biological rep3


title: [C05INF] Patient C05 inflamed mucosa

type: genomic

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description: Sample name in processed data: C05INF

hyb_protocol: ULS-labeled tumor and genomic reference DNA was hybridized on Agilent SurePrint G3 Human CGH Microarrays 4 X 180 K or 8 X 60 K (Agilent), according to the manufacturer's protocol version 3.1.

scan_protocol: Slides were scanned with microarray scanner G2565BA (Agilent).

data_processing:
Images were analyzed by Feature Extraction software version 10.7.1.1 (Agilent). The aCGH data were visualized and analyzed using Nexus Copy Number software version 8.0 (BioDiscovery, Inc., El Segundo, CA, USA).
value definition in data matrix: Log2(copy number of segment/2)

molecule: genomic DNA

source_name: inflamed mucosa

label_protocol: Isolated FFPE DNA was labeled using the Genomic DNA ULS Labeling Kit (Agilent) according to the manufacturer's protocol version 3.1. Sex-matched human genomic DNA (Promega) was used as reference. Tumor DNA was labeled with ULS-Cy3 and genomic reference DNA with ULS-Cy5, respectively.

extract_protocol: DNA was isolated from formalin-fixed paraffin-embedded tissue after histopathologic determination of tumor areas on H&E sections, avoiding foci of inflammation as well as foci of high mucin and low cellular content. Tissue was deparaffinized in 1 ml of Histochoice Clearing Agent (Amresco, Solon, OH) in a thermomixer at 65 °C and two rounds of agitations at 1,100 rpm for 20 min. The tissue pieces were then washed with 1 ml of 50% ethanol/TE buffer and air dried before incubation in 400 ul of 1 M sodium thiocyanate at 65 °C, followed by agitation at 450 rpm for 2 hr. After washing once in 400 ul of TE buffer, Proteinase K digestion, RNase A treatment, and subsequent spin column purification of the extracted DNA were done using DNeasy Blood and Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA concentration was measured by fluorometric quantitation (Qubit 3.0 Fluorometer, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies). DNA integrity was evaluated based on Bioanalyzer traces (2100 Bioanalyzer Instrument, Agilent) using the High Sensitivity DNA kit (Agilent).

value: inflamed mucosa

tag: sample preparation

value: FFPE

tag: crc etiology

value: Crohn's disease

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

value: male

tag: ajcc stage

value: IV

tag: carcioma associated to fistula

tag: special histology

tag: microsatellite/hypermutation status

value: microsatellite stable

source_name: normal reference DNA

tag: manufacturer

value: Promega


title: 50_Treg


title: [C05CA] Patient C05 carcinoma

description: Sample name in processed data: C05CA

source_name: carcinoma

value: carcinoma

value: no


title: [C04INF] Patient C04 inflamed mucosa

description: Sample name in processed data: C04INF

value: II


title: 42_Treg


title: DRG3

value: pooled donor RNA


title: 41_Treg

value: CD4 Treg


title: Heart2


title: non invasive RB, biological rep2

value: non-invasive retinoblastoma

tag: age

value: 2 years


title: MDM4

source_name: human macrophage

value: healthy donor


title: [C03CA] Patient C03 carcinoma

description: Sample name in processed data: C03CA

value: I


title: [C17CA] Patient C17 carcinoma

description: Sample name in processed data: C17CA

value: III


title: adult retina, biological rep3

description: Gene expression data from retina

source_name: Cadaveric Retina

value: retina

value: 17 years


title: DRG2


title: H1_HLCs

source_name: hepatocyte-like cells (HLCs) derived from human embryonic stem cells

tag: cell type

value: HLCs


title: 44_Treg

value: PWD

value: Female

value: VitD low


title: Class III miRNA rep-2

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description:
raw files: 0_ are Hy3; 1_ are Hy5
The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 1000 ng total RNA from sample and control was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled control RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 11 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for various species registered in the miRBASE version 16.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). The probes were annotated according to miRBase 16. The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled control RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 11 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for various species registered in the miRBASE version 16.0 at the Sanger Institute.

organism: Drosophila melanogaster

source_name: Class III Peripheral nervous system (PNS)

label_protocol: 1000 ng total RNA from sample(Class I, Class III and Class IV RNA) and control was labelled with Hy3 and Hy5 fluorescent label,respectively,using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: The isolation and purification of Class I, Class III and Class IV da neurons was performed as previously described (Iyer et al., 2009). Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL80ppk.1.9; GAL4221 (CI), GAL80ppk.1.9, GAL4ppk,(CIII) or GAL4ppk.1.9 (CIV)  drivers were collected and washed several times in ddH20. The larvae were then rinsed in RNAse away, ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate is then incubated with superparamagnetic beads (Dynabeads MyOne Streptavidin T1, Invitrogen) coupled with biotinylated mouse anti-CD8a antibody (eBioscience) for 60 minutes. Finally the da neurons attached to the magnetic beads were then separated using a powerful magnetic field. The isolated neurons were washed at least five times with PBS to remove any potential non-specific cells and the quality and purity of isolated neurons was assessed under a stereo-fluorescent microscope equipped with phase contrast for examining the number of fluorescent vs. non-fluorescent cells. Only if the isolated cells were free of cellular debris and non-specific (i.e. non-fluorescing) contaminants were they retained. The purified CI and C-IV neuron populations were then lysed in miRCURY™ (Exiqon) RNA lysis buffer followed by storage at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

tag: developemental stage

value: Third Instar Larvae

tag: strain background

value: Oregon-R

tag: genotype/variation

value: GAL80ppk.1.9, GAL4ppk,UAS-mCD8::GFP

tag: tissue type

value: Dendritic arborization neuron of PNS

source_name: Whole Larvae


title: adult retina, biological rep2

description: Gene expression data from retina

value: 12 years


title: 56_Treg

value: CD4 Treg

tag: strain/background

tag: Sex

value: Male

tag: diet


title: [C07INF] Patient C07 inflamed mucosa

description: Sample name in processed data: C07INF

tag: tissue

value: inflamed mucosa

tag: sample preparation

value: FFPE

tag: crc etiology

value: Crohn's disease

value: female

value: microsatellite stable

value: Promega


title: MDM2

tag: sample type

value: healthy male


title: Heart1

value: pooled donor RNA


title: adult retina, biological rep1

description: Gene expression data from retina

value: retina

value: 26 years


title: 23_Treg

value: VitD low


title: 5_Treg


title: MDM1

value: healthy female


title: [C02CA] Patient C02 carcinoma

description: Sample name in processed data: C02CA

value: carcinoma

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

value: male

tag: ajcc stage

value: II

tag: carcioma associated to fistula

value: yes

value: mucinous


title: 64_Treg

value: CD4 Treg

value: Male

value: VitD high


title: DRG1


title: [C01LN] Patient C01 lymph node metastasis

description: Sample name in processed data: C01LN

source_name: lymph node metastasis

value: lymph node metastasis

value: FFPE

value: Crohn's disease

value: III

tag: special histology

tag: microsatellite/hypermutation status

tag: manufacturer


title: 20_Treg

tag: cell type


title: [C01INF2] Patient C01 inflamed mucosa 2

description: Sample name in processed data: C01INF2

value: inflamed mucosa

value: microsatellite stable

value: Promega


title: 21_Treg


title: MDM3

value: healthy male


title: [C01INF1] Patient C01 inflamed mucosa 1

description: Sample name in processed data: C01INF1


title: 61_Treg

value: Female

value: VitD low


title: [C01DYS] Patient C01 dysplasia

description: Sample name in processed data: C01DYS

source_name: dysplasia

value: dysplasia

value: male


title: Meg_Cont_rep4

city: Fukuoka

first: Taro

last: Tochigi

address: Maidashi

country: Japan

institute: Kyushu university

description: Gene expression of megakaryocytes generated in the absence of lenalidomide

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies).

source_name: Megakaryocyte, control, replicate 4

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized with Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using Isogen2 (NIPPON GENE) according to the manufacturer's instructions.

treatment_protocol: Hematopoietic stem/progenitor cells from healthy volunteers were cultured for 10 days in IMDM supplemented with 20% BIT, low-density lipoprotein, and 2-mercaptoethanol in the presence of cytokine cocktail including SCF, TPO, IL-6, IL-9.10 µM lenalidomide was added into the media where indicated. All of the cultures were incubated at 39ºC in a humidified chamber under 10% CO2.

value: Hematopoieti stem/progenitor cells-derived megakaryocyte


title: [C01CA2] Patient C01 carcinoma 2

description: Sample name in processed data: C01CA2

value: carcinoma

value: no

value: mucinous


title: 10_Treg

value: CD4 Treg


title: 60_Treg


title: 1_Treg

value: Male

value: VitD high


title: [C01CA3] Patient C01 carcinoma 3

description: Sample name in processed data: C01CA3

value: FFPE

value: Crohn's disease

value: mucinous, signet ring


title: 9_Treg


title: ADPKD patients without hemodialysis treatment TN5

city: Lodz

first: Wojciech

last: Fendler

state: Lodzkie

address: 15 Mazowiecka Str.

department: Department of Biostatistics and Tranalational Medicine

country: Poland

institute: Medical University of Lodz

description: No dialysis

data_processing:
The normalization was performed by subtracting avarage from all detected miRNA for each patients. Data analysis were performed using Microsoft Excel 2013.
Fold Dialysis / Controls = 2^(-(mean (Controls) - mean (Dialysis))); Fold No Dialysis / Controls = 2^(-(mean (Controls) - mean (No Dialysis))); Fold Dialysis / No dialysis  = 2^(-(mean (No dialysis) - mean (Dialysis)))

label: SYBR Green

source_name: Serum

label_protocol: PCR arrays with locked nucleic acid-containing primers (miRCURY LNA; Exiqon, Copenhagen, Denmark) for serum profiling were used following the Manufacturer’s instructions. RNA spike-in control (UniSp6) was used to test the efficiency of the reverse transcription reaction. Exiqon real-time PCR human miRNA arrays I and II quantify expression of 752 miRNAs detectable in serum.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: age


title: ADPKD patients without hemodialysis treatment TN22

description: No dialysis

value: female


title: Meg_Cont_rep3

source_name: Megakaryocyte, control, replicate 3


title: 26_Treg


title: Meg_Len_rep3

description: Gene expression of megakaryocytes generated in the presence of lenalidomide

source_name: Megakaryocyte, lenalidomide, replicate 3


title: 57_Treg


title: ADPKD patients without hemodialysis treatment TN2

description: No dialysis


title: Meg_Len_rep4

source_name: Megakaryocyte, lenalidomide, replicate 4


title: Meg_Cont_rep1

source_name: Megakaryocyte, control, replicate 1


title: Meg_Len_rep1

source_name: Megakaryocyte, lenalidomide, replicate 1


title: Meg_Cont_rep2

source_name: Megakaryocyte, control, replicate 2


title: Meg_Len_rep2

source_name: Megakaryocyte, lenalidomide, replicate 2


title: AN24h2_HZ: HZ mice cochlea -24 hours post-noise exposure

city: Madrid

first: Sara

last: Pulido

address: Arturo Duperier, 4.

