title: BEL-7404_ShCENPK_rep3

city: Xi’an

first: Jianlin

state: shaanxi

address: 127 West Changle Street

institute: Fourth Military Medical University

description: gene expression after CENPK-knockdown in BEL-7404 cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method

source_name: BEL-7404 transfected with ShCENPK

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: Cells were transfected with scramble or shCENPK lentiviral plasmids

tag: genotype

value: CENPK knockdown


title: LPM011a_B

status: Public on May 30 2018

type: RNA

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

country: USA

institute: MD Anderson Cancer Center

description: Gene expression analysis of follicular lymphoma B-cells

hyb_protocol: Overnight hybridization according to Affymetrix Protocol

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 and GCOS software

data_processing: CEL files were RMA normalized using GenePattern ExpressionFileCreator module

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Follicular lymphoma tumor

label_protocol: Biotin labelled with Affymetrix GeneChip reagents according to the manufacturers protocol

growth_protocol: Cells were not cultured

extract_protocol: Qiagen AllPrep Mini Kit

treatment_protocol: Tumors were stained with antibodies specific for CD19, CD20, CD10 and CD5. Tumor B-cells (CD19+CD20+CD10+) and tumor-infiltrating T-cells (CD19-CD5+) were sorted on a BD FACS Aria. Sorted cells were processed immediately using Qiagen AllPrep Mini Kit.

tag: disease state

value: follicular lymphoma

tag: cell type

value: B-cells

tag: condition

value: Diagnosis


title: LPM005b_B

value: Relapse 1


title: p19; undifferentiated; Ctcfl overexpression

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: RMA expression value derived from Expression Console software

hyb_protocol: According to manufacturers instructions without modifications.

data_processing: Raw data was analysed using Affymetrix software (Expression console & Transcriptome analysis console).

label: biotin

organism: Mus musculus

source_name: mouse embryonic carcinoma cells

label_protocol: Biotinylated cRNA was prepared according to the appropriate Affymetrix protocol without further amplification.

growth_protocol: WT cells were grown normally in DMEM Medium supplemented with 10% FCS. CTCFL inducible P19 clone was grown in the presence of 2 µg/ml Doxycyclin to repress CTCFL expression (Tet-Off)

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen)

treatment_protocol: Differentiation of P19 cells was achieved by addition of 10 µM retinoic acid to the growth medium for four days. Overexpression of CTCFL was achieved by growing in P19 clone cells in medium lacking Doxycyclin for two days.

tag: cell line

tag: stable integrate

value: pBI-EGFP-FLAG-mCtcfl and pTA-N

tag: treatment 1

value: Removal of 2 ug/ml Doxycyline 2 days before extraction

tag: treatment 2

value: vehicle (ethanol)


title: XYL-CONS-1

type: SRA

city: Medford

first: Nikhil

middle: Unni

last: Nair

state: Massachusetts

address: 4 Colby St, STC 276

department: Chemical & Biological Engineering

institute: Tufts University

description: W303-1a obtained from Euroscarf

library_source: transcriptomic

data_processing:
Possible adapter sequences and nucleotides with poor quality were trimmed, sequence reads shorter than 50 bp were excluded and the remaining were aligned to the reference genome W303 obtained from Saccharomyces Genome Database (http://www.yeastgenome.org) along with XYLA*3 sequence.
Genome_build: W303
Supplementary_files_format_and_content: RNA-Seq

organism: Saccharomyces cerevisiae

source_name: Strain without xylose regulon but constitutively expressing XYL*3, XKS1, TAL1 and GAL2-2.1, and grown in xylose

growth_protocol: The strains were grown overnight in  SC-Ura-His-Trp-Leu medium supplemented with sucrose (2%). They were washed thrice in the YP medium with xylose (2%) or galactose (2%) and then diluted to an initial OD600 of 0.1 in the same medium.

extract_protocol:
The strains were grown in their respective carbon source (galactose or xylose) till mid exponential phase and approximately 2 × 10^7 cells were washed twice in water, pelleted and stored at -80 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: carbon source grown in

value: Xylose

tag: mode of control for carbon source utilization

value: Unregulated constitutive expression


title: BEL-7404_ShCENPK_rep1

last: Wang

country: China

tag: tissue

value: hepatocellular carcinoma


title: XYL-CONS-2

description: W303-1a obtained from Euroscarf


title: LPM011b_B


title: p19; differentiated; Ctcfl overexpression

scan_protocol: According to manufacturers instructions without modifications.

value: 10 uM retinoic acid


title: BEL-7404_Scramble_rep2

description: gene expression after Scramble in BEL-7404 cell lines

source_name: BEL-7404 transfected with scramble

value: scramble


title: BEL-7404_ShCENPK_rep2


title: XYL-REG-3

description: W303-1a obtained from Euroscarf

source_name: GAL-adapted xylose regulon with XYLA*3, XKS1, TAL1 and GAL2-2.1, necessary for growth in xylose and grown in xylose

value: GAL-type XYL regulon


title: BEL-7404_Scramble_rep1


title: XYL-REG-2

description: W303-1a obtained from Euroscarf


title: XYL-CONS-3

description: W303-1a obtained from Euroscarf


title: ex-vivo_patient_ID:_11014_2010-2012_Kilifi_Kenya

type: genomic

first: Margaret

middle: Jane

last: Mackinnon

country: Australia

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, competitive hybridizations of each test sample against the reference isolate, P4, derived from a field isolate, were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning was performed as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v4.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data were filtered for poor quality spots (less than 6 pixels, or with size that greatly differed from that in the GAL file) then normalised for spot intensity within arrays using the ‘normexp’ and ‘robustspline’ methods, and for between-array variation using the “quantile” method using the limma package in R. Data from genes encoding the variant antigen gene families of var, rifin and stevor, and other multi-copy or highly variable genes, ribosomal RNAs, and pseudogenes were excluded from further analyses. Data from probes were excluded if they contained a SNP (based on data from 129 genomes in PlasmoDB) or if they matched multiple genes in Version 3 of the 3D7 genome.

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: P. falciparum (ex vivo), Kilifi, Kenya

label_protocol: Labeling was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Blood samples from children (3-5ml) were obtained by venesection.  Aliquots of whole blood were frozen at -80 degrees C.

extract_protocol: For samples from Kilifi, genomic DNA was extracted using the phenol chloroform method. For samples from Sudan and Kisumu, DNA was extracted from using the automated ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems).

treatment_protocol: After centrifugation, the plasma and buffy coat were removed in order to minimize contaminating human host DNA. For samples from Kilifi, 30-200 μl of parasite-infected red blood cells (iRBCs) were stored frozen then thawed on ice and saponified in order to remove intact parasites from RBCs. For samples from Sudan and Kisumu, 100 μl of iRBCs were stored frozen then thawed prior to DNA extraction.

tag: sample type(culture type, patient id,  year, location, country

source_name: P. falciparum lab-adapted strain P4

value: strain P4


title: ex-vivo_patient_ID:_11057_2010-2012_Kilifi_Kenya


title: LPJ128a_B


title: p19; undifferentiated

value: WT

value: 2 ug/ml Doxycyline


title: GAL-CONS-3

description: W303-1a obtained from Euroscarf

source_name: Yeast strain with GAL4 knock out, but GAL1, GAL10 and GAL7 genes expressed under constitutive TEF1p, TPI1p and GPM1p promoters, grown in galactose

value: Galactose


title: p19; differentiated


title: ex-vivo_patient_ID:_10966_2010-2012_Kilifi_Kenya


title: XYL-REG-1

description: W303-1a obtained from Euroscarf


title: GAL-CONS-1

description: W303-1a obtained from Euroscarf


title: GAL-CONS-2

description: W303-1a obtained from Euroscarf


title: LPJ040b_B

value: follicular lymphoma


title: ex-vivo_patient_ID:_10941_2010-2012_Kilifi_Kenya


title: LPM001a_B

value: B-cells


title: ex-vivo_patient_ID:_10904_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10929_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10923_2010-2012_Kilifi_Kenya


title: B cell, Trisomic 21, biological rep3

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Gene expression data from B cell with Trisomic 21

hyb_protocol: Chips were hybridized for 16-18 hours in Hybridization Oven 645 at 45°C.  Chips were stained with the Affymetrix GeneChip(r) Hybridization, Wash, and Stain Kit on Fluidics Station 450 with Fluidics Script 002.

scan_protocol: All chips were scanned with the Affymetrix GeneChip(r) Scanner 3000 7G System using the standard protocol.

data_processing: Affymetrix CEL files were summaried and normalized using RMA, followed by the SVA package for removing batch effects and other unwanted variation.

source_name: B cell with Trisomic 21

label_protocol: Purified RNA was processed as follows: Labeling Protocol, targets were prepared with the NuGEN Ovation Pico WTA System V2 with Ribo-SPIA® amplification for cDNA.  The NuGEN Encore® Biotin Module was used to label the samples prior to loading on to Affymetrix Human Genome U133 Plus 2.0 Array.

growth_protocol: Disomic and trisomic isogenic iPS cells were differentiated in parallel, and after co-culture with MS5 cells, CD45+ CD34- CD19+ cells were isolated by FACS.

extract_protocol: Cells were sorted into TRIzol (ThermoFisher Scientific) and RNA was isolated using the RNeasy Plus Mini Kit or RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's protocol. cDNA was synthesized with the iScript cDNA synthesis kit (Bio-Rad) from purified RNA. Real-time (RT) PCR was performed using the iQ SYBR Green Supermix (Bio-Rad). Relative expression was quantified using the ΔΔCt method.

value: B cell

value: Trisomic 21


title: ex-vivo_patient_ID:_10902_2010-2012_Kilifi_Kenya


title: B cell, Trisomic 21, biological rep1

treatment_protocol: Disomic and trisomic isogenic iPS cells were differentiated in parallel, and after co-culture with MS5 cells, CD45+ CD34- CD19+ cells were isolated by FACS.


title: B cell, Trisomic 21, biological rep2


title: GAL-REG (WT)-2

description: W303-1a obtained from Euroscarf

source_name: Wildtype yeast strain with intact GAL regulon grown in galactose

value: GAL regulon


title: Ihh_Dhh_dKO::3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression from ovary, Dhh/Ihh DKO, 2 months

hyb_protocol: 4.6 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: ovary, Dhh/Ihh DKO, 2 months

label_protocol: Fifty (50) ng of total RNA was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

extract_protocol: Total RNA was isolated from ovaries using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA) according to the manufacturer’s protocol. 50 ng of total RNA was amplified with the WT-Ovation Pico RNA Amplification System, and labeled with biotin following the Encore Biotin Module protocols for further microarray procedures.

treatment_protocol: ovary specific gene deletion

tag: organ

value: ovary

tag: age

value: 2 month old


title: S1P2-KO_bleomycin#2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene expression in alveolar macrophages between bleomycin–treated S1pr2-/- mice.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_20120201). These data were analyzed further with GeneSpring GX12.5 software (Agilent Technologies). Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array; 4, per-gene normalization, in which the data were normalized to control (wild type) samples.

source_name: alveolar macrophages from  bleomycin–treated S1pr2-/- mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification 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: Mice were housed in a temperature-controlled conventional facility (24 °C) under a 12:12 h light–dark cycle with free access to regular chow and water.

