title: Fine root

city: Xi'an

first: Li

last: Guo

state: Shaanxi

address: 28 Xianning West Road

institute: Xi'an Jiao Tong University

data_processing:
Data quality is checked by FastQC. Low quality reads were trimmed using Trimmomatic v0.32 using a sliding widow of 4 bp and quality score >30
High quality reads were aligned to reference genome using Hisat2 v2.1.0 using default settings
Stringtie v1.3.3 was used to discover transcripts and estimate the transcript abundance with Ballgown method.
Genome_build: opium_poppy reference genome
Supplementary_files_format_and_content: Discovered transcripts and their abundance were presented in GTF format.

organism: Papaver somniferum

source_name: Fine root

growth_protocol: Self-pollinated progeny of the HN1 plant selected for genome sequencing was grown in Maxi RootrainersTM as described above except for the growth substrate, which consisted of 50% sand and 50% Terragreen (Oil-Dri Ltd, Wisbech, UK) to allow easy access to clean root material. The plants were watered daily with a modified Magnavaca nutrient solution. Concentrations of nutrients in the solution were 1 mM KCl, 1.5 mM NH4NO3, 1.5 mM CaCl2,, 50 µM KH2PO4, 200 µM MgSO4, 500 µM Mg(NO3)2, 155 µM MgCl2, 8.26 µM MnCl2, 23.1 µM H3BO3, 2.14 µM ZnSO4, 0.56 µM CuSO4, 0.75 µM Na2MoO2, 77 µM Fe-HEDTA (ferric hydroxyethyl-ethylene diaminetriacetate). The pH of the nutrient solution was adjusted to 5.5 using sodium hydroxide.

extract_protocol:
Samples were harvested into liquid nitrogen, then stored at -80°C until extraction. Grinding was performed in jars chilled in liquid nitrogen on the Qiagen TissueLyser as follows: 15 seconds at 20Hz, followed by re-chilling in liquid nitrogen, then a further 15 seconds at 20Hz. 100mg of ground material was used per RNA extraction. RNA was prepared using the Direct-zol RNA Miniprep kit (Zymo Research, USA) according to the manufacturer’s instructions.
We used 400 ng high quality total RNA per pooled sample for mRNA sequencing library preparation. NEBNext® RNA Ultra Directional Library preparation kit for Illumina,  NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs Inc.), and NEBNext® single 6bp indexing primers, were used according to the manufacturer’s instructions.

value: Fine root

tag: cultivar

value: High Noscapine 1 (HN1)

tag: Stage

value: 1 day after onset of anthesis


title: Tap root

status: Public on Sep 01 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

source_name: Tap root

tag: tissue

value: Tap root


title: GATA2R396Q rep1

type: RNA

city: Toulouse

first: Eric

last: DELABESSE

address: 1 avenue Irène Joliot-Curie

country: France

institute: Institut Universitaire de Cancérologie de Toulouse, site Oncopôle CHU de Toulouse

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Probe-signal intensities were normalized and summarized using the robust multiarray average (RMA) method with the Affymetrix’s Expression Console software.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0

label: Biotin

organism: Mus musculus

source_name: GATA2R396Q cDNA EGFP transduction of murine hematopoietic stem cells

label_protocol: RNA samples were purified and prepared according to the manufacturer's protocol using the Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) and hybridized on Affymetrix GeneChip Mouse Exon 1.0 ST arrays.

growth_protocol: C57BL/6 8-week female were treated with 5-fluorouracil (5-FU) at 150mg/kg 6 days prior to bone marrow cell harvesting. Bone marrow cells from C57BL/6 8-week female mice were sorted according to stem cell surface markers (Lin-Sca+Kit+) using autoMACS (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA was extracted using Rneasy plus MiniKit (Qiagen) and its quality was assessed with the RNA Screen Tape on Agilent 2200 Tapestation Bioanalyzer (Agilent Technologies).

treatment_protocol: The bone marrow cells were infected with MIE, WT and R396Q retroviral particles. One hundred thousand cells per condition were infected twice with retroviral vector-based particles by centrifugation at 3,000xg for 2 hours at 32°C with 2µg Polybrene (Hexadimethrine bromide, 400µg/uL) on 2 consecutive days. GFP-positive cells were sorted after 72h of culture.

tag: strain

value: Blood

tag: cell type

value: HSC

tag: genotype

value: GATA2 R396Q


title: PCOS 151B

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

description: Gene expression data from ovary biopt material

hyb_protocol: Hybridization was performed according to Affymetrix protocols.

scan_protocol: Chips were scanned on an Affymetrix Scanner according to the manufacturers protocol.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using GCRMA with default settings and quantile normalization method. The data is log2 transformed.

label: biotin

organism: Homo sapiens

source_name: PCOS, ovary sample

label_protocol: cRNA was biotin-labeled.

growth_protocol: All tissue samples were snap frozen in liquid nitrogen immediately after collection.

extract_protocol: Total RNA was extracted from Ovary biopsies using TRIZOL reagent (Invitrogen, Breda, The Netherlands) as per manufacturer's instructions.  After Trizol purification, RNA was repurified using  the Rneasy Mini Kit (Qiagen, Venlo., The Netherlands) according to manufacturer's instructions.  Total RNA was quantified by OD260/OD280 measurement and with RiboGreen RNA Quantitation Kit (Moleular Probes, Leiden, The Netherlands). RNA quality was assessed on a 6000 nanochip using Agilent 2100 bioanalyzer (Agilent Technologys, Waldbronn, Germany).

treatment_protocol: There was no treatment on the tissues.

tag: gender

value: female

tag: disease state

value: PCOS

value: ovary


title: Stem-5D

source_name: Stem (five days after the onset of anthesis)

value: Stem

value: 5 days after onset of anthesis


title: GATA2WT rep1

source_name: GATA2WT cDNA EGFP transduction of murine hematopoietic stem cells

value: GATA2 wild type


title: Capsule-5D

source_name: Capsule (five days after the onset of anthesis)

value: Capsule


title: GATA2WT rep2


title: GATA2WT rep3


title: MIE rep3

source_name: Empty EGFP vector (MIE) transduction of murine hematopoietic stem cells

value: control


title: Stamen

source_name: Stamen

value: Stamen


title: SSC047 [methylation]

type: genomic

city: Dallas

first: Quan

last: Li

state: TX

address: 6001 Forest Park Rd

department: Immunology

country: USA

institute: UTSW

description:
9933448144_R06C02
Case

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

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

data_processing: BeadStudio software v3.2

molecule: genomic DNA

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: F

value: PBMC

tag: diagnosis

value: SSc


title: SSC065 [methylation]

description:
9933448144_R04C02
Case


title: SSC067 [methylation]

description:
9933448144_R05C02
Case


title: MIE rep1


title: Leaf

source_name: Leaf

value: Leaf

value: High Noscapine 1 (HN1)

value: 1 day after onset of anthesis


title: Mixed Culture (N_mix) rep2

city: Urbana

first: Brendan

last: Harley

state: Illinois

address: 110 Roger Adams Laboratory MC 712

department: Chemical and Biomolecular Engineering

institute: University of Illinois Urbana Champaign

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina) was used to generate fastq files.
Trimmomatic (version 0.36_Java_1.8.0_121) was used to remove low-quality reads using the following parameters - ILLUMINACLIP:myAdapters.fa:2:30:10 LEADING:28 TRAILING:28 MINLEN:30. Trimmed libraries were subsequently aligned to the human genome (GRCh38.p10) using STAR (version 2.5.3a) .
featureCounts (Subread version 1.5.2) was used to categorize the aligned reads to genes and other genomic features.
Tab-delimited text files of raw read counts per gene per sample were used directly in edgeR (version 3.18.1) for statistical analysis and thus are the "normalized" data.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: raw read counts are in column G of the featCounts.txt files

source_name: Human umbilical vein endothelial cells (HUVEC), normal human lung fibroblasts (NHLF), U87-MG

growth_protocol: HUVECs were cultured in EGM-2 media containing 2% FBS and supplements such as hEGF, hydrocortisone, VEGF, hFGF-B, R3-IGF-1, ascorbic acid, heparin, and gentamicin/amphotericin-B (Lonza, Walkersville, MD). NHLFs were cultured in FGM-2 media containing 2% FBS and supplements such as hFGF-B, insulin, and gentamicin/amphotericin-B (Lonza, Walkersville, MD). U87-MG cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin. All cell types were cultured at 37 °C in 5% CO2.

