title: KAP1_Knockdown_R2

city: Bath

first: Keith

middle: W

last: Vance

address: Claverton Down

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

hyb_protocol: Labelled sense single stranded DNA was hybridised to Mouse Gene 1.0 ST Arrays using the Affymetrix Hybridization, Wash, and Stain Kit as described by the manufacturer. Gene Chips were washed and stained on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Gene Chips were scanned on an Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages

source_name: Neuroblastoma cells

label_protocol: 200 ng RNA was used to generate labelled sense single stranded DNA using the Ambion WT Expression Kit, the Affymetrix WT Terminal Labelling and Controls Kit following manufacturers instructions.

growth_protocol: N2A cells were grown in DMEM supplemented with 10% foetal bovine serum.

extract_protocol: Total RNA was isolated from triplicate control and KAP1 knockdown cells using the Qiagen Mini RNeasy kit following the manufacturer’s instructions. RNA samples with a RNA Integrity Number greater than 8, as assessed on a BioAnalyzer (Agilent Technologies) were used.

treatment_protocol: Approximately 2x10^5 N2A cells were plated per well in a six well plate. 16–24 h later cells were transfected with 1.5 ug Kap1 shRNA expression construct or scrambled control and 300 ng (5:1 ratio) pTK-Hyg. Three days after transfection, cells were trypsinised, resuspended in growth medium containing 200 mg/ml Hygromycin B and plated onto a 6 cm dish. Drug resistant cells were grown for 7 days and then harvested for total RNA purification.

value: Neuro-2A cells

value: KAP1 knockdown


title: KAP1_Knockdown_R3

status: Public on Feb 02 2018

type: RNA

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: genotype/variation


title: Sciatic nerves_CT_1

city: Zürich

first: Laura

last: Montani

state: ZH

address: Otto Stern Weg 7

country: Switzerland

institute: IMHS - ETH Zürich

hyb_protocol: Following fragmentation, 10 ug of cRNA per sample were hybridized for 16 hr at 45C on Affymetrix MG-430 PM Array Strips. Strips were washed and stained using the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: An Affymetrix GeneAtlas Imaging Station was used to measure the fluorescent intensity emitted by the labeled targets.

data_processing: Signal estimates were calculated using RMA in Bioconductor (v.2.11).

label: biotin

source_name: Sciatic nerves_CT

label_protocol: Biotinylated cRNA were prepared using the GeneAtlasTM 3’IVT Express Kit (Affymetrix) from 100ng total RNA

extract_protocol: total RNA by Trizol/chloroform/ethanol extraction

treatment_protocol: P60 mice were euthanized and tissue immediately dissected, transferred to eppendorfs and snap frozen in liquid nitrogen. Tissues were stored at -80C to be subsequently processed for total RNA extraction.

tag: strain background

value: mixed

value: control; DhhCre- Fasn lox/lox

tag: age

tag: tissue

value: Sciatic nerve


title: KAP1_Knockdown_R1


title: Acetate_1

city: La Jolla

first: Nathan

last: Lewis

state: California

address: 9500 Gilman Drive

department: Pediatrics

country: USA

institute: University of California, San Diego

hyb_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

data_processing: Affymetrix CEL files were normalized using GCRMA (version 2.20.0) implemented in R (version 2.11.1)

organism: Escherichia coli

source_name: E. coli K-12 MG1655, aerobic conditions on 0.2% (w/v) acetate M9 minimal media at 37°C

growth_protocol: E. coli K12 MG1655 was grown and expression profiled on 0.2% (w/v) glucose M9 minimal media or 0.2% (w/v) fructose M9 minimal media or 0.2% (w/v) acetate M9 minimal media at 37°C. Each experimental condition was tested in triplicate in the respective carbon sources using independent cultures. Cultures were grown to mid-exponential growth phase aerobically (OD600 = 0.3) in minimal media, supplemented with the appropriate carbon source.

extract_protocol: total RNA

treatment_protocol: Addition of 0.2% v/v carbon source to the M9 media

tag: strain

tag: treatment


title: N2A_Control_R2

value: scrambled control


title: N2A_Control_R1


title: Blood _day3_pt2

status: Public on Feb 01 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

source_name: Blood from SAH pt2

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: The blood and CSF samples on day 3 were sampled from two SAH patients. Sample from non-SAH patient was used as control sample.

extract_protocol: RNA samples were extracted from CSF and blood using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: Exosomes were isolated from 500 µL of plasma and 1 mL of CSF, and total RNA was isolated from exosome samples

tag: disease

value: SAH patient


title: Blood _day3_pt1

source_name: Blood from SAH pt1


title: Blood _day0_ptcontrol

description: BloodCON

source_name: Blood from control pt

value: control patient


title: N2A_Control_R3


title: Negative control 2

city: Beijing

first: Wei

last: Han

address: Dongdansantiao 5

country: China

institute: CAMS&PUMC

description: Gene expression after control vector transfection, replicate 2

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: T98G glioma cell, Negative control

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

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany))and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Control vector and FHL3 plasmids were purified using the EndoFree Plasmid Maxi Kit (QIAGEN) and transfected into T98G cells using FuGENE6 (Promega), including 3 technical replicates. After transfection for 72h, total RNA was extracted for microarray analysis.

value: T98G glioma cell line

value: control


title: CSF_day3_pt2

source_name: CSF from SAH pt2


title: CSF_day3_pt1

source_name: CSF from SAH pt1


title: Negative control 3

description: Gene expression after control vector transfection, replicate 3


title: FHL3 ovexpression 2

description: Gene expression after FHL3 overexpression, replicate 2

source_name: T98G glioma cell, FHL3 ovexpression

value: FHL3 ovexpression


title: FHL3 ovexpression 1

description: Gene expression after FHL3 overexpression, replicate 1


title: Negative control 1

description: Gene expression after control vector transfection, replicate 1


title: FHL3 ovexpression 3

description: Gene expression after FHL3 overexpression, replicate 3


title: Spleen_Tcm-a3

city: Minneapolis

first: Marissa

last: Macchietto

state: MN

department: Institute of Health Informatics

institute: University of Minnesota

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The probe data were then preprocessed and normalized with RMA (Robust Multiarray Average) from the “affy” R/Bioconductor package (Gautier et al. 2004).

source_name: FACS-sorted CD8+ Thy1.1+ P14 TCM (CD62Lhi CD69-) cells from spleen

label_protocol: Affymetrix protocol

extract_protocol: CD8+ Thy1.1+ P14 TCM (CD62Lhi CD69-) and SLO TRM (CD62Llo CD69+) populations were sorted from spleen, and CD69+ TRM were isolated (as described, Thompson et al) and sorted from FRT of LCMV immune chimeras using a BD FACSAria II. Sorted cells were homogenized using QIAshredder columns (Qiagen) and RNA was extracted using an RNeasy kit (Qiagen) per the manufacturer’s instructions. RNA quality was assessed using the Agilent Model 2100 Bioanalyzer.

value: Spleen


title: Spleen_Tcm-a1


title: Spleen_Tcm-a2


title: FRT_CD69pos-2

source_name: FACS-sorted CD69+CD103lo TRM cells from female reproductive tract

value: Female Reproductive Tract


title: Spleen_Trm-3

source_name: FACS-sorted SLO TRM (CD62Llo CD69+) cells from spleen


title: FRT_CD69pos-3


title: Invasive front_rep5

city: Tokyo

first: Akiko

last: Kunita

address: 7-3-1, Hongo, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: Gene expression data from cells located at the invasive front of mouse squamous cell carcinomas

hyb_protocol: The fragmented cRNA (15μg) was used in a hybridization cocktail containing spiked controls (Affymetrix). A total of 200μl of this hybridization cocktail was hybridized at 45°C for 16 hours to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: Following hybridization, the arrays were processed using a GeneChip Fluidics Station 400 according to recommended protocols (FS450_0001, Affymetrix). Fluorescent images of arrays were captured using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Image data were acquired and analyzed using the GeneChip Operating Software (GCOS, Affymetrix).

source_name: 7 months old HPV/E2 mouse treated with oestrogen

label_protocol: Preparation of in vitro transcription (IVT) products was performed according to Affymetrix protocols (GeneChip Expression Analysis Technical manual, Rev. 5), with minor modifications.

growth_protocol: 7 months old HPV/E2 mouse

extract_protocol: Total cellular RNA was isolated with the PicoPure RNA isolation kit (Arcturus, USA), with minor modifications. The optional DNase treatment step to remove potential genomic DNA contamination was omitted and the centrifugation times during washing were reduced to 30 seconds.

treatment_protocol: Chronico oestrogen treatment via implantation of oestorgen capsules

value: cervical invasive squamous cell carcinoma


title: Tumor mass_rep5

description: Gene expression data from cells located in the tumor mass of mouse squamous cell carcinomas


title: Spleen_Trm-2


title: Tumor mass_rep4


title: FRT_CD69pos-1


title: Invasive front_rep6


title: Invasive front_rep4


title: Spleen_Trm-1


title: Tumor mass_rep1


title: Tumor mass_rep2


title: CSF_day0_ptcontrol

description: CSFCON

source_name: CSF from control pt


title: Tumor mass_rep3


title: MEF wt d3 II

type: genomic

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

country: Germany

institute: University Regensburg

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: The values represent  M-values= log2(R/G), normalized by qspline (a natural cubic spline interpolation method followed by linear interpolation of outlier values, Bioconductor aCGH.Spline_2.2.tar), each array was normalized separately.

molecule: genomic DNA

source_name: nucleolar DNA

label_protocol: 2µg of DNA were submitted to NimbleGen and steps were performed as service there.