extract_protocol: Total RNA was prepared from BALF cells of WT or S1pr2-/- mice on day22 after bleomycin instillation using RNeasy® Lipid Tissue Mini Kit according to the manufacturer’s instructions.

treatment_protocol: Mice were challenged with intraperitoneal bleomycin at 0.035 U/g twice weekly.

value: alveolar macrophages

tag: treatment

value: bleomycin


title: Wt_bleomycin#1

description: Gene expression in alveolar macrophages between bleomycin–treated wild-type mice.

source_name: alveolar macrophages from bleomycin–treated wild-type mice


title: B cell, Disomic 21, biological rep3

description: Gene expression data from B cell with Disomic 21

source_name: B cell with Disomic 21

value: Disomic 21


title: LPJ040a2_B

value: Diagnosis


title: S1P2-KO_bleomycin#1


title: LPM005a_B


title: ex-vivo_patient_ID:_10898_2010-2012_Kilifi_Kenya


title: B cell, Disomic 21, biological rep2


title: Ihh_Dhh_dKO::2


title: ex-vivo_patient_ID:_10895_2010-2012_Kilifi_Kenya


title: Ihh_Dhh_dKO::1


title: GAL-REG (WT)-3

description: W303-1a obtained from Euroscarf


title: GAL-REG (WT)-1

description: W303-1a obtained from Euroscarf


title: Wt_bleomycin#2


title: ex-vivo_patient_ID:_10882_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10849_2010-2012_Kilifi_Kenya


title: 48 hours Mock BR3 TR2 [48mkIII_S29_L007]

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

data_processing:
After aligning the reads to maize genome v4 using STAR (Dobin et al., 2013).
Read counts were calculated using featureCounts (Liao et al., 2014).
The counts were then normalized using the TMM method (Robinson and Oshlack, (2010),
Differential gene expression between samples was assessed using generalized linear models based on negative binomial distribution with the R package edgeR (Robinson et al., 2010; McCarthy et al., 2012). The FDR was controlled using the method of Benjamini and Hochberg (1995)
K mreans clustering was performed to identify gen expression patterns over time in the treated samples
Genome_build: Zea mays AGP version 4; release 32 [genome build]
Supplementary_files_format_and_content: csv; raw and normalized counts for gene expresion. The cluster analysis results have been submitted as supplentary tables in the manuscript  [processed data files format and content]

organism: Zea mays

source_name: Maize 7-day old seedlings

growth_protocol: Seeds of maize B73 were germinated on wetted filter paper at 30°C in 100 ml glass bottles for two days. Thereafter, the bottles were transfered to 23°C for 7 days at a light intensity of 70 micromoles m-2 s-1.

extract_protocol:
Complementary DNA libraries were generated from the RNA samples and subjected to DNA sequencing (150 bp, paired end) on an Illumina Hiseq 3000 analyzer
RNA sequencing libraries were prepared using TruSeq RNA Sample Prep Kits (Illumina Inc., San Diego, CA) and samples sequenced by 2 × 150 bps paired-end sequencing on an Illumina HiSeq 3000 instrument at the Iowa State DNA facility
Illumina Hi- Seq3000 150PE

treatment_protocol: Seedlings were treated with 5 micrograms ml-1 of tunicamycin for 0h, 3h, 6h, 12h, 24h, 36h, 48h. A 48h mock sample was included. Roots were harvested and flash frozen in liquid nitrogen for further processing.  RNA was extracted using the mirVANATM miRNA isolation kit from Invitrogen (Thermo Fisher Scientific) and analyzed for quantity and quality on an Agilent 2100 BioAnalyzer (http://www.agilent.com).

tag: time point

value: 48 hours Mock

tag: agent

value: Mock


title: 48 hours Mock BR2 TR2 [48IIImk_S26_L006]


title: ex-vivo_patient_ID:_10832_2010-2012_Kilifi_Kenya

value: strain P4


title: B cell, Disomic 21, biological rep1

tag: genotype


title: Normal-LC, biological rep3

city: New York

first: Jiajing

last: Qiu

state: NY

address: 1468 Madison Ave, ANBG bldg 24-10

department: Hematology/Oncology Department of Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
c1_011916
Gene expression data from normal  human splenic littoral cells

hyb_protocol: aRNAs were hybridized to Affymetrix human genome U133 Plus 2.0 array.

scan_protocol: GeneChip Scanner 3000

data_processing:
GeneChip Command Console software
Probe-level gene expression values were calculated using RMA normalization

source_name: human normal littoral cells

label_protocol: biotin labeled aRNA was synthesized using MessageAmpTM II aRNA Amplificaiton Kit (Ambion)

growth_protocol: Fresly processed human spleen specimens

extract_protocol: Total RNA was individually extracted from 0.5-1x105 freshly isolated viable LCs or SVECs using RNeasy Micro Kit (Qiagen). In vitro RNA amplification was performed using MessageAmpTM II aRNA Amplificaiton Kit (Ambion)

treatment_protocol: Fresh spleen specimens were minced and ground over a sieve. The remainning tissues that did not pass through the mesh were digested suing Collagenase B. CD45+ cells were immunomegnetically depleted and the remaining RBCs were lysed.  Viable CD34-CD8a+CD31+CD3-CD45- LCs and CD34+CD8a-CD31+CD3-CD45- SVECs were isolated using Flow cytometric sorting.

tag: subject status

value: healthy donors

value: normal spleen

tag: cell phenotype


title: ex-vivo_patient_ID:_10846_2010-2012_Kilifi_Kenya


title: Normal-SVEC, biological rep3

description:
c2_011916
Gene expression data from normal human splenic vascular endothelial cells

source_name: human normal splenic vascular endothelial cells


title: Dhh_KO ::3

description: gene expression from ovary, Dhh_KO, 2 months

source_name: ovary, Dhh_KO, 2 months


title: ex-vivo_patient_ID:_10836_2010-2012_Kilifi_Kenya


title: Ihh_KO :: 3

description: gene expression from ovary, Ihh_KO, 2 months

source_name: ovary, Ihh_KO, 2 months


title: Normal-SVEC, biological rep2

description:
5b_061515
Gene expression data from normal human splenic vascular endothelial cells


title: Normal-SVEC, biological rep1

description:
3b_061515
Gene expression data from normal human splenic vascular endothelial cells


title: Normal-LC, biological rep2

description:
4b_061515
Gene expression data from normal  human splenic littoral cells


title: ex-vivo_patient_ID:_10848_2010-2012_Kilifi_Kenya


title: Ihh_Dhh_dhet::8

description: gene expression from ovary, Ihh_Dhh_dhet, 2 months

source_name: ovary, Ihh_Dhh_dhet, 2 months


title: Ihh_KO :: 2


title: Ihh_KO :: 1


title: ex-vivo_patient_ID:_10843_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10820_2010-2012_Kilifi_Kenya


title: Dhh_KO :: 4


title: Ihh_KO :: 4


title: Dhh_KO ::1


title: Dhh_KO ::2


title: Ihh_Dhh_dhet::7


title: 48 hours Mock BR1 TR2 [48mkII_S28_L007]


title: ex-vivo_patient_ID:_10814_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10760_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10779_2010-2012_Kilifi_Kenya


title: MF-SVEC, biological rep3

description:
3_041315
Gene expression data from myelofibrotic human splenic vascular endothelial cells

source_name: human MF splenic vascular endothelial cells

value: patients with advanced forms of MF

value: myelofibrotic spleen


title: ex-vivo_patient_ID:_10770_2010-2012_Kilifi_Kenya


title: Ihh_Dhh_dhet::6


title: 48 hours Post Treatment BR3 TR2 [48IImk_S18_L006]

value: 48 hours Post Treatment

value: tunicamycin


title: MF-SVEC, biological rep2

description:
d#4(E26)
Gene expression data from myelofibrotic human splenic vascular endothelial cells


title: MF-LC, biological rep3

description:
5_041315
Gene expression data from myelofibrotic human splenic littoral cells

source_name: human MF littoral cells


title: MF-LC, biological rep2

description:
d3#(L26)
Gene expression data from myelofibrotic human splenic littoral cells


title: Ihh_Dhh_dhet::4


title: Ihh_Dhh_dhet::3


title: human-paracancerous normal tissues-biological rep10

city: Nanning

first: Guangqiang

last: Ye

address: NO.22 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

description:
Raw file: US10313827_256740610336_S01_GE2_1105_Oct12_1_1
the para-cancerous tissues come from the same patients as the tumor samples.

hyb_protocol: 100 μL of the hybridization solution was applied to the hybrid coverslip, and the hybridization cassette was mounted on the rotor of the Hybridization Oven G2545A and hybridized at 45°C for 12 hours.

scan_protocol: Scan the cleaned chip with Agilent G2565CA Microarray Scanner to get a hybrid picture

data_processing: Hybrid images were analyzed and data extracted using Agilent Feature Extraction (v10.7) software.Then use Agilent GeneSpring software to normalize and analyze the data.  A file with all raw data, normalized data, detection flags and probe annotation is available on the series record.

source_name: paracancerous normal tissues

label_protocol: The volume of the cDNA product obtained after reverse transcription and purification was concentrated to 14 μL, and cy3-dCTP/cy5-dCTP was added and placed on a PCR machine (reaction at 37°C for 1.5 hours, reaction at 70°C for 5 minutes, retention at 4°C). Then, the cDNA was purified using the Nucleospin ® Extract II (MN, Cat. No. 740609.250) kit, and the fluorescently labeled product was subjected to fluorescence incorporation and nucleic acid quantification using an ultraviolet spectrophotometer.

growth_protocol: The tissues that was harvested individually from  hepatocellular carcinoma and paracancerous normal tissues were stored at liquid nitrogen temperatures with protected by Rnasin inhibitor

extract_protocol: Trizol (Invitrogen, USA) extracted total RNA from the tissue mass. Further column purification of total RNA was performed using the NucleoSpin ® RNA clean-up kit (740.948.250). It is then quantified using the Qubit method and its integrity is tested using the Agilent 2100 method.

treatment_protocol: After grinded under the ice , hepatocellular carcinoma and paracancerous normal tissues were collected for further total RNA extraction

value: liver

tag: disease state

value: the paracancerous normal tissues is 2 cm away from the cancer tissue

tag: patient id

tag: sample id


title: 48 hours Post Treatment BR2 TR2 [48mkI_S27_L007]


title: Normal-LC, biological rep1

description:
2b_061515
Gene expression data from normal  human splenic littoral cells


title: MF-LC, biological rep1

description:
d#1 (L25)
Gene expression data from myelofibrotic  human splenic littoral cells


title: 48 hours Post Treatment BR1 TR2 [48Imk_S10_L006]


title: Ihh_Dhh_dhet::5

value: ovary


title: human-paracancerous normal tissues-biological rep12

description:
Raw file: US10313827_256740610336_S01_GE2_1105_Oct12_1_3
the para-cancerous tissues come from the same patients as the tumor samples.


title: 36 hours Post Treatment BR3 TR2 [48III_S25_L007]

value: 36 hours Post Treatment


title: Ihh_Dhh_dhet::1

value: 2 month old


title: 24 hours Post Treatment BR3 TR2 [48II_S17_L006]

value: 24 hours Post Treatment


title: human-paracancerous normal tissues-biological rep11

description:
Raw file: US10313827_256740610336_S01_GE2_1105_Oct12_1_2
the para-cancerous tissues come from the same patients as the tumor samples.