extract_protocol:
Hydrogels were collected at Day 7 and stored at -80 °C until RNA extraction. Hydrogels were crushed on dry ice using micropestles, and RNA was extracted using an RNeasy Plant Mini Kit, followed by DNase digestion using a RNase-free DNase set (Qiagen, Hilden, Germany).
Mixed samples were constructed by mixing RNA from GBM-only and Perivascular-only cultures such that the NHLF fraction of the Tri-Culture and Mixed samples were equal. Libraries for RNA sequencing were prepared using the TruSeq Stranded mRNAseq Sample Prep Kit (Illumina, San Diego, CA), with Read1 aligning to the antisense strand.

treatment_protocol: GBM-only cultures were formed by re-suspending 1 × 10^5 U87-MGs/mL in GelMA polymer solution. Perivascular-only cultures were formed by re-suspending 1 × 10^6 HUVECs/mL and 2 × 10^6 NHLFs/mL in GelMA polymer solution. Tri-Cultures were formed by re-suspending 1 × 10^6 HUVECs/mL, 2 × 10^6 NHLFs/mL, and 1 × 10^5 U87-MGs/mL in GelMA polymer solution. Cell-laden solutions were subsequently pipetted into circular Teflon molds with a diameter of 5 mm and a thickness of 1 mm, and exposed to UV light at a wavelength of 365 nm and intensity of 5.69 mW/cm2 for 30 s to form cell-seeded hydrogels.  Hydrogels were maintained for 7 days in a 48-well plate with daily EGM-2 media changes.

tag: protocol

value: HUVECs and NHLFs were cultured together in one hydrogel, while U87-MG cells were cultured in a separate hydrogel


title: Capsule

source_name: Capsule


title: SSC040 [methylation]

description:
9933448144_R01C02
Case


title: SSC028 [methylation]

description:
9933448144_R06C01
Case

value: M


title: Mixed Culture (N_mix) rep3


title: Stem

source_name: Stem


title: SSC049 [methylation]

description:
9933448144_R02C02
Case


title: SSC052 [methylation]

description:
9933448144_R03C02
Case


title: SSC005 [methylation]

description:
9933448143_R04C02
Case


title: SSC018 [methylation]

description:
9933448144_R05C01
Case


title: Tumor Relapse - L002

city: Seattle

first: Kelly

middle: Garneski

last: Paulson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: raw.expMatrix.csv

data_processing:
Guide barcode reads - Read length: Read 1: 26 (cell-barcode 16bp, UMI 10bp)  , Index read 2 (i5): 8, Read 2: 91 (RNA read)
Raw base BCL files were demultiplexed using the Cell Ranger version 2.1.0 mkfastq pipeline into sample-specific FASTQ files.
FASTQ files were processed individually using the Cell Ranger count pipeline, which made use of  the STAR software to align cDNA reads to the GRCh38 and the Merkel cell polyomavirus sequence (HM011556.1).
Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads.
Samples were respectively aggregated together using the Cell Ranger aggr pipeline resulting in one gene-barcode count matrix to be used for downstream analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data delimited text file includes raw count values; barcodes that are followed by -1 represent cells from the PBMC sample and -2 represent cells from the tumor digest sample

source_name: Tumor

extract_protocol:
PBMC were isolated with standard FICOLL, tumor tissues were digested in RPMI with DNAse, Collagenase, and hyaluronidase, strained and frozen.  All samples were thawed on same day and immediately processed
10x Genomics 5' Chromium single cell RNA sequencing Gene expression per manufacturer's instructions

value: Tumor

tag: time point

value: Relapse D+565

tag: lane


title: MIE rep2

value: Blood

value: HSC


title: Tumor Relapse - L001

description: raw.expMatrix.csv


title: SSC004 [methylation]

description:
9933448143_R03C02
Case


title: Petal

source_name: Petal

value: Petal


title: Mixed Culture (N_mix) rep1


title: SSC039 [methylation]

description:
9933448144_R02C01
Case


title: SSC010 [methylation]

description:
9933448144_R04C01
Case


title: SSC053 [methylation]

description:
9933448143_R06C02
Case


title: PBMC Relapse  - L002

description: raw.expMatrix.csv

source_name: PBMC

value: Relapse D+559


title: Tri-Culture (N_3_100) rep2

value: HUVECs, NHLFs, and U87-MG cells were cultured together in the same hydrogel


title: Tri-Culture (N_3_100) rep3


title: SSC023 [methylation]

description:
9933448144_R01C01
Case


title: PBMC Relapse - L001

description: raw.expMatrix.csv


title: Tri-Culture (N_3_100) rep1


title: SSC006 [methylation]

description:
9933448143_R05C02
Case


title: NC085 [methylation]

description:
9933448142_R05C01
Control

value: NC


title: Hippocampus TBI 1yr post injury, rep4

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: Hippocampus TBI 1yr post injury, rep4

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample.  Briefly, Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

growth_protocol: Rats were prepared for fluid percussion traumatic brain injury or sham injury (Naive rats had no anesthesia and were not handled in any way and gene expression in their brains serve as baseline data) and sacrificed 24 hr, 2 week, 3 month, 6 month and 1 year post-injury, hippocampi and cortex were obtained, and stored in RNA later.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation.  Quality and quantity of the Total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies; Santa Clara, CA).

treatment_protocol: Moderate Fluid percussion injury (TBI), sham and Naive at various time points (24hr, 2 week,3,6 and 12 month)

value: Sprague-Dawley


title: CITED1 OE D2-rep3

city: Shanghai

first: Yanli

last: Xu

state: Shanghai

address: 320 Yue Yang Road

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression data from ESCs transfected with Cited1.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CITED1 OE E14T ESCs

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: E14T ESCs were cultured on gelatin-coated plates in standard ESC medium consisting of GMEM (Glasgow's modified Eagle’s medium) (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2 mM Glutamax (Gibco), 0.1% beta-mercaptoethanol (Sigma), 1 mM MEM pyruvate sodium (Gibco), 0.1 mM MEM nonessential amino acid (Gibco), 1% Penicillin/Streptomycin (Hyclone), and 1000 U/ml recombinant leukemia inhibitory factor (Millipore).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: ESCs overexpressing CITED1 or empty vector were washed twice with PBS buffer, trypsinized and washed twice with PBS, and placed on ice in the Trizol solution (Invitrogen).

tag: cell line

value: ESCs

tag: transfection


title: SSC003 [methylation]

description:
9933448143_R02C02
Case

value: F

value: PBMC


title: SSC001 [methylation]

description:
9933448143_R06C01
Case

value: SSc


title: Hippocampus TBI 1yr post injury, rep3

source_name: Hippocampus TBI 1yr post injury, rep3


title: At_7d Combination treatment _rep3

city: Bielefeld

first: Vijay

last: Kumar

address: University Street 25

country: Germany

institute: Bielefeld University

description: Gene expression data from hypoxia combined with As-treated plant samples

hyb_protocol: 3,8 µg of fragmented and labeled ss cDNA were hybridized to Affymetrix Arabidopsis Gene 1.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix Gene Chip Expression Console v1.4 Software. The generated “.cel” files were analyzed further using the Expression Console version 1.4.1 (Affymetrix) and Transcriptome Analysis Console version 3.1 (Affymetrix).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana (Col-0) roots after 7d of treatment (39d old plant)

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).

extract_protocol: RNA was isolated using the LiCl precipitation method. Cells were extracted with 750 µl of Tris-buffer (100 mM; pH 7.8) containing SDS (4%), NaCl (600 mM) and EDTA (20 mM) and 750 µl phenol: chloroform: isoamylalcohol (PCI, 25: 24: 1). After shaking for 30 min, the samples were centrifuged (16,000xg, 20 min). The collected uppermost layer was cleared by adding 750 µl PCI to remove proteins and other metabolites leaving behind nucleic acids. After centrifugation, RNA were precipitated by adding 8 M LiCl (0.75 volume of the sample) and incubating overnight at 4°C. The RNA pellet was resuspended in autoclaved distilled water (200 µl). After addition of 50 µl sodium acetate (3 M, pH 5.2) and 1 ml EtOH (96%, -20°C), the samples were incubated at -80°C for 1h. RNA precipitates collected after centrifugation were washed two times with 70% EtOH (-20°C) to remove salts. The precipitates were dried at 56°C and dissolved in RNase free water at 56°C with shaking.