department: Department of Endocrine and Nervous Systems Pathophysiology

country: Spain

institute: Alberto Sols Biomedical Research Institute (Spanish National Research Council - Autonomous University of Madrid)

data_processing: The open source NormFinder  v.5 software was used to identify a pair of stable genes, which were Bag1 and Sesn2, used as reference genes for the normalization of the data. Normalization was performed using the geometric mean normalization method and the data subsequently  filtered to discard the genes whose expression was undetermined (Ct values > 35) in at least 90 % of the samples in the dataset.

source_name: Cochlea

label_protocol: Genes involved in p53 Signaling Pathway were studied with the “Mouse Inflammasomes RT² Profiler PCR Array” (PAMM-097ZA, SABiosciences Corp., Frederick, MD, USA). It includes a panel of 84 target genes and 5 housekeeping genes. First-strand cDNA was synthesised using the RT2 first strand kit (C-03, SABiosciences Corp.) and PCR arrays were then processed on an Applied Biosystems 7900HT Real-Time PCR System, to obtain the Ct values.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro Kit after cochleae homogenisation.

treatment_protocol: Six month-old wild type and Igf1 heterozygous mice were exposed to a violet swept sine noise (frequency range 2–20 kHz) at 110 dB SPL for 30 minutes.

value: Cochlea

tag: genotype

value: Igf1 heterozygous

value: 6 months

tag: noise insult

value: 24 hours post-noise exposure


title: non invasive RB, biological rep3

source_name: RB primary tumor

value: non-invasive retinoblastoma

value: 2 years


title: AN24h3_WT: WT mice cochlea -24 hours post-noise exposure

value: wild type


title: ADPKD patients without hemodialysis treatment TN3

description: No dialysis

tag: Sex


title: AN24h1_HZ: HZ mice cochlea -24 hours post-noise exposure


title: [C01CA1] Patient C01 carcinoma 1

description: Sample name in processed data: C01CA1

source_name: carcinoma

value: carcinoma

value: male

value: III

value: microsatellite stable

source_name: normal reference DNA

value: Promega


title: AN24h3_HZ: HZ mice cochlea -24 hours post-noise exposure


title: ADPKD patients without hemodialysis treatment TN6

description: No dialysis


title: [C02INF] Patient C02 inflamed mucosa

description: Sample name in processed data: C02INF

source_name: inflamed mucosa

value: inflamed mucosa

value: II


title: 34_Treg

source_name: spleen

value: CD4 Treg

tag: strain/background

value: PWD

value: Female

tag: diet

value: VitD low


title: 8_Treg

value: VitD high


title: 7_Treg


title: AN24h2_WT: WT mice cochlea -24 hours post-noise exposure

tag: tissue

value: Cochlea

value: 6 months


title: 27_PWD_M_B_4_

value: CD4 T effector

value: Male


title: 15_PWD_M_B_3_


title: ADPKD patients without hemodialysis treatment TN23

description: No dialysis

value: female


title: AN24h1_WT: WT mice cochlea -24 hours post-noise exposure

value: wild type

value: 24 hours post-noise exposure


title: 14_PWD_M_B_2_


title: AN2h1_HZ: HZ mice cochlea -2 hours post-noise exposure

value: Igf1 heterozygous

value: 2 hours post-noise exposure


title: ADPKD patients without hemodialysis treatment TN7

description: No dialysis

value: male


title: ADPKD patients without hemodialysis treatment TN4

description: No dialysis


title: 13_PWD_M_B_1_


title: ADPKD patients without hemodialysis treatment TN24

description: No dialysis


title: C3HZ: HZ mice cochlea - without noise exposure

description: control

value: without noise exposure


title: ADPKD patients without hemodialysis treatment TN1

description: No dialysis


title: ADPKD patient on hemodialysis therapy TN16

description: Dialysis


title: AN2h1_WT: WT mice cochlea -2 hours post-noise exposure


title: 46_PWD_M_A_3_


title: 47_PWD_M_A_4_


title: ATSC_IRI_rep03

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Adipose tissue deirved mesenchymal stem cells, ischemia-reperfusion injury, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Agilent One-Color Quick Amp labeling kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA extraction was performed using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and the extraction was done according to the manufacturer’s instructions. The quantity and quality of each RNA sample was determined using NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) RNA Pico Kit.

treatment_protocol: ATSC were harvested from the subcutaneous fat of male Sprague-Dawley rats. The subcutaneous adipose tissue was washed \with sterile phosphate buffered saline (PBS) and then treated with 0.1% collagenase in PBS for 30 minutes at 37°C with gentle agitation.  After filtration through 100-μm mesh filter to remove debris, the filtrate was washed three times and completely suspended in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine. The cultures were maintained in an incubator with a humidified atmosphere of 5% CO2.

value: Adipose tissue

value: mesenchymal stem cells


title: ATSC_non-IRI_rep03

source_name: Adipose tissue deirved mesenchymal stem cells, non-ischemia-reperfusion injury, replicate 3


title: ATSC_IRI_rep02

source_name: Adipose tissue deirved mesenchymal stem cells, ischemia-reperfusion injury, replicate 2


title: ATSC_non-IRI_rep01

source_name: Adipose tissue deirved mesenchymal stem cells, non-ischemia-reperfusion injury, replicate 1


title: ATSC_non-IRI_rep04

source_name: Adipose tissue deirved mesenchymal stem cells, non-ischemia-reperfusion injury, replicate 4


title: ADPKD patient on hemodialysis therapy TN14

description: Dialysis

source_name: Serum


title: 12_PWD_M_A_2_

value: PWD


title: C2HZ: HZ mice cochlea - without noise exposure

description: control


title: AN2h2_HZ: HZ mice cochlea -2 hours post-noise exposure


title: ATSC_IRI_rep01

source_name: Adipose tissue deirved mesenchymal stem cells, ischemia-reperfusion injury, replicate 1


title: ADPKD patient on hemodialysis therapy TN19

description: Dialysis


title: AN2h2_WT: WT mice cochlea -2 hours post-noise exposure


title: 11_PWD_M_A_1_


title: Dap5_rep2_total_polysome

type: SRA

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

library_source: transcriptomic

data_processing:
Sequenced reads were aligned and quantified using STAR v2.6.0a using UCSC hg19 genome
counts for heavy and moderate labeled ns within each sample were added for comparison to heavy Dap5 counts
Differential analysis was performed using voom normalization / Limma linear modeling
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each gene of each sample

growth_protocol: MDA-MB-231 cells containing either stable doxycycline inducible non-silencing (NS) construct or sh Dap5 were grown to 70-80 % confluency.

extract_protocol:
Cells were lysed in buffer intended for isolation of cytoplasmic fractions and enrichment of ribosomes.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Cells were treated to with 1ug/mL of doxycycline for 6 days before polysome profiling was performed.

tag: cell line

tag: shRNA

value: sh Dap5


title: Dap5_rep2_heavy_polysome


title: non invasive RB, biological rep1

value: non-invasive retinoblastoma

value: 2 months


title: 53_PWD_F_B_4_

value: Female

value: VitD low


title: Dap5_rep2_light_polysome


title: ADPKD patient on hemodialysis therapy TN11

description: Dialysis


title: ADPKD patient on hemodialysis therapy TN21

description: Dialysis


title: Dap5_rep1_total_polysome


title: Dap5_rep1_heavy_polysome


title: C3WT: WT mice cochlea - without noise exposure

description: control

value: Cochlea

value: 6 months


title: 45_PWD_F_B_3_

value: CD4 T effector


title: C2WT: WT mice cochlea - without noise exposure

description: control

value: wild type


title: Dap5_rep1_light_polysome


title: C1HZ: HZ mice cochlea - without noise exposure

description: control


title: NS_rep2_total

value: non-silencing (NS) construct


title: ADPKD patient on hemodialysis therapy TN10

description: Dialysis

value: female


title: C1WT: WT mice cochlea - without noise exposure

description: control


title: NS_rep2_moderate_polysome


title: 39_PWD_F_B_1_


title: ATSC_in-vitro_rep1

source_name: Basal expression of the ATSC, in in-vitro culture, replicate 1


title: ADPKD patient on hemodialysis therapy TN13

description: Dialysis


title: NS_rep2_light_polysome


title: 52_PWD_F_A_4_

value: VitD high


title: [C04CA1] Patient C04 carcinoma 1

description: Sample name in processed data: C04CA1

value: carcinoma

tag: sample preparation

value: FFPE

tag: crc etiology

value: Crohn's disease

tag: age at crc diagnosis, years

value: male

value: II

value: no

value: mucinous

value: microsatellite stable

value: Promega


title: ADPKD patient on hemodialysis therapy TN15

description: Dialysis


title: [C04CA2] Patient C04 carcinoma 2

description: Sample name in processed data: C04CA2

tag: duration of cd at crc diagnosis, years

tag: ajcc stage

tag: carcioma associated to fistula


title: 50_PWD_F_A_3_

value: PWD

value: Female


title: NS_rep2_heavy_polysome


title: ADPKD patient on hemodialysis therapy TN20

description: Dialysis


title: 43_PWD_F_A_2_


title: 40_PWD_F_A_1_


title: ADPKD patient on hemodialysis therapy TN12

description: Dialysis


title: Healthy control 67

description: Controls


title: 44_PWD_F_B_2_

value: VitD low


title: NS_rep1_moderate_polysome


title: 65_B6_M_B_3_

value: CD4 T effector

value: Male


title: 66_B6_M_B_4_


title: Healthy control 5

description: Controls


title: Healthy control 58

description: Controls


title: Wild type_Col-0

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

country: China

institute: Guizhou University

description: Gene expression data from 2-week-old seedlings of the wild-type(col)

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis ATH1 Genome  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Genesystem Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: Arabidopsis wild-type (Columbia-0:Col )

growth_protocol: seedlings of the wild-type NO and duf761-1, and seedlings of the Col-0 and OE6, grown on 1/2 MS medium containing 2% sucrose at 22˚C  under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1.