title: 36 hours Post Treatment BR1 TR2 [48II_S17_L007]


title: MF-SVEC, biological rep1

description:
d#2(E25)
Gene expression data from myelofibrotic human splenic vascular endothelial cells


title: ex-vivo_patient_ID:_10748_2010-2012_Kilifi_Kenya

source_name: P. falciparum (ex vivo), Kilifi, Kenya

source_name: P. falciparum lab-adapted strain P4


title: ex-vivo_patient_ID:_10738_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10727_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10739_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10726_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10737_2010-2012_Kilifi_Kenya


title: 12 hours Post Treatment BR3 TR2 [36III_S24_L007]

value: 12 hours Post Treatment


title: Ihh_Dhh_dhet::2


title: human-paracancerous normal tissues-biological rep9

description:
Raw file: US10313827_256740610336_S01_GE2_1105_Oct12_1_4
the para-cancerous tissues come from the same patients as the tumor samples.


title: 12 hours Post Treatment BR2 TR2 [36III_S24_L006]


title: 24 hours Post Treatment BR2 TR2 [48I_S9_L007]


title: 24 hours Post Treatment BR1 TR2 [48I_S9_L006]


title: 6 hours Post Treatment BR3 TR2 [36II_S16_L006]

value: 6 hours Post Treatment


title: human-paracancerous normal tissues-biological rep8

description:
Raw file: US10313827_256740610335_S01_GE2_1105_Oct12_1_3
the para-cancerous tissues come from the same patients as the tumor samples.


title: human-paracancerous normal tissues-biological rep5


title: HUES9-derived cortical neurons shBMI1 rep1, rep2, rep3

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Boul. l’Assomption

country: Canada

institute: Hopital Maisonneuve-Rosemont

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Lumi package in Flexarray

source_name: Cortical neurons

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

growth_protocol: By default cortical differentiation by inhibiting BMP4

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

treatment_protocol: At day 24 of differentiation, neural progenitors were infected with lentiviruses for the expression of a shRNA targetting a scrambled sequence or BMI1

tag: cell line

value: HUES9-derived cortical neurons

tag: days of differentiation

value: 1.5 months

tag: shRNA lentiviral infection

value: yes, shRNA BMI1


title: Undifferentiated hESC line HUES9 rep1, rep2, rep3

source_name: hESC

value: Undifferentiated hESC line HUES9


title: human-paracancerous normal tissues-biological rep4

description:
Raw file: US10313827_256740610333_S01_GE2_1105_Oct12_1_4
the para-cancerous tissues come from the same patients as the tumor samples.


title: human-paracancerous normal tissues-biological rep7

description:
Raw file: US10313827_256740610335_S01_GE2_1105_Oct12_1_2
the para-cancerous tissues come from the same patients as the tumor samples.


title: ex-vivo_patient_ID:_10676_2010-2012_Kilifi_Kenya

tag: strain

value: strain P4


title: 12 hours Post Treatment BR1 TR2 [36II_S16_L007]


title: 3 hours Post Treatment BR3 TR2 [24III_S23_L007]

value: 3 hours Post Treatment


title: HUES9-derived cortical neurons rep1, rep2, rep3

value: yes, shRNA scramble


title: ex-vivo_patient_ID:_10747_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10725_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10614_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10615_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10724_2010-2012_Kilifi_Kenya


title: human-paracancerous normal tissues-biological rep1

description:
Raw file: US10313827_256740610333_S01_GE2_1105_Oct12_1_1
the para-cancerous tissues come from the same patients as the tumor samples.

tag: tissue


title: human-paracancerous normal tissues-biological rep6

description:
Raw file: US10313827_256740610335_S01_GE2_1105_Oct12_1_1
the para-cancerous tissues come from the same patients as the tumor samples.


title: human-HCC-biological rep11

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: 6 hours Post Treatment BR2 TR2 [36I_S8_L007]

value: tunicamycin


title: ex-vivo_patient_ID:_10608_2010-2012_Kilifi_Kenya

tag: sample type(culture type, patient id,  year, location, country


title: human-paracancerous normal tissues-biological rep2

description:
Raw file: US10313827_256740610333_S01_GE2_1105_Oct12_1_2
the para-cancerous tissues come from the same patients as the tumor samples.

value: liver


title: O hours Post Treatment BR2 TR2 [24I_S7_L007]

value: O hours Post Treatment


title: 6 hours Post Treatment BR1 TR2 [36I_S8_L006]


title: human-HCC-biological rep12


title: human-paracancerous normal tissues-biological rep3

description:
Raw file: US10313827_256740610333_S01_GE2_1105_Oct12_1_3
the para-cancerous tissues come from the same patients as the tumor samples.

value: the paracancerous normal tissues is 2 cm away from the cancer tissue


title: human-HCC-biological rep10


title: ex-vivo_patient_ID:_10596_2010-2012_Kilifi_Kenya


title: human-HCC-biological rep7


title: O hours Post Treatment BR3 TR2 [24II_S15_L006]


title: 3 hours Post Treatment BR2 TR2 [24III_S23_L006]


title: ex-vivo_patient_ID:_10612_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10609_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10581_2010-2012_Kilifi_Kenya


title: 48 hours Mock BR3 TR1 [12III_S22_L007]

value: 48 hours Mock


title: human-HCC-biological rep8


title: O hours Post Treatment BR1 TR1 [24I_S7_L006]


title: ex-vivo_patient_ID:_10599_2010-2012_Kilifi_Kenya


title: 48 hours Mock BR2 TR1 [12III_S22_L006]


title: ex-vivo_patient_ID:_10580_2010-2012_Kilifi_Kenya


title: 48 hours Post Treatment BR2 TR1 [12I_S6_L007]

value: 48 hours Post Treatment


title: ex-vivo_patient_ID:_10576_2010-2012_Kilifi_Kenya


title: human-HCC-biological rep6


title: human-HCC-biological rep4


title: 48 hours Mock BR1 TR1 [12II_S14_L007]


title: human-HCC-biological rep5


title: human-HCC-biological rep3


title: 48 hours Post Treatment BR1 TR1 [12I_S6_L006]


title: ex-vivo_patient_ID:_10574_2010-2012_Kilifi_Kenya


title: 36 hours Post Treatment BR3 TR1 [6III_S21_L007]

value: 36 hours Post Treatment


title: human-HCC-biological rep9


title: ex-vivo_patient_ID:_10565_2010-2012_Kilifi_Kenya


title: human-HCC-biological rep2


title: ex-vivo_patient_ID:_10578_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10566_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10532_2010-2012_Kilifi_Kenya


title: ex-vivo_patient_ID:_10526_2010-2012_Kilifi_Kenya


title: human-HCC-biological rep1


title: 36 hours Post Treatment BR1 TR1 [6II_S13_L007]


title: 36 hours Post Treatment BR2 TR1 [6III_S21_L006]


title: 24 hours Post Treatment BR3 TR1 [6II_S13_L006]

value: 24 hours Post Treatment


title: 48 hours Post Treatment BR3 TR1 [12II_S14_L006]


title: ex-vivo_patient_ID:_3180_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1980_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1959_1994-1996_Kilifi_Kenya


title: 3 hours Post Treatment BR1 TR2 [24II_S15_L007]

description:
The read counts were very low and hence excluded it from statistical analysis
24II_S15_L007


title: ChIP-Seq T cells TCR 2 days

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: ChIP-Seq P4 T cells TCR 2 days using anti-ZNF341

library_source: genomic

data_processing:
Basecalls performed using CASAVA 1.8. Raw reads were aligned to the human hg19 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to bam format using samtools and bedGraph files are converted using bedtools. ChIP-Seq peaks are called using Model-based Analysis of ChIP-Seq (MACS) version 1.4.2. RPKM (reads per kilobase per million reads) was calculated using unpublished python script to normalize gene expression values and R package edgeR is used to identify differentially expressed genes. Browser-extensible data files are converted to binary tiled data files (TDFs) with IGVTools 2.3.32 for browser viewing.
Genome_build: hg19
Supplementary_files_format_and_content: text file with RPKM for RNA-seq samples, bedGraph files with genome-wide coverage data (20-bp window) for ChIP-seq.

source_name: T cells (Patient 4) with T-Cell Receptor stimulation (anti-CD3 + anti-CD28)

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density centrifugation (Amersham-Pharmacia-Biotech) from cytopheresis or whole-blood samples obtained from healthy volunteers and patients, respectively. PBMCs, PHA blasts and Epstein Barr virus-immortalized lymphoblastoid cell lines (EBV-B cells) were cultured in RPMI-1640 medium supplemented with 10% FCS (referred to hereafter as complete medium).

extract_protocol: For RNA-Seq, total RNA extracted using the RNeasy Mini Kit (Qiagen). Poly(A)+ RNA was selected twice from total RNA using Dynal oligo magnetic beads (Invitrogen). Double-stranded cDNA was synthesized using SuperScript (Invitrogen) and fragmented using Bioraptor (Diagenode). Adaptors (Illumina) were ligated to the dsDNA using T4 DNA ligase (New England Biolabs) after end-repair using End-It kit (Epicentre) and dA addition. Libraries were size-selected for 250-400 bp fragments, purified using 2% E-Gel (Invitrogen), and amplified for 18 cycles by PCR with PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix. For ChIP-Seq, chromatin was isolated from 10 million cells, after cross-linking with 1% methanol-free formaldehyde (Thermo Fisher Scientific). Chromatin was fragmented by sonication and subjected to immunoprecipitation with 10 µg of either mouse IgG (Santa Cruz Biotechnology, Dallas TX) or mouse monoclonal anti-ZNF341 (8B3.1) antibodies prebound to Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). The immunoprecipitate was washed and cross-linked, and ChIP-Seq DNA libraries were then prepared with the fragmented DNA and the KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA)

treatment_protocol: EBV-B cells were transduced with ZNF341 WT isoforms (iso 1 or iso 2) or empty vectors. TCR stimulation: Fresh isolated CD3+ T cells were activated by incubation for 24 or 48 hours with antibodies against CD3 and CD28.