value: Treated-root


title: At_7d Arsenic treatment _rep3

description: Gene expression data from As-treated plant samples


title: SSC002 [methylation]

description:
9933448143_R01C02
Case


title: At_7d treatment control_rep3

description: Gene expression data from experimental control samples

value: Un-treated root


title: CITED1 OE D1-rep3


title: CITED1 OE D2-rep1


title: CITED1 OE D1-rep1


title: Hippocampus TBI 1yr post injury, rep1

source_name: Hippocampus TBI 1yr post injury, rep1


title: CITED1 OE D2-rep2


title: At_7d Hypoxia treatment _rep3

description: Gene expression data from hypoxia-treated plant samples


title: CITED1 OE D1-rep2


title: HMEPIC_VA_E018

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

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

data_processing: Normalisation was performed using the preprocessFunnorm() function from the Bioconductor package minfi.

label: Cy5 and Cy3

source_name: Visceral adipocytes

label_protocol: Standard Illumina Protocol.

extract_protocol: Freshly isolated visceral adipose tissue samples were weighed and minced with surgical scissors. For each gram of minced tissue, 1.25 mg/mL of Collagenase I (Sigma Aldrich, CAT#C6885-1G) was added to 2 mL of HEPES buffer containing 7.9 g/L NaCl, 323 mg/L CaCl2.2H2O, 308 mg/L MgSO4.7H2O, 154.3 mg/L Na2HPO4 (anhydrous), 5 mL/L of 1M Hepes (Sigma Aldrich), 450 mg/L D-glucose, pH 7.2 – 7.4, 20 g/L BSA. The tissue was incubated for 30-45 minutes at 37ºC before being diluted 1:9 with additional HEPES buffer. The mixture was passed through a 250 micron mesh before being centrifuged at 300 rcf for 6 minutes at room temperature. The top lipid layer was removed and the adipocytes collected for snap-freezing in liquid nitrogen.

value: Female

tag: tissue origin

value: Visceral adipose

value: Visceral (omental) adipocytes


title: NC086 [methylation]

description:
9933448142_R03C01
Control


title: At_7d Combination treatment _rep2


title: HMEPIC_VA_E013


title: Hippocampus Sham 1yr post injury, rep4

source_name: Hippocampus Sham 1yr post injury, rep4


title: pPy OE D2-rep3

description: Gene expression data from ESCs transfected with pPy.

source_name: Control E14T ESCs

value: empty vector


title: At_7d Hypoxia treatment _rep2


title: NC053 [methylation]

description:
9933448142_R02C01
Control

value: M


title: Hippocampus TBI 1yr post injury, rep2

source_name: Hippocampus TBI 1yr post injury, rep2


title: NC239 [methylation]

description:
9933448142_R01C01
Control

source_name: Blood


title: NC231 [methylation]

description:
9933448121_R05C02
Control


title: HMEPIC_VA_E023


title: Hippocampus Sham 1yr post injury, rep2

source_name: Hippocampus Sham 1yr post injury, rep2


title: NC230 [methylation]

description:
9933448121_R04C02
Control


title: NC198 [methylation]

description:
9611519083_R01C01
Control


title: NC180 [methylation]

description:
9933448121_R03C02
Control


title: Hippocampus Sham 1yr post injury, rep3

source_name: Hippocampus Sham 1yr post injury, rep3


title: pPy OE D2-rep1


title: Hippocampus Naive 1yr, rep3

source_name: Hippocampus Naive 1yr, rep3


title: Hippocampus Sham 1yr post injury, rep1

source_name: Hippocampus Sham 1yr post injury, rep1


title: At_7d treatment control_rep2


title: pPy OE D2-rep2


title: At_7d Arsenic treatment _rep2


title: NC211 [methylation]

description:
9611519083_R02C01
Control


title: pPy OE D1-rep3


title: pPy OE D1-rep2


title: At_7d Arsenic treatment _rep1


title: NC063 [methylation]

description:
9933448121_R02C02
Control


title: NC062 [methylation]

description:
9933448121_R01C02
Control


title: NC055 [methylation]

description:
9611519043_R04C02
Control


title: Hippocampus Naive 1yr, rep4

source_name: Hippocampus Naive 1yr, rep4


title: ES-rep3

description: Gene expression data from ESCs.

source_name: E14T ESCs


title: PBMC Disc Early

description:
Early PostRx Peripheral Blood
raw.expMatrix_PBMC.csv

data_processing:
Guide barcode reads - Read length: Read 1: 26 (cell-barcode, UMI), Index read 2 (i5): 8, Read 2: 98 (RNA read)
Raw base BCL files were demultiplexed using the Cell Ranger mkfastq pipeline into sample-specific FASTQ files.
FASTQ files were processed individually using the Cell Ranger count pipeline, which made use of  the STAR software to align cDNA reads to the GRCh38 and the Merkel cell polyomavirus sequence (HM011556.1).
Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads.
Tumor and PBMC samples were respectively aggregated together using the Cell Ranger aggr pipeline resulting in two gene-barcode count matrices (tumor and PBMC) to be used for downstream analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for tumor and PBMC

source_name: PBMC

growth_protocol: N/A - ex vivo

extract_protocol:
PBMC were isolated with standard FICOLL, tumor tissues were digested in RPMI with DNAse, Collagenase, and hyaluronidase, strained and frozen.  All samples were thawed on same day and immediately processed
10x Genomics Gene Expression 3' Chromium V 2.0 per manufacturer's instructions

tag: chromium index


title: Hippocampus Naive 1yr, rep1

source_name: Hippocampus Naive 1yr, rep1


title: At_7d treatment control_rep1


title: PBMC Disc AR

description:
Acquired Resistance Peripheral Blood
raw.expMatrix_PBMC.csv


title: Hippocampus Naive 1yr, rep2

source_name: Hippocampus Naive 1yr, rep2


title: NC050 [methylation]

description:
9933448121_R06C01
Control


title: Hippocampus TBI 6mo post injury, rep4

source_name: Hippocampus TBI 6mo post injury, rep4


title: At_7d Combination treatment _rep1

source_name: Arabidopsis thaliana (Col-0) roots after 7d of treatment (39d old plant)


title: At_7d Hypoxia treatment _rep1


title: ES-rep1

description: Gene expression data from ESCs.


title: NC011 [methylation]

description:
9933448121_R02C01
Control


title: PBMC Pre

description:
PreRx Peripheral Blood
raw.expMatrix_PBMC.csv

value: PreRx


title: NC042 [methylation]

description:
9933448121_R05C01
Control


title: Hippocampus TBI 6mo post injury, rep3

source_name: Hippocampus TBI 6mo post injury, rep3


title: ES-rep2

description: Gene expression data from ESCs.


title: pPy OE D1-rep1


title: Tumor Disc AR

description:
Acquired Resistance Tumor Digest
raw.expMatrix_Tumor.csv

source_name: Tumor

value: Merkel Cell Carcinoma Tumor


title: Tumor Disc Pre

description:
PreRx MCC Tumor Digest
raw.expMatrix_Tumor.csv


title: NC010 [methylation]

description:
9611519043_R01C02
Control


title: 83B936 ko rep 2

city: Erlangen

first: Soeren

last: Lukassen

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Friedrich-Alexander Universitaet Erlangen Nuernberg

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Affymetrix Expression Console 1.4.1

source_name: whole testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using Trizol according to manufacturer instructions.

value: testis

value: Phf13 knockout


title: Hippocampus TBI 6mo post injury, rep1

source_name: Hippocampus TBI 6mo post injury, rep1


title: Hippocampus TBI 6mo post injury, rep2

source_name: Hippocampus TBI 6mo post injury, rep2


title: RB_0

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13
ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:25"
PhiX Screen - Bowtie-2.2.1 "-N 1"
MAPPING - SHRiMP_2_2_3 "--qv-offset 33 --all-contigs"
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing fpkm values of all samples

source_name: Primary AML patient specimen

extract_protocol:
Qiagen Rneasy Plus
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer’s protocols.
mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’-adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

treatment_protocol: Cells were stained with CellROX dye at 5 uM for 30 min prior to surface staining and sorting.