extract_protocol: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany)

value: whole plant

tag: cultivar

value: wildtype

value: 2-week-old seedlings


title: duf761-1 mutant

description: Gene expression data from 2-week-old seedlings of the duf761-1 mutant grown on 1/2 MS medium containing 2% sucrose at 22˚C

source_name: Arabidopsis duf761-1 mutant RATM11-0975-1_H

value: Nössen

value: duf761-1 mutant


title: OE6

description: Gene expression data from 2-week-old seedlings of the OE6

source_name: Transgenic plant overexpressing DUF761-1 (OE6) plants

value: duf761-1 over-expression


title: 22_B6_M_B_2_

tag: cell type


title: 5_B6_M_B_1_


title: NS_rep1_heavy_polysome

value: non-silencing (NS) construct


title: Healthy control 31

description: Controls

value: female

tag: age


title: Wild type_NO

description: Gene expression data from 2-week-old seedlings of the wild-type(NO) grown on 1/2 MS medium containing 2% sucrose at 22˚C

source_name: Arabidopsis wild-type (Nössen:NO)

tag: genotype


title: NS_rep1_total


title: Healthy control 3

description: Controls

value: male


title: Cldn18 kock-out  [5511168014_G]

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

description:
Replicate 1
5511168014_G

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: lung AT2 cells

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

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

tag: strain

value: mixed 129S6/SvEvTac, C57BL/6J, Balb/c

value: lung AT2 cells

tag: genotype/variation

value: Cldn18 kock-out


title: Cldn18 wild-type [5511168014_H]

description:
Replicate 4
5511168014_H

value: Cldn18 wild-type


title: 64_B6_M_A_4_

tag: strain/background

tag: Sex

value: VitD high


title: Cldn18 kock-out  [5511168014_F]

description:
Replicate 2
5511168014_F


title: Healthy control 19

description: Controls


title: NS_rep1_light_polysome


title: Healthy control 18

description: Controls


title: 3_B6_M_A_2_

tag: diet


title: Cldn18 wild-type [5511168014_E]

description:
Replicate 2
5511168014_E


title: Pro-B Mll1 KO, rep3

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description: Gene expression data with or without Mll1 deletion in pro-B cells

hyb_protocol: The labeled products were hybridized to Affymetrix mouse 430 2.0 Arrays at the Dartmouth Genomics and Microarray Laboratory

scan_protocol: Arrays were scanned using the Genechip 3000 7G scanner and exported as standard .CEL files

data_processing: Expression was extracted using Bioconductor in R using the GCRMA package

source_name: pro-B cell

label_protocol: Input RNA was 250ng and labeled using the Affymetrix GeneChip 3' IVT PLUS Reagent Kit

growth_protocol: Bone marrow was crushed, lineage+ cells were depleted with dynal beads and viable (PI excluding) Hardy Fraction B (IgM-/CD43+/CD24+/BP-1-) cells were sorted using a FACS Aria. Cells were transferred to Trizol and processed to isolate total RNA.

extract_protocol: Cells were lysed in Trizol (Invitrogen) and total RNA was further purified using  RNeasy mini columns (Qiagen). RNA was quantified with a Bioanalyzer 2100 (Agilent).

tag: gender

value: 3 weeks postnatal


title: Pro-B Mll1 KO, rep4


title: 1_B6_M_A_1_

value: CD4 T effector


title: Cldn18 wild-type [5511168014_D]

description:
Replicate 1
5511168014_D


title: Cldn18 kock-out  [5511168014_C]

description:
Replicate 4
5511168014_C


title: Pro-B Mll1 KO, rep1


title: Pro-B Mll1 KO, rep2


title: Healthy control 2

description: Controls


title: 59_B6_F_B_3_

value: Female

value: VitD low


title: 10_B6_F_B_2_


title: Healthy control 17

description: Controls


title: 9_B6_F_B_1_


title: Cldn18 wild-type [5511168014_B]

description:
Replicate 3
5511168014_B


title: 8_B6_F_A_2_


title: 26_B6_F_A_3_


title: 60_B6_F_B_3_


title: 7_B6_F_A_1_


title: 63_B6_M_A_3__

value: Male


title: 58_B6_F_A_4_


title: Cldn18 kock-out  [5511168014_A]

description:
Replicate 3
5511168014_A


title: Pro-B Control, rep3


title: Pro-B Control, rep1


title: CHINFAM-151: Blood_SCZ_Non_Famine51

status: Public on Jun 29 2018

city: Utrecht

first: M

middle: P

last: Boks

address: Heidelberglaan 100

department: Psychiatry

country: Netherlands

institute: UMC Utrecht

description: Human whole blood DNA methylation sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Intensity read outs, quality control parameters and methylation measures were obtained from the genome studio software. X chromosome, Y chromosome, and non-specific binding probes were removed. Failed probes were excluded based on a detection p-value larger than 0.001 and bead count lower than 5. In addition, probes with SNPs of Minor Allele Frequency(MAF) larger than 5 percent within 10 base pairs of the primer were excluded after constructing ancestry estimates based on their principal components as proposed by Barfield et al (lists of CpG sites available at http://genetics.emory.edu/research/conneely/annotation-r-code.html). DNA methylation analysis was performed in R, using minfi (providing routines to handle Illumina BeadStudio data and functional normalization) and bumphunter (for statistical routines). The data was normalized to remove systematic differences in overall signal distribution using functional normalization as implemented in the minfi package.
Average M value after functional normalization
Unmethylated and methylated signal intensities

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood with the Gentra Puregene Kit (Qiagen, Valencia, CA, USA) following manufacturer's protocol. DNA concentration and integrity was assessed using riboGreen and BioAnalyser.

treatment_protocol: Bisulphite conversion was conducted with Zimo kits (ZYMO Research, Orange, CA, USA) using standard procedures.

tag: tissue

value: Whole blood

tag: schizophrenia

value: TRUE

tag: famine

value: No

tag: group

value: M

tag: nk

tag: bcell

tag: mono

tag: city

value: FALSE

tag: sentrix

tag: position


title: CHINFAM-146: Blood_SCZ_Non_Famine49

tag: age


title: CHINFAM-153: Blood_CTR_Non_Famine54

value: F


title: CHINFAM-144: Blood_CTR_Famine23

value: Yes


title: CHINFAM-150: Blood_CTR_Non_Famine53


title: CHINFAM-142: Blood_SCZ_Non_Famine46


title: CHINFAM-139: Blood_CTR_Famine22


title: CHINFAM-140: Blood_CTR_Non_Famine51


title: CHINFAM-145: Blood_SCZ_Non_Famine48


title: CHINFAM-148: Blood_CTR_Famine24


title: Pro-B Control, rep2

tag: strain

value: female

tag: genotype


title: Healthy control 14

description: Controls


title: Pro-B Control, rep4


title: CHINFAM-143: Blood_SCZ_Non_Famine47


title: CHINFAM-135: Blood_CTR_Non_Famine49


title: CHINFAM-137: Blood_CTR_Famine21


title: CHINFAM-133: Blood_CTR_Famine20


title: CHINFAM-152: Blood_CTR_Famine25


title: CHINFAM-132: Blood_SCZ_Famine21


title: ATSC_non-IRI_rep02

source_name: Adipose tissue deirved mesenchymal stem cells, non-ischemia-reperfusion injury, replicate 2