tag: patient diagnosis

value: hyper-IgE syndrome (HIES)

tag: cell type

value: T cells

tag: antibodies


title: Rabbit iPS cells rbEKA-mid cell line culture replicate 1

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Rabbit Agilent Custom Gene Expression Oligo Microarrays (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 037293_D_F_20111104). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryctolagus cuniculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling 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.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes a DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell features

value: Rabbit B19-EOS iPS cells  further transfected with a piggy Bac vector containing human KLF2 and KLF4


title: ex-vivo_patient_ID:_1915_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_10495_2010-2012_Kilifi_Kenya


title: Rabbit iPS cells rbEKA-high cell line culture replicate 3


title: Rabbit iPS cells rbEKA-mid cell line culture replicate 2


title: 24 hours Post Treatment BR2 TR1 [6I_S5_L007]

tag: time point

tag: agent


title: Rabbit iPS cells rbEKA-high cell line culture replicate 2


title: Rabbit iPS cells rbEKA-high cell line culture replicate 1


title: Rabbit iPS cells B19 EOS cell line culture replicate 3

value: Rabbit B19 iPS cells infected L-SIN-EOS-C(3)-EiP (EOS) lentiviral vector (Hotta 2009)


title: ex-vivo_patient_ID:_1920_1994-1996_Kilifi_Kenya


title: Rabbit iPS cells rbEKA-mid cell line culture replicate 3


title: 12 hours Post Treatment BR3 TR1 [3III_S20_L007]

value: 12 hours Post Treatment


title: 12 hours Post Treatment BR1 TR1 [3II_S12_L007]


title: ex-vivo_patient_ID:_1914_1994-1996_Kilifi_Kenya

value: strain P4


title: Rabbit iPS cells B19 EOS cell line culture replicate 1


title: ChIP-Seq P4-EBV Iso 1(ZNF341)

description: ChIP-Seq P4-EBV Iso 1 using anti-ZNF341

source_name: EBV (Patient 4)_ZNF341 isoform 1

value: EBV-B


title: 6 hours Post Treatment BR2 TR1 [3I_S4_L007]

value: 6 hours Post Treatment


title: 6 hours Post Treatment BR1 TR1 [3I_S4_L006]


title: 6 hours Post Treatment BR3 TR1 [3II_S12_L006]


title: ChIP-Seq P4-EBV Iso 2(ZNF341)

description: ChIP-Seq P4-EBV Iso 2 using anti-ZNF341

source_name: EBV (Patient 4)_ZNF341 isoform 2


title: ChIP-Seq P4-EBV EV

description: ChIP-Seq P4-EBV Empty Vector control using anti-ZNF341

source_name: EBV (Patient 4)_empty vector


title: ex-vivo_patient_ID:_1779_1994-1996_Kilifi_Kenya


title: 3 hours Post Treatment BR3 TR1 [0III_S19_L007]

source_name: Maize 7-day old seedlings

value: 3 hours Post Treatment


title: ChIP-Seq P4-EBV Iso 2

description: ChIP-Seq P4-EBV IgG control


title: ex-vivo_patient_ID:_1859_1994-1996_Kilifi_Kenya


title: Rabbit iPS cells B29 cell line culture replicate 1

value: Rabbit iPS obtained from Adult rabbit fibroblasts by 4 retrovirus transfection coding for human Oct4, Sox2, c-Myc, Klf4


title: ex-vivo_patient_ID:_1801_1994-1996_Kilifi_Kenya


title: Rabbit iPS cells B29 cell line culture replicate 2


title: 3 hours Post Treatment BR1 TR1 [0II_S11_L007]

value: tunicamycin


title: ex-vivo_patient_ID:_1768_1994-1996_Kilifi_Kenya


title: Rabbit iPS cells B19 line culture replicate 1


title: Rabbit iPS cells B19 line culture replicate 2


title: Rabbit iPS cells B19 line culture replicate 3


title: RNA-Seq P4-EBV Iso 2(ZNF341)

description: RNA-Seq P4-EBV Iso 2(ZNF341)


title: Adult Rabbit Fibroblast   - culture replicate 3

value: Adult rabbit fibroblasts


title: 3 hours Post Treatment BR2 TR1 [0III_S19_L006]


title: O hours Post Treatment BR3 TR1 [0II_S11_L006]

value: O hours Post Treatment


title: O hours Post Treatment BR2 TR1 [0I_S3_L007]


title: ex-vivo_patient_ID:_1695_1994-1996_Kilifi_Kenya


title: RNA-Seq P4-EBV Iso 1(ZNF341)

description: RNA-Seq P4-EBV Iso 1(ZNF341)


title: RNA-Seq P4-EBV EV

description: RNA-Seq P4-EBV Empty Vector


title: O hours Post Treatment BR1 TR1 [0I_S3_L006]


title: ex-vivo_patient_ID:_1727_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1690_1994-1996_Kilifi_Kenya


title: Adult Rabbit Fibroblast   - culture replicate 2


title: GFP-ZmbZIP17C [GFP-91III]

description: Maize protoplasts

data_processing:
One sample (GFP-60III) was dropped due to poor read quality. Short Read sequences were trimmed using Trimmomatic ver 0.36.
Reads were aligned to maize genome version 4 using bwa-mem and the BAM files for each condition was merged
Peaks were called using the macs2 peak caller using the merged GFP636 BAM files as control
Peak intersection with upstream promoter regions were computed using bedtools
Genome_build: Zea mays AGP version 4
Supplementary_files_format_and_content: Text/BED format; peaks and summit details

source_name: Maize B73 leaf protoplast

growth_protocol: Sterilized seeds of maize B73 were germinated on wetted filter paper at 30°C in 100 ml glass bottles for two days. Thereafter, the bottles were transfered to 23°C for 7 days at a light intensity of 70 micromoles m-2 s-1.

extract_protocol:
Protoplasts were extracted from the leaves for the B73 plants and transformed with GFP-bZIP60 and GFP-bZIP91. The protoplasts expressing the transgene were fixed, pelleted and frozen. Nuclei extraction was followed by chromatin shearing and pull down using GFP ab. The GFP vector alone was used as a control
Illumina TruSeq libraries were constructed according to manufacturer’s instructions and 150-cycle HiSEQ 3000
ChIP-Seq Hiseq3000 150 cycle

treatment_protocol: seedlings were treated with 5 mg ml-1 tunicamycin in DMSO

tag: line

tag: protocol


title: ex-vivo_patient_ID:_1629_1994-1996_Kilifi_Kenya


title: Adult Rabbit Fibroblast   - culture replicate 1


title: GFP-ZmbZIP17C [GFP-91I]

description: Maize protoplasts


title: GFP-ZmbZIP60C  [GFP-60III]

description: Maize protoplasts


title: GFP-ZmbZIP60C  [GFP-60II]

description: Maize protoplasts


title: ex-vivo_patient_ID:_1706_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1623_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1590_1994-1996_Kilifi_Kenya


title: RNA-Seq T cells TCR 2 days

description: RNA-Seq P4 T cells TCR 2 days


title: GFP-ZmbZIP60C  [GFP-60I]

description: Maize protoplasts


title: Vector Control [GFP-636III]

description: Maize protoplasts

value: Vector Control


title: Vector Control [GFP-636II]

description: Maize protoplasts


title: RNA-Seq T cells TCR 1 day

description: RNA-Seq P4 T cells TCR 1 day


title: RNA-Seq Fresh T cells

description: RNA-Seq P4 Fresh T cells

source_name: T cells (Patient 4)_fresh T cells with no stimulation


title: ex-vivo_patient_ID:_1506_1994-1996_Kilifi_Kenya


title: GFP-ZmbZIP17C [GFP-91II]

description: Maize protoplasts


title: ex-vivo_patient_ID:_1520_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1394_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1624_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1537_1994-1996_Kilifi_Kenya


title: Gibbon_WGBS

city: Portland

first: Lucia

last: Carbone

state: Oregon

address: 3303 SW Bond Ave.

institute: Oregon Health & Science University

description: Gibbon

data_processing:
Adapters and low quality reads were removed using trim_galore v0.4.0.
Trimmed reads were mapped to the respective genome using Bismark v0.12.5 and CpG methylation was calculated at each cytosine genome-wide.
Genome_build: Nleu3.0, RheMac8 (Mmul_8.0.1)
Supplementary_files_format_and_content: *-WGBS-methylation.bedgraph: bedGraph files

organism: Nomascus leucogenys

source_name: Blood

extract_protocol:
White-blood cells were isolated using Ficoll gradient on fresh blood received in a heparin tube.
Genomic DNA was extracted from opportunistic whole blood samples from one gibbon individual and one rhesus individual and fragmented (Fragmentase Reaction Buffer v2, Fragmentase (New England Biolab)), end-repaired (T4 DNA Ligase Buffer, dNTP, T4 DNA polymerase, T4 PNK), A-tailed (NEB buffer 2, 1mM dATP, Klenow exo-) and ligated to 30mM methylated forked Illumina adaptors (Quick Ligase Reaction Buffer, Quick Ligase). Ligated fragments were size-selected (250-500bp) and bisulfite converted using the Qiagen EpiTect bisulfite kit.

value: White blood cells

tag: age

value: adult


title: ex-vivo_patient_ID:_1380_1994-1996_Kilifi_Kenya


title: R2-3 6 hours

description: Maize protoplasts

data_processing:
Reads were trimmed off Nextera Adapters using cutadapt ver 1.11
Reads were aligned to maize genome version 4 using bowtie2 version 2.2.6
Reads aligning to chloroplast and mitochnondri awere excluded and from the remaining only those with MAPQ>=10 were retained
Peaks were called on each sample using macs2 peak caller after removing duplicates. We had the -broad paramter on and -nomodel -q 0.05 --nomodel --shift 0 --extsize 73
Resulting Bedgraph files were all converted to bigwig and the peak scores over a 1000 base upstream region of each gene was calculated
DEseq2 was used to calculate differential peak scores representing changes in promoter openness
Genome_build: Zea mays AGP version 4
Supplementary_files_format_and_content: Text/BED format; peaks and summit details

source_name: Maize root

extract_protocol:
Nucleus was isolated from flash frozen from tunicamycin treated maize root samples, purified, followed by Nextera transposition reaction and and purification
Std ATACseq library preparation (Buenrostro  et  al.,  2015)
Hiseq3000 150 cycle

value: 6 hours


title: Vector Control [GFP-636I]

description: Maize protoplasts


title: ex-vivo_patient_ID:_1349_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1354_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1518_1994-1996_Kilifi_Kenya


title: R3-2 12 hours

description: Maize protoplasts

value: 12 hours


title: R3-1 12 hours

description: Maize protoplasts


title: R2-2 6 hours

description: Maize protoplasts


title: ex-vivo_patient_ID:_1387_1994-1996_Kilifi_Kenya


title: Primary tumor tissue of patient 3 PrE-3

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

description:
Gene expression data from FACS sorted co-culture
Primary tumor tissue of PrE-3

hyb_protocol: Hybridization followed the GeneChip Pico Reagent Kit (Affymetrix) protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were processed using the Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific)

source_name: Macrodissected primary prostate tumor

label_protocol: Labeling followed the GeneChip Pico Reagent Kit (Affymetrix) protocol

growth_protocol: Primary prostate epithelial (PrE) and stromal (PrS) cells were grown independently in 2D, mixed, and seeded into 3D matrigel and cultured for 7 to 14 days prior to harvest

extract_protocol: Matrigel from 3D cultures was dissociated, cells were trypsinized to form single cell suspension and sorted by fluorescent associated cell sorting according to EpCAM. RNA extracted using the TRIzol method.

treatment_protocol: PrE dervied organoids were cultured with or without PrS cells

value: Tissue


title: R2-1 6 hours

description: Maize protoplasts


title: R1-2 0 hour

description: Maize protoplasts

value: 0 hour


title: R1-3 0 hour

description: Maize protoplasts


title: ex-vivo_patient_ID:_1299_1994-1996_Kilifi_Kenya


title: Stromal cells in 3D co-culture with benign organoids PrE-4

description:
Gene expression data from FACS sorted co-culture
PrS mix co-culture with PrE-4

source_name: Primary prostate stromal cell

value: Stromal cell from co-culture


title: ex-vivo_patient_ID:_1212_1994-1996_Kilifi_Kenya


title: R1-1 0 hour

description: Maize protoplasts


title: Primary tumor tissue of patient 4 PrE-4

description:
Gene expression data from FACS sorted co-culture
Primary tumor tissue of PrE-4


title: ex-vivo_patient_ID:_1077_1994-1996_Kilifi_Kenya


title: ex-vivo_patient_ID:_1013_1994-1996_Kilifi_Kenya


title: Gibbon_input

description:
Chromatin
processed data file: NLE-ChIP-H3K4me3-final-peaks.bw

data_processing:
Removed adapter using Trimmomatic.
De-duplicated reads using fastx-toolkit v0.0.13.
Mapped to the reference genome using BWA-mem v0.7.9a.
Used phantompeakqualtools v2.0 to run SPP to obtain a loose set of peaks.
Performed an irreproducibility discovery rate (IDR) analysis using ENCODE guidelines.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: NLE-ChIP-H3K4me3-final-peaks.bw: bigWig tracks of final H3K4me3 ChIP-seq peaks.