tag: individual

value: Primary AML patient

tag: treatment

value: untreated

value: bone marrow mononuclear cells


title: Hippocampus Sham 6mo post injury, rep4

source_name: Hippocampus Sham 6mo post injury, rep4

value: Sprague-Dawley


title: FJ_6

source_name: Primary AML patient specimen, treated

value: venetoclax and azacitidine


title: Hippocampus Sham 6mo post injury, rep3

source_name: Hippocampus Sham 6mo post injury, rep3


title: 83B935 wt rep 3

value: wild type


title: RB_7


title: 83B906 wt rep 2


title: PBMC Disc Resp

description:
Responding PostRx Peripheral Blood
raw.expMatrix_PBMC.csv

value: PBMC


title: NC003 [methylation]

description:
9933448121_R01C01
Control

source_name: Blood

value: F

value: NC


title: 83B937 ko rep 3


title: Hippocampus Sham 6mo post injury, rep2

source_name: Hippocampus Sham 6mo post injury, rep2


title: 83B882 wt rep 1


title: 83B907 ko rep 1


title: Hippocampus Sham 6mo post injury, rep1

source_name: Hippocampus Sham 6mo post injury, rep1


title: 1020_6


title: FJ_0


title: 839742 ko rep 3


title: 1020_0


title: Hippocampus Naive 6mo, rep4

source_name: Hippocampus Naive 6mo, rep4


title: NC005 [methylation]

description:
9611519043_R04C01
Control


title: 839613 wt rep 3


title: Hippocampus Naive 6mo, rep2

source_name: Hippocampus Naive 6mo, rep2


title: Hippocampus Naive 6mo, rep3

source_name: Hippocampus Naive 6mo, rep3


title: hCTB (3) cultured 3h, exposed to 1µM BDE-47 for 24h

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description:
hCTB 3_T3h_24h_BDE_47
3999442056_R04C02

hyb_protocol: Converted DNA was amplified, fragmented and hybridized to Illumina Infinium 450k Bead Array

data_processing: BeadStudio software v3.2; Methylation data was processed via Illumina standard background subtraction and control probe normalization, and converted to M values, using the minfi package and BRB Array Tools (NCI) software package

source_name: hCTB cultured 3h_exposed to 1µM BDE-47 for 24h

label_protocol: Downstream processing of genomic DNA bisulfite conversion was performed using the EZ DNA Methylation Kit (ZymoResearch) and Infinium HumanMethylation450 bead arrays (Illumina) following the manufacturer’s protocols.

growth_protocol: As described  (Robinson et al., 2017), cytotrophoblasts (CTBs) were isolated from 2nd trimester human placentas. CTBs were cultured at a density of 500,000 CTBs/well in 1.5 ml medium containing DME/H-21, 2% Nutridoma (Roche), 1% sodium pyruvate (Sigma), 1% Hepes buffer (Invitrogen), 1% glutamate plus (Atlanta Biologicals), and 1% penicillin/streptomycin (Invitrogen) on Matrigel substrate.

extract_protocol: Immediately following a 24h exposure duration, CTBs were washed once with PBS and trypsinized (0.05%, Gibco, 5min). Cell pellets were washed 2X with PBS (centrifugation at 5min/800 rpm) and stored at -80oC. To extract genomic DNA, CTBs were digested with 1mg/ml proteinase K in lysis buffer (50mM Tris, pH 8.0, 1mM EDTA pH 8.0, 0.5% SDS) overnight at 55⁰C. Following RNase treatment, DNA was isolated using the Phenol-Chloroform Isoamyl Alcohol (PCI) method, followed by precipitation with ethanol, and resuspended in TE. The DNA concentration and quality were estimated by using a Nanodrop spectrometer (Thermo Scientific) and the Agilent RNA 6000 Nano LabChip Kit and Bioanalyzer 2100 system. DNA was extracted from exposed and control cultures from 3 independent experiments (~1 million cells/sample).

treatment_protocol: Cells were incubated at 37oC in 5% CO2/ 95% air. Following attachment (t=3h) or the next morning (t=15h), fresh media was supplied and CTBs were exposed to vehicle control (0.1% DMSO) or 1µM BDE-47.

value: primary villous cytotrophoblast (2nd trimester; hCTB)

tag: gestational age

tag: exposed to

tag: exposure duration


title: RNA-seq_siRNA #2 SLNCR rep1

city: Boston

first: Carl

last: Novina

state: MA

address: 450 Brookline Ave

department: Cancer Immunology

institute: Dana-Farber Cancer Institute

data_processing:
Raw FASTQ sequence was mapped using Bowtie (Langmead et al., 2009)
Normalized read counts (FPKM) were generated in Cufflinks v2.1.1 (http://cole-trapnell-lab.github.io/cufflinks/) by mapping onto the hg19 build of the human transcriptome (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
Differentially expressed genes were identified using CuffDiff (http://cufflinks.cbcb.umd.edu/)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, and log2 fold change values compared to scrambled siRNA control

source_name: cell culture

growth_protocol: WM1976 cells were maintained in DMEM plus 10% FBS.

extract_protocol:
Cells were harvested 48 hours post-transfection RNA was isolated using Trizol® (Life Technologies) and Qiagen RNeasy Mini Kit and treated with DNase.
Libraries were prepared using Illumina TruSeq Rna sample preparation kit (v2).

treatment_protocol: Cells were transfected with scrambled siRNA control, or siRNA targeting SLNCR1 24 hours post-seeding using RNAiMAX (Invitrogen)

tag: tissue

value: skin

tag: tumor stage

value: malignant melanoma

tag: genotype/variation

value: SLNCR siRNA #2


title: 839604 wt rep 2

tag: genotype


title: 839744 wt rep 4


title: hCTB (3) cultured 15h, exposed to 1µM BDE-47 for 24h

description:
hCTB 3_T15h_24h_BDE_47
3999442056_R06C02

source_name: hCTB cultured 15h_exposed to 1µM BDE-47 for 24h

tag: cell type


title: hCTB (3) cultured 3h, exposed to 0.1% DMSO for 24h

description:
hCTB 3_T3h_24h_vehicle
3999442056_R03C02

source_name: hCTB cultured 3h_exposed to 0.1% DMSO for 24h


title: RNA-seq_siRNA #1 SLNCR rep2

value: SLNCR siRNA #1


title: Hippocampus Naive 6mo, rep1

source_name: Hippocampus Naive 6mo, rep1

tag: strain


title: Hippocampus TBI 2wk post injury, rep4

source_name: Hippocampus TBI 2wk post injury, rep4


title: 839603 ko rep 2

source_name: whole testis


title: RNA-seq_siRNA #1 SLNCR rep1


title: 839498 wt rep 1


title: hCTB (2) cultured 15h, exposed to 1µM BDE-47 for 24h

description:
hCTB 2_T15h_24h_BDE_47
3999442056_R02C02


title: hCTB (2) cultured 15h, exposed to 0.1% DMSO for 24h

description:
hCTB 2_T15h_24h_vehicle
3999442056_R01C02

source_name: hCTB cultured 15h_exposed to 0.1% DMSO for 24h


title: Hippocampus TBI 2wk post injury, rep2

source_name: Hippocampus TBI 2wk post injury, rep2


title: hCTB (2) cultured 3h, exposed to 1µM BDE-47 for 24h

description:
hCTB 2_T3h_24h_BDE_47
3999442056_R06C01


title: RNA-seq_scrambled control rep2

value: scrambled control


title: RNA-seq_siRNA #2 SLNCR rep2


title: PrEC

description: normal prostate epithelial cell line

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 using Tophat v2.0.8b with parameters –library-type fr-secondstrand
Read counts over the aligned BAM file were extracted using bedtools multicov, for core loci common to both HuGene2.0st and HTA2.0 arrays.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing read counts extracted for the given ranges using bedtools multicov

source_name: Normal prostate epithelial cell line

growth_protocol: LNCaP: As per Song JZ, Stirzaker C, Harrison J, Melki JR, Clark SJ. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene. 2002;21:1048–61. PrEC: As per Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol. 2010;12:235–46.

extract_protocol:
Total RNA was isolated with TRIzol reagent from exponentially growing LNCaP and PrEC cells that were 80% confluent and treated with DNaseI.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PrEC

value: Normal prostate epithelial

tag: passage

value: cell line at passage 6


title: LNCaP

description: prostate cancer epithelial cell line

source_name: Cancerous prostate epithelial cell line

value: LNCaP

value: Cancerous prostate epithelial

value: cell line at passage 69


title: hCTB (2) cultured 3h, exposed to 0.1% DMSO for 24h

description:
hCTB 2_T3h_24h_vehicle
3999442056_R05C01


title: Hippocampus TBI 2wk post injury, rep1

source_name: Hippocampus TBI 2wk post injury, rep1

value: Sprague-Dawley


title: Male_Meth#2 Heart Trial 2

city: Honolulu

first: April

middle: L

last: Darrow

state: HI

address: 651 Ilalo St.

institute: University of Hawaii

description: Gene expression in the heart of a male C57BL/6 mouse after 5 months of methamphetamine exposure

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 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 manufacturer's instructions. Upon 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 Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent),