growth_protocol: MEF cells were grown under standard conditions: 37°C, 5 % CO2, DMEM-GlutaMAX, high Glucose (4 g/L), 10 % FCS

extract_protocol: 1x10^8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. After washing cells 2 times with ice-cold PBS they were scraped off and pooled in 100 mL 1xPBS and centrifuged (750 g, 5 min, 4°C). Supernatant was discarded and cells were resuspended in 1 mL HMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 12 mM MgCl2, 1 mM TCEP, PI). Cells were then sonified with the Bioruptor 30 sec on 30 sec off for 3x5min with high mode. After ceintrifugation the pellet was respuspended in 1mL LMg (10 mM Hepes pH 7.4, 0.88 M sucrose, 1 mM MgCl2, 1 mM TCEP, PI) buffer and sonified again with the same settings. Supernatant was discarded and the pellet was resuspended in 200 µL 20 mM Tris pH 8.1. RNA was digested by adding 3 µL of RNAse A (10 mg/mL) and incubation for 1 h at 37°C. Proteins were digested by adding 5 µL Proteinase K and incubation for 8 h at 37°C and the cross-link was reversed for 8 h at 65°C. Finally DNA was precipitated.

treatment_protocol: For UBF knock-out MEF cells were treated for 4h with 50 nM 4-hydroxytamoxifen.

value: MEF UBFwt/wt / ER-Cre+/+ / p53−/−

value: 72h after UBF ko

tag: molecule type

value: nucleolar DNA

source_name: MEF genomic DNA


title: Invasive front_rep3


title: Tumor mass_rep6


title: thymus_day7TBI_rep3

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

description: Gene expression from CD45- thymic stromal cells; SL-TBI was given at a dose of 550 cGy from a cesium source mouse irradiator with no hematopoietic rescue

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. Used Bioconductor Affy for normalization (GC-RMA) and gene annotation

source_name: Mouse thymus harvested 7 days post SL-TBI

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with Invitrogen Superscriptase.

treatment_protocol: Thymic non-hematopoietic stromal cells were isolated using CD45 MACS cell depletion. To obtain sufficient RNA for every timepoint, thymic ECs of several mice were pooled

tag: gender

value: female

value: thymus

tag: cell type

value: thymic non-hematopoietic stromal cells


title: Invasive front_rep2


title: MEF wt d0 II

value: untreated


title: MEF flox d3 I

value: MEF UBFfl/fl / ER-Cre+/+ / p53−/−


title: thymus_day7TBI_rep1


title: thymus_untreated_rep2

description: Gene expression from CD45- thymic stromal cells

source_name: Mouse thymus harvested, no damage


title: thymus_day7TBI_rep2


title: GS_PBS_88119

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: All mice were housed at 21 ±1 C and an alternating 12 hour light and 12 hour dark cycle. Standard chow (Sniff, Soest, Germany) and tap water were provided ad libitum.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with RMA using PartekGS default analysis settings

source_name: murine liver tissue

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

extract_protocol: Total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: 8-9 week old male mice were rendered hypothyroid for three weeks giving 0.02% methimazol, 0.5% perchlorate and 0.3% saccharine via drinking water and feeding a low iodine diet (TD.95007, Harlan-Teklad, USA). T3 was intraperitoneally injected at a concentration of 20 µg/100 g body weight and mice were sacrified after 6 hours and liver tissue was isolated and shock frozen in liquid nitrogen.

tag: genotype

value: Thyroid hormone receptor beta E125G, G126S mutant (C57BL/6J background)


title: thymus_untreated_rep1


title: Invasive front_rep1


title: MEF wt d3 I


title: GS_PBS_92933


title: GS_PBS_106407


title: MEF wt d0 I


title: GS_T3_85889


title: MEF flox d3 II


title: GS_T3_92928


title: KO_PBS_105815

value: Thyroid hormone receptor beta knock out (C57BL/6J background)


title: GS_T3_106403


title: thymus_day4TBI_rep3

source_name: Mouse thymus harvested 4 days post SL-TBI


title: KO_PBS_105809


title: MEF flox d0 II


title: iMEF wt d0 II

value: iMEF UBFwt/wt / ER-Cre+/+ / SvT


title: iMEF flox d0 I

value: iMEF UBFfl/fl / ER- Cre+/+ / SvT


title: KO_T3_105814


title: U2OS_Input

type: SRA

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: input sample (mix of all treatments)

library_source: genomic

data_processing:
Quality control of reads was performed with FastQC software
Reads were mapped to the human genome (hg19) with Bowtie2.0.4
Peak detection was carried with the MACS program (detected peaks are given in bed files)
p65 target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Peak intersections and their genomic coordinates were found using Bedtools software
The significance of differences between control untreated cells and cells subjected to TNFα and IR was estimated using MACS software; the FDR=0.05 level was selected as the significance threshold.
Genome_build: hg19
Supplementary_files_format_and_content: fastq - raw data from Illumina sequencer; bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: U2OS cells

growth_protocol: The wild-type U2-OS cells were purchased from ATCC (HTB-96) and used as a primary model. Cells were grown in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (HyClone) and gentamicin (40 mg/mL; Krka) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
2x10^6 cells were inoculated on 10 cm2 dish 2 days before experiments. At the appointed experimental points a two-step cross-linking procedure was applied for an efficient fixation of NF-κB dimers with DNA [27]. Cells were washed twice with PBS, a solution of DSG (disuccinimidyl glutarate) in PBS was added to the final concentration of 2 mM, and then cells were incubated for 45 minutes at RT with rotation. Next, cells were washed twice with PBS and the second fixation was performed using 1% formaldehyde for 10 min at RT. Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 15 cycles of 30 sec shearing followed by 30 sec of standby; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 3µl/sample of anti-RelA(p65) polyclonal antibody (C15310256, Diagenode) or without antibody (mock-IP), according to the manufacturer protocol.
Immunoprecipitated DNA fragments and input DNA were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

treatment_protocol: Any treatment started 48 h after inoculation of cells; all steps, with the exception of irradiation, were carried out at 37 °C and 5% CO2. For ChIP-Seq analysis wild-type cells were harvested after 0.5 and 4 hours of stimulation with TNFα (30ng/ml). Alternatively, cells were irradiated with 10 Gy IR dose at a 1Gy/min dose rate using 6 MeV photons (generated by linear accelerator Clinac 600, Varian), the medium was replaced with a fresh one, and cells were analyzed 2 or 4 hours after irradiation.

value: U2OS cells

value: osteosarcoma

tag: Sex

value: 15 years

tag: tissue/cells

value: bone

tag: chip antibody


title: KO_T3_105818


title: iMEF wt d3 II


title: WT_T3_89651

value: wild type (C57BL/6J background)


title: WT_T3_90288


title: WT_PBS_88121


title: WT_PBS_107237


title: KO_PBS_105816


title: iMEF flox d3 I


title: KO_T3_105807


title: thymus_day4TBI_rep1


title: thymus_day4TBI_rep2


title: iMEF flox d3 II


title: WT_PBS_88123


title: MEF flox d0 I


title: iMEF flox d0 II


title: Raji Control Replicate 2

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

description: Gene expression data from Raji Cells as Controls

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMAExpress which performs background adjustments and quantile normalization

source_name: Raji Cells

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: SUDHL10 and Raji cell lines were grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Cells were treated with Cerulenin for 48 hours at 12.5uM.

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

treatment_protocol: Cells were treated with cerulenin for 48 hours at 12.5uM.

value: Raji

value: Diffuse Large B Cell Lymphoma

value: Control


title: WT_T3_90286


title: thymus_untreated_rep3

value: female


title: Raji Cerulenin Replicate 3

description: Gene expression data from Raji Cells with 12.5uM of Cerulenin treatment for 48 hours

source_name: Raji Cells with Cerulenin Treatment

value: 12.5uM of Cerulenin for 48 Hours


title: Raji Control Replicate 1


title: SUDHL10 Control Replicate 3

description: Gene expression data from SUDHL10 Cells as Controls

source_name: SUDHL10 Cells


title: SUDHL10 Control Replicate 1


title: SUDHL10 Cerulenin Replicate 1

description: Gene expression data from SUDHL10 Cells with 12.5uM of Cerulenin treatment for 48 hours

source_name: SUDHL10 Cells with Cerulenin Treatment


title: SUDHL10 Cerulenin Replicate 3


title: SUDHL10 Control Replicate 2


title: SUDHL10 Cerulenin Replicate 2


title: SKO_16M

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

hyb_protocol: Fragmented and Labeled products were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix part# 902500). Washing and staining of arrays took place on the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G system

data_processing: Raw .CEL files were were analyzed with in the Affymetrix Expression Console software v.1.3.1.187 using rma-sketch normalization with Affymetrix default analysis settings to generate .CHP files.

source_name: IL10 WT, STING knockout

label_protocol: 300ng of Total RNA per sample was prepared using the GeneChip WT PLUS Reagent Kit (Affymetrix part#902280) and yielded cDNA product for fragmentation and labeling

growth_protocol: We extracted the colon from each genotype mice.

extract_protocol: total RNA extraction using QIAGEN RNeasy mini kit following kit instruction

value: colon


title: SKO_14M


title: WT_3M

source_name: IL10 WT, STING WT


title: WT_4M


title: DKO_10M

source_name: IL10 knockout, STING knockout


title: IL10KO_29M

source_name: IL10 knockout, STING WT


title: SKO_15M


title: WT_5M


title: DKO_9M


title: DKO_8M


title: IL10KO_27M


title: MyD88KO LPS-1

description: gBarber_MoGene2.0_A9_MyD88KO LPS-1_1252017

source_name: LPS treatment

growth_protocol: We isolataed the mouse embryonic fibroblast from WT, SKO, or MyD99KO mice.

treatment_protocol: The cells were trasfected with dsDNA or treated with LPS. Untreated cells were used as a control.

value: MyD88KO murine embryonic fibroblasts


title: SKO mock-1

description: gBarber_MoGene2.0_A4_SKO mock-1_1252017

source_name: Control

value: SKO murine embryonic fibroblasts

value: STING-/-


title: SKO ISD-1

description: gBarber_MoGene2.0_A5_SKO ISD-1_1252017

source_name: dsDNA transfection


title: MyD88KO mock-1

description: gBarber_MoGene2.0_A7_MyD88KO mock-1_1252017


title: MyD88KO ISD-1

description: gBarber_MoGene2.0_A8_MyD88KO ISD-1_1252017


title: WT LPS-1

description: gBarber_MoGene2.0_A3_WT LPS-1_1252017

value: WT murine embryonic fibroblasts

value: STING+/+


title: AML Compound, biological repeat rep3

city: Tianjin

first: Hui

last: Cheng

address: 288 Nanjing road

institute: Institute of Hematology

description: Gene expression data from Compound inducible 24h leukemia cells

hyb_protocol: Following fragmentation,  Labeled cRNA was hybridized to Mouse Gene 2.0 ST GeneChip® arrays (Affymetrix, America).