value: Adipose tissue

tag: cell type

value: mesenchymal stem cells


title: CHINFAM-131: Blood_CTR_Non_Famine48


title: CHINFAM-149: Blood_CTR_Non_Famine52


title: CHINFAM-147: Blood_SCZ_Non_Famine50


title: CHINFAM-141: Blood_SCZ_Non_Famine45


title: CHINFAM-130: Blood_SCZ_Famine20


title: CHINFAM-129: Blood_SCZ_Non_Famine43


title: CHINFAM-128: Blood_CTR_Famine19


title: CHINFAM-138: Blood_CTR_Non_Famine50


title: CHINFAM-127: Blood_SCZ_Famine19


title: CHINFAM-125: Blood_SCZ_Non_Famine42


title: CHINFAM-122: Blood_CTR_Non_Famine45


title: CHINFAM-136: Blood_SCZ_Famine22


title: CHINFAM-126: Blood_CTR_Non_Famine47


title: CHINFAM-120: Blood_SCZ_Famine18


title: CHINFAM-124: Blood_CTR_Non_Famine46


title: CHINFAM-119: Blood_SCZ_Non_Famine40


title: CHINFAM-123: Blood_SCZ_Non_Famine41


title: CHINFAM-117: Blood_CTR_Non_Famine43


title: CHINFAM-118: Blood_CTR_Non_Famine44


title: CHINFAM-134: Blood_SCZ_Non_Famine44


title: CHINFAM-115: Blood_SCZ_Non_Famine39


title: CHINFAM-112: Blood_SCZ_Famine17


title: CHINFAM-111: Blood_SCZ_Famine16


title: CHINFAM-116: Blood_CTR_Famine17


title: CHINFAM-114: Blood_CTR_Non_Famine42


title: CHINFAM-110: Blood_SCZ_Non_Famine38


title: CHINFAM-109: Blood_CTR_Non_Famine40


title: CHINFAM-108: Blood_SCZ_Non_Famine37


title: CHINFAM-107: Blood_SCZ_Non_Famine36


title: CHINFAM-105: Blood_CTR_Famine15


title: CHINFAM-106: Blood_CTR_Famine16


title: CHINFAM-101: Blood_CTR_Non_Famine38


title: CHINFAM-100: Blood_SCZ_Non_Famine34


title: CHINFAM-102: Blood_SCZ_Non_Famine35


title: CHINFAM-104: Blood_SCZ_Famine15


title: CHINFAM-121: Blood_CTR_Famine18


title: CHINFAM-98: Blood_CTR_Non_Famine37


title: CHINFAM-97: Blood_CTR_Non_Famine36


title: CHINFAM-96: Blood_SCZ_Non_Famine32


title: CHINFAM-95: Blood_CTR_Famine14


title: CHINFAM-113: Blood_CTR_Non_Famine41


title: CHINFAM-94: Blood_CTR_Non_Famine35


title: CHINFAM-99: Blood_SCZ_Non_Famine33


title: CHINFAM-90: Blood_CTR_Non_Famine33


title: CHINFAM-89: Blood_SCZ_Non_Famine29


title: CHINFAM-88: Blood_CTR_Famine13


title: CHINFAM-87: Blood_SCZ_Famine14


title: CHINFAM-91: Blood_CTR_Non_Famine34


title: CHINFAM-86: Blood_CTR_Non_Famine32


title: CHINFAM-82: Blood_SCZ_Non_Famine27


title: CHINFAM-85: Blood_SCZ_Non_Famine28


title: CHINFAM-84: Blood_CTR_Non_Famine31


title: CHINFAM-93: Blood_SCZ_Non_Famine31


title: CHINFAM-80: Blood_CTR_Non_Famine30


title: CHINFAM-81: Blood_SCZ_Non_Famine26


title: CHINFAM-77: Blood_CTR_Non_Famine27


title: CHINFAM-103: Blood_CTR_Non_Famine39


title: CHINFAM-75: Blood_SCZ_Non_Famine24


title: CHINFAM-76: Blood_SCZ_Non_Famine25


title: CHINFAM-73: Blood_CTR_Non_Famine26


title: CHINFAM-74: Blood_SCZ_Non_Famine23


title: CHINFAM-70: Blood_SCZ_Famine12


title: CHINFAM-69: Blood_SCZ_Non_Famine22


title: CHINFAM-67: Blood_CTR_Famine10


title: CHINFAM-72: Blood_CTR_Non_Famine25


title: CHINFAM-83: Blood_CTR_Famine12


title: CHINFAM-65: Blood_CTR_Non_Famine23


title: CHINFAM-66: Blood_CTR_Non_Famine24


title: CHINFAM-92: Blood_SCZ_Non_Famine30


title: CHINFAM-59: Blood_SCZ_Non_Famine20


title: CHINFAM-60: Blood_CTR_Non_Famine22


title: CHINFAM-63: Blood_SCZ_Famine11


title: CHINFAM-79: Blood_CTR_Non_Famine29


title: CHINFAM-62: Blood_CTR_Famine9


title: CHINFAM-56: Blood_SCZ_Non_Famine18


title: CHINFAM-78: Blood_CTR_Non_Famine28


title: mESC_WT_H3_ChIP

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description: WT H3 ChIP

library_source: genomic

data_processing:
Reads were mapped to the mm10 genome in paired-end mode with bowtie2 (Galaxy Version 2.3.0.1) using parameters: --sensitive, --end-to-end
Coverage files were generated with deepTools2 (Galaxy Version 2.5.1.0.0) bamCompare, binsize of 2. Duplicate reads and reads with a mapping quality < 10 were removed, the X chromosome was ignored for scaling.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: bigWig files, containing H4K16ac ChIP log2foldchange-normalized over H3 input ChIP

source_name: mouse embryonic stem cells

growth_protocol: All cell culture was performed in a humidified incubator at 37C and 5% CO2. The parental male Mouse embryonic stem cells were kindly donated by the Buhler laboratory, FMI Basel  and cultivated on Attachment Factor in 2i Media: KnockOutTM DMEM supplemented with 15% KnockOutTM Serum Replacement, 0.1mM MEAA,1nM Na Pyruvate, 0.1mM 2-mercaptoethanol, 4mM GlutaMAXTM, 5 ug/ml Insulin (sigma I0516), 50U/ml Pen/Strep, 200U/ml LIF,  1uM PD0325901 (StemGent 04-0006), 3uM CHIR99021 (StemGent 04-0003)

extract_protocol:
15 cm dishes were fixed in PBS containing 1% methanol-free formaldehyde for 8 min at RT. Chromatin was purified using Paro-washes as described in Baubec et al., Nature. Chromatin was fragmented using MNase as for the Drosophila ChIP protocol but digesting at 37C and adding SDS to 0.1% final concentration after addition of EDTA-containing buffer. Cleared chromatin was incubated for 6-8h with antibody, before addition of Protein A dynabeads for 1h. Beads were washed 3 x in RIPA, 1 x LiCl-DOC and 2 x in TE buffer. Chromatin was further processed according to standard procedures.
NEB Next Ultra II

tag: chip antibody

value: H3(Active Motif, MABI 0301, 39763)

value: male

tag: genotype/variation

value: wild type


title: mESC_Msl2KO_H4K16ac_ChIP

description:
mESC_Msl2KO_K16ac_vs_H3_log2FC.bw
Msl2 KO H4K16ac ChIP

value: H4K16ac(Merck Milipore, 07-329)

tag: gender


title: mESC_WT_H4K16ac_ChIP

description:
mESC_WT_K16ac_vs_H3_log2FC.bw
WT H4K16ac ChIP


title: CHINFAM-55: Blood_CTR_Non_Famine20

tag: tissue


title: mESC_Msl2KO_H3_ChIP

description: Msl2 KO H3 ChIP


title: CHINFAM-71: Blood_SCZ_Famine13

tag: schizophrenia


title: CHINFAM-68: Blood_CTR_Famine11

tag: famine


title: CHINFAM-52: Blood_SCZ_Non_Famine17

tag: group


title: CHINFAM-54: Blood_CTR_Non_Famine19

tag: nk


title: CHINFAM-53: Blood_CTR_Non_Famine18

tag: bcell


title: CHINFAM-61: Blood_CTR_Famine8

tag: mono


title: CHINFAM-47: Blood_CTR_Non_Famine17

tag: city


title: CHINFAM-58: Blood_CTR_Non_Famine21

tag: sentrix


title: CHINFAM-64: Blood_SCZ_Non_Famine21

tag: position


title: CHINFAM-48: Blood_SCZ_Famine10

tag: age


title: CHINFAM-57: Blood_SCZ_Non_Famine19


title: CHINFAM-44: Blood_SCZ_Non_Famine14


title: CHINFAM-49: Blood_SCZ_Non_Famine16


title: CHINFAM-46: Blood_SCZ_Non_Famine15


title: CHINFAM-43: Blood_CTR_Non_Famine16


title: CHINFAM-50: Blood_CTR_Famine6


title: CHINFAM-42: Blood_SCZ_Non_Famine13


title: CHINFAM-40: Blood_SCZ_Famine8


title: CHINFAM-41: Blood_SCZ_Famine9


title: CHINFAM-51: Blood_CTR_Famine7


title: CHINFAM-45: Blood_CTR_Famine5


title: CHINFAM-39: Blood_CTR_Non_Famine15


title: CHINFAM-38: Blood_CTR_Non_Famine14


title: CHINFAM-37: Blood_CTR_Non_Famine13


title: CHINFAM-35: Blood_SCZ_Famine7


title: CHINFAM-36: Blood_CTR_Non_Famine12


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E169)

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Expression analysis of 6 milk samples from dairy cows with endometritis. Milk cells from dairy cows were collected in cooperation with local conventional dairy farms, as well as the Large Animal Clinic for Internal Medicine and the Clinic for Ruminants and Swine of the University of Leipzig (Faculty of Veterinary Medicine), Germany. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Diseased cows were in their 1st to 8th lactation within 10-220 dpp.

hyb_protocol: Hybridization was performed for 16 hours in a GeneChip® Hybridization Oven 645 (Affymetrix, CA, USA). Afterwards, arrays were washed and stained using the Fluidics Station FS450 (Affymetrix, CA, USA) and the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, CA, USA) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix, CA, USA).

data_processing: Affymetrix microarrays have been analysed by using R and Bioconductor. Background adjustment and between array normalization was performed by Robust Multiarray Average (RMA) with estimation of non-specific probe binding [Jean Wu and Rafael Irizarry with contributions from James MacDonald, Jeff Gentry (2016). gcrma: Background Adjustment Using Sequence Information.]. Only probes with an intensity above background signal and non-specific variance above a pre-defined cutoff were retained for differential expression analysis. In detail, only probes with intensities >= log2(30) in at least 4 of 18 arrays and an interquartile range of IQR>=0.5 passed the non-specific filter [R. Gentleman, V. Carey, W. Huber and F. Hahne (2016). genefilter: methods for filtering genes from high-throughput experiments.]. Linear models were fitted using the R package limma [Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.] and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment [Benjamini, Yoav; Hochberg, Yosef (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B. 57 (1): 289–300.].

organism: Bos taurus

source_name: Milk cells from dairy cows with endometritis

label_protocol: All samples were prepared using the GeneChip®3′ IVT Express Kit (Affymetrix, CA, USA). RNA amplification, cDNA synthesis, labelling and array hybridization were performed according to manufacturer’s instructions using 100 ng total RNA. All samples were concentrated in a lyophilizer for 2 hours. Thereafter, 12 µg labelled RNA was used for fragmentation followed by hybridization on Affymetrix GeneChip® bovine Genome arrays using 10 µg of labelled and fragmented RNA.

extract_protocol: Total RNA was extracted using TRI® Reagent (Sigma-Aldrich, Steinheim, Germany) according to the manufacturer’s protocol. To remove residual genomic DNA, RNA was incubated with RNase-free DNase I (VWR International - Germany GmbH, Darmstadt, Germany) as instructed in the manual. If required, RNA cleanup was performed with RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) to the manufacturer’s protocol. RNA purity and integrity was checked with the Agilent Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using Agilent RNA 6000 Nano Kit. Only samples with an RNA integrity number (RIN) > 6 were used for further analysis.

tag: sample type

value: Milk cell samples


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M91)

description: Expression analysis of 6 milk samples from dairy cows with mastitis. Milk cells from dairy cows were collected in cooperation with local conventional dairy farms, as well as the Large Animal Clinic for Internal Medicine and the Clinic for Ruminants and Swine of the University of Leipzig (Faculty of Veterinary Medicine), Germany. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Diseased cows were in their 1st to 8th lactation within 10-220 dpp.

source_name: Milk cells from dairy cows with mastitis


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E158)


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E157)


title: CHINFAM-34: Blood_SCZ_Non_Famine12


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E108)


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M144)


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M82)


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E156)


title: Expression analysis of milk samples from dairy cows with endometritis (sample 20110816_OnFarm_E177)


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M88)


title: CHINFAM-33: Blood_CTR_Famine4


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M87)


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K74)

description: Expression analysis of 6 control milk samples. Milk cells from healthy dairy cows were collected in cooperation with local conventional dairy farms, as well as the Large Animal Clinic for Internal Medicine and the Clinic for Ruminants and Swine of the University of Leipzig (Faculty of Veterinary Medicine), Germany. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Control animals (2-4 years old, 1st to 3th lactation, one animal 4th and one 8th lactation) showed no clinical signs of disease and had no abnormalities in the udder or milk. Their somatic cell count (SCC) was less than 100,000 cells/ml milk. Most of the control samples were taken during early lactation (10-100 days post-partum, dpp).

source_name: Milk cells from healthy dairy cows


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K69)


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K70)


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K175)


title: Expression analysis of milk samples from dairy cows with mastitis (sample 20110816_OnFarm_M139)


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K165)


title: Expression analysis of milk samples from healthy dairy cows (sample 20110816_OnFarm_K176)


title: CHINFAM-30: Blood_SCZ_Famine6


title: CHINFAM-31: Blood_CTR_Non_Famine11


title: CHINFAM-28: Blood_CTR_Non_Famine10


title: CHINFAM-29: Blood_SCZ_Non_Famine10


title: HCC4_shRNA_CTRL_REP2

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

country: France

institute: Institut Pasteur

hyb_protocol: Subsequent hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit and the manufacturer's protocols were followed. Briefly, each fragmented and labeled single-strand cDNA target sample (approximately 3.5 µg) was individually hybridized to a GeneChip Mouse Gene 2.0 ST Array at 45°C for 16 h in Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix Mouse Gene 2.0 ST array intensity data were preprocessed altogether for the two shRNA experiments (2 shRNA against Prdm5 in ICC, 2 shRNA against Tbx3 in CCC, each with biological duplicates, and two biological duplicates for shRNA control in each cell type, i.e. 12 arrays).
Normalized log-scaled and filtered expression data were further considered for differential analysis with limma.
Please note that sample data table contains the data on which the biological conclusions (described in the study) are based. After RMA normalization, all the probes considered as not-expressed, or ambiguously annotated/unannotated probes were removed and additional normalization considering potential surrogate with SVA was applied, resulting in a reduced data set of 17,668 rows.