source_name: Lymphoblasts

extract_protocol:
EBV-transformed cells were cross-linked and lysed with Lysis buffer (0.1% SDS, 0.5% Triton X-100, 20mM Tris-HCl pH 8.0, 150mM NaCl and protease inhibitor cocktail). Lysate was sheared using the Bioruptor sonicator until the lysate was cleared. Lysate was incubated with 1ug of anti-H3K4me3 antibody (Abcam, ab8580). Prepared Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific) were added to lysates, incubated for 2 hour at 4°C and then washed four times with TBST (25mM Tris-HCl pH 7.6, 250mM NaCl, 0.05% Tween-20), once with LiCl Wash Buffer (10mM Tris-HCl pH 8.0, 0.5M LiCl, 1mM EDTA, 0.05% Tween-20), once with Lysis Buffer and once with 1X TE. Elution reactions were pooled and incubated with NaCl overnight at 65°C to reverse crosslinks. The elution product was used to generate libraries.
Libraries were constructed using NEBNext Ultra II DNA Library preparation Kit (NEB, E7645S).

value: EBV-transformed cell line

tag: chip antibody


title: D586 WT  DSS colitis

city: Chongqin

first: Xiaodong

last: Xie

address: 30, gaotanyan Street, shapingba District

institute: Army medical university

description: control

data_processing:
The normalization and all the data analysis were performed by Qinshan, Ni.
The technical replicates were combined using the mean of the two replicates.
All the NA are replicated with ct value 40. For the normalization it uses the average of two housekeeping genes: GAPDH, ACTB.
Target gene signals normalized to housekeeping genes, deltaCt = Ct_Target − Ct_house keeping genes.
Normalized data were used to analysis the differential gene expression based on the published method---limma (Ann Appl Stat 10 (2016) 946-963.).
Matrix non-normalized worksheet reports non-normalized raw signal, each target has two technical replicates (eg. ABCB5_TechReps.1, ABCB5_TechReps.2).
Log FC represents the Log values of the Fold Change.

label: BRYT Green

source_name: colon

label_protocol: Reverse transcription was performed from 1ug total RNA using the PrimeScriptTM RT reagent kit with gDNA Eraser (Takara). Quantitative real-time PCR were performed (ViiA7, Life technology, USA) with 40 cycles at 95℃ for 5 min, followed by 40 cycles of 95℃ for 30s and 60℃ for 45s.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen)

tag: regent

value: DSS

tag: time

value: 9 Days

tag: genotype/variation

value: WT


title: D582 WT  DSS colitis

description: control


title: Stromal cells in 3D co-culture with cancer organoids PrECa-4

description:
Gene expression data from FACS sorted co-culture
PrS mix co-culture with PrECa-4


title: Gibbon_H3K4me3_rep2


title: Cancer organoid in 3D co-culture PrECa-4

description:
Gene expression data from FACS sorted co-culture
PrECa-4 co-culture

source_name: Primary prostate epithelial organoid

value: Epithelial organoid co-culture


title: Stromal cells in 3D co-culture with benign organoids PrE-3

description:
Gene expression data from FACS sorted co-culture
PrS mix co-culture with PrE-3


title: Benign organoid in 3D co-culture PrE-4

description:
Gene expression data from FACS sorted co-culture
PrE-4 co-culture


title: D581 WT  DSS colitis

description: control


title: Cancer organoid in 3D co-culture PrECa-3

description:
Gene expression data from FACS sorted co-culture
PrECa-3 co-culture


title: Stromal cells in 3D co-culture with cancer organoids PrECa-3

description:
Gene expression data from FACS sorted co-culture
PrS mix co-culture with PrECa-3


title: Gibbon_H3K4me3_rep1


title: D519 Rab32  DSS colitis

description: Test


title: Gibbon_Hi-C

data_processing:
Raw Hi-C data was processed with the Juicer package.
TADtool was used to call TADs using the directionality index method.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Gibbon_TAD_boundaries_500kb-1Mb.bed: Bed file containing the positions of the boundaries of all TADs that range in 500kb-1Mb in size.

extract_protocol:
EBV-transformed cells were cross-linked, washed, bound to AMPure XP beads and digested with DpnII. After incorporation of biotin-dCTP, chromatin proximity ligation was carried out.
Libraries were constructed using NEBNext Ultra II DNA Library preparation Kit (NEB, E7645S).


title: 36 hours Post Treatment BR2 TR2 [48III_S25_L006]

value: 36 hours Post Treatment


title: Cancer organoid in 3D mono-culture PrECa-4

description:
Gene expression data from FACS sorted co-culture
PrECa-4 mono-culture

value: Epithelial organoid mono-culture


title: ex-vivo_patient_ID:_1300_1994-1996_Kilifi_Kenya

data_processing: Data were filtered for poor quality spots (less than 6 pixels, or with size that greatly differed from that in the GAL file) then normalised for spot intensity within arrays using the ‘normexp’ and ‘robustspline’ methods, and for between-array variation using the “quantile” method using the limma package in R. Data from genes encoding the variant antigen gene families of var, rifin and stevor, and other multi-copy or highly variable genes, ribosomal RNAs, and pseudogenes were excluded from further analyses. Data from probes were excluded if they contained a SNP (based on data from 129 genomes in PlasmoDB) or if they matched multiple genes in Version 3 of the 3D7 genome.

source_name: P. falciparum (ex vivo), Kilifi, Kenya

extract_protocol: For samples from Kilifi, genomic DNA was extracted using the phenol chloroform method. For samples from Sudan and Kisumu, DNA was extracted from using the automated ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems).

source_name: P. falciparum lab-adapted strain P4

value: strain P4


title: D515 Rab32  DSS colitis

description: Test


title: Benign organoid in 3D mono-culture PrE-4

description:
Gene expression data from FACS sorted co-culture
PrE-4 mono-culture


title: D513 Rab32  DSS colitis

description: Test


title: FSHD2B_MB

status: Public on May 29 2018

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description:
FSHD2 myoblast B
MTMB_gencode19_novel.csv

data_processing:
Trimmed 3' adapters and aligned reads to genome build hg19 uisng GSNAP (v2014-12-19) allowing two mismatches per read.
Retained one copy of duplicated reads to mitigate the effects of PCR amplification bias.
Genomic features were collected from Gencode v19, UCSC tRNA, novel miRNAs predicted by mirDeer2 and novel ncRNA predicted by in-house algorithm.
Due to overlapping features, the precedence of counting hits was given to the non-coding features, including tRNA, miRNA and ncRNA, and then to protein-coding features.
The assinged coutns were adjusted by the number of reported multiple alignments of each read.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts saved in both CSV and RDA format. The RDA file can be opened from R workspace and it contain the Bioconductor RangedSummarizedExpriment instances.

source_name: FSHD2B MB

growth_protocol: Primary myoblast cell lines were routinely maintained in F-10 Medium (Invitrogen) supplemented with 20% fetal bovine serum (Atlanta Biologicals, GA, USA), 1% Pen/Strep, 10 ng/ml hrFGF (Promega), and 1μM Dexamethasone (Sigma) (Growth media).  Myoblasts were induced to differentiation to myotubes with DMEM, 1% heat-inactivated horse serum, 10 ug/ml insulin (Sigma) and 10 ug/ml transferrin (Sigma) (Differentiation media) for 48 hours. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA from myoblasts (MB) and myotubes (MT) from two control and two FSHD2 individuals was isolated using TRIZOL (Invitrogen) according to the manufacturer’s instructions. The isolated RNA was treated with DNase twice to remove contaminating DNA prior cDNA generation.  First, isolated RNA was treated with RNase-free DNaseI (Sigma-Aldrich, #04716728001 ROCHE) followed by acidic phenol/chloroform extraction, and then treated with TURBO RNase-free DNase (Ambion) followed by inactivation reagent treatment. The DNaseI-treated RNA was tested for genomic DNA contamination by PCR and RNA quality by RNA gel.
small RNA libraries were prepared using Illumina TruSeq small RNA protocol

value: Myoblast

tag: phenotype

tag: cell line


title: FSHD2A_MT

description:
FSHD2 mytube A
MTMB_gencode19_novel.csv

source_name: FSHD2A MT

value: Myotube


title: controlB_MT

description:
Control myotube B
MTMB_gencode19_novel.csv

source_name: controlB MT

value: control

value: Control B


title: Benign organoid in 3D mono-culture PrE-3

description:
Gene expression data from FACS sorted co-culture
PrE-3 mono-culture


title: controlB_MB

description:
Control myoblast B
MTMB_gencode19_novel.csv

source_name: controlB MB


title: FSHD2A_MB

description:
FSHD2 myoblast A
MTMB_gencode19_novel.csv

source_name: FSHD2A MB


title: R3-3 12 hours

description: Maize protoplasts

value: tunicamycin


title: controlA_MT

description:
Control myotube A
MTMB_gencode19_novel.csv

source_name: controlA MT

value: Control A


title: controlA_MB

description:
Control myoblast A
MTMB_gencode19_novel.csv

source_name: controlA MB


title: controlA_lenti-GFP

description:
Lenti virus on control A cell line to overexpress GFP
DUX4GFP_gencode_novel.csv

source_name: controlA lenti-GFP

value: Lenti

value: GFP


title: 12 hours Post Treatment BR2 TR1 [3III_S20_L006]

source_name: Maize 7-day old seedlings

value: 12 hours Post Treatment


title: FSHD2B_MT

source_name: FSHD2B MT


title: controlA_Lenti-DUX4

description:
Lenti virus on control A cell line to overexpress DUX4
DUX4GFP_gencode_novel.csv

source_name: controlA Lenti-DUX4


title: Cancer organoid in 3D mono-culture PrECa-3

description:
Gene expression data from FACS sorted co-culture
PrECa-3 mono-culture


title: 24 hours Post Treatment BR1 TR1 [6I_S5_L006]

value: 24 hours Post Treatment


title: Sample197_Systemic JIA

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Reads were mapped to the human genome (hg19) with TopHat 2.0.13 using default parameters,
aligned reads were transformed with SAMtools to quantify number of reads at the gene level with HTSeq-0.6.1 using default “union” mode.
counts were transformed to RPKM to follow GTEx QC guidelines, retaining 11,924 genes with RPKM>1 and >6 read counts in at least 10 individuals
finally, original raw counts of the retained genes were normalized using TMM normalization with edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts or normalized read counts at the gene level for each sample

source_name: Whole Blood

extract_protocol:
Blood was collected via Tempus Tube and RNA was extracted with Tempus Spin RNA isolation kit.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq stranded mRNA library kit and sequenced on the Illumina HiSeq Rapid Run with paired-end 100-bp reads (Illumina, San Diego, CA).