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000 7G

data_processing: Raw data (CEL files) were normalized at transcript level using robust multiaverage method (RMA workflow).

source_name: Leukemia cells (MLL-AF9) after Compound induction 24h

label_protocol: RNA was labeled using the GeneChip® WT Terminal Labeling and Controls Kit combined with the Ambion® WT Expression Kit.

growth_protocol: leukemia cells and normal HSPCs were sorted by FACS from 4F mice and treated with Dox and compound (VC6T) in vitro for 24h.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Canada) and purified using RNeasy Mini Kit (Qiagen, German), including a DNase digestion treatment. RNA concentrations were determined by NanoDrop 2000 (Thermo, America).

treatment_protocol: After treatment, cells were centrifuged at 1400rpm and Trizol were added into the tube

tag: disease state

value: AML

value: BM

value: leukemia cells

tag: protocol

value: reprogramming compound treatment 24h


title: SKO LPS-1

description: gBarber_MoGene2.0_A6_SKO LPS-1_1252017


title: Raji Control Replicate 3

tag: cell line


title: IL10KO_26M


title: LSK Dox, biological repeat rep3

description: Gene expression data from Dox inducible 24h Normal HSPCs

source_name: Normal HSPCs (LSK) after Dox induction 24h

value: control

value: Normal HSPCs

value: Dox induction of OSKM expression 24h


title: Raji Cerulenin Replicate 1

value: Raji

value: Diffuse Large B Cell Lymphoma


title: LSK Control, biological repeat rep2

description: Gene expression data from control Normal HSPCs

source_name: Normal HSPCs (LSK) of control group


title: WT mock-1

description: gBarber_MoGene2.0_A1_WT mock-1_1252017


title: WT ISD-1

description: gBarber_MoGene2.0_A2_WT ISD-1_1252017


title: LSK Dox, biological repeat rep1


title: LSK Compound, biological repeat rep3

description: Gene expression data from Compound inducible 24h Normal HSPCs

source_name: Normal HSPCs (LSK) after Compound induction 24h


title: AML Dox, biological repeat rep2

description: Gene expression data from Dox inducible 24h leukemia cells

source_name: Leukemia cells (MLL-AF9) after Dox induction 24h


title: LSK Control, biological repeat rep1


title: AML Compound, biological repeat rep2


title: AML Control, biological repeat rep3

description: Gene expression data from control leukemia cells

source_name: Leukemia cells (MLL-AF9) of control group


title: AML Dox, biological repeat rep3


title: AML Dox, biological repeat rep1


title: TH3639_ccnk_7

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Reads were aligned to mouse genome assembly mm9 or mm10 using STAR with default parameters.
Read count tables were created using FeatureCounts using UCSC refFlat gene models
Genome_build: mm9 (Setd1aKO) mm10 (Ccnk CRISPR)
Supplementary_files_format_and_content: read count of each transcript

source_name: mouse MLL-AF9 leukemia_Ccnk sgRNA CRISPR

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Total RNA was purified with RNeasy Mini kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Tamoxifen was treated for 24 hours. Dox was treated for 4 days.

tag: genotype/variation

value: Ccnk sgRNA CRISPR


title: LSK Compound, biological repeat rep2


title: LSK Compound, biological repeat rep1


title: Ccnk_4


title: AML Compound, biological repeat rep1


title: LSK Control, biological repeat rep3


title: Ccnk_3


title: LSK Dox, biological repeat rep2


title: AML Control, biological repeat rep1


title: TH3639_ccnk_8


title: TH3639_ccnk_3

source_name: mouse MLL-AF9 leukemia_Control

value: Control


title: TH3639_ccnk_2


title: TH3639_ccnk_1


title: Emp_1


title: MLL-AF9_WT2_K27Ac

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
Duplicate reads were removed
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 1 million reads

source_name: mouse MLL-AF9 leukemia

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3. NIH3T3 cells were grown in DMEM media supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Cells were fixed with 2mM DSG for 30 min followed by 1% formaldehyde for 10 min  and treated with 0.125M Glycine for 5 min. Washed cells were suspended in ChIP Lysis Buffer  and shredded using Bioruptor (Diagenode) or E220 Focused-ultrasonicator (Covaris). Histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed with the ThruPLEX DNA-seq Kit following the manufacturer’s recommended protocol (Rubicon genomics).

value: Setd1a wild-type

value: H3K27Ac (abcam Cat#ab4729)


title: NIH3T3_3T3 Setd1a-2 SETD1A

source_name: mouse NIH3T3 cell line

value: Setd1a knockdown

value: SETD1A (abcam Cat#ab70378)


title: NIH3T3_3T3 Ren SETD1A


title: MLL-AF9_E6-TAM CCNK

value: CCNK (Bethyl Laboratories Cat#301-939A)


title: NIH3T3_3T3 Ren Pol2

value: RNAP2 (diagenode Cat#C15100055)


title: MLL-AF9_E6+TAM CCNK

value: Setd1a knockout


title: MLL-AF9_WT2_K4me3

value: H3K4me3 (abcam Cat#ab8580)


title: NIH3T3_3T3 Setd1a-2 Pol2


title: Testo_100nM_1

city: Illkirch

first: Angélique

last: Quartier

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description:
Processed data file(s):
hNSCs_batch1_androgens_24h_Deanalysis

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 / 1.18.61 and CASAVA 1.8.2.
Tophat v1.4.1 with bowtie v0.12.7 was used for read mapping.
Gene expression was quantified using HTSeq v0.5.3p5 and gene annotations from Ensembl release 72.
Normalization was performed using the DESeq2 Bioconductor package (v1.0.19).
Genome_build: hg19
Supplementary_files_format_and_content: .csv file(s) with raw read counts and normalized counts

source_name: Neural Stem Cells

growth_protocol: ES cell–derived hNSC cells were routinely maintained on poly-ornithine and laminin-coated dishes in Dulbecco's modified Eagle's medium/F12 Glutamax and Neurobasal medium (1:1) supplemented with N2, B27 and 50µM 2-mercaptoethanol containing brain-derived growth factor (20ng/mL), fibroblast growth factor-2 (10ng/mL) and epidermal growth factor (10ng/mL).

extract_protocol:
Total RNA were extracted from treated cells using TRI reagent, treated with DNase I recombinant (1U/µg of nucleic acids) during 30min at 37°C and then purify by using the RNeasy mini kit.
RNA libraries were prepared for high throughput DNA sequencing using “TruSeq™ RNA Sample Preparation v2 Kit” protocol.

treatment_protocol: Cells were placed in depleted medium (phenol-red free medium without N2 and B27) during 48h hours before androgen treatments and thus treated with DMSO, DHT 100nM , 10nM, Testosterone 100nM, 10nM, R1881 1nM, retinoic acid 1µM during 24h hours.

value: ES-derived neural stem cells

value: Testo 100nM 24 hours


title: R1881_1nM_1

value: R1881 1nM 24 hours


title: Testo_10nM_1

value: Testo 10nM 24 hours


title: Testo_10nM_2


title: RA_1µM_3

value: RA 1µM 24 hours


title: Testo_100nM_2


title: Testo_100nM_3


title: RA_1µM_1


title: RA_1µM_2


title: R1881_1nM_3


title: R1881_1nM_2


title: DHT_10nM_3

value: DHT 10nM 24 hours


title: MLL-AF9_WT1_K4me3

value: leukemia cells


title: MLL-AF9_HO2_K27Ac


title: MLL-AF9_WT1_Input

value: no antibody


title: MLL-AF9_WT2_Input


title: MLL-AF9_HO2_Input


title: MLL-AF9_WT1_K27Ac


title: DHT_10nM_2


title: MLL-AF9_HO2_K4me3


title: DHT_10nM_1


title: GIST48-siFOXF1-H3K4Me1

first: Yuedan

last: Chen

state: NY

department: HOPP

data_processing:
The sequenced reads from fastq files were aligned to the human genome (hg 19) using the Bowtie alignment software, and duplicate reads were eliminated for subsequent analysis. Peak calling was performed using MACS 2.1 comparing immunoprecipitated chromatin with input chromatin, using a false-discovery rate cutoff of q<10-3.
Genome_build: hg19

growth_protocol: All media were supplemented with l-glutamine (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml), and 10% heat-inactivated fetal bovine serum (FBS) except the medium used for GIST882 cells was supplemented with 15% FBS.

extract_protocol:
GIST cells were transfected with siRNAs using DharmaFECT2 (GE healthcare) according to the manufacture’s protocol. In brief, transfection was performed under serum free conditions, using 20nM siRNA in Opti-MEM.
cells were crosslinked for 15 min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using Bioruptor (Diagenode) to fragments of approximately 150 base pairs and was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with primary antibody,
ChIP libraries were prepared for sequencing using standard Illumina protocols


title: GIST48-siFOXF1-H3K4Me3


title: GIST48-siFOXF1-ETV1


title: Testo_10nM_3


title: GIST48-siETV1-H3K4Me3


title: GIST48-siFOXF1-FOXF1


title: GIST48-siFOXF1-Input


title: GIST48-siETV1-H3K4Me1


title: GIST48-siETV1-FOXF1


title: HR42.180D

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Chronic SIV-infected

data_processing:
QuantStudio run files representing all treatment groups and timepoints were analyzed first using ExpressionSuite Software (Thermo Fisher). The output file from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) was saved as a tab-delimited text file, imported and analyzed using the Omics Office StatMiner qPCR analysis software (TIBCO Spotfire, Perkin Elmer, Waltham, MA) using the non-parametric Mann-Whitney U test.
miRNA expression data was analyzed using global normalization method.
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Multiple comparisons correction was performed using Benjamini-Hochberg method for false discovery rate.
Omics Office StatMiner qPCR analysis software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio files. Comparisons between the two groups were made using non-parametric Mann-Whitney U test.
Fold Change worksheet reports test/control (i.e., Chronic-SIV vs uninfected control) ratios.