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Methamphetamine-treated male heart, trial#2

label_protocol: Total RNA was converted into double-stranded cDNA and then into Cy-3 labeled cRNA using the Agilent Quick Amp Labeling Kit (Santa Clara, CA) according to the manufacturer’s instructions. Following purification, 1.65 µg of Cy3 dye-labeled cRNA, as measured by NanoDrop 2000c spectrophotometer (Thermo Scientific, Bellerica, MA), was used for subsequent array analysis.

extract_protocol: RNA was extracted from homogenized heart tissue using TriReagent® (Molecular Research Center, Cincinnati, OH) following the manufacture’s protocol.  The RNA was further purified using an RNeasy® Mini Kit (Qiagen, Valencia, CA), quantified on the Qubit fluorometer (Invitrogen, Carlsbad, CA) and examined on a 1% agarose-EthBr gel to confirm integrity.

treatment_protocol: After 5 months of dosing, heart tissue from methamphetamine-treated mice and the PBS controls was excised,  snap frozen in liquid nitrogen, and stored at -80C prior to mechanical homogenization.

tag: gender

value: Male

value: methamphetamine hydrochloride

tag: heart

value: heart


title: Male_PBS#1 Heart Trial 2

description: Gene expression in the heart of a male C57BL/6 control mouse after 5 months of PBS injections

source_name: PBS control male heart, trial#2

value: PBS


title: Male_Meth#1 Heart Trial 2


title: Male_PBS#2 Heart Trial 2


title: Hippocampus TBI 2wk post injury, rep3

source_name: Hippocampus TBI 2wk post injury, rep3


title: Female_Meth#3 Heart Trial 1

description: Gene expression in the heart of a female C57BL/6 mouse after 5 months of methamphetamine exposure

source_name: Methamphetamine-treated female heart, trial#2

value: Female


title: Female_Meth#2 Heart Trial 1

source_name: Methamphetamine-treated female heart, trial#1


title: Hippocampus Naive 2wk, rep3

source_name: Hippocampus Naive 2wk, rep3


title: hCTB (1) cultured 15h, exposed to 0.1% DMSO for 24h

description:
hCTB 1_T15h_24h_vehicle
3999442056_R03C01

value: primary villous cytotrophoblast (2nd trimester; hCTB)


title: Hippocampus Sham 2wk post injury, rep4

source_name: Hippocampus Sham 2wk post injury, rep4


title: Hippocampus Naive 2wk, rep4

source_name: Hippocampus Naive 2wk, rep4


title: Hippocampus Naive 2wk, rep2

source_name: Hippocampus Naive 2wk, rep2


title: Female_PBS#2 Heart Trial 1

description: Gene expression in the heart of a female C57BL/6 control mouse after 5 months of PBS injections

source_name: PBS control female heart, trial#1


title: Female_PBS#3 Heart Trial 1

source_name: PBS control female heart, trial#2


title: Hippocampus Naive 2wk, rep1

source_name: Hippocampus Naive 2wk, rep1


title: hCTB (1) cultured 15h, exposed to 1µM BDE-47 for 24h

description:
hCTB 1_T15h_24h_BDE_47
3999442056_R04C01

source_name: hCTB cultured 15h_exposed to 1µM BDE-47 for 24h


title: hCTB (1) cultured 3h, exposed to 1µM BDE-47 for 24h

description:
hCTB 1_T3h_24h_BDE_47
3999442056_R02C01

source_name: hCTB cultured 3h_exposed to 1µM BDE-47 for 24h


title: Hippocampus Sham 2wk post injury, rep1

source_name: Hippocampus Sham 2wk post injury, rep1


title: Hippocampus Sham 2wk post injury, rep3

source_name: Hippocampus Sham 2wk post injury, rep3


title: Female_Meth#4 Heart Trial 1


title: H5N1_1hr [mRNA]

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

data_processing:
Basecalls performed using Illumina pipeline version 1.3.
The sequencing reads were trimmed with adapters, homopolymers, and residue rRNA sequences, and were then aligned to the Genome Reference Consortium Human Build 37 (GRCh37) using CLC Genomics Workbench (CLC bio, Cambridge, MA).
Genome_build: GRCh37
Supplementary_files_format_and_content: Table files containing the read counts for each gene in each sample.
Supplementary_files_format_and_content: Excel file containing the normalized gene expression (RPKM) for genes with read count greater than 10.

source_name: macrophage cell type

extract_protocol:
The macrophages were infected with H1N1 and H5N1 separately at a MOI of two. The cells were washed with warm culture medium and incubated in macrophage serum free medium (Invitrogen) supplemented with 0.6 mg/l penicillin and 60 mg/l streptomycin. The total RNA was extracted from cells at 1-, 3-, and 6-hr post-infection using the mirVana miRNA Isolation Kit (Ambion, Inc. TX, USA).
The rRNAs were removed from 1 µg total RNA with the RiboMinus™ Transcriptome Isolation kit (Human/Mouse) (Invitrogen, Carlsbad, CA). The rRNA-depleted RNA from 1 µg total RNA was fragmented by incubation for 5 min at 94 °C in 5x Array Fragmentation Buffer (Ambion, TX). Double stranded cDNA was synthesized with the SuperScript Double Stranded cDNA synthesis kit (Invitrogen). The RNA was purified on a QiaQuick PCR column (Qiagen, Valencia, CA), and Illumina pair-ended adapter was ligated to the end of DNA fragments with the Quick Ligation™ Kit (NEB, Ipswich, MA) by incubation for 15 min at room temperature.

treatment_protocol: Primary human macrophage was separated from peripheral-blood leucocytes from healthy blood donors. The macrophages were seeded onto tissue culture plates in RPMI 1640 medium (Sigma-Aldrich) supplemented with 5% heat-inactivated autologous plasma.

tag: sample type

value: Highly pathogenic

tag: molecule

value: rRNA-depleted RNA

tag: time point


title: H5N1_6hr [mRNA]


title: hCTB (3) cultured 15h, exposed to 0.1% DMSO for 24h

description:
hCTB 3_T15h_24h_vehicle
3999442056_R05C02

source_name: hCTB cultured 15h_exposed to 0.1% DMSO for 24h


title: Female_PBS#1 Heart Trial 1


title: hCTB (1) cultured 3h, exposed to 0.1% DMSO for 24h

description:
hCTB 1_T3h_24h_vehicle
3999442056_R01C01

source_name: hCTB cultured 3h_exposed to 0.1% DMSO for 24h


title: H5N1_3hr [mRNA]


title: Male_PBS#2 Heart Trial 1

source_name: PBS control male heart, trial#1


title: Cortex TBI 1yr post injury, rep4

source_name: Cortex TBI 1yr post injury, rep4


title: Cortex TBI 1yr post injury, rep3

source_name: Cortex TBI 1yr post injury, rep3


title: Male_PBS#1 Heart Trial 1


title: H1N1_3hr [mRNA]

value: Low virulence


title: H1N1_1hr [mRNA]


title: Female_Meth#1 Heart Trial 1

source_name: Methamphetamine-treated female heart, trial#1


title: Mock_6hr [mRNA]

value: Mock control


title: Mock_3hr [mRNA]


title: human control

city: Bar Harbor

first: Petko

last: Petkov

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: human control

library_source: genomic

data_processing:
Sequence reads were trimmed using trimmomative version 0.32
ChIP-Seq reads were aligned to the GRC38m/mm10 or GRC38h/hg38 genome assembly or using BWA v0.7.9a
Potential PCR duplicates were removed from alignments using Samtools v0.1.19
Alignments were filtered for highest mapping quality score with no indels
Blacklist peaks were found in input/control samples utilizing custom code and filtered from Chip-Seq samples
Genome_build: GRC38m/mm10
Genome_build: GRC38h/hg38
Supplementary_files_format_and_content: Peaks were called utilizing MACS v1.4.2
Supplementary_files_format_and_content: Motif data was generated using Meme v4.9.0.3

source_name: human genomic DNA

extract_protocol:
phenol-chlorophorm
Illumina  Nextera DNA

value: cell culture

tag: age

value: not applicable

value: NIST RM 8398


title: Mock_1hr [mRNA]


title: H1N1_6hr [mRNA]


title: NC001 [methylation]

description:
9611519043_R01C01
Control

source_name: Blood

value: F

value: PBMC

tag: diagnosis

value: NC


title: Cortex Sham 1yr post injury, rep4

source_name: Cortex Sham 1yr post injury, rep4

value: Sprague-Dawley


title: Cortex TBI 1yr post injury, rep2

source_name: Cortex TBI 1yr post injury, rep2


title: Cortex TBI 1yr post injury, rep1

source_name: Cortex TBI 1yr post injury, rep1


title: hZFY

description: hZFY


title: Male_Meth#2 Heart Trial 1

source_name: Methamphetamine-treated male heart, trial#1

value: Male

tag: treatment


title: Cortex Sham 1yr post injury, rep3

source_name: Cortex Sham 1yr post injury, rep3


title: SSC047

description: Systemic sclerosis

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

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

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

tag: race

value: Chinese

value: SSc


title: Cortex Naive 1yr, rep4

source_name: Cortex Naive 1yr, rep4


title: Male_Meth#1 Heart Trial 1

value: methamphetamine hydrochloride

value: heart


title: Cortex Sham 1yr post injury, rep1

source_name: Cortex Sham 1yr post injury, rep1


title: FoxO1 KO BMDMs, M1

city: Hefei

first: Jingbo

last: Yang

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

description:
Gene expression of FoxO1 KO M1 BMDMs
F BMDM 1

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Agilent Feature Extraction Software (FES) was used to read out and process the Microarray Image files. The software determines feature intensities (including background substraction), rejects outliers, and calculates statistical confidences.Microarray results were analyzed with GeneSpring GX software. Normalization method: signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.