tag: gender

value: Male

tag: age at diagnosis

tag: ancestry

value: White

tag: disease state (diagnosis)

value: Systemic JIA

tag: tissue

value: Whole Blood


title: Sample196_Systemic JIA

value: Female

value: Black


title: Sample202_Crohn's Disease

value: Crohn's Disease


title: Sample201_Polyarticular JIA

value: Polyarticular JIA


title: Sample200_Polyarticular JIA


title: Sample199_Polyarticular JIA


title: Sample198_Systemic JIA


title: Sample187_Control

value: Control


title: Sample194_Systemic JIA


title: Sample193_Oligoarticular JIA

value: Oligoarticular JIA


title: Sample192_Polyarticular JIA


title: Sample195_Oligoarticular JIA


title: Sample189_Polyarticular JIA


title: Sample191_Polyarticular JIA


title: Sample188_Polyarticular JIA


title: Sample179_Control


title: Sample182_Control


title: Sample186_Control


title: Sample177_Control


title: Sample185_Control


title: Sample184_Control


title: Sample183_Control


title: Sample181_Control


title: Sample178_Control


title: Sample190_Polyarticular JIA


title: Sample176_Control


title: Sample175_Crohn's Disease


title: Sample171_Systemic JIA


title: Sample172_Oligoarticular JIA


title: Sample173_Polyarticular JIA


title: Sample174_Crohn's Disease


title: Sample168_Systemic JIA


title: Sample169_Polyarticular JIA


title: Sample161_Crohn's Disease


title: Sample167_Oligoarticular JIA


title: Sample166_Polyarticular JIA


title: Sample165_Polyarticular JIA


title: Sample163_Crohn's Disease


title: Sample180_Control


title: Sample160_Ulcerative Colitis

value: Ulcerative Colitis


title: Sample164_Polyarticular JIA


title: Sample159_Crohn's Disease


title: Sample158_Oligoarticular JIA


title: Sample156_Oligoarticular JIA


title: Sample154_Oligoarticular JIA


title: Sample157_Systemic JIA


title: Sample153_Polyarticular JIA


title: Sample155_Oligoarticular JIA


title: Sample152_Polyarticular JIA


title: Sample151_Polyarticular JIA


title: Sample150_Crohn's Disease


title: Sample170_Oligoarticular JIA


title: Sample149_Crohn's Disease


title: Sample148_Crohn's Disease


title: Sample162_Crohn's Disease


title: Sample147_Ulcerative Colitis


title: Sample143_Systemic JIA


title: Sample145_Crohn's Disease


title: Sample144_Crohn's Disease


title: Sample146_Ulcerative Colitis


title: Sample142_Oligoarticular JIA


title: Sample141_Oligoarticular JIA


title: Sample140_Oligoarticular JIA


title: Sample139_Oligoarticular JIA


title: Sample137_Oligoarticular JIA


title: Sample136_Systemic JIA


title: Sample135_Oligoarticular JIA


title: Sample138_Oligoarticular JIA


title: Sample134_Oligoarticular JIA


title: Sample133_Polyarticular JIA


title: Sample132_Crohn's Disease


title: Sample131_Crohn's Disease


title: Sample130_Crohn's Disease


title: Sample128_Crohn's Disease


title: Rabbit iPS cells B19 EOS cell line culture replicate 2

tag: cell features

value: Rabbit B19 iPS cells infected L-SIN-EOS-C(3)-EiP (EOS) lentiviral vector (Hotta 2009)


title: Sample127_Crohn's Disease


title: Emc2

city: Cambridge

first: Jonathan

middle: S

last: Weissman

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

description:
ribosome protected mRNA fragment
HeLa_RPKMs.txt

data_processing:
Library strategy: ribosome profiling
base calls were called with Illumina CASAVA software (1.6-1.8)
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3 for yeast) or to UCSC known gene cDNA sequences (hg19)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3 and hg19
Supplementary_files_format_and_content: tab delimited file containing gene annotations, count (yeast) and rpkm (HeLa) data

source_name: HeLa

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6. HeLa Cells were cultured in 15 cm plates with Dulbecco modified eagle medium (DMEM) with 10% fetal bovine serum (Gibco) until ~80% confluency.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.  HeLa cells were lysed using 500 µl per polysome lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton x-100, 1 mM DTT, 8% glycerol, 100 µg/ml CHX, 24 U/ml Turbo DNase) per plate using a rubber cell scraper to facilitate lysis.
Footprinting was performed with RNase I (yeast) or MNase (HeLa cells), monosomes were purified on 10-50% sucrose gradients (yeast) or a sucrose cushion (HeLa). For proximity-specific samples, biotinylated ribosomes were purified on streptavidin dynabeads.  RNA was extracted with trizol and protected fragments gel purified.  Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Yeast cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction then induced with 10 nM biotin.  HeLa cells were treated with 100 ug/ml CHX for 2 min.

tag: strain/cell line

value: HeLa

tag: genotype

tag: lentivirally transduced transgenes

value: dCas9-BFP-KRAB; sgEmc2 Puro-T2A-BFP


title: Gal4

value: dCas9-BFP-KRAB; sgGal4 Puro-T2A-BFP


title: Sample126_Ulcerative Colitis


title: Sample129_Crohn's Disease


title: Sample124_Systemic JIA


title: Sample123_Oligoarticular JIA


title: Sample122_Systemic JIA


title: Sample121_Systemic JIA


title: dCas9


title: ex-vivo_patient_ID:_1895_1994-1996_Kilifi_Kenya

tag: sample type(culture type, patient id,  year, location, country

tag: strain

value: strain P4


title: Sample120_Oligoarticular JIA


title: Sample119_Polyarticular JIA


title: Sample125_Systemic JIA


title: Sample118_Polyarticular JIA


title: Sample116_Crohn's Disease


title: Sample115_Crohn's Disease


title: Sample114_Ulcerative Colitis


title: Sample113_Crohn's Disease


title: Sample112_Crohn's Disease


title: Sample111_Crohn's Disease


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 49 dpi biological rep1

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: Gene expression data from PSTVd-S23 inoculated leaves at 49 dpi

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized on GeneChip Tomato Gene 1.0 ST Array in the Affymetrix according to standard Affymetrix protocol.     scan protocol  GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

scan_protocol: The chips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

organism: Solanum lycopersicum

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol.

growth_protocol: Inoculated tomato plants were maintained in a greenhouse at 28-30ºC for 16 h and at 25ºC for 8 h in the dark.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit according to manufacturer’s instruction (Qiagen). Contaminating DNA was removed from the extracted RNA using TURBO DNase-free TM Kit (Ambion).

treatment_protocol: Tomato seedlings with true leaves were mechanically inoculated with purified plasmids (2 μg/plant) containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control. Tomato leaves were collected at 8, 17, 24 and 49 days post inoculation.

value: leaves


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 49 dpi biological rep3

description: Gene expression data from PSTVd-M inoculated leaves at 49 dpi


title: Solanum lycopersicum leaves inoculated with pUC9 at 49 dpi biological rep1

description: Gene expression data from pUC9 inoculated leaves at 49 dpi


title: Sample110_Systemic JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 49 dpi biological rep3


title: Sample109_Oligoarticular JIA

value: Male


title: Solanum lycopersicum leaves inoculated with pUC9 at 49 dpi biological rep3


title: Solanum lycopersicum leaves inoculated with pUC9 at 49 dpi biological rep2


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 49 dpi biological rep2


title: Sample117_Polyarticular JIA

value: White


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 24 dpi biological rep3

description: Gene expression data from PSTVd-S23 inoculated leaves at 24 dpi


title: Sample108_Polyarticular JIA


title: Solanum lycopersicum leaves inoculated with pUC9 at 24 dpi biological rep1

description: Gene expression data from pUC9 inoculated leaves at 24 dpi


title: Solanum lycopersicum leaves inoculated with pUC9 at 24 dpi biological rep3


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 49 dpi biological rep2


title: Sample107_Oligoarticular JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 49 dpi biological rep1


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 24 dpi biological rep2


title: Solanum lycopersicum leaves inoculated with pUC9 at 24 dpi biological rep2


title: Sample106_Systemic JIA

value: Systemic JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 24 dpi biological rep3

description: Gene expression data from PSTVd-M inoculated leaves at 24 dpi


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 24 dpi biological rep1


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 24 dpi biological rep2


title: Sample105_Oligoarticular JIA

value: Whole Blood


title: Solanum lycopersicum leaves inoculated with pUC9 at 17 dpi biological rep3

description: Gene expression data from pUC9 inoculated leaves at 17 dpi


title: Sample104_Oligoarticular JIA

value: Female


title: Solanum lycopersicum leaves inoculated with pUC9 at 17 dpi biological rep2


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 24 dpi biological rep1


title: Sample103_Oligoarticular JIA


title: Sample102_Systemic JIA


title: Sample101_Polyarticular JIA

value: Black


title: Solanum lycopersicum leaves inoculated with pUC9 at 17 dpi biological rep1


title: Sample100_Crohn's Disease

value: Crohn's Disease


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 17 dpi biological rep3

description: Gene expression data from PSTVd-S23 inoculated leaves at 17 dpi


title: Sample096_Oligoarticular JIA


title: Sample098_Crohn's Disease


title: Sample097_Crohn's Disease


title: Sample094_Oligoarticular JIA


title: Sample099_Ulcerative Colitis


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 17 dpi biological rep2


title: Sample095_Systemic JIA


title: Sample093_Oligoarticular JIA


title: Sample092_Oligoarticular JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 17 dpi biological rep1


title: Solanum lycopersicum leaves inoculated with pUC9 at 8 dpi biological rep3

description: Gene expression data from pUC9 inoculated leaves at 8 dpi


title: Solanum lycopersicum leaves inoculated with pUC9 at 8 dpi biological rep1


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 17 dpi biological rep1

description: Gene expression data from PSTVd-M inoculated leaves at 17 dpi


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 17 dpi biological rep3


title: Sample090_Polyarticular JIA

value: Polyarticular JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 8 dpi biological rep2

description: Gene expression data from PSTVd-S23 inoculated leaves at 8 dpi


title: Solanum lycopersicum leaves inoculated with pUC9 at 8 dpi biological rep2


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 17 dpi biological rep2


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 8 dpi biological rep1


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 8 dpi biological rep2

description: Gene expression data from PSTVd-M inoculated leaves at 8 dpi


title: Solanum lycopersicum leaves inoculated with PSTVd-S23 at 8 dpi biological rep3


title: Sample089_Polyarticular JIA


title: Solanum lycopersicum leaves inoculated with PSTVd-M at 8 dpi biological rep1


title: Sample088_Polyarticular JIA


title: Sample087_Polyarticular JIA


title: Sample086_Polyarticular JIA


title: Sample085_Polyarticular JIA


title: Sample084_Crohn's Disease


title: Sample091_Polyarticular JIA


title: Sample081_Ulcerative Colitis


title: Sample080_Polyarticular JIA


title: Sample078_Oligoarticular JIA


title: SSEA3- GATA6+

city: Los Angeles

first: Thomas

last: Allison

state: California

address: 615 Charles E Young Drive South

institute: UCLA

data_processing:
Raw reads were converted to a BAM file using bcl2fastq followed by Picard FastqToSam
Cellular barcode extraction was performed  with TagBamWithReadSequenceExtended followed by molecular barcode  using the same software. Number of bases below quality was set to 1 to remove poor quality base reads. Low quality reads in which the cell or molecular barcodes have low quality bases were removed using FilterBAM software. TrimStartingSequence was used to remove extra sequences present in reads, primarily the SMART adapter on the 5' end of the reads. PolyATrimmer was used to remove the PolyA tail from reads by looking for 6 contiguous A's within the read with 0 mismatches. SamtoFastq was used to convert processed BAM file to Fastq for alignment
Alignment was performed using STAR
SortSam was used to generate the output from alignment in queryname order, as well as converting the aligned SAM to BAM. MergeBAMAlignment was then used to merge the sorted aligment with the unaligned BAM to recover lost BAM tags during alignment. TagReadWithGeneExon is a drop-seq specific program used to add a BAM tag 'GE' onto reads that overlap an exon of a gene, utilised within the final DGE. DetectBeadSynthesisError was used to identify aberrant fixed UMI bases. DigitalExpression was then used to generate the final DGE matrix.
Genome_build: hg38
Supplementary_files_format_and_content: TSV files were generated with the DGE matrix information

source_name: cell line

growth_protocol: hESCs were growin in KO serum on MEFs.