organism: Macaca mulatta

source_name: Colonic Epithelium

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 8 animals were infected intravenously with 100 TCID50 SIVmac251 and 4 (3 THC only and 1 vehicle only) remained uninfected

value: Chronic SIV


title: HV48

description: Chronic SIV-infected


title: GIST48-siETV1-Input


title: GIST48-siETV1-ETV1


title: GIST48-siSCR-H3K4Me1


title: GIST48-siSCR-H3K4Me3


title: GIST48-siSCR-FOXF1


title: GIST48-siSCR-ETV1


title: MLL-AF9_HO1_Input


title: MLL-AF9_HO1_K27Ac


title: GA19

description: Chronic SIV-infected


title: GIST48-siSCR-Input


title: HB31

description: Chronic SIV-infected


title: MLL-AF9_HO1_K4me3


title: AML Control, biological repeat rep2

value: AML

value: BM

value: control


title: HG45

description: Chronic SIV-infected


title: HD08.90D

description: Chronic SIV-infected


title: HH07.180D

description: Chronic SIV-infected


title: HF54.180D

description: Chronic SIV-infected


title: HI68

description: Chronic SIV-infected


title: MDA-PCa2b-ETV1

extract_protocol:
cells were crosslinked for 15 min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using Bioruptor (Diagenode) to fragments of approximately 150 base pairs and was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with primary antibody,
ChIP libraries were prepared for sequencing using standard Illumina protocols


title: FT11

description: Chronic SIV-infected


title: FE24

description: Chronic SIV-infected


title: HN15

description: Chronic SIV-infected


title: MDA-PCa2b-Input


title: GIST-T1-FOXF1


title: GIST-T1-input-2


title: Raji Cerulenin Replicate 2

source_name: Raji Cells with Cerulenin Treatment

value: Raji

value: Diffuse Large B Cell Lymphoma

value: 12.5uM of Cerulenin for 48 Hours


title: EJ34

description: Control

value: Uninfected


title: GIST-T1-ETV1


title: GIST-T1-input-1


title: HT73

description: Control


title: IT05

description: Control


title: HR42.Preinfection

description: Control


title: GIST48-input


title: HH07.Preinfection

description: Control


title: HF54.Preinfection

description: Control


title: GIST48-FOXF1


title: HD08.Preinfection

description: Control


title: T1-siFOXF1_ATAC-seq

data_processing:
ATAC-seq reads were quality and adapter trimmed using ‘trim_galore’ before aligning to human genome assembly hg19 with bowtie2 using the default parameters. Aligned reads with the same start position and orientation were collapsed to a single read before subsequent analysis. Density profiles were created by extending each read to the average library fragment size and then computing density using the BEDTools suite, with subsequent normalization to a sequencing depth of ten million reads for each library.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of raw data

extract_protocol:
cell nuclei were prepared from 50,000 cells, and incubated with 2.5 μl of transposase (Illumina) in a 50-μl reaction for 30 min at 37 °C.
ATAC libraries were prepared for sequencing using standard Illumina protocols, After purification of transposase-fragmented DNA, the library was amplified by PCR and subjected to paired-end 50 base-pair high-throughput sequencing on an Illumina HiSeq2500 platform.

treatment_protocol: GIST cells were transfected with siRNAs using DharmaFECT2 (GE healthcare) according to the manufacture’s protocol. GIST48, GIST-T1 and GIST882 cells with siRNA-mediated downregulations of FOXF1, ETV1 or scramble controls at a time point (48-72 hours after siRNA transfection) before any remarkable growth suppression or cell death was observed


title: 7C6-rep3 [LFDA_9]

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5).
Raw gene counts were generated from STAR output
Differential gene expression was analyzed by DESeq2 (version 3.5)
Supplementary_files_format_and_content: STAR.csv: Comma-separated text file includes raw gene counts for each sample.

source_name: Human NK cells_A375-7C6-hIgG1

growth_protocol: RPMI-1640 media with 10% FBS

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, # 74134) following the manufacturer’s protocol.
Standard mRNA library preparation kit (Kapa mRNAseq kit (KapaBiosystems)) was used for library preparation.

treatment_protocol: NK cells were co-cultured for 6 hours with A375 cells treated with either isotype control or MICA/B antibody (clone 7C6-hIgG1)

value: Human NK cells

tag: cocultivated with

value: A375 tumor cells

tag: a375 pretreated with

value: MICA/B antibody (clone 7C6-hIgG1)


title: 7C6-rep2 [LFDA_8]


title: 7C6-rep1 [LFDA_7]


title: Isotype_rep2 [LFDA_5]

source_name: Human NK cells_A375-isotype

value: isotype control (BioXcell BE0096) antibodies


title: Isotype_rep1 [LFDA_4]


title: Isotype_rep3 [LFDA_6]


title: G882-siETV1_ATAC-seq


title: G882-siSCR_ATAC-seq


title: G882-siFOXF1_ATAC-seq


title: T1-siSCR_ATAC-seq


title: G48-siETV1_ATAC-seq


title: T1-siETV1_ATAC-seq


title: G48-siFOXF1_ATAC-seq


title: G48-siSCR_ATAC-seq


title: IH95

description: Control


title: ILC1 donor 1 + PDGF-DD

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: immune subset

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Human 1.0 ST Array in the GeneChip Hypridization Oven 640 for 18hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Sation 450

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

data_processing: Data were processed using the AffySTExpressionFileCreator function of GenePattern from the Broad Institute using quantile normalization and background correction. Data were analzyed using Multiplot Studio from the Broad Institute.

source_name: tonsil

label_protocol: Biotyinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

growth_protocol: CD3-CD19-NKp44+CD103+ ILC1 sorted from enriched tonsilar CD56+ cells were expanded in IL-2 (10 ng/ml, Peprotech) for 10 days prior to PDGF-DD stimulation.

extract_protocol: Qiagen RNAeasy Plus Micro kit was used to extract RNA from freshly sorted human myeloid cell subsets.

treatment_protocol: Tonsil ICL1 were stimulated with or without 250 ng/ml PDGF-DD (R&D systems) for 16h prior to RNA isolation

tag: agent

value: 50 ng/ml PDGF-DD


title: ILC1 donor 2 medium

description: immune subset


title: reil1-1 reil2-1_20°C->10°C_3W_rep2

city: Potsdam-Golm

first: Dirk

last: Walther

address: Am Mühlenberg 1

department: Bioinformatics

institute: Max Planck Institute for Molecular Plant Physiology

description: 20°C->10°C acclimated

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides. The scanned images were analyzed with GeneSpring (Agilent). Percentile normalization (75 percentile) was performed for each chip.

data_processing: ID_REF =  VALUE = Quantile normalized, log-2 transformed signal intensity

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) 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-1000 Spectrophotometer.

growth_protocol: Constant optimized temperature conditions at 20°C. Seedlings were transferred to soil after 10 days of in vitro cultivation at 20°C. Plants were acclimated to soil in short days with an 8h/16h day/night cycle at 20°C/18°C, 100-150 µmol m-2 s-1 light intensity, and 60%-70% relative humidity using a controlled-environment chamber. After a total of 4 weeks, namely 10 days in vitro cultivation and 18 days on soil, the wildtype reached stage ~1.10.

extract_protocol: Total plant RNA of samples from the time points 0 (non-acclimated, i.e. before transfer), 1 day, 1 week, and 3 weeks was isolated from leaf tissue using the RNeasy Plant Mini Kit and RNase free DNAse (Qiagen, Hilden, Germany). RNA integrity number (RIN) was evaluated and calculated by microfluidic electrophoresis using an Agilent 2100 Bioanalyzer and 2100 Expert software (Agilent Technologies GmbH & Co. KG, Waldbronn, Germany). RNA samples with RIN > 8.0 were sent to the 4×44K Agilent expression profiling service of ATLAS Biolabs GmbH (Berlin, Germany).

treatment_protocol: Temperature shift from 20°C to 10°C. At stage ~1.10 plants were transferred from optimized conditions to a controlled-environment chamber that was set to long days with a 16h/8h day/night cycle at 10°C/8°C, 100-150 µmol m-2 s-1 light intensity and 60%-70% relative humidity. Mature leaves of plant rosettes were harvested at 0 (non-acclimated, i.e. before transfer),  24 hour after acclimation and furthermore at 1 and 3  weeks after acclimation.

tag: tissue

value: rosette DS 1.14 (leaf number)

value: cold treatment

tag: time point

value: reil1-1 reil2-1


title: ILC1 donor 1 medium

description: immune subset


title: Col-0_20°C->10°C_3W_rep3

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_3W_rep3

value: rosette DS 1.35 (leaf number)

tag: treatment

value: wild type Col-0


title: Col-0_20°C->10°C_3W_rep1

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_3W_rep1


title: reil1-1 reil2-1_20°C->10°C_3W_rep1

description: 20°C->10°C acclimated


title: reil1-1 reil2-1_20°C->10°C_1W_rep3

description: 20°C->10°C acclimated

value: rosette DS 1.10 (leaf number)


title: Col-0_20°C->10°C_1W_rep3

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_1W_rep3


title: Glioblastoma stem-like cells transfected with the empty vector rep3

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing:
Affymetrix HuGene-1_0-st chip with bioconductor cdf (hugene10stv1cdf); The data were normalized with Bioconductor software using RMA algorithm.
The versions of the software used in the analysis were: R 2.15.0, Bioconductor 2.11 and affy package 1.36.0.