source_name: FoxO1 KO BMDMs, M1

label_protocol: Standard Agilent protocol

growth_protocol: Bone marrow cells were cultured with 10% L929 cultured medium, for 7 days

extract_protocol: BMDMs were lysis with RNAiso Plus and extracted as the protocol described.

treatment_protocol: M0 BMDMs without addition treatment, M1 BMDMs were treated with 100ng/ml LPS plus 20ng/mL IFN-γ, M2 BMDMs were treated with 10ng/ml IL-4 plus 10ng/ml IL-13, both last for 24 hours.

value: bone marrow derived macrophages

value: LysMcre FoxO1 Fl/Fl

tag: polarization state

value: M1 polarization


title: SSC065

description: Systemic sclerosis


title: Cortex Naive 1yr, rep2

source_name: Cortex Naive 1yr, rep2


title: WT BMDMs, M1

description:
Gene expression of M1 BMDMs
W BMDM 1

source_name: WT BMDMs, M1

value: FoxO1 Fl/Fl


title: SSC067

description: Systemic sclerosis


title: Cortex Sham 1yr post injury, rep2

source_name: Cortex Sham 1yr post injury, rep2


title: FoxO1 KO BMDMs, M2

description:
Gene expression of FoxO1 KO M2 BMDMs
F BMDM 2

source_name: FoxO1 KO BMDMs, M2

value: M2 polarization


title: FoxO1 KO BMDMs, M0

description:
Gene expression of FoxO1 KO M0 BMDMs
F BMDM 0

source_name: FoxO1 KO BMDMs, M0

value: M0 unstimulated state


title: SSC052

description: Systemic sclerosis


title: WT BMDMs, M0

description:
Gene expression of M0 BMDMs
W BMDM 0

source_name: WT BMDMs, M0


title: SSC040

description: Systemic sclerosis


title: Cortex Naive 1yr, rep1

source_name: Cortex Naive 1yr, rep1


title: WT BMDMs, M2

description:
Gene expression of M2 BMDMs
W BMDM 2

source_name: WT BMDMs, M2


title: SSC049

description: Systemic sclerosis

source_name: Blood


title: SSC018

description: Systemic sclerosis


title: 839460 ko rep 1

source_name: whole testis

tag: tissue

value: testis

value: Phf13 knockout


title: Cortex Naive 1yr, rep3

source_name: Cortex Naive 1yr, rep3


title: Cortex TBI 6mo post injury, rep1

source_name: Cortex TBI 6mo post injury, rep1


title: RNA-seq_scrambled control rep1

source_name: cell culture

tag: cell line

value: skin

tag: tumor stage

value: malignant melanoma

value: scrambled control


title: Cortex TBI 6mo post injury, rep4

source_name: Cortex TBI 6mo post injury, rep4

value: Sprague-Dawley


title: Cortex TBI 6mo post injury, rep2

source_name: Cortex TBI 6mo post injury, rep2


title: Cortex TBI 6mo post injury, rep3

source_name: Cortex TBI 6mo post injury, rep3


title: Cortex Sham 6mo post injury, rep4

source_name: Cortex Sham 6mo post injury, rep4


title: SSC010

description: Systemic sclerosis

value: PBMC


title: SSC039

description: Systemic sclerosis

value: Chinese


title: SSC028

description: Systemic sclerosis

value: SSc


title: Cortex Sham 6mo post injury, rep2

source_name: Cortex Sham 6mo post injury, rep2


title: Cortex Sham 6mo post injury, rep3

source_name: Cortex Sham 6mo post injury, rep3


title: Hippocampus Sham 2wk post injury, rep2

source_name: Hippocampus Sham 2wk post injury, rep2


title: Cortex Naive 6mo, rep3

source_name: Cortex Naive 6mo, rep3


title: Cortex Sham 6mo post injury, rep1

source_name: Cortex Sham 6mo post injury, rep1


title: Cortex Naive 6mo, rep4

source_name: Cortex Naive 6mo, rep4


title: Cortex TBI 3mo post injury, rep4

source_name: Cortex TBI 3mo post injury, rep4


title: Cortex Naive 6mo, rep2

source_name: Cortex Naive 6mo, rep2


title: SSC053

description: Systemic sclerosis

source_name: Blood


title: SSC003

description: Systemic sclerosis


title: Cortex Naive 6mo, rep1

source_name: Cortex Naive 6mo, rep1


title: SSC005

description: Systemic sclerosis


title: NC086

description: normal control

value: NC


title: SSC002

description: Systemic sclerosis


title: SSC004

description: Systemic sclerosis


title: SSC001

description: Systemic sclerosis


title: Cortex Sham 3mo post injury, rep2

source_name: Cortex Sham 3mo post injury, rep2


title: Cortex TBI 3mo post injury, rep3

source_name: Cortex TBI 3mo post injury, rep3


title: Cortex Sham 3mo post injury, rep3

source_name: Cortex Sham 3mo post injury, rep3


title: NC085

description: normal control


title: Cortex TBI 3mo post injury, rep1

source_name: Cortex TBI 3mo post injury, rep1


title: NC231

description: normal control


title: NC211

description: normal control


title: SSC023

description: Systemic sclerosis


title: Cortex Naive 3mo, rep4

source_name: Cortex Naive 3mo, rep4


title: Cortex Sham 3mo post injury, rep4

source_name: Cortex Sham 3mo post injury, rep4


title: Cortex TBI 3mo post injury, rep2

source_name: Cortex TBI 3mo post injury, rep2


title: NC230

description: normal control


title: NC053

description: normal control


title: S8_60_2rp

city: Jena

first: Falk

last: Hillmann

address: Adolf-Reichwein-Straße 23

department: Evolution of Microbial Interactions

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

data_processing:
Demultiplexing of all libraries for each sequencing lane using the Illumina bcl2fastq 2.17.1.14 software
quality control of raw read data with FastQC, quality and adapter trimming with Trimmomatic v0.32; PE -threads 3 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:15:25 MINLEN:30
mapping of reads against the combined reference genomes of Candida parapsilosis and Protostelium aurantium with TopHat v2.1.0; -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive –no-coverage-search
assigning reads to features and counting reads per feature with FeatureCounts v1.4.5; -T 5 -s 0 -t exon -g gene_id
differential expression analysis with Deseq, DEseq2, SAMseq, Limma, EdgeR and BaySeq, adjusted p-value cutoff 0.01
Genome_build: Candida parapsilosis CDC317 s01-m03-r11; Protostelium aurantium var. fungivorum J1 ASM302417v1
Supplementary_files_format_and_content: Tab-delimited text files include counts for each gene per sample

organism:
Candida parapsilosis
Planoprotostelium fungivorum

source_name: Candida parapsilosis, Protostelium aurantium

growth_protocol: Amoeba were pre-cultured in 20 x wMY medium at 22°C, yeast cells were grown exponentially in YPD medium at 30°C

extract_protocol:
For RNA isolation, frozen pellets were resuspended in TES lysis buffer. Primary extraction was achieved by acidic phenol:chloroform, heating at 65°C and shaking in the presence of zirconia beads. After freezing at -80°C, samples were centrifuged for the phase separation, followed by two extraction step with phenol:chloroform and chloroform:isoamyl alcohol. RNA was precipitated in ice-cold ethanol, equilibrated with 3M sodium acetate at -20°C. After washing with 70 % ethanol, RNA was resuspended in DEPC-treated water.
Illumina library was prepared by LGC Genomics using the Encore Rapid DR Multiplex system (Nugen) according the manual. Prior to library construction, mRNA was isolated via oligo dT binding, cDNA was synthetised using NEBNext RNA First and Second Strand Synthesis Modules (New England Biolabs). Libraries were amplified in a volume of 100µl for 15 cycles using MyTaq (Bioline) and standard Illumina primers. Size selection was done on a preparative Agarose Gel selecting fragments between 200 and 500bp

treatment_protocol: Amoeba cells were harvested using cell scraper, centrifuged for 10 min/800g and resuspended in 20 x wMY. Yeast cells were hravested by centrifugation and washed twice with 20 x wMY. Both organisms were counted in a CASY Cell Counter. Amoeba nad yeast cells were mixed at an MOI of 10 and spread on the 20 x wMY agar . At indicated time points, cells were washed off the plate, centrifuged and immediately frozen in the liquid nitrogen.