extract_protocol:
mRNA extraction with drop-seq as described in Mackosko et al (2015)
libraries were prepared using illuminas instructions for single cell libraries using the Nextera XT kit. Sequencing was performed on the HiSeq2500 following the manufacters protocol

tag: cell type

value: human embryonic stem cell

tag: expression status

value: SSEA3- GATA6+


title: SSEA3+ GATA6 High

value: SSEA3+ GATA6 High


title: Sample079_Oligoarticular JIA

value: Oligoarticular JIA


title: SSEA3+ GATA6 Low

value: SSEA3+ GATA6 Low


title: SSEA3+ GATA6-

value: SSEA3+ GATA6-


title: Sample075_Oligoarticular JIA


title: Sample073_Polyarticular JIA


title: Sample077_Systemic JIA


title: Sample074_Systemic JIA


title: Sample083_Crohn's Disease


title: Sample072_Polyarticular JIA


title: PMDC05_rep3

city: Koto

first: Kana

last: Sakamoto

state: Tokyo

institute: Japanese Foundation for Cancer Research

hyb_protocol: Total RNA was prepared for hybridization using the GeneChip 3' IVT PLUS Kit and GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (ThermoFisher Scientific, Waltham, MA, USA).

data_processing: Gene expression data were analyzed using GeneSpring 14.9 (Agilent Technologies, Santa Clara, CA, USA) and were normalized and summarized via the Robust Multi-array Average (RMA) approach with default setting.

label_protocol: Total RNA was labelled using the GeneChip 3' IVT PLUS Kit (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s instructions.

growth_protocol: Cells were grown in RPMI 1640 supplemented with GlutaMAX (Thermo Fisher Scientific, Waltham, MA, USA) and 10% fetal bovine serum in a 5% CO2 atmosphere at 37°C in a humidified cell culture incubator.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

value: PMDC05 (MYC-BPDCN)

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells

tag: disease state


title: Sample082_Crohn's Disease


title: CAL1_JQ1_non_rep2

source_name: CAL1, JQ1-nontreated

treatment_protocol: CAL-1 cells were treated with 400 nM JQ1 for 24 hours.

value: CAL-1 (MYC+BPDCN)

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)

tag: agent

value: control


title: Sample071_Crohn's Disease

value: White


title: CAL1_JQ1_24h_rep1

source_name: CAL1, JQ1-treated, 24h


title: PMDC05_rep2


title: CAL1_rep3


title: PMDC05_rep1


title: CAL1_JQ1_non_rep1


title: CAL1_JQ1_24h_rep2


title: CAL1_rep2


title: CAL1_rep1


title: CAL1_JQ1_24h_rep3


title: CAL1_JQ1_non_rep3


title: Sample070_Crohn's Disease

value: Male

value: Whole Blood


title: Sample068_Ulcerative Colitis

value: Ulcerative Colitis


title: Sample076_Systemic JIA

value: Systemic JIA


title: Sample067_Crohn's Disease

value: Female

value: Crohn's Disease


title: Sample063_Polyarticular JIA

value: Polyarticular JIA


title: Sample065_Crohn's Disease

value: Black


title: Sample064_Polyarticular JIA


title: Sample061_Polyarticular JIA


title: Sample062_Oligoarticular JIA

value: Oligoarticular JIA


title: Sample060_Oligoarticular JIA


title: Sample057_Oligoarticular JIA


title: Sample059_Oligoarticular JIA


title: Sample056_Polyarticular JIA


title: Sample069_Crohn's Disease


title: Sample055_Polyarticular JIA


title: Sample052_Ulcerative Colitis


title: Sample051_Crohn's Disease


title: Sample050_Ulcerative Colitis


title: Sample049_Ulcerative Colitis


title: Sample053_Polyarticular JIA


title: Sample046_Crohn's Disease


title: Sample054_Polyarticular JIA


title: Sample048_Crohn's Disease


title: Sample047_Ulcerative Colitis


title: Sample066_Crohn's Disease


title: Sample044_Oligoarticular JIA


title: Sample042_Crohn's Disease


title: Sample041_Crohn's Disease


title: Sample040_Ulcerative Colitis


title: Sample043_Crohn's Disease


title: Sample045_Oligoarticular JIA


title: Sample038_Crohn's Disease


title: Sample037_Crohn's Disease


title: Sample036_Crohn's Disease


title: Sample039_Crohn's Disease


title: Sample058_Systemic JIA


title: Sample032_Crohn's Disease


title: Sample034_Crohn's Disease


title: Sample033_Crohn's Disease


title: Sample031_Crohn's Disease


title: Sample027_Oligoarticular JIA


title: Sample028_Systemic JIA


title: Sample024_Systemic JIA


title: Sample026_Oligoarticular JIA


title: Sample025_Systemic JIA


title: Sample021_Crohn's Disease


title: Sample020_Crohn's Disease


title: Sample022_Polyarticular JIA


title: Sample017_Polyarticular JIA


title: Sample015_Oligoarticular JIA


title: Sample014_Systemic JIA


title: Sample016_Oligoarticular JIA


title: Sample018_Crohn's Disease


title: Sample011_Oligoarticular JIA


title: Sample012_Oligoarticular JIA


title: Sample013_Systemic JIA


title: Sample029_Polyarticular JIA


title: Sample008_Polyarticular JIA


title: Sample030_Crohn's Disease


title: Sample007_Crohn's Disease


title: Sample005_Crohn's Disease


title: Sample035_Crohn's Disease


title: Sample006_Crohn's Disease


title: Sample004_Ulcerative Colitis


title: Sample001_Crohn's Disease


title: Sample002_Crohn's Disease


title: Sample023_Polyarticular JIA


title: Sample019_Ulcerative Colitis


title: Sample010_Polyarticular JIA


title: Sample003_Crohn's Disease


title: Sample009_Polyarticular JIA


title: Sample 22: diet14071611_pooled_hypo_2

city: Beijing

first: John

last: Speakman

address: No. 1 West Beichen Road,

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: diet D14071611

data_processing:
All sequencing was carried out using the Illumina NextSeq 500 sequencer.
Paired-end reads were mapped to the Mus musculus genome (GRCm38) using Bowtie 2-2.1.0 with bowtie2-build -f, TopHat-2.0.10, and Samtools-0.1.19 with samtools sort -n ;
Uniquely mapped reads for each gene were counted against the GTF file of GRCm38 provided by Ensembl (release 83) using HTSeq-0.6.1p1 using htseq-count -r name -s reverse;
After read count data were obtained from the TopHat-HTSeq pipeline, counts per million (CPM) value for each gene was calculated by using the R package ‘edgeR’ (version 3.12.0, R version 3.2.2) to normalize the count data by the size of the library of each sample. Genes with the CPM value ≥ 1 in at least one of the 24 diets group were retained (Anders et al., 2013).
Genome_build: GRCm38 provided by Ensembl (release 83)
Supplementary_files_format_and_content: Ninety-six ".count" files for all  the 96 samples containing read count for each gene from the TopHat-HTSeq pipeline; also two ".xls" files for the two tissue types, hypothalamus and white adipose tissue, containing counts per million (CPM) values for genes with the CPM value ≥ 1 in at least one of the 24 diet groups.

source_name: Hypothalamus

growth_protocol: All mice were fed a standard diet with 10% fat and 20% protein (D12450B, Research Diets Ltd) for 2 weeks as the baseline period. Following 2 weeks of baseline monitoring (at age 12 weeks), all mice were randomly allocated to different groups and switched to the experimental diets for 12 weeks. After 12 weeks all mice were sacrificed and dissected.

extract_protocol:
From each diet group, the hypothalami of 8/20 individuals were collected. The left halves of two, and the right halves of another two, were pooled together as one sample, and the same was performed with the other 4 hypothalami, resulting in each diet group having 2 pooled samples of 4 hypothalami (n = 48 samples in total across 24 diets). From each diet group, the sWAT and eWAT of 12/20 individuals were also collected. A small piece from each of six sWAT collections were pooled together as one sample, and the same was performed with the other six eWAT collections. In this way each diet group had one pooled sWAT sample and one pooled eWAT sample (also n = 48 across 24 diets). The total RNA of the hypothalamus and WAT was isolated using the RNeasy Mini Kit (QIAGEN, 74104) according to manufacturer's protocol.
All sequencing was carried out using the Illumina NextSeq 500 sequencer using standard Illumina protocols

treatment_protocol: In total, mice were fed on 4 diet series, each series consisting of 6 different diets (total = 24 diets). In the first two series (Series 1: D14071601–D14071606 and series 2: D14071607 – D14071612) we fixed the level of fat by energy, and varied the protein content. The protein source was casein. The balance was made up by carbohydrate (roughly equal mix of corn starch and maltodextrose). The source of fat was a mix of cocoa butter, coconut oil, menhaden oil, palm oil and sunflower oil. This mix was designed to match the balance of saturated, mono-unsaturated and polyunsaturated fats (ratio 47.5: 36.8: 15.8) and the n-6: n-3 ratio (14.7: 1) in the typical western diet. The proportions of the different fat constituents and hence fatty acid distributions did not change as the total fat content changed. Sucrose and cellulose were both fixed 5% by energy and weight respectively, and all diets were supplemented with a standard vitamin and mineral mix. In the second two series of diets (series 3: D14071613 – D14071618 and series 4: D14071619 – D14071624) we fixed the level of protein by energy and then allowed the fat content to vary.  In these diets the sucrose, cellulose and vitamin and mineral contents were the same as the diets in series 1 and 2. All these diets can be ordered direct from research diets (www.researchdiets.com) using the diet codes provided.