source_name: GSCs_empty vector

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: GBM cells were maintained in serum-free DMEM/F12 medium (Life Technologies, Paisley, UK) and plated at a density of 3x10^6 live cells/60-mm plate. Primary neurospheres were dissociated every 4 days to facilitate cell growth.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: No prior treatment

tag: sample source

value: Surgical specimen from glioblastoma patients

value: Glioblastoma stem-like cells (GSCs)

tag: transfected with

value: empty vector


title: Glioblastoma stem-like cells transfected with the intracellular fragment of ODZ1 rep2

tag: cell type

value: intracellular fragment of ODZ1


title: Col-0_20°C->10°C_1W_rep2

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_1W_rep2


title: Glioblastoma stem-like cells transfected with the empty vector rep1


title: reil1-1 reil2-1_20°C->10°C_1W_rep2

description: 20°C->10°C acclimated


title: ILC1 donor 2 + PDGF-DD

description: immune subset


title: Glioblastoma stem-like cells transfected with the intracellular fragment of ODZ1 rep1


title: Glioblastoma stem-like cells transfected with the intracellular fragment of ODZ1 rep3


title: reil1-1 reil2-1_20°C->10°C_3W_rep3

description: 20°C->10°C acclimated


title: reil1-1 reil2-1_20°C->10°C_24hr_rep2

description: 20°C->10°C acclimated


title: Glioblastoma stem-like cells transfected with the empty vector rep2


title: reil1-1 reil2-1_20°C->10°C_24hr_rep3

description: 20°C->10°C acclimated


title: Col-0_20°C->10°C_3W_rep2

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_3W_rep2


title: Col-0_20°C->10°C_1W_rep1

description: 20°C->10°C acclimated

source_name: plant rosette_Col-0_20°C->10°C_1W_rep1


title: reil1-1 reil2-1_20°C->10°C_1W_rep1

description: 20°C->10°C acclimated


title: reil1-1 reil2-1_20°C_rep5

description: 20°C non acclimated

source_name: plant rosette_reil1-1 reil2-1_20°C_rep5

value: non-treatment


title: Col-0_20°C_rep6

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep6


title: Col-0_20°C->10°C_24hr_rep2

description: 20°C->10°C acclimated


title: Col-0_20°C_rep4

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep4


title: reil1-1 reil2-1_20°C_rep4

description: 20°C non acclimated

source_name: plant rosette_reil1-1 reil2-1_20°C_rep4


title: BS13_38Ba

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip MoGene-1.0 ST-V1 microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: Liver from adult mice

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: Liver

tag: genotype

tag: diet

value: high-fat diet


title: Col-0_20°C->10°C_24hr_rep1

description: 20°C->10°C acclimated


title: Col-0_20°C_rep2

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep2


title: BS15_39Bb


title: BS16_41Ba


title: Col-0_20°C->10°C_24hr_rep3

description: 20°C->10°C acclimated


title: BS14_39Ba


title: Col-0_20°C_rep3

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep3


title: reil1-1 reil2-1_20°C->10°C_24hr_rep1

description: 20°C->10°C acclimated


title: reil1-1 reil2-1_20°C_rep1

description: 20°C non acclimated

source_name: plant rosette_reil1-1 reil2-1_20°C_rep1


title: reil1-1 reil2-1_20°C_rep3

description: 20°C non acclimated

source_name: plant rosette_reil1-1 reil2-1_20°C_rep3


title: Col-0_20°C_rep5

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep5


title: Col-0_20°C_rep1

description: 20°C non acclimated

source_name: plant rosette_Col-0_20°C_rep1


title: BS11_30Ba


title: BS06_55Ba

value: Control Diet


title: BS12_30Bb


title: reil1-1 reil2-1_20°C_rep2

description: 20°C non acclimated

source_name: plant rosette_reil1-1 reil2-1_20°C_rep2


title: BS09_45Bc


title: BS05_54Ba


title: BS10_46Ba


title: BS07_55Bc


title: BS02_42Bb


title: BS03_47Bc


title: BS08_35Bb


title: BS04_42Bc


title: EL-5 Control Replicate 3

description: Gene expression data from EL-5 Cells as Controls

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were corrected by normalizing to the housekpeeking genes and then quantile normalization with GenePattern Illumina Normalizer Module.

source_name: EL-5 Cells

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

growth_protocol: SUDHL4, SUHDL10, EL-2, EL-5 and Raji cell line was grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C.

treatment_protocol: No treatment of cells


title: EL-2 Control Replicate 3

description: Gene expression data from EL-2 Cells as Controls

source_name: EL-2 Cells


title: EL-5 Control Replicate 2


title: Raji Control Replicate 2

source_name: Raji Cells

value: Raji


title: BS01_46Bb


title: EL-2 Control Replicate 1


title: Raji Control Replicate 1


title: EL-2 Control Replicate 2


title: SUDHL10 Control Replicate 5

source_name: SUDHL10 Cells


title: SUDHL10 Control Replicate 3


title: SUDHL10 Control Replicate 6


title: Raji Control Replicate 3


title: EL-5 Control Replicate 1


title: SUDHL4 Control Replicate 6

description: Gene expression data from SUDHL4 Cells as Controls

source_name: SUDHL4 Cells


title: SUDHL10 Control Replicate 2


title: 2147

city: Leeds

first: Mihaela

last: Lorger

address: Beckett street

department: Leeds Institute of Cancer and Pathology

institute: University of Leeds

description: sample name: s2147_B

data_processing:
Data analysis was performed by Novogene. Quality control raw data (raw reads) in fastq format were firstly processed through in-house perl scripts
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data
Index of the reference genome was built using Bowtie v2.2.3 and single-end clean reads were aligned to the reference genome using TopHat v2.0.12
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene (Quantification of gene expression level). FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: text file with raw read counts or fpkm.

source_name: Intracranial tumor

growth_protocol: B16 cells (1x10^5) were implanted into the brain of C57Bl6 mice; established tumours were isolated after 9 days;

extract_protocol:
Tissue was lysed in lysis buffer (RNAqueous-Micro Total RNA isolation kit; Ambion) immediately after isolation and RNA extracted according to the manufacurer's protocol.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: Treatment differed between groups and is specified for each sample;

tag: strain

tag: tumor presence in mice

value: Intracranial  and extracranial tumor

value: anti-PD-1 plus anti-CTLA-4


title: SUDHL10 Control Replicate 1


title: SUDHL4 Control Replicate 5


title: SUDHL4 Control Replicate 3 (2)


title: 2139

description: sample name: s2139_B2

value: IgG


title: SUDHL10 Control Replicate 4


title: 2135

description: sample name: s2135_B


title: 2140

description: sample name: s2140_B


title: 2131

description: sample name: s2131_B

value: Intracranial tumor


title: SUDHL4 Control Replicate 1 (2)


title: SUDHL10 TVB3567 Replicate 2

description: Gene expression data from SUDHL10 Cells with IC50 concentration of TVB3567 treatment for 48 hours

source_name: SUDHL10 Cells with TVB3567 Treatment

growth_protocol: SUDHL2, SUHDL10, and Raji cell line was grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Cells were treated with 12.5uM Cerulenin, or IC50 drug concentrations for TVB3567 and TVB3166 for 48 hours.

value: SUDHL10 Cells


title: SUDHL10 TVB3166 Replicate 2

description: Gene expression data from SUDHL10 Cells with IC50 concentration of TVB3166 treatment for 48 hours

source_name: SUDHL10 Cells with TVB3166 Treatment

treatment_protocol: Cells were treated with 12.5uM Cerulenin, or IC50 drug concentrations for TVB3567 and TVB3166 for 48 hours.


title: SUDHL10 TVB3567 Replicate 3


title: 2144

description: sample name: s2144_B


title: SUDHL10 TVB3166 Replicate 3


title: SUDHL10 Control 1% FBS Replicate 2

description: Gene expression data from SUDHL10 Cells as Controls with 1% FBS

source_name: SUDHL10 Cells 1% FBS

value: 1% FBS Control


title: SUDHL10 Control 1% FBS Replicate 1


title: SUDHL4 Control Replicate 4


title: SUDHL10 Control 1% FBS Replicate 3


title: Raji TVB3166 Replicate 1

description: Gene expression data from Raji Cells with IC50 concentration of TVB3166 treatment for 48 hours

source_name: Raji Cells with TVB3166 Treatment

value: Raji Cells


title: 2130

description: sample name: s2130_B


title: Raji TVB3567 Replicate 2

description: Gene expression data from Raji Cells with IC50 concentration of TVB3567 treatment for 48 hours

source_name: Raji Cells with TVB3567 Treatment


title: Raji TVB3166 Replicate 3


title: soma_wt1

city: Paris

first: Remi-Xavier

last: Coux

address: 25 rue du docteur Roux

department: Developmental and Stem Cell Biology dpt

institute: Pasteur Institute

description:
PolyA RNA
processed data file: Soma_RNAseq.xlsx

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software (Illumina).
Reads were aligned to the fly genome (build dm3/BDGP5) using the splice-aware STAR aligner (Dobin et al., 2013)
PCR duplicates were removed using the Picard toolkit (https://broadinstitute.github.io/picard/)
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exons (Anders et al., 2015).
These counts were then used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: dm3/BDGP5
Supplementary_files_format_and_content: Soma_RNAseq.xlsx: Excel spreadsheet contains differential expression per experiment, as well as normalized counts.
Supplementary_files_format_and_content: *.bw: Normalized bigwig files.

organism: Drosophila melanogaster

source_name: somatic ovaries (ovaries devoid of germ cells)

growth_protocol: Flies were maintained at 25˚C following standard procedures.

extract_protocol:
Somatic ovaries: 60-70 ovaries from females of maternal tud[1]/tud[B42] and zygotic l(3)mbt[GM76]/+ (control) or l(3)mbt[GM76]/Df genotypes were dissected in cold PBS and RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
Libraries were generated from 1µg of total RNA using the NEBNext Poly(A) magnetic Isolation Module (NEB #7490) and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB # E7420). Libraries from 3 biological replicates were sequenced on an Illumina Hi-Seq2000, paired-end 50 run.