value: whole organism

value: 60 min

tag: candida parapsilosis strain

tag: protostelium aurantium strain


title: Cortex Sham 3mo post injury, rep1

source_name: Cortex Sham 3mo post injury, rep1

tag: strain


title: S9_60_3rp


title: Cortex Naive 3mo, rep3

source_name: Cortex Naive 3mo, rep3


title: S7_60_1rp


title: NC180

description: normal control

tag: cell type


title: PJL_T

city: San Francisco

first: Anne

last: de Bruyn Kops

state: California

address: UCSF Mission Bay, Genentech Hall N376, Guthrie Lab, 600 16th St

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  S288C genome with bowtie v 1.1.2
To identify regions of Brr6 binding, smoothed ChIP signal from the tagged samples (B6N) were divided by the signal from the untagged sample (PJL) after normalizing to the total number of aligned reads. A sliding window of 200 bp moving in increments of 20 bp was used to detect regions that had at least 2-fold enrichment of signal in the tagged sample over the untagged sample. Regions that had at least 50% overlap in both replicates were selected. Only the overlapping portion of the region was considered for further analysis steps. Finally, the average read density (in RPKM) was calculated in each region of Brr6 binding for tagged and untagged and then normalized to the signal from the corresponding whole cell extract from that sample.
Genome_build: R64-2-1_20150113

organism: Saccharomyces cerevisiae

growth_protocol: 10 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

extract_protocol:
Cells were washed 2x in TBS, and resuspended in IP buffer (50 mM Tris [pH 7.4], 125 mM KCl, and 0.1% NP40) plus protease inhibitors (100 μM phenylmethanesulphonylfluoride [PMSF], Sigma and Complete protease tablet (Roche). Cells lysates generated by bead beating (5x1', separated by 2' on ice) were bath-sonicated 4x 7.5’ and clarified 2x 10' at 18,000 RCF. Extracts were incubated (350ul/sample) O/N with 40ul EZview Red anti-FLAG M2 affinity gel (Sigma) and washed twice with 1ml lysis buffer, once with 1ml lysis buffer + 500mM NaCl at 4˚C and once with TE at room temperature.
Crosslinks were reversed and DNA libraries prepared as described in Inada, M. et al.,(2016). NAR 44(19):9180-9189 (PMID:27402158 except that the Thermo Fast End Repair Kit was used for DNA end repair.
Libraries were size selected (200-400bp) and quality checked by bioanalyzer using the Agilent High Sensitivity DNA Kit prior to multiplexing for Illumina sequencing (single end, 50bp reads).

treatment_protocol: Cells  (80ml, OD600=1) were crosslinked in 15’ in 1% formaldehyde, quenched 15’ with 125mM glycine

tag: genotype

value: wild type (empty vector)

value: DNA


title: PJL_b

growth_protocol: 9 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

value: M2 anti-FLAG Affinity purified DNA


title: NC239

city: Dallas

first: Quan

last: Li

institute: UTSW

description: normal control


title: PJL_a

growth_protocol: 8 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.


title: NC063

description: normal control


title: NC062

description: normal control


title: NC198

description: normal control


title: Cortex TBI 2wk post injury, rep4

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Cortex TBI 2wk post injury, rep4

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation.  Quality and quantity of the Total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies; Santa Clara, CA).


title: SSC006

description: Systemic sclerosis


title: deltaC4N_T

growth_protocol: 7 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

value: W303, pPGAL_NLS-brr6deltaC4N

value: FLAG-tagged Brr6deltaC4N


title: Striatum of the brain from mice with Thr-Dio2 gene 39

city: Chicago

first: Gustavo

middle: Werpel

last: Fernandes

address: 5841 South Maryland Av.

department: Endocrinology

institute: University of Chicago

description:
Gene expression data from the striatum of Thr92D2 mice
Thr Striatum Cortex 39

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized on GeneChip Affymetrix Clariom S Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips underwent a process of scanning, visualization of arrays and quality control analysis.

data_processing: RMA method .The data were analyzed using Affymetrix analysis.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10uL with concentration at least 250ng/3uL (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All animals were kept at room temperature (22°C) under a 12-h dark/light cycle, and main-tained on a chow diet and water Ad libitum

tag: background strain

value: brain

tag: tissue region

value: Striatum

value: 8-10 weeks-old


title: Striatum of the brain from mice with Thr-Dio2 gene 38

description:
Gene expression data from the striatum of Thr92D2 mice
Thr Striatum Cortex 38


title: Striatum of the brain from mice with Thr-Dio2 gene 40

description:
Gene expression data from the striatum of Thr92D2 mice
Thr Striatum Cortex 40


title: Cortex TBI 2wk post injury, rep1

source_name: Cortex TBI 2wk post injury, rep1


title: Cortex Naive 3mo, rep2

source_name: Cortex Naive 3mo, rep2


title: Cortex TBI 2wk post injury, rep3

source_name: Cortex TBI 2wk post injury, rep3


title: NC050

address: 6001 Forest Park Rd

description: normal control


title: NC055

description: normal control


title: Striatum of the brain from mice with Thr-Dio2 gene 37

description:
Gene expression data from the striatum of Thr92D2 mice
Thr Striatum Cortex 37


title: NC042

description: normal control


title: NC011

description: normal control


title: Cortex TBI 2wk post injury, rep2

source_name: Cortex TBI 2wk post injury, rep2


title: Striatum of the brain from mice with Ala-Dio2 gene 34

description:
Gene expression data from the striatum of Ala92D2 mice
Ala Striatum Cortex 34


title: deltaC4N_b

growth_protocol: 6 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

tag: molecule


title: Cortex Sham 2wk post injury, rep4

source_name: Cortex Sham 2wk post injury, rep4


title: Striatum of the brain from mice with Ala-Dio2 gene 35

description:
Gene expression data from the striatum of Ala92D2 mice
Ala Striatum Cortex 35


title: Cortex Sham 2wk post injury, rep3

source_name: Cortex Sham 2wk post injury, rep3


title: deltaC4N_a

growth_protocol: 5 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.


title: Striatum of the brain from mice with Ala-Dio2 gene 36

description:
Gene expression data from the striatum of Ala92D2 mice
Ala Striatum Cortex 36


title: Striatum of the brain from mice with Ala-Dio2 gene 33

description:
Gene expression data from the striatum of Ala92D2 mice
Ala Striatum Cortex 33


title: Cortex Sham 2wk post injury, rep2

source_name: Cortex Sham 2wk post injury, rep2


title: B6N_T

growth_protocol: 4 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

value: W303, pPGAL_NLS-BRR6N

value: FLAG-tagged Brr6N


title: NC005

description: normal control

source_name: Blood


title: B6N_b

growth_protocol: 3 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

value: M2 anti-FLAGAffinity purified DNA


title: brr6-1_gal_B

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  S288C genome with Tophat
Reads in annotated transcripts were counted with Htseq-count
Genome_build: R64-2-1_20150113

growth_protocol: Cells (12mls, 2 biological replicates) were grown at 30 ˚C in 2% glucose (samples 1,2,5,6) or raffinose/0.04% sucrose YEP media followed by addition of galactose (2%)  and incubation for 2hrs (samples 3,4,7,8). Cells were harvested in mid-log phase.

extract_protocol:
RNA was extracted using an established hot acid phenol protocol. Ribosomal RNA was removed using a Ribominus transcriptome isolation kit for yeast and concentration module (Invitrogen).
RNA was cleaned and DNAse treated using  the RNA Clean and Concentrator Kit (Zymo Research). RNA quality was checked by bioanalyzer using the Agilent RNA 6000 Pico Kit.RNA libraries were prepared using a NEBNext Ultra Directional RNA Library Prep kit for Illumina (E7420) and standard NEB protocol for ribosome-depleted RNA. Libraries were size selected (200-400bp) and quality checked by bioanalyzer using the Agilent High Sensitivity DNA Kit prior to multiplexing for Illumina sequencing (single end, 50bp reads).
Libraries were size selected (200-400bp) and quality checked by bioanalyzer using the Agilent High Sensitivity DNA Kit prior to multiplexing for Illumina sequencing (single end, 50bp reads).