value: Hypothalamus

value: male

tag: age

value: 24 weeks

value: wild type


title: Sample 7: diet14071604_pooled_hypo_1

description: diet D14071604


title: Sample 6: diet14071603_pooled_hypo_2

description: diet D14071603


title: Sample 21: diet14071611_pooled_hypo_1

description: diet D14071611


title: Sample 3: diet14071602_pooled_hypo_1

description: diet D14071602


title: Sample 5: diet14071603_pooled_hypo_1

description: diet D14071603


title: Sample 9: diet14071605_pooled_hypo_1

description: diet D14071605


title: Sample 15: diet14071608_pooled_hypo_1

description: diet D14071608


title: Sample 1: diet14071601_pooled_hypo_1

description: diet D14071601


title: Sample 17: diet14071609_pooled_hypo_1

description: diet D14071609


title: Sample 16: diet14071608_pooled_hypo_2

description: diet D14071608


title: Sample 19: diet14071610_pooled_hypo_1

description: diet D14071610


title: Sample 12: diet14071606_pooled_hypo_2

description: diet D14071606


title: Sample 10: diet14071605_pooled_hypo_2

description: diet D14071605


title: Sample 2: diet14071601_pooled_hypo_2

description: diet D14071601


title: Sample 11: diet14071606_pooled_hypo_1

description: diet D14071606


title: Sample 4: diet14071602_pooled_hypo_2

description: diet D14071602


title: Sample 13: diet14071607_pooled_hypo_1

description: diet D14071607


title: Sample 96: diet14071624_pooled_ewat

description: diet D14071624

source_name: Epididymal White Adipose Tissue

value: Epididymal White Adipose Tissue


title: Sample 94: diet14071623_pooled_ewat

description: diet D14071623


title: Sample 20: diet14071610_pooled_hypo_2

description: diet D14071610


title: Sample 95: diet14071624_pooled_swat

description: diet D14071624

source_name: Subcutaneous White Adipose Tissue

value: Subcutaneous White Adipose Tissue


title: Sample 93: diet14071623_pooled_swat

description: diet D14071623


title: Sample 8: diet14071604_pooled_hypo_2

description: diet D14071604


title: Sample 18: diet14071609_pooled_hypo_2

description: diet D14071609


title: Sample 14: diet14071607_pooled_hypo_2

description: diet D14071607


title: Sample 92: diet14071622_pooled_ewat

description: diet D14071622


title: Sample 91: diet14071622_pooled_swat

description: diet D14071622


title: Sample 90: diet14071621_pooled_ewat

description: diet D14071621


title: Sample 85: diet14071619_pooled_swat

description: diet D14071619


title: Sample 87: diet14071620_pooled_swat

description: diet D14071620


title: Sample 88: diet14071620_pooled_ewat

description: diet D14071620


title: Sample 71: diet14071612_pooled_swat

description: diet D14071612


title: Sample 89: diet14071621_pooled_swat

description: diet D14071621


title: Sample 68: diet14071610_pooled_ewat

description: diet D14071610


title: Sample 83: diet14071618_pooled_swat

description: diet D14071618


title: Sample 79: diet14071616_pooled_swat

description: diet D14071616


title: Sample 86: diet14071619_pooled_ewat

description: diet D14071619


title: Sample 81: diet14071617_pooled_swat

description: diet D14071617


title: Sample 82: diet14071617_pooled_ewat

description: diet D14071617


title: Sample 70: diet14071611_pooled_ewat

description: diet D14071611


title: Sample 75: diet14071614_pooled_swat

description: diet D14071614


title: Sample 67: diet14071610_pooled_swat

description: diet D14071610


title: Sample 74: diet14071613_pooled_ewat

description: diet D14071613


title: Sample 66: diet14071609_pooled_ewat

description: diet D14071609


title: Sample 78: diet14071615_pooled_ewat

description: diet D14071615


title: Sample 77: diet14071615_pooled_swat

description: diet D14071615


title: Sample 80: diet14071616_pooled_ewat

description: diet D14071616


title: Sample 69: diet14071611_pooled_swat

description: diet D14071611


title: Sample 65: diet14071609_pooled_swat

description: diet D14071609


title: Sample 72: diet14071612_pooled_ewat

description: diet D14071612


title: Sample 73: diet14071613_pooled_swat

description: diet D14071613


title: Sample 84: diet14071618_pooled_ewat

description: diet D14071618


title: Sample 63: diet14071608_pooled_swat

description: diet D14071608


title: Surviving cells from siRNA library-infected neural stem cells with MNNG treatment

city: Baltimore

first: Ted

middle: M

last: Dawson

address: 733 N. Broadway, MRB SUITE 731

department: Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

description:
JZha-NCD-MNNG-1a

The ANSO4E neural cell line was derived from a transgenic animal described in PMID 8631266.  The background strain was C57BL/6JxSJL/JF1 oocytes fertilized with BDF1 sperm.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’s GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Starting from the CEL files, the data were normalized using RMA.

source_name: Mouse neural stem cells (ANSO4E) treated with GeneNetTM mouse 40K Lentiviral siRNA Library and MNNG

label_protocol: One round amplification protocol for total RNA following Affymetrix’s specifications using the T7 promoter oligo dT primer for cDNA synthesis, and the ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual).

growth_protocol: Culture medium: 20ng/ml of b-FGF, 20ng/ml of EGF in D-MEM/F-12 medium. 37 °C, 95%O2/5%CO2.

extract_protocol: Genomic DNA was extracted from neural stem cells by using the QIAGEN DNeasy Blood & Tissue Kit. siRNA inserts were amplified and biotin-labeled by using the PCR kit provided by SBI.

treatment_protocol: 500 µM MNNG (N-methyl-N′-nitro-N-nitrosoguanidine) treatment for 15 minutes.

tag: cell line

value: neural stem cells

value: treated


title: Sample 64: diet14071608_pooled_ewat

description: diet D14071608

tag: gender


title: Sample 76: diet14071614_pooled_ewat

description: diet D14071614


title: siRNA library-infected neural stem cells without MNNG treatment

description:
JZha-NCD-C-1a

The ANSO4E neural cell line was derived from a transgenic animal described in PMID 8631266.  The background strain was C57BL/6JxSJL/JF1 oocytes fertilized with BDF1 sperm.

source_name: Mouse neural stem cells (ANSO4E) treated with GeneNetTM mouse 40K Lentiviral siRNA Library

value: untreated


title: Sample 62: diet14071607_pooled_ewat

description: diet D14071607


title: Sample 61: diet14071607_pooled_swat

description: diet D14071607


title: reanalyzed_Sec63,input

description:
ribosome protected mRNA fragment
originally accessioned as: GSM2281591
yeast_codon_counts.txt

value: sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: Sample 58: diet14071605_pooled_ewat

description: diet D14071605


title: Sample 56: diet14071604_pooled_ewat

description: diet D14071604


title: Sample 43: diet14071622_pooled_hypo_1

description: diet D14071622


title: Sample 52: diet14071602_pooled_ewat

description: diet D14071602


title: Sample 45: diet14071623_pooled_hypo_1

description: diet D14071623


title: Sample 49: diet14071601_pooled_swat

description: diet D14071601


title: Sample 47: diet14071624_pooled_hypo_1

description: diet D14071624


title: Sample 48: diet14071624_pooled_hypo_2

description: diet D14071624


title: Sample 57: diet14071605_pooled_swat

description: diet D14071605


title: Sample 55: diet14071604_pooled_swat

description: diet D14071604


title: Sample 59: diet14071606_pooled_swat

description: diet D14071606


title: Sample 51: diet14071602_pooled_swat

description: diet D14071602


title: Sample 44: diet14071622_pooled_hypo_2

description: diet D14071622


title: Sample 38: diet14071619_pooled_hypo_2

description: diet D14071619


title: Sample 42: diet14071621_pooled_hypo_2

description: diet D14071621


title: Sample 50: diet14071601_pooled_ewat

description: diet D14071601


title: Sample 46: diet14071623_pooled_hypo_2

description: diet D14071623


title: Sample 40: diet14071620_pooled_hypo_2

description: diet D14071620


title: reanalyzed_Sec63,pulldown

description:
ribosome protected mRNA fragment
originally accessioned as: GSM2281592
yeast_codon_counts.txt


title: Sample 54: diet14071603_pooled_ewat

description: diet D14071603


title: Sample 39: diet14071620_pooled_hypo_1

description: diet D14071620


title: Sample 37: diet14071619_pooled_hypo_1

description: diet D14071619


title: Sample 53: diet14071603_pooled_swat

description: diet D14071603


title: Sample 36: diet14071618_pooled_hypo_2

description: diet D14071618


title: Sample 60: diet14071606_pooled_ewat

description: diet D14071606


title: Sample 35: diet14071618_pooled_hypo_1

description: diet D14071618


title: Sample 41: diet14071621_pooled_hypo_1

description: diet D14071621


title: expr_monocytes_cebpa_wt_Rep3

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaløes Vej 5, 4.

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
The reads were mapped to mouse genome (mm9) using STAR (default parameters) (Dobin et al., 2013) and expression levels for non-redundant set of genes (N=21,147) were quantified using featureCounts (Liao et al., 2013). Read counts were normalized using RLE method (Love et al., 2014).
Differential gene expression analysis between preGM WT and KO populations, and between CFU-G and CFU-M populations was performed using DESeq2 (Love et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM.

source_name: Monocytes

growth_protocol: Cells sorted from freshly harvested murine bone marrow

extract_protocol:
Total RNA was extracted from LSK, preGMs, GMP, CFU-G, CFU-M, granulocytes and monocytes in biological triplicates, using RNeasy Micro Kit (Qiagen).
RNA was processed for double-stranded cDNA synthesis using the Ovation RNA-Seq System V2 (NuGEN Technologies).  Subsequently the sheared cDNA (fragment size from 150 – 550 bp) was subjected to library preparation using the Ovation Ultralow System V2 (NuGEN Technologies). The indexed cDNA libraries were pooled in equimolar ratios and subjected to 75-cycles sequencing on NextSeq 500 System (Illumina).

value: wt

value: bone marrow

tag: cell markers

value: Ter119- B220- CD3- NK1.1- CD115+ cKit- CD34- FcgRII/III+ Ly6G- CD11b+


title: expr_monocytes_cebpa_wt_Rep2


title: expr_monocytes_cebpa_wt_Rep1


title: expr_granulocytes_cebpa_wt_Rep3

source_name: Granulocytes


title: Sample 34: diet14071617_pooled_hypo_2

description: diet D14071617


title: Sample 33: diet14071617_pooled_hypo_1

description: diet D14071617


title: expr_gmp_cebpa_wt_Rep2

source_name: GMP

value: Lin-, Sca-1-, ckit+, CD150-, FcgRII/III+


title: expr_granulocytes_cebpa_wt_Rep1


title: expr_gmpM_cebpa_wt_Rep2

description: Colony Forming Unit - Monocyte

source_name: CFU-M

value: Lin- Sca1- cKit+ CD150- CD41- FcgRII/III(hi) CD115+


title: expr_granulocytes_cebpa_wt_Rep2


title: expr_gmpM_cebpa_wt_Rep3

description: Colony Forming Unit - Monocyte


title: Sample 32: diet14071616_pooled_hypo_2

description: diet D14071616


title: expr_gmpG_cebpa_wt_Rep2

description: Colony Forming Unit - Granulocyte

source_name: CFU-G

value: Lin- Sca1-cKit+ CD150- CD41- FcgRII/III(hi) CD115-


title: Sample 30: diet14071615_pooled_hypo_2

description: diet D14071615


title: expr_gmpG_cebpa_wt_Rep3

description: Colony Forming Unit - Granulocyte


title: Sample 28: diet14071614_pooled_hypo_2

description: diet D14071614