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: Cells were grown in DMEM with 10% FCS in 7.5% CO2

extract_protocol: RNA was extracted using the QIAGEN RNAeasy Plus kit according to the manufacturer's instructions.

treatment_protocol: Successful infected cells were selected with puromycin (2.5 µg/ml for HCC and 3.75 µg/ml for ICC). Expression of shRNAs was induced with Doxycyclin (5 µg/ml) 4 starting 4 days before extraction.

tag: strain

tag: cell line source tumor type

value: Hepatocellular carcinoma (HCC)

tag: shRNA


title: CHINFAM-27: Blood_CTR_Non_Famine9


title: HCC4_shRNA_TBX3_2_REP2


title: HCC4_shRNA_TBX3_1_REP1


title: GC2 siFGFR1 3

city: Toulouse

first: VALERIE

last: GOUAZE-ANDERSSON

address: 2 avenue Hubert Curien, CS 5317

department: Glioblastoma radioresistance: from signaling pathways to clinical trials

institute: CRCT

hyb_protocol: All subsequent sample handling, labeling, and GeneChip (Human Gene 2.0 ST arrays, Affymetrix) processing was performed at the Genotoul Get laboratory (Toulouse, France; http://www.get.genotoul.fr).

data_processing: The affymetrix chips were standardized by the RMA method (R software version 3.3.2, Bioconductor version 3.4). The differences between the different conditions were tested using an ANOVA (R software version 3.3.2) corrected for multiple tests using the Benjamini & Hochberg method. The gene lists were compared to different databases GeneOntology C5, Reactome ) using the ZE Autocompare software based on an exact Zelen test.

source_name: glioblastoma

growth_protocol: The GBM samples were processed in order to obtain the corresponding primary neurospheres (NS) cell lines shown by other groups to be enriched in Glioblastoma stem-like cells, neurospheres GSLC lines were maintained in DMEM-F12 (Lonza, Levallois-Perret, France) supplemented with B27 and N2, 25 ng/ml of FGF-2 and EGF at 37 °C in 5% CO2 humidified incubators.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen), and eluted with nuclease-free water.

treatment_protocol: Cells were transfected with different small interfering RNAs (siRNA): an aleatory sequence, SiScramble siRNA  andsiRNAs specific for FGFR1. Cells were transfected with 20 nM of the different siRNAs using the Lipofectamine RNAiMAX transfection reagent according to the manufacturer conditions (Invitrogen).

value: brain

tag: transfection

value: siRNA FGFR1


title: HCC4_shRNA_TBX3_2_REP1

tag: gender


title: HCC4_shRNA_TBX3_1_REP2


title: CHINFAM-32: Blood_SCZ_Non_Famine11

tag: tissue

value: Whole blood

value: TRUE


title: ICC10_shRNA_PRDM5_2_REP2

value: Intrahepatic cholangiocarcinoma (ICC)


title: GC2 siFGFR1 2

scan_protocol: All subsequent sample handling, labeling, and GeneChip (Human Gene 2.0 ST arrays, Affymetrix) processing was performed at the Genotoul Get laboratory (Toulouse, France; http://www.get.genotoul.fr).


title: GC2 siCtl 3

value: siRNA control


title: ICC10_shRNA_CTRL_REP1


title: GC2 siCtl 2


title: CHINFAM-21: Blood_SCZ_Famine5

tag: schizophrenia

value: M


title: CHINFAM-26: Blood_CTR_Non_Famine8

value: FALSE

tag: famine

value: No

value: F


title: ICC10_shRNA_PRDM5_2_REP1

value: female


title: CHINFAM-25: Blood_SCZ_Non_Famine9

tag: group


title: GC2 siFGFR1 1


title: GC2 siCtl 1


title: ICC10_shRNA_CTRL_REP2


title: CHINFAM-24: Blood_SCZ_Non_Famine8

tag: nk


title: ICC10_shRNA_PRDM5_1_REP2


title: CHINFAM-20: Blood_SCZ_Non_Famine7

tag: bcell


title: CHINFAM-17: Blood_CTR_Non_Famine7

tag: mono


title: CHINFAM-23: Blood_SCZ_Famine5

value: Yes

tag: city


title: ICC10_shRNA_PRDM5_1_REP1


title: CHINFAM-16: Blood_SCZ_Non_Famine5

tag: sentrix


title: CHINFAM-22: Blood_CTR_Famine3

tag: position


title: CHINFAM-18: Blood_SCZ_Non_Famine6

tag: age


title: CHINFAM-14: Blood_CTR_Non_Famine6


title: CHINFAM-19: Blood_CTR_Famine2


title: CHINFAM-15: Blood_SCZ_Famine4


title: CHINFAM-13: Blood_CTR_Non_Famine5


title: CHINFAM-12: Blood_SCZ_Famine3


title: CHINFAM-11: Blood_CTR_Famine1


title: CHINFAM-08: Blood_SCZ_Non_Famine3


title: CHINFAM-06: Blood_CTR_Non_Famine3


title: CHINFAM-03: Blood_SCZ_Non_Famine1


title: CHINFAM-10: Blood_SCZ_Non_Famine4


title: CHINFAM-04: Blood_CTR_Non_Famine2


title: CHINFAM-05: Blood_SCZ_Non_Famine2


title: CHINFAM-07: Blood_SCZ_Famine2


title: CHINFAM-02: Blood_CTR_Non_Famine1


title: HCC4_shRNA_CTRL_REP1

value: male


title: WT_MF_Serum_rep3

description: WT control serum

data_processing:
Reads were mapped to the mm10 genome using Hisat2 (v2.0.0.0-beta) with default parameters. Only uniquely mapped reads were kept.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.1) and DeepTools2 (v2.4.1)
Primary alignments were counted using featureCounts (v1.4.6-p2)
Differential experesssion analysis was performed using DESeq2 (1.8.2). Only genes with FDR<0.05 in both Msl2 knock-out clones (A2 and D12 as replicates) were considered differentially expressed.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: featureCounts count table output

molecule: polyA RNA

growth_protocol: All cell culture was performed in a humidified incubator at 37°C and 5% CO2. The parental male Mouse embryonic stem cells were kindly donated by the Bühler laboratory, FMI Basel  and cultivated on Attachment Factor in two different ESC culture media.  2i Media: KnockOutTM DMEM supplemented with 15% KnockOutTM Serum Replacement, 0.1mM MEAA,1nM Na Pyruvate, 0.1mM 2-mercaptoethanol, 4mM GlutaMAXTM, 5 μg/ml Insulin (sigma I0516), 50U/ml Pen/Strep, 200U/ml LIF,  1μM PD0325901 (StemGent 04-0006), 3μM CHIR99021 (StemGent 04-0003)  serum media: DMEM supplemented with 15% FCS (PAN, PANSera Lot n. P1302077ES), 0.1mM MEAA,1nM Na Pyruvate, 0.1mM 2-mercaptoethanol, 4mM GlutaMAXTM, 50U/ml Pen/Strep, 400U/ml LIF

extract_protocol:
RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research)
TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: genotype

value: wild-type

tag: culture media

value: serum


title: WT_MF_Serum_rep1

description: WT control serum


title: WT_MF_Serum_rep4

description: WT control serum


title: WT_MF_Serum_rep2

description: WT control serum


title: CHINFAM-01: Blood_SCZ_Famine1


title: DUTCHSCZ-64: Blood_Schizophrenia_15

value: SCZ


title: WT_MF_2i_rep1

description: WT control 2i medium


title: WT_MF_2i_rep2

description: WT control 2i medium


title: Msl2KO_D12_Serum_rep4

description: Msl2 KO serum

value: msl2 deletion clone D12


title: Msl2KO_D12_Serum_rep2

description: Msl2 KO serum


title: Msl2KO_D12_2i_rep3

description: Msl2 KO 2i medium


title: DUTCHSCZ-62: Blood_Control_48

value: CTR


title: Msl2KO_D12_Serum_rep1

description: Msl2 KO serum


title: DUTCHSCZ-61: Blood_Control_47


title: CHINFAM-09: Blood_CTR_Non_Famine4


title: Msl2KO_D12_2i_rep2

description: Msl2 KO 2i medium


title: WT_MF_2i_rep3

description: WT control 2i medium


title: Msl2KO_D12_2i_rep1

description: Msl2 KO 2i medium


title: DUTCHSCZ-60: Blood_Control_46


title: Msl2KO_A2_Serum_rep4

description: Msl2 KO serum

value: msl2 deletion clone A2


title: Msl2KO_D12_Serum_rep3

description: Msl2 KO serum


title: DUTCHSCZ-58: Blood_Control_44

value: Whole blood


title: Msl2KO_A2_Serum_rep3

description: Msl2 KO serum


title: Msl2KO_A2_Serum_rep1

description: Msl2 KO serum


title: DUTCHSCZ-59: Blood_Control_45


title: Msl2KO_A2_Serum_rep2

description: Msl2 KO serum


title: Msl2KO_A2_2i_rep3

description: Msl2 KO 2i medium


title: Msl2KO_A2_2i_rep2

description: Msl2 KO 2i medium


title: DUTCHSCZ-57: Blood_Control_43


title: DUTCHSCZ-63: Blood_Control_49


title: DUTCHSCZ-56: Blood_Control_42


title: DUTCHSCZ-51: Blood_Control_37


title: DUTCHSCZ-52: Blood_Control_38


title: DUTCHSCZ-50: Blood_Control_36


title: Msl2KO_A2_2i_rep1

description: Msl2 KO 2i medium


title: DUTCHSCZ-54: Blood_Control_40


title: DUTCHSCZ-53: Blood_Control_39


title: DUTCHSCZ-55: Blood_Control_41


title: DUTCHSCZ-49: Blood_Schizophrenia_14


title: DUTCHSCZ-48: Blood_Control_35


title: DUTCHSCZ-44: Blood_Control_32


title: DUTCHSCZ-47: Blood_Schizophrenia_13


title: DUTCHSCZ-45: Blood_Control_33


title: DUTCHSCZ-43: Blood_Control_31


title: DUTCHSCZ-42: Blood_Control_30


title: DUTCHSCZ-41: Blood_Control_29


title: DUTCHSCZ-39: Blood_Control_28


title: DUTCHSCZ-40: Blood_Schizophrenia_12


title: DUTCHSCZ-38: Blood_Control_27


title: DUTCHSCZ-46: Blood_Control_34


title: DUTCHSCZ-36: Blood_Control_25


title: DUTCHSCZ-37: Blood_Control_26


title: DUTCHSCZ-34: Blood_Schizophrenia_11


title: DUTCHSCZ-35: Blood_Control_24


title: DUTCHSCZ-32: Blood_Control_23


title: DUTCHSCZ-31: Blood_Schizophrenia_9


title: DUTCHSCZ-30: Blood_Control_22


title: LATE STAGE rep3

city: Columbus

first: Carlo

middle: M.