value: somatic ovaries

tag: maternal genotype

tag: zygotic genotype

tag: Stage

value: 2-3 day old females


title: Raji Control 1% FBS Replicate 3

description: Gene expression data from Raji Cells as Controls with 1% FBS

source_name: Raji Cells 1% FBS

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)


title: SUDHL10 TVB3166 Replicate 1


title: Raji TVB3567 Replicate 1


title: 2142

description: sample name: s2142_B


title: Raji TVB3166 Replicate 2


title: 2125

description: sample name: s2125_B


title: SUDHL4 Control Replicate 2 (2)


title: 2118

description: sample name: s2118_B


title: 2117

description: sample name: s2117_B


title: 2124

description: sample name: s2124_B


title: mouse_resection_48_2

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: University of Pittsburgh

description:
mouse_surgery_48_2
M48_r2

data_processing:
Tophat 2 was used to align paired-end sequence reads to the GRCm30 genome for mouse and GRCz10 genome for zebrafish29
For mouse and zebrafish samples, Cufflinks was used to estimate gene expression levels in aligned reads and the resulting data was processed with Cuffdiff to identify differentially expressed genes between resected and sham groups at each time point and species
Trinity was used to produce a de novo transcriptome for Axolotl.
RSEM was used to analyzed Axolotl data.
Genome_build: GRCm30 (mouse), GRCz10 (zebrafish); FASTA for Axolotl transcripts is available on the series record.
Supplementary_files_format_and_content: text files with expression values (TPM, FPKM)

source_name: Heart ventricles

extract_protocol:
Total RNA from the lower half of the ventricle of resected and sham hearts was isolated using Trizol at three different time points: 12, 24, and 48 hours post-surgery. Three biological replicates were used for each time point and condition in each species. For neonatal mice and axolotls, each replicate represents myocardium from a single animal. Due to the smaller size of the zebrafish, each biological replicate represents three pooled tissue samples. Poly-adenylated mRNA was isolated using the Wafergen #400047 protocol.
RNA-sequencing libraries were prepared with the IntegenX Directional PrepX mRNA kit. Paired-end (50 base pairs) sequencing was performed using an Illumina HiSeq 2500.

treatment_protocol: neonatal CD1 mice, adult axoltol and zebrafish are subjected to apical resection to remove ~15% of the ventricular mass. Sham surgeries are performed as control.

value: Heart ventricles

tag: timepoint

value: 48 hours post resection

tag: surgical treatment

value: apical resection


title: mouse_resection_48_1

description:
mouse_surgery_48_1
M48_r1


title: mouse_resection_48_3

description:
mouse_surgery_48_3
M48_r3


title: SUDHL10 TVB3567 Replicate 1


title: Raji TVB3567 Replicate 3


title: SUDHL2 Cerulenin Replicate 2

description: Gene expression data from SUDHL2 Cells with 12.5uM of Cerulenin treatment for 48 hours

source_name: SUDHL2 Cells with Cerulenin Treatment

value: Cerulenin

value: SUDHL2 Cells


title: mouse_sham_48_3

description:
mouse_sham_48_3
M48_s4

value: sham surgery


title: Raji Control 1% FBS Replicate 2


title: Raji Control 1% FBS Replicate 1


title: SUDHL2 Cerulenin Replicate 1


title: SUDHL2 TVB3567 Replicate 3

description: Gene expression data from SUDHL2 Cells with IC50 concentration of TVB3567 treatment for 48 hours

source_name: SUDHL2 Cells with TVB3567 Treatment


title: SHED vs SHED-Hep Replicate 5

city: Fukuoka

first: Haruyoshi

last: yamaza

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

department: Division of Oral Health, Growth & Development

institute: Faculty of Dental Science, Kyushu University

description: Biological replicate 3 of 3

hyb_protocol: labeled DNA was hybridized to a 60K 60-mer oligomicroarray ( Human CGH 4x180K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The data was analyzed with Agilent Genomic Workbench 7.0.4 using default parameters.

source_name: SHED

label_protocol: DNA was labelled using a SureTag DNA Labeling Kit (Agilent Technologies).

growth_protocol: SHED were grown with a growth medium consisting of 15% fetal bovine serum, 100 uM L-ascorbic acid 2-phosphate, 2 mM L-glutamine, and premixed antibiotics containing 100 U/ml penicillin and 100 ug/ml streptomycin in alpha Modification of Eagle's Medium.

extract_protocol: Genomic DNA extracted using Dneasy Blood&Tissue Kit following manufacturer's instructions

treatment_protocol: SHED were initially incubated with 20 ng/mL EGF and 10 ng/mL FGF2 for 2 days, and then stimulated with 10 ng/mL FGF2 , 20 ng/mL HGF and 0.61 g/Lnicoti amide for 7 days. Finally the cells were induced under a stimulation of 20 ng/mL oncostatin M, 1 uM dexamethasone and 1xITS premix for 21 days. Each medium was changed twice weekly during the culture.

value: undifferentiated SHED

source_name: SHED-derived hepatocyte-like cells

value: hepatocyte differentiated SHED


title: SUDHL2 Cerulenin Replicate 3


title: SHED vs SHED-Hep Replicate 3

description: Biological replicate 2 of 3


title: SUDHL2 TVB3567 Replicate 2


title: SUDHL2 Control 1% FBS Replicate 1

description: Gene expression data from SUDHL2 Cells as Controls with 1% FBS

source_name: SUDHL2 Cells 1% FBS


title: SUDHL2 TVB3166 Replicate 3

description: Gene expression data from SUDHL2 Cells with IC50 concentration of TVB3166 treatment for 48 hours

source_name: SUDHL2 Cells with TVB3166 Treatment


title: Ovarian tumor from patient 10

city: LYON

first: Daniel

last: PISSALOUX

address: 28 rue Laënnec

department: Biopathology

institute: Centre Léon Bérard

description: FFPE sample

hyb_protocol: Co-hybridization was performed on 4x180K Agilent SurePrint G3 Human whole-genome oligonucleotide arrays (Agilent #G4449A) at 65°C for 24 hours, in a rotating oven at 20rpm. Slides were then washed with Oligo aCGH Wash Buffer 1 at room temperature for 5 min followed by 1 min wash with Oligo aCGH Wash Buffer 2 at 37°C. Finally, slides were dried.

scan_protocol: Slides were scanned using Agilent Surescan scanner G2600D with 3 μm resolution.

data_processing:
Scan images were processed using Agilent Feature Extraction Software V11.0 and the analysis was carried out using the Agilent Genomic Workbench software V7.0. The identification of aberrant copy number segments was based on ADM-2 segmentation algorithm with a threshold of 7.
Basically, chromosomal loci were considered as amplified if log2ratio were ≥ 1.6, and were considered as homozygously deleted if log2ratio were ≤ −1. However, these thresholds were manually adapted according to the percentage of tumor cells.

source_name: Ovarian tumor from yo-PCD patient 10

label_protocol: Fragmentation and labeling were done according to the manufacturer’s recommendation for the CGH arrays (Agilent Technologies, Santa Clara, CA) with some modifications. In brief, reference and tumor DNA were heat-denatured and fragmented during 10min at 95°C. Then, tumor DNA was chemically labeled with Universal Linkage System (ULS™, Agilent #5190-0450) Cy5-dye, whereas reference DNA was labeled with Cy3-dye. The labeled samples were then purified using Agilent KREApure columns (Agilent #5190-0418).

growth_protocol: FFPE archived samples of ovarian tumors

extract_protocol: DNA extraction was performed using the QIAamp DNA Micro kit (Qiagen #56304, Sussex, UK) according to the manufacturer’s instructions, and DNA was eluted in 25 μl of water.

treatment_protocol: Small amounts of tumor tissues were collected by scrapping 20 unstained slides containing 8 μm FFPE sections. Paraffin was removed using the Deparaffinization Solution (Qiagen #19093)

tag: tumor type

value: High grade serous carcinoma

tag: age at tumor diagnosis

tag: staging at tumor diagnosis

value: II

tag: percentage of tumor cells

source_name: Male reference DNA, commercial

tag: reference

value: Promega #G1471


title: SUDHL2 TVB3166 Replicate 2

first: Afshin

last: Beheshti

tag: treatment


title: SUDHL2 Control Replicate 1

description: Gene expression data from SUDHL2 Cells as Controls

source_name: SUDHL2 Cells

value: Control


title: SHED vs SHED-Hep Replicate 2

description: Biological replicate 1 of 3


title: Ovarian tumor from patient 24

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 24

value: Carcinosarcoma type

value: III


title: Ovarian tumor from patient 16

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 16

value: IV


title: SUDHL2 TVB3567 Replicate 1


title: SUDHL2 Control Replicate 2


title: mouse_sham_48_2

description:
mouse_sham_48_2
M48_s2

tag: tissue


title: SUDHL2 Control Replicate 3

tag: cell type


title: SUDHL2 TVB3166 Replicate 1


title: Ovarian tumor from patient 13

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 13


title: mouse_sham_48_1

description:
mouse_sham_48_1
M48_s1


title: mouse_resection_24_3

description:
mouse_surgery_24_3
M24_r4

value: 24 hours post resection


title: Ovarian tumor from patient 21

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 21

value: Clear cell carcinoma type

value: I


title: SUDHL2 Control 1% FBS Replicate 2

value: 1% FBS Control


title: SUDHL4 LDS Replicate 2

description:
LDS-02
Gene expression data from SUDHL4 Cells with LDS treatment for 48 hours

data_processing: The data were corrected by normalizing to the housekeeking genes and then quantile normalization with GenePattern Illumina Normalizer Module.

source_name: SUDHL4 Cells with LDS Treatment

growth_protocol: SUDHL4 cell line was grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Cells were treated with 12.5uM Cerulenin, 5.7uM TVB3567, and LDS for 48 hours.

tag: cell line

value: Diffuse Large B Cell Lymphoma

value: LDS for 48 hours


title: SUDHL4 LDS Replicate 3

description:
LDS-03
Gene expression data from SUDHL4 Cells with LDS treatment for 48 hours

treatment_protocol: Cells were treated with 12.5uM Cerulenin, 5.7uM TVB3567, and LDS for 48 hours.


title: SUDHL2 Control 1% FBS Replicate 3

value: SUDHL2 Cells


title: mouse_resection_24_2

description:
mouse_surgery_24_2
M24_r2

value: Heart ventricles

value: apical resection


title: mouse_resection_24_1

description:
mouse_surgery_24_1
M24_r1


title: Ovarian tumor from patient 11

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 11


title: mouse_sham_24_3

description:
mouse_sham_24_3
M24_s9

value: sham surgery


title: mouse_sham_24_2

description:
mouse_sham_24_2
M24_s2


title: SUDHL4 Cerulenin Replicate 3

description:
Cerulenin_12.5uM-03
Gene expression data from SUDHL4 Cells with 12.5uM of Cerulenin treatment for 48 hours

source_name: SUDHL4 Cells with Cerulenin Treatment

value: 12.5uM of Cerulenin for 48 Hours


title: SUDHL4 Cerulenin Replicate 1

description:
Cerulenin_12.5uM-01
Gene expression data from SUDHL4 Cells with 12.5uM of Cerulenin treatment for 48 hours


title: SUDHL4 TVB3567 Replicate 1

description:
TVB_3567_5.7uM-01
Gene expression data from SUDHL4 Cells with 5.7uM of TVB3567 treatment for 48 hours

source_name: SUDHL4 Cells with TVB Treatment

value: 5.7uM of TVB3567 for 48 Hours


title: SUDHL4 TVB3567 Replicate 2

description:
TVB_3567_5.7uM-02
Gene expression data from SUDHL4 Cells with 5.7uM of TVB3567 treatment for 48 hours


title: SUDHL4 TVB3567 Replicate 3

description:
TVB_3567_5.7uM-03
Gene expression data from SUDHL4 Cells with 5.7uM of TVB3567 treatment for 48 hours


title: mouse_sham_24_1

description:
mouse_sham_24_1
M24_s1

source_name: Heart ventricles


title: SUDHL4 LDS Replicate 1

description:
LDS-01
Gene expression data from SUDHL4 Cells with LDS treatment for 48 hours


title: SUDHL4 Control Replicate 1

description:
Untreated_Control-01
Gene expression data from SUDHL4 Cells as Controls

source_name: SUDHL4 Cells


title: SUDHL4 Control Replicate 2

description:
Untreated_Control-02
Gene expression data from SUDHL4 Cells as Controls


title: mouse_resection_12_3

description:
mouse_surgery_12_3
M12_r3

value: 12 hours post resection


title: SUDHL4 Cerulenin Replicate 2

description:
Cerulenin_12.5uM-02
Gene expression data from SUDHL4 Cells with 12.5uM of Cerulenin treatment for 48 hours


title: Ovarian tumor from patient 1

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 1

value: High grade serous carcinoma

value: Promega #G1471


title: Ovarian tumor from patient 8

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 8


title: Ovarian tumor from patient 18

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 18


title: SUDHL4 Control Replicate 3

description:
Untreated_Control-03
Gene expression data from SUDHL4 Cells as Controls

value: Control


title: L_24_57

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina BeadArray Assay System Manual.

data_processing: For each probe, replicated measurements (beads) were averaged after removing outliers by GenomeStudio software v.3 (Illumina). Data were then normalized using cubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

source_name: MDA-MB-231 cultured with post-mastectomy IF, low invasiveness

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Serum-free DMEM with 1% post-mastectomy fluid for 24h.

value: breast cancer cell line

value: interstitial fluid (IF) from post-mastectomy breast cancer patient

tag: patient id

tag: in vitro transwell invasiveness

value: low


title: L_24_85

scan_protocol: Refer to the Illumina BeadArray Assay System Manual.


title: Ovarian tumor from patient 9

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 9

value: III


title: H_24_71

source_name: MDA-MB-231 cultured with post-mastectomy IF, high invasiveness

label_protocol: Refer to the Illumina BeadArray Assay System Manual.

value: high


title: L_24_100


title: mouse_resection_12_2

description:
mouse_surgery_12_2
M12_r2

tag: strain


title: Setd1aWT-A7

data_processing:
Reads were aligned to mouse genome assembly mm9 or mm10 using STAR with default parameters.
Read count tables were created using FeatureCounts using UCSC refFlat gene models
Genome_build: mm9 (Setd1aKO) mm10 (Ccnk CRISPR)
Supplementary_files_format_and_content: read count of each transcript

source_name: mouse MLL-AF9 leukemia_Setd1a wild-type

extract_protocol:
Total RNA was purified with RNeasy Mini kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

value: leukemia cells

tag: genotype/variation

value: Setd1a wild-type


title: Setd1aWT-B6


title: Setd1aHO-E6

source_name: mouse MLL-AF9 leukemia_Setd1a knockout

value: Setd1a knockout


title: Setd1aWT-A5


title: Ovarian tumor from patient 7

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 7

source_name: Male reference DNA, commercial


title: mouse_resection_12_1

description:
mouse_surgery_12_1
M12_r1

value: Heart ventricles


title: Setd1aHO-E11


title: mouse_sham_12_3

description:
mouse_sham_12_3
M12_s3


title: Setd1aHO-E10


title: MLL-AF9_Setd1b shRNA MA9 H3K4me3

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
Duplicate reads were removed
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 1 million reads

source_name: mouse MLL-AF9 leukemia

extract_protocol:
Cells were fixed with 2mM DSG for 30 min followed by 1% formaldehyde for 10 min  and treated with 0.125M Glycine for 5 min. Washed cells were suspended in ChIP Lysis Buffer  and shredded using Bioruptor (Diagenode) or E220 Focused-ultrasonicator (Covaris). Histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed with the ThruPLEX DNA-seq Kit following the manufacturer’s recommended protocol (Rubicon genomics).

tag: genotype

value: Setd1b knockdown

tag: chip antibody

value: H3K4me3 (abcam Cat#ab8580)


title: L_24_48


title: Ovarian tumor from patient 14

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 14


title: MLL-AF9_Setd1a shRNA MA9 H3K4me3

value: Setd1a knockdown


title: Ovarian tumor from patient 25

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 25


title: MLL-AF9_Ren shRNA MA9 H3K4me3

value: Renilla luciferase knockdown


title: SL262684

city: Columbus

first: Emily

last: Nordquist

state: OH

address: 575 Children's Crossroad

department: Department of Cardiovascular Research

institute: Nationwide Children's Hospital

description: aortic heart valves from 5-6 adult mice, pooled

data_processing:
The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (3 nucleotides at the left end of the R1 reads and 1 nt at the left end of the R2 reads).
Sequence alignment was performed using TopHat v2.1.0 to the mm10 genome.
For exon and gene level counting Bioconductor easyRNASeq v. 2.4.7 package running on R version 3.2.2 platform was used.
The RPKM values were filtered to retain a list of genes with a minimum of approximately 50 mapped reads in 25% or more samples.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files include raw exon counts and raw gene counts for each sample

source_name: aortic heart valve at 4 months, biological replicate 3

extract_protocol:
Mice were euthanized and aortic valves were isolated on cold 1xPBS, then flash frozen in liquid nitrogen and stored at -80. Total RNA was isolated using TRI reagent.
Amplified cDNA libraries were prepared from 200 nanograms on DNA-free total RNA using TruSeq Stranded Total mRNA Library Prep Kit LT

value: aortic valve

tag: age

value: 4 months

value: wild type


title: SL262682

source_name: aortic heart valve at 4 months, biological replicate 1


title: SL262681

description: aortic heart valves from 5-6 pups, pooled

source_name: aortic heart valve at postnatal day 2, biological replicate 3

value: postnatal day 2


title: SL262683

source_name: aortic heart valve at 4 months, biological replicate 2


title: H_24_61

value: breast cancer cell line


title: SL262679

source_name: aortic heart valve at postnatal day 2, biological replicate 1


title: SL262680

source_name: aortic heart valve at postnatal day 2, biological replicate 2


title: mouse_sham_12_2

description:
mouse_sham_12_2
M12_s2

source_name: Heart ventricles

tag: timepoint

value: 12 hours post resection

tag: surgical treatment

value: sham surgery


title: H_24_56

value: interstitial fluid (IF) from post-mastectomy breast cancer patient


title: Ovarian tumor from patient 6

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 6

tag: tumor type

value: High grade serous carcinoma

tag: age at tumor diagnosis

value: II

value: Promega #G1471


title: H_24_46

value: high


title: mouse_sham_12_1

description:
mouse_sham_12_1
M12_s1

value: Heart ventricles


title: zebrafish_resection_48_1

description:
zebrafish_surgery_48_1
Z48_r1

organism: Danio rerio

value: Wild-type AB, wild-type TuAB

value: 48 hours post resection

value: apical resection


title: zebrafish_resection_48_2

description:
zebrafish_surgery_48_2
Z48_r2


title: zebrafish_resection_48_3

description:
zebrafish_surgery_48_3
Z48_r3


title: IHCC cells cultured with EM or DM

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

description: Gene expression profiling between EM and DM

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: EM

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: IHCC cells were expanded in EM that includes EGF and R-spondin1.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: Differentiation of IHCC cells performed by culture with DM that includes EGF, HGF, FGF19, DAPT, BMP7 and dexamethasone.

value: Human intrahepatic cholangiocarcinoma cells

tag: protocol

value: EM

source_name: DM

value: DM


title: zebrafish_sham_48_3

description:
zebrafish_sham_48_3
Z48_s3


title: zebrafish_sham_48_2

description:
zebrafish_sham_48_2
Z48_s2


title: zebrafish_resection_24_3

description:
zebrafish_surgery_24_3
Z24_r3

value: 24 hours post resection


title: Ovarian tumor from patient 2

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 2

tag: staging at tumor diagnosis

value: I

tag: percentage of tumor cells

tag: reference


title: OP50 24hours rep4

city: Manhattan

first: Michael

middle: A

last: Herman

state: KS

address: 266 Chalmers Hall

department: Division of Biology

institute: Kansas State University, Ecological Genomics Institute

description: RMA Call summary of mean expression

hyb_protocol: Performed by NimbleGen Gene Expression Services (Roche NimbleGen Inc.)