last: Croce

state: Ohio

address: 460 West 12th Avenue

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

description:
L3
miRNA editing profiling from PEV

data_processing:
The detection and quantification analysis of modification events from sRNAseq data were based on two principal phases: 1) detection of miRNA editing sites by applying the Alon-Eisenberg pipeline (PMID:23872974) and 2) differential expression analysis of miRNA editing hotspots.
Briefly, we filtered all reads according to a Phred quality ≥20, with at most three positions with a lower quality. In addition, we removed sequences identified as 5' or 3' adaptors. Subsequently, we also removed reads whose length did not fall within the typical length range for a mature miRNA (16-27 bases).
Subsequently, all filtered reads were aligned to the human genome (hg19) employing the Bowtie software (PMID:19261174), allowing for one mismatch at most and trimming the last two bases of the read (PMID:20719920) (Bowtie parameters: -e 50 -a -m 1 -trim3 2 -best -strata). All the reads mapped to the known pre-miRNA sequences were considered for downstream analysis.
Finally, all miRNA MEs with the mismatch base quality score ≥30 and a Bonferroni-adjusted P-value <0.05, were taken into account for downstream analysis. The expression of each filtered miRNA MEs was calculated in RPMs. Among miRNA MEs, we have selected those which we consider to be high confidence miRNA editing sites, namely, having geometric mean of ED miRNA expression >1 RPM and geometric mean of editing level ≥5, in at least one condition (normal or tumor).
Finally, we identified as miRNA editing hotspots all high confidence miRNA editing sites present in ≥50% of samples, in at least one condition (tumor or normal).
Genome_build: hg19
Supplementary_files_format_and_content: Txt files contains the abundance measurements for all miRNAs in each sample.

source_name: Plasma-derived exosome

growth_protocol: PEVs were isolated using the Izon qEV size exclusion column (Izon qEV, iZON science, Cambridge MA). 190uL of plasma (centrifuged for 10 minutes at 10,000xG) was added to the column membrane, followed by 310uL of PBS.  PBS was then added in 500uL increments for a total of 32 fractions. The fractions were run on a NuPAGE Bis-Tris gel to evaluate protein contamination.  Fractions 7-9 were combined as the EV fraction and fractions 12-32 were combined as the depleted fraction.  Both the EV and depleted fractions were concentrated to ~150uL using an Amicon Ultra-4 10K centrifugal filter (Millipore cat#UFC801024).

extract_protocol:
Total RNA from all 3 fractions (whole plasma, EVs and EV-depleted) was isolated using the Qiagen miRNeasy kit (Qiagen) and eluted twice with 30uL H2O. RNA was isolated from 100 uL of plasma using the Qiagen miRNeasy Mini prep kit and eluted from the binding column in 15 uL H2O. The quality and quantity of RNA was checked with Bioanalyzer.
The small RNA sequencing library was constructed with NEBNext library construction kit following manufacture's instruction. The library with proper insert size was selected by using PippinHT from Sage Scientific. For pooling samples, NEBNext Library Quant Kit was used to quantify the library and equimolar amount of libraries from different samples was pooled for sequencing using Illumina NextSeq 500 (50 bp single-end reads were generated).

tag: dissease state

value: late stage NSCLC

tag: Stage

value: IV

tag: Sex

value: Female

tag: sample type

value: PEV


title: LATE STAGE rep7

description:
L7
miRNA editing profiling from PEV

value: II

value: Male


title: LATE STAGE rep4

description:
L4
miRNA editing profiling from PEV


title: LATE STAGE rep5

description:
L5
miRNA editing profiling from PEV

value: III


title: DUTCHSCZ-29: Blood_Control_21

tag: tissue

tag: gender

value: M


title: LATE STAGE rep2

description:
L2
miRNA editing profiling from PEV


title: DUTCHSCZ-28: Blood_Control_20

value: F


title: LATE STAGE rep1

description:
L1
miRNA editing profiling from PEV


title: EARLY STAGE rep10

description:
E10
miRNA editing profiling from PEV

value: early stage NSCLC

value: IA


title: DUTCHSCZ-27: Blood_Control_19


title: EARLY STAGE rep11

description:
E11
miRNA editing profiling from PEV

value: IB


title: DUTCHSCZ-33: Blood_Schizophrenia_10

value: SCZ


title: DUTCHSCZ-26: Blood_Schizophrenia_8


title: EARLY STAGE rep9

description:
E9
miRNA editing profiling from PEV


title: DUTCHSCZ-25: Blood_Control_18


title: LATE STAGE rep8

description:
L8
miRNA editing profiling from PEV


title: EARLY STAGE rep5

description:
E5
miRNA editing profiling from PEV


title: EARLY STAGE rep6

description:
E6
miRNA editing profiling from PEV


title: DUTCHSCZ-23: Blood_Schizophrenia_7


title: EARLY STAGE rep3

description:
E3
miRNA editing profiling from PEV


title: EARLY STAGE rep2

description:
E2
miRNA editing profiling from PEV


title: CTRL rep7

description:
C7
miRNA editing profiling from PEV

value: control

value: No NODULES


title: EARLY STAGE rep1

description:
E1
miRNA editing profiling from PEV


title: CTRL rep6

description:
C6
miRNA editing profiling from PEV


title: DUTCHSCZ-21: Blood_Schizophrenia_6


title: CTRL rep5

description:
C5
miRNA editing profiling from PEV


title: LATE STAGE rep6

description:
L6
miRNA editing profiling from PEV


title: EARLY STAGE rep8

description:
E8
miRNA editing profiling from PEV


title: CTRL rep3

description:
C3
miRNA editing profiling from PEV


title: CTRL rep2

description:
C2
miRNA editing profiling from PEV


title: CTRL rep1

description:
C1
miRNA editing profiling from PEV


title: DUTCHSCZ-18: Blood_Control_14

value: CTR


title: DUTCHSCZ-22: Blood_Control_16

value: Whole blood


title: DUTCHSCZ-16: Blood_Control_12


title: DUTCHSCZ-20: Blood_Control_15


title: DUTCHSCZ-17: Blood_Control_13


title: DUTCHSCZ-14: Blood_Control_10


title: CTRL rep4

description:
C4
miRNA editing profiling from PEV


title: DUTCHSCZ-19: Blood_Schizophrenia_5


title: DUTCHSCZ-15: Blood_Control_11


title: MG12: Mut lig rep 3

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

data_processing:
Sequencing was carried out at a concentration of 1.8pM on a Illumina NextSeq 500, NCS v2.1.2, 43bp paired end protocol.
Basecalling was done using the standard Illumina parameters (RTA 2.4.11)
Reads were demulitplexed using Illumina bcl2fastq v2.17 and then were aligned using STAR v2.5.0b.
Transcript abundance was estimated using Illumina's RnaReadCounter tool and differential expression analysis performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with matrix table containing raw counts of sequencing reads

source_name: Mut lig rep 3

extract_protocol:
Macrophages were derived from femur and tibia bone marrows. Macrophage RNA was extracted using Trizol reagent and genomic DNA was eliminated with Buffer GE (Qiagen). mRNA was enriched with oligo dT  paramagnetic beads
Libraries were constructed using the Kapa Stranded mRNA-Seq Kit (Cat#KK8421) with 12 cycles of PCR enrichment.

treatment_protocol: Mice were fed a Western diet (34,15% Sucrose, 21% Milk fat, 0,15% Cholesterol; 5TFH/Breslow Western Diet, Test Diet Limited, UK) for 12 weeks ad libitum.

tag: strain

value: 20-week old

value: Macrophage


title: MG10: Mut lig rep 1

source_name: Mut lig rep 1


title: MG11: Mut lig rep 2

source_name: Mut lig rep 2


title: DUTCHSCZ-24: Blood_Control_17

tag: group


title: MG13: Mut no lig rep 3

source_name: Mut no lig rep 3


title: MG8: Mut no lig rep 2

source_name: Mut no lig rep 2


title: MG7: Mut no lig rep 1

source_name: Mut no lig rep 1


title: MG6: WT lig rep 3

source_name: WT lig rep 3

value: WT-LdlrKO


title: DUTCHSCZ-12: Blood_Schizophrenia_4

tag: nk


title: MG3: WT no lig rep 3

source_name: WT no lig rep 3


title: MG4: WT lig rep1

source_name: WT lig rep1


title: MG2: WT no lig rep 2

source_name: WT no lig rep 2


title: DUTCHSCZ-10: Blood_Schizophrenia_3

source_name: Whole blood

tag: bcell


title: MG5: WT lig rep 2

source_name: WT lig rep 2


title: DUTCHSCZ-11: Blood_Control_8

tag: mono


title: DUTCHSCZ-13: Blood_Control_9


title: DUTCHSCZ-08: Blood_Control_6


title: DUTCHSCZ-07: Blood_Control_5


title: DUTCHSCZ-06: Blood_Schizophrenia_2


title: DUTCHSCZ-05: Blood_Schizophrenia_1


title: DUTCHSCZ-04: Blood_Control_4


title: LGP2_KO

city: Bunkyo-ku

first: Kumiko

last: Ui-Tei

state: Tokyo

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy-3 labeled RNAs were fragmented by Gene Expression Hybridization kit (Agilent Techinologies) and hybridized to SurePrint G3 Human GE microarray ver.3 (Agilent Techinologies) at 65°C for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing:
Signals were quantified by Feature Extraction 10.5.1.1 (Agilent Techinologies).
Normalized signal intensity

label_protocol: Cy-3 labeled RNA were synthesized by Quick Amp Labeling kit for One color (Agilent Techinologies).