organism: Caenorhabditis elegans

source_name: nematode,  OP50, 24hrs

label_protocol: cDNA was synthesized using the SMARTer PCR cDNA synthesis kit (Clontech), amplified and optimized using the Advantage 2 PCR Kit (Clontech). Double-stranded cDNA was purified using the PureLinkTM Quick PCR Purification Kit (Invitrogen) and ethanol precipitation. Purified cDNA was sent to NimbleGen Gene Expression Services (Roche NimbleGen Inc.) for labeling.

growth_protocol: Synchronized wild-type nematodes were reared at 20˚C on E. coli OP50 from egg to larval stage 4 (L4).

extract_protocol: After 24 hours of feeding on the treatment bacteria at 25˚C, young adult nematodes were collected in M9 buffer and lysed in TRIzol® reagent (Life Technologies). This bulk extraction was considered one biological replicate and was repeated four times for each bacterial treatment. RNA extraction and DNAse treatment were performed using the PureLink RNA Mini Kit (Invitrogen) and on-column PureLink® DNase Treatment (Invitrogen).

treatment_protocol: L4s were then washed off the rearing plates with M9 buffer and placed onto lawns of S. maltophilia JCMS, K279a or E. coli OP50.

tag: bacterial strain

value: OP50 avirulent E.coli

tag: developmental stage

value: Young adult


title: Ovarian tumor from patient 20

description: FFPE sample

source_name: Ovarian tumor from yo-PCD patient 20

value: III


title: K279a 24hours rep3

description: RMA Call summary of mean expression

scan_protocol: Performed by NimbleGen Gene Expression Services (Roche NimbleGen Inc.)

source_name: nematode,  K279a, 24hrs

value: K279a avirulent S. maltophilia


title: K279a 24hours rep4

description: RMA Call summary of mean expression

data_processing: Performed by NimbleGen Gene Expression Services (Roche NimbleGen Inc.)


title: OP50 24hours rep3

description: RMA Call summary of mean expression


title: K279a 24hours rep1

description: RMA Call summary of mean expression


title: K279a 24hours rep2

description: RMA Call summary of mean expression


title: JCMS 24hours rep2

description: RMA Call summary of mean expression

source_name: nematode,  JCMS, 24hrs

value: JCMS virulent S. maltophilia


title: zebrafish_resection_12_2

description:
zebrafish_surgery_12_2
Z12_r2

tag: tissue

value: 12 hours post resection


title: zebrafish_sham_24_1

description:
zebrafish_sham_24_1
Z24_s1

value: sham surgery


title: zebrafish_sham_24_2

description:
zebrafish_sham_24_2
none
sample failed quality control and was not included in the final analysis.


title: zebrafish_resection_24_2

description:
zebrafish_surgery_24_2
Z24_r2


title: zebrafish_sham_24_3

description:
zebrafish_sham_24_3
Z24_s3


title: zebrafish_resection_24_1

description:
zebrafish_surgery_24_1
none
The gene level analysis was not included for this sample.


title: zebrafish_resection_12_1

description:
zebrafish_surgery_12_1
Z12_r1


title: JCMS 24hours rep3

description: RMA Call summary of mean expression


title: zebrafish_sham_48_1

description:
zebrafish_sham_48_1
Z48_s1


title: OP50 24hours rep1

description: RMA Call summary of mean expression


title: OP50 24hours rep2

description: RMA Call summary of mean expression


title: germline_l(3)mbt_mut1

description:
PolyA RNA
processed data file: Germline_RNAseq.xlsx

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software (Illumina).
Reads were aligned to the fly genome (build dm3/BDGP5) using the splice-aware STAR aligner (Dobin et al., 2013).
PCR duplicates were removed using the Picard toolkit (https://broadinstitute.github.io/picard/).
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exons (Anders et al., 2015).
These counts were then used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: dm3/BDGP5
Supplementary_files_format_and_content: Germline_RNAseq.xlsx: Excel spreadsheet contains differential expression per experiment, as well as normalized counts.
Supplementary_files_format_and_content: *.bw: Normalized bigwig files.

source_name: embryos

extract_protocol:
Early embryos, TJ>UAS-l(3)mbt::myc;l(3)mbt[GM76]/+ and TJ>UAS-l(3)mbt::myc;l(3)mbtGM76/Df females were allowed to lay for 30 minutes to 1 hour on agar plates. Embryos were dechorionated in 50% bleach for 5 minutes, rinsed with PBS, and then lysed in TRIzol following manufacturer's guidelines.
Libraries were generated from 1µg of total RNA using the NEBNext Poly(A) magnetic Isolation Module (NEB #7490) and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB # E7420). Libraries from 2 biological replicates were sequenced on an Illumina Hi-Seq2500, paired-end 50 run.

value: embryos

tag: Stage

value: 30 mins to 1 hour

tag: maternal genotype


title: germline_wt2


title: zebrafish_resection_12_3

description:
zebrafish_surgery_12_3
Z12_r3

value: Heart ventricles

tag: strain

value: Wild-type AB, wild-type TuAB


title: zebrafish_sham_12_1

description:
zebrafish_sham_12_1
Z12_s1


title: zebrafish_sham_12_3

description:
zebrafish_sham_12_3
Z12_s3


title: JCMS 24hours rep1

description: RMA Call summary of mean expression


title: zebrafish_sham_12_2

description:
zebrafish_sham_12_2
Z12_s2


title: Huh28_TGFb_1

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

description: TGFb-treated  Huh28 cell line - Replicate 1

hyb_protocol: 600 ng of Cy3-labelled 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 manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (V2) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 039494_D_F_20120411). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded. Normalization was based on the 75th percentile shift.

source_name: TGFb-treated  Huh28 cell line

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions.

growth_protocol: HuCCT1 (RCB-1960) and Huh28 (RCB-1943) CCA cell lines were purchased at the RIKEN BioResource Center (Tsukuba-shi, Japan). Cells were grown in RPMI-1640 (HuCCT1) or MEM (Huh28) medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cells were cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted and purified using the miRNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Overnight serum starvation was performed before each treatment. Cells were treated with 1ng/mL recombinant human TGFβ (R&D system, Minneapolis, USA) for 16hrs. Triplicate experiments were performed.

tag: cell line

tag: agent

value: TGFβ


title: Huh28_Control_3

description: Untreated control Huh28 cell line - Replicate 3

source_name: Untreated control Huh28 cell line

value: Control


title: SAMPLE 13_H1417 DMSO 72h

city: Fujisawa

first: SHINJI

last: TAKAGI

address: 26-1 Muraoka Higashi 2-chome

department: Oncology Drug Discovery Unit

institute: Takeda Pharmaceutical Company

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: H1417 DMSO 72h

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit with DNase I treatment with  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Treatment with test article or DMSO for 72 hours

tag: cell type

value: small cell lung cancer (SCLC) cell line

tag: treated with

value: DMSO for 72hrs


title: HuCCT1_TGFb_3

description: TGFb-treated  HuCCT1 cell line - Replicate 3

source_name: TGFb-treated  HuCCT1 cell line


title: Huh28_Control_2

description: Untreated control Huh28 cell line - Replicate 2


title: Huh28_Control_1

description: Untreated control Huh28 cell line - Replicate 1


title: SAMPLE 18_H1417 T-3775440 500 nmol/L 72h


title: SAMPLE 8_H526 DMSO 72h

source_name: H526 DMSO 72h


title: HuCCT1_Control_1

description: Untreated control HuCCT1 cell line - Replicate 1

source_name: Untreated control HuCCT1 cell line


title: SAMPLE 10_H526 T-3775440 500 nmol/L 72h


title: Huh28_TGFb_2

description: TGFb-treated  Huh28 cell line - Replicate 2


title: SAMPLE 15_H1417 DMSO 72h


title: SAMPLE 7_H526 DMSO 72h


title: SAMPLE 14_H1417 DMSO 72h


title: HuCCT1_Control_2

description: Untreated control HuCCT1 cell line - Replicate 2


title: SAMPLE 16_H1417 T-3775440 500 nmol/L 72h


title: SAMPLE 11_H526 T-3775440 500 nmol/L 72h


title: HuCCT1_Control_3

description: Untreated control HuCCT1 cell line - Replicate 3


title: HuCCT1_TGFb_2

description: TGFb-treated  HuCCT1 cell line - Replicate 2


title: 5day_after_molt

city: Hefei

first: Xing young

last: Chen

address: 130, Changjiang Xi Road

institute: Anhui Agricultural University

description: gene expression 5 day after molt

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Anser sp.

source_name: skin sample from ventral

label_protocol: The microarrays were performed following Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol and RNA Spike-In-One Color. We used about 400 ng total RNA as the starting material for amplification and labelling. Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

growth_protocol: The geese were reared on a floor system in open-sided houses. At 10 wk of age the birds were transferred to pens (3×3 m2) in groups of 25 per pen. Each pen contained on one side a 3×3 m2 outside ground area with a water bath. When half geese were going to molting, six randomly selected geese were reared on a separated pen with same conditions. The experimental geese were fed a commercial maize-soybean-based diet containing 155 g CP/kg feed with a metabolic energy content of 10.87 MJ/kg and sufficient forage. The birds had free access to feed and water.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: time

value: 5 days after molt

value: skin

tag: gender

value: female


title: 10day_after_molt

description: gene expression 10 day after molt

value: 10 days after molt


title: SAMPLE 17_H1417 T-3775440 500 nmol/L 72h


title: Huh28_TGFb_3

description: TGFb-treated  Huh28 cell line - Replicate 3


title: HuCCT1_TGFb_1

description: TGFb-treated  HuCCT1 cell line - Replicate 1


title: SAMPLE 9_H526 DMSO 72h


title: SAMPLE 12_H526 T-3775440 500 nmol/L 72h


title: SAMPLE 6_H510 T-3775440 500 nmol/L 72h