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (Wako) containing 10% fetal bovine serum (Gibco) at 37°C with 5% CO2.

extract_protocol: Total RNAs were extracted by RNeasy mini kit (QIAGEN).

treatment_protocol: Non treated

tag: disease

value: cervical cancer cells

tag: cell line

value: HeLa

tag: genotype/variation

value: LGP2 knockout

value: female


title: HeLa_WT

description: Gene expression

value: WT


title: DUTCHSCZ-09: Blood_Control_7

value: F

tag: age

tag: sentrix

tag: position


title: DUTCHSCZ-01: Blood_Control_1


title: Dmel_male_MSL2Flag_Input

data_processing:
Paired-end 75 bp reads were mapped to dm6 with bowtie2 (Galaxy Version 2.3.0.1) using parameters: --sensitive, --end-to-end for histones and --sensitive --local for all other profiles. For Msl2 ChIP-seq, read-pairs with a minimal overlap of 10 bp were merged and Illumina adpters were trimmed using bbmerge (v7.3), resulting in small (≤140 bp) and large (>140 bp) fragments. Merged, single end reads and unmerged, paired-end reads were then mapped separately.
Peaks were called with MACS2 (Galaxy Version 2.1.1.20160309.0) on each replicated and merged using cat, BEDtools sort (Galaxy Version 2.27.0.0) followed by BEDtools merge with 10 bp option.
Coverage files were generated with deepTools2 (Galaxy Version 2.5.1.0.0) bamCompare, binsize of 2. Duplicate reads and reads with a mapping quality < 10 were removed, the X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H3, H4K16ac, H3K36me3, H4ac, H3ac; Input subtraction for Drosophila MSL2-Flag, untagged-Flag, MLE, MSL1, NSL1 (S2 cells), MSL2 (S2 cells); 1 x Coverage for Drosophila H4K16ac, H3K36me3, H3ac, H4ac shown in Figure 1d and 2a; mESC H4K16ac log2FC over H3.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files of uniquely mapped reads, bed files of Msl2 peaks

source_name: third instar larvae

growth_protocol: Drosophila melanogaster were reared on a cornflour-molasses fruit fly medium [1l water, 12g agar-agar threads, 18g bakery yeast, 10g soya flour, 80g corn flour, 22g molasses, 80g malt extract, 2.4g 4-hydroxibenzoic acid methylester (Nipagin), 6.25ml propionic acid] at 25¡C, 70% relative humidity and 12 hr dark/12 hr light cycle.

extract_protocol:
Larvae were dissected and the front part fixed at RT for 15 min with 1% or 0.2% Formaldehyde. Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using Phenol-Chloroform Extraction and Ethanol precipitation.
NEB Next Ultra II

value: msl-2227/msl-2km ; tub-Gal4 / UAS-msl-2::3Flag


title: Dmel_female_MSL2Flag_Input


title: Dmel_female_MSL2Flag_ChIP


title: Dmel_male_MLE

data_processing:
forward and reverse reads having a minimal overlap of 30 nt were merged using bbmerge (v7.3)
merged reads and unmerged forward reads were mapped to the dm6 genome using bowtie2 (2.2.3) with default parameters
only mapped reads having a mapping quality score of more than 10 were kept, filtering was done with Samtools(v1.1)
PCR-duplicate removalwas performed based on the random tags contained in the custom-made adapters using a custom-made Python script.
Coverage signal tracks (bigWigs) of PCR duplicates removed, uniquely mapped reads were generated with DeepTools2 (v2.4.1)
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files, containing uniquely mapped, PCR duplicates removed coverage signal

extract_protocol:
Larvae were dissected and the front part was homogenized and UV crossllinked at 0.15 mJ/cm2. The homogenate was cleared using a sucrose cushion followed by 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before pull-down of the protein of interest.
After a brief RNaseI-digestion, RNA 3'-ends were healed with T4-PNK. Custom-made barcoded adapters are ligated using T4 RNA Ligase1 for 1 hr at 25˚C. Custom FLASH adapters contained index barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNNNNTTTTTTNN (N: random tag nucleotide, T: index nucleotide). Index nucleotides were used to separate samples. Random tags were used to merge PCR-duplicates. Excess adapters are washed away and RNA is isolated with Proteinase K treatment and column purification. Isolated RNA is reverse-transcribed and RNaseH-treated. cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 or HiSeq 3000 in paired-end mode.

value: White-eyed (w1118) Oregon-R

tag: rip antibody

value: Rat-anti-MLE (Ilik et al. Mol Cell. 2013 Jul 25;51(2):156-73)


title: Dmel_male_MSL2

value: Anti-HA magnetic beads (Thermo Fisher, 88836)


title: Dmel_female_MLE


title: Dmel_male_msl2null_H4K16ac_ChIP

value: msl-2-delta-7 / msl-2-delta-10

tag: chip antibody

value: H4K16ac(Merck Milipore, 07-329)


title: Dmel_male_msl2null_H3_H4K16ac_Input


title: Dmel_male_WOR


title: Dmel_female_WOR


title: Dmel_male_msl2null_H3_ChIP

value: H3(Active Motif, MABI 0301, 39763)


title: Dmel_female_MSL2


title: Dmel_male_msl2het_H4K16ac_ChIP

value: msl-2-delta-7/10 / CyO-GFP


title: EARLY STAGE rep4

description:
E4
miRNA editing profiling from PEV

tag: dissease state

value: early stage NSCLC

tag: Stage

value: IA

tag: Sex

value: Female

value: PEV


title: Dmel_male_msl2het_H3_H4K16ac_Input


title: DUTCHSCZ-03: Blood_Control_3

tag: tissue

value: Whole blood

value: CTR

tag: gender


title: Dmel_male_msl2het_H3_ChIP

tag: strain


title: Dmel_male_UntaggedFlag_Input


title: DUTCHSCZ-02: Blood_Control_2

tag: group

tag: nk


title: Dmel_male_MLE_Input


title: Dmel_male_MSL2Flag_ChIP


title: Dmel_male_MLE_ChIP


title: Dmel_male_H4ac_ChIP

value: PanAc H4(Merck Milipore, 06-598)


title: Dmel_male_H4_ChIP

value: H4(Active Motif, 61521)


title: Dmel_male_H3_H4K16ac_Input


title: Dmel_male_H4K16ac_ChIP


title: Dmel_male_H3ac_ChIP

value: PanAc H3(Merck Milipore, 06-599)


title: Dmel_male_H3_ChIP


title: MG1: WT no lig rep 1

source_name: WT no lig rep 1

value: 20-week old

tag: genotype

value: WT-LdlrKO

value: Macrophage


title: Dmel_female_msl2null_H4K16ac_ChIP


title: Dmel_male_H3K36me3_ChIP

value: White-eyed (w1118) Oregon-R

value: H3K36me3(Active Motif, 61102)


title: Dmel_male_UntaggedFlag_ChIP

value: Monoclonal ANTI-FLAG® M2 antibody(Sigma, F1804)


title: Dmel_female_msl2null_H3_H4K16ac_Input

value: msl-2-delta-7 / msl-2-delta-10


title: Dmel_female_msl2null_H3_ChIP

value: H3(Active Motif, MABI 0301, 39763)


title: Dmel_female_msl2het_H4K16ac_ChIP

value: msl-2-delta-7/10 / CyO-GFP

value: H4K16ac(Merck Milipore, 07-329)


title: Dmel_female_msl2het_H3_ChIP


title: Dmel_female_msl2het_H3_H4K16ac_Input


title: Follicular helper T cell rep7

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: Replicate 7

hyb_protocol: After quality control assessment, 1.5 µg of cRNA was mixed with the hybridization controls and it was hybridized to the array. The array was hybridized for 16 hours in a hybridization oven with a rocking platform at 58°C. The array chip then was subjected to a series of washes before it was stained with streptavidin-Cy3. After the staining, it went through a final wash and drying.

scan_protocol: BeadChips were scanned on the Illumina iScan at the Yale Center for Genome Analysis.

data_processing: Data were made positive by adding an offset to remove negative values, log2 transformed, and subjected to the VST variance-stabilizing transformation, then quantile normalized using procedures in the R 2.13 bioconductor lumi 2.4.0 package.

source_name: Human tonsils

label_protocol: Double stranded cDNA and biotin-labeled cRNA were synthesized and purified according to the manufacturer's  protocol using a TotalPrep RNA Amplification kit (Thermofisher). Samples of 400ng of total RNA were reverse transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled via incorporation of biotin-16-UTP.

extract_protocol: RNA was prepared using the Qiagen RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Chronically inflamed tonsils were obtained from routine pediatric tonsilectomy from Yale Childeren's hospital (age: Between 2-18). The study was approved by Institutional Review Board (IRB) at Yale University School of Medicine.  Patient name, chart number, gender and date of birth were deidentified. We sorted four CD4 T cell subgroups from three tonsils ex vivo and extracted mRNA.

value: Low

value: High


title: Dmel_female_UntaggedFlag_Input


title: Follicular helper T cell rep9

description: Replicate 9


title: PSGL-1 high PD-1 high CXCR5 high cell rep6

description: Replicate 6


title: Dmel_female_UntaggedFlag_ChIP


title: Dmel_female_MLE_Input


title: PSGL-1 high PD-1 high CXCR5 high cell rep8

description: Replicate 8


title: PSGL-1 high PD-1 high CXCR5 high cell rep2

description: Replicate 2


title: PSGL-1 high PD-1 high CXCR5 high cell rep9

description: Replicate 9


title: PSGL-1 high PD-1 high CXCR5 high cell rep4

description: Replicate 4


title: PSGL-1 high PD-1 high CXCR5 high cell rep7

description: Replicate 7


title: PSGL-1 high PD-1 high CXCR5 high cell rep5

description: Replicate 5


title: Follicular helper T cell rep5

description: Replicate 5


title: Dmel_female_MLE_ChIP

value: Rat-anti-MLE (Ilik et al. Mol Cell. 2013 Jul 25;51(2):156-73)


title: Follicular helper T cell rep1

description: Replicate 1


title: Follicular helper T cell rep2

description: Replicate 2


title: Follicular helper T cell rep8

description: Replicate 8


title: Follicular helper T cell rep3

description: Replicate 3


title: Follicular helper T cell rep6

description: Replicate 6


title: PSGL-1 high PD-1 high CXCR5 high cell rep1

description: Replicate 1


title: Follicular helper T cell rep4

description: Replicate 4


title: Effector memory T cell rep2

description: Replicate 2


title: CD45RA+ T cell rep3

description: Replicate 3


title: Effector memory T cell rep3

description: Replicate 3


title: Effector memory T cell rep1

description: Replicate 1


title: CD45RA+ T cell rep2

description: Replicate 2


title: PSGL-1 high PD-1 high CXCR5 high cell rep3

description: Replicate 3


title: Dmel_female_H4ac_ChIP


title: Dmel_female_H4_ChIP


title: Dmel_female_H4K16ac_ChIP


title: Dmel_female_H3ac_ChIP


title: Dmel_female_H3_ChIP


title: Dmel_female_H3_H4K16ac_Input


title: CD45RA+ T cell rep1

description: Replicate 1


title: PAD-140

status: Public on Jun 28 2018

city: Cambridge

first: Mike

last: Chapman

address: Long Road

department: Haematology

institute: University of Cambridge

data_processing:
Read quality was checked for each sample using FastQC v0.11.4
High-quality reads were imported into TopHat v2.0.10 for alignment into BAM files.
Read counts were generated by mapping the bam files against the human transcriptome using the Rsubread package version 1.20.6
Genome_build: NCBI 37.2
Supplementary_files_format_and_content: Comma separated file with raw count values

source_name: patient enrolled into the PADIMAC study_Bortezomib-standard

extract_protocol:
CD138+ myeloma cells were isolated using magnetic activated cell sorting CD138 MicroBeads (Miltenyi Biotech), resulting in cell suspensions with purity of greater than 90%. Total RNA isolation was carried out using PureLink RNA Micro Kit RNAqueous kit (Invitrogen). Samples were only processed if they had an RNA integrity number of greater than 6, as determined by the RNA 6000 Nano Kit (Agilent).
Libraries were prepared from 250ng total RNA with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) according to the manufacturer’s instructions, apart from a 10-minute fragmentation and 14 cycles of PCR. The average insert size was 150bp.

tag: iss stage

value: I

tag: subtype

value: IgA

tag: bortezomib response

value: Bortezomib-standard

tag: cell type

value: CD138 selected bone marrow cells


title: PAD-148

tag: age

value: II

value: IgG


title: PAD-150

value: III


title: PAD-153


title: PAD-145


title: PAD-146

source_name: patient enrolled into the PADIMAC study_Bortezomib-good

value: Bortezomib-good


title: PAD-141


title: PAD-152


title: Dmel_female_H3K36me3_ChIP

value: White-eyed (w1118) Oregon-R

value: H3K36me3(Active Motif, 61102)


title: BRAF Inhibitor Resistant Rep 1

city: Cold Spring Harbor

first: Molly

middle: Gale

last: Hammell

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Base calls performed using CASAVA
TEsmall called cutadapt under which read adapters were trimmed and filtered for lengths between 16-36 nucleotides
Tesmall called bowtie v1.2.1 to first map ribosomal derived reads with the option bowtie -v 2 -k 1, then map remaining sRNA reads with option bowtie -v 0 -a -m 100
Tesmall compiled annotation and count files using UCSC annotation tracks
Summary count file was filtered to exclude row sum across samples < 20
Count file was subject to statstical analysis by DEseq2 to normalize counts and calculate differential expression
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited files containing TE small raw count data and DE seq2 output

growth_protocol: Parental cell lines were cultured in standard growth media (DMEM with 10% FBS) Resistant cell lines were supplemented with a 1uM concentration of BRAF inhibitor vemurafenib

extract_protocol:
Total RNA was extracted using the Ambion PureLink RNA Mini Kit to extract up to 2ug of total RNA
Small RNA sequencing libraries were prepared with Illumina TruSeq Small RNA library preparation kit using 1.2 ug of input total RNA

value: primary tissue derived melanoma cell line

tag: drug treatment

value: vemurafenib

tag: cell line


title: Parental Rep 2

value: vector


title: BRAF Inhibitor Resistant Rep 2


title: Parental Rep 1


title: PAD-149


title: PAD-127

value: Light chain


title: PAD-129


title: PAD-131


title: EARLY STAGE rep7

description:
E7
miRNA editing profiling from PEV

source_name: Plasma-derived exosome

value: early stage NSCLC

value: IA

value: Male

tag: sample type

value: PEV


title: PAD-130

value: I

value: IgA


title: PAD-126

value: CD138 selected bone marrow cells


title: PAD-125

value: II

value: Bortezomib-standard


title: PAD-135

value: III

value: IgG


title: PAD-119


title: PAD-120

value: Bortezomib-good


title: PAD-112


title: PAD-139


title: PAD-109


title: PAD-098


title: PAD-080


title: PAD-111


title: PAD-128


title: PAD-050


title: PAD-078


title: PAD-049


title: PAD-039


title: PAD-124


title: PAD-025


title: PAD-034


title: PAD-024


title: PAD-021


title: PAD-061


title: PAD-018


title: PAD-027


title: PAD-017


title: PAD-066


title: PAD-075


title: PAD-056


title: PAD-004


title: PAD-095


title: PAD-035


title: Hs578T TET1_KO_3_2

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Library strategy: Dream-seq
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards). Summary table lists methylation percent values supported by more than 19 equencing reads at individual CCCGGG sites.

growth_protocol: Hs578T cells were cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA).
Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB).
Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

treatment_protocol: gRNAs targeting 2 different TET1 exons were cloned into the Lenti CRISPR V2 plasmid.  gRNAs targeted exon 11 (ATTCCCCGAATCAAGCGGAA, KO-1 and KO-2) and exon 3 (AAGTTTTAAAGGTAATCAGC, KO-3).  Lentiviruses were generated using HEK293T cells by transfecting with packaging plasmid (psPAX2, Addgene 12260), envelope plasmid (pMD2.G, Addgene 12259) and lenti-CRISPR V2 plasmid (Addgene 52961).  Cells were transfected using Lipofectamine 2000.  Viral supernatant was collected at 48 and 72 hours, filtered with 0.45µm membrane and incubated on Hs578T cells for 7 hours in the presence of polybrene (6µg/mL, Millipore).  We puromycin selected (1µg/mL) the cells for three days, followed by single cell cloning using serial dilution in 96 well plates.  After selection, cells were maintained in normal media supplemented with 0.25 µg/mL puromycin.

tag: phenotype

value: Triple negative breast cancer cell line

value: adult

tag: genotype/variation

value: TET1 KO_3 single clone 13_D8 (gRNA AAGTTTTAAAGGTAATCAGC targeting exon 3)


title: Hs578T TET1_KO_3_3


title: Hs578T TET1_KO_2_2

value: TET1 KO_1 single clone Both_C6 (gRNA ATTCCCCGAATCAAGCGGAA targeting exon 11)


title: Hs578T TET1_KO_3_1


title: Hs578T TET1_KO_2_1


title: Hs578T TET1_KO_1_3

value: TET1 KO_1 single clone Both_B5 (gRNA ATTCCCCGAATCAAGCGGAA targeting exon 11)


title: DAXX-NC NCI-H727 cells

first: Kaoru

last: Mogushi

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description: Gene expression profile of ALDH high QGP1 cells

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using affy package (version 1.40.0) and R statistical software (version 3.0.3).

source_name: Human bronchial NET cell line QGP1

label_protocol: Amplified RNA was prepared using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies). All samples had RNA Integrity Number (RIN) greater than 7.0.

treatment_protocol: Cells were transfected with small interfering RNA (siRNA) of DAXX (SASI_Hs01_00138404 and SASI_Hs01_00138407; Sigma-Aldrich Japan) or negative control (Mission siRNA Universal Negative Control; Sigma-Aldrich Japan) to give a final concentration of 50 nM by using Neon electroporation system (Thermo Fisher Scientific).

tag: treatment

value: Control


title: DAXX-NC QGP1 cells

source_name: Human pNET cell line QGP1


title: DAXX-KD NCI-H727 cells

value: DAXX knockdown


title: Hs578T Empty Vector_3

value: Empty vector single clone D5


title: Hs578T TET1_KO_1_1


title: Hs578T TET1_KO_1_2


title: Hs578T TET1_KO_2_3


title: Hs578T Empty Vector_2

value: Empty vector single clone C5


title: MT14.GlutamineDeficient.WT1.Rep2

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

data_processing:
Basecalls performed in phred64
Sequenced reads were mapped to hg19 whole genome using Tophat2 with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using CuffDiff with default settings (FDR <= 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: Summary files describe the results of CuffDiff differential expression analysis for core comparisons as well as FPKM matrix for all replicates created using Cufflinks suite.

growth_protocol: Total RNA was isolated from HCT116 cells after 48 hours of glutamine starvation (GD) (Cetinbas et al., 2016) or complete medium (CM)

extract_protocol:
Qiagen RNA extraction kit. (74104, Quigen)
PolyA, paired end sequencing on Illumina NextSeq500 at the Beatson Institute of Cancer Research, UK

tag: tissue

value: human colon cancer cell line

tag: growth medium

value: 48hr glutamine starvation


title: MT17.GlutamineDeficient.WT2.Rep2


title: Hs578T Empty Vector_1

value: Empty vector single clone B5


title: MT6.CompleteMedium.WT2.Rep3

value: Grown in complete medium


title: MT18.GlutamineDeficient.WT2.Rep3


title: MT16.GlutamineDeficient.WT2.Rep1


title: MT15.GlutamineDeficient.WT1.Rep3


title: MT13.GlutamineDeficient.WT1.Rep1


title: DAXX-KD QGP1 cells


title: MT5.CompleteMedium.WT2.Rep2


title: BC08_TUMOR2

city: New York

first: Ambrose

last: Carr

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

data_processing:
InDrop v2 RNA-seq data was processed from raw fastq files to count matrices with SEQC v0.2.1 (see https://github.com/ambrosejcarr/seqc.git)
Genome_build: Gencode GRCh38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format

extract_protocol:
InDrop v2
CD45+ cells from tumor were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter  and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

value: CD45+ leukocytes

tag: donor age (years)

tag: resident tissue

value: breast tumor


title: BC08_TUMOR3


title: MT4.CompleteMedium.WT2.Rep1


title: BC07_TUMOR3


title: BC08_TUMOR1