value: brr6-1 mutant

value: rRNA depleted total RNA


title: brr6-1_gal_A


title: brr6-1_glu_B


title: NC001

description: normal control

value: Chinese

value: PBMC


title: brr6-1_glu_A


title: NC010

description: normal control

value: NC


title: Cortex Sham 2wk post injury, rep1

source_name: Cortex Sham 2wk post injury, rep1

growth_protocol: Rats were prepared for fluid percussion traumatic brain injury or sham injury (Naive rats had no anesthesia and were not handled in any way and gene expression in their brains serve as baseline data) and sacrificed 24 hr, 2 week, 3 month, 6 month and 1 year post-injury, hippocampi and cortex were obtained, and stored in RNA later.

value: Sprague-Dawley


title: Prefrontal Cortex of the brain from mice with Thr-Dio2 gene 30

description:
Gene expression data from the prefrontal cortex of Thr92D2 mice
Thr Prefrontal Cortex 30

value: Prefrontal Cortex


title: Prefrontal Cortex of the brain from mice with Thr-Dio2 gene 29

description:
Gene expression data from the prefrontal cortex of Thr92D2 mice
Thr Prefrontal Cortex 29


title: YPH399_gal_B

value: wild type


title: Cortex Naive 2wk, rep4

source_name: Cortex Naive 2wk, rep4


title: Cortex Naive 2wk, rep3

source_name: Cortex Naive 2wk, rep3


title: Prefrontal Cortex of the brain from mice with Ala-Dio2 gene 26

description:
Gene expression data from the prefrontal cortex of Ala92D2 mice
Ala Prefrontal Cortex 26


title: B6N_a

growth_protocol: 2 biological replicates were grown to mid-log phase in YEP media containing 2%Raffinose/0.04% sucrose, diluted into media containing 2% galactose/0.04% sucrose and grown O/N.

value: M2 anti-FLAG Affinity purified DNA


title: Cortex Naive 2wk, rep2

source_name: Cortex Naive 2wk, rep2


title: Cortex Naive 2wk, rep1

source_name: Cortex Naive 2wk, rep1


title: Cortex TBI 24hr post injury, rep4

source_name: Cortex TBI 24hr post injury, rep4


title: YPH399_gal_A


title: Prefrontal Cortex of the brain from mice with Thr-Dio2 gene 31

description:
Gene expression data from the prefrontal cortex of Thr92D2 mice
Thr Prefrontal Cortex 31


title: Prefrontal Cortex of the brain from mice with Ala-Dio2 gene 28

description:
Gene expression data from the prefrontal cortex of Ala92D2 mice
Ala Prefrontal Cortex 28


title: Prefrontal Cortex of the brain from mice with Ala-Dio2 gene 27

description:
Gene expression data from the prefrontal cortex of Ala92D2 mice
Ala Prefrontal Cortex 27


title: Prefrontal Cortex of the brain from mice with Thr-Dio2 gene 32

description:
Gene expression data from the prefrontal cortex of Thr92D2 mice
Thr Prefrontal Cortex 32


title: Prefrontal Cortex of the brain from mice with Ala-Dio2 gene 25

description:
Gene expression data from the prefrontal cortex of Ala92D2 mice
Ala Prefrontal Cortex 25


title: Hippocampus of the brain from mice with Thr-Dio2 gene 24

description:
Gene expression data from the hippocampus of Thr92D2 mice
Thr Hippocampus 24

value: Hippocampus


title: Cortex TBI 24hr post injury, rep3

source_name: Cortex TBI 24hr post injury, rep3


title: Hippocampus of the brain from mice with Thr-Dio2 gene 23

description:
Gene expression data from the hippocampus of Thr92D2 mice
Thr Hippocampus 23


title: NC003

description: normal control


title: YPH399_glu_B


title: YPH399_glu_A


title: S5_30_2rp

source_name: Candida parapsilosis, Protostelium aurantium

value: whole organism

tag: time point

value: 30 min


title: S6_30_3rp


title: Hippocampus of the brain from mice with Thr-Dio2 gene 22

description:
Gene expression data from the hippocampus of Thr92D2 mice
Thr Hippocampus 22

value: brain

tag: age


title: Cortex TBI 24hr post injury, rep2

source_name: Cortex TBI 24hr post injury, rep2


title: S3_0_3rp

value: 0 min


title: Cortex Sham 24hr post injury, rep4

source_name: Cortex Sham 24hr post injury, rep4


title: Cortex TBI 24hr post injury, rep1

source_name: Cortex TBI 24hr post injury, rep1


title: S2_0_2rp


title: Hippocampus of the brain from mice with Thr-Dio2 gene 21

description:
Gene expression data from the hippocampus of Thr92D2 mice
Thr Hippocampus 21

value: 8-10 weeks-old


title: Cortex Sham 24hr post injury, rep2

source_name: Cortex Sham 24hr post injury, rep2


title: Hippocampus of the brain from mice with Ala-Dio2 gene 20

description:
Gene expression data from the hippocampus of Ala92D2 mice
Ala Hippocampus 20


title: 60min_3RP

data_processing:
Demultiplexing of all libraries for each sequencing lane using the Illumina bcl2fastq 2.17.1.14 software
quality control of raw read data with FastQC, quality and adapter trimming with Trimmomatic v0.32; PE -threads 3 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:15:25 MINLEN:30
mapping of reads against the combined reference genomes of Candida albicans and Candida parapsilosis with TopHat2 v2.1.0; tophat2 -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive –no-coverage-search
assigning reads to features and counting reads per feature with FeatureCounts v1.4.5; -T 5 -s 0 -t exon -g gene_id
differential expression analysis with Deseq, DEseq2, SAMseq, Limma, EdgeR and BaySeq, adjusted p-value cutoff 0.01
Genome_build: Candida albicans SC5314 A22-s05-m04-r04; Candida glabrata CBS138 s02-m05-r02
Supplementary_files_format_and_content: Tab-delimited text files include counts for each gene per sample

organism:
Candida albicans
Nakaseomyces glabratus
Planoprotostelium fungivorum

source_name: Candida albicans, Candida glabrata, Protostelium aurantium

value: 60 min

tag: candida albicans strain

tag: candida glabrata strain


title: S1_0_1rp


title: Cortex Sham 24hr post injury, rep1

source_name: Cortex Sham 24hr post injury, rep1


title: Hippocampus of the brain from mice with Ala-Dio2 gene 19

description:
Gene expression data from the hippocampus of Ala92D2 mice
Ala Hippocampus 19


title: Cortex Sham 24hr post injury, rep3

source_name: Cortex Sham 24hr post injury, rep3


title: Cortex Naive 24hr, rep3

source_name: Cortex Naive 24hr, rep3


title: Cortex Naive 24hr, rep2

source_name: Cortex Naive 24hr, rep2


title: Cortex Naive 24hr, rep4

source_name: Cortex Naive 24hr, rep4


title: Hippocampus of the brain from mice with Ala-Dio2 gene 18

description:
Gene expression data from the hippocampus of Ala92D2 mice
Ala Hippocampus 18


title: Hippocampus of the brain from mice with Ala-Dio2 gene 17

description:
Gene expression data from the hippocampus of Ala92D2 mice
Ala Hippocampus 17


title: Cortex Naive 24hr, rep1

source_name: Cortex Naive 24hr, rep1


title: S4_30_1rp


title: 60min_2RP


title: Cerebellum of the brain from mice with Thr-Dio2 gene 14

description:
Gene expression data from the cerebellum of Thr92D2 mice
Thr Cerebellum 14

value: Cerebellum


title: Cerebellum of the brain from mice with Thr-Dio2 gene 15

description:
Gene expression data from the cerebellum of Thr92D2 mice
Thr Cerebellum 15


title: 30min_3RP


title: 0min_3RP


title: 30min_2RP


title: Vehicle6

city: Sapporo

first: Tsutomu

last: Oshigiri

state: Hokkaido

address: 1,minami 1jou nisi 17choume, chuoku

department: Orthopaedic Surgery

country: Japan

institute: Sapporo Medical University

description: gene expression data in brain after infused vehicle in SCI rat

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

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

data_processing: The data were analyzed with Expression console software using Affymetrix default analysis settings and global scaling using SST-RMA algorithm.

source_name: brain of SCI rat at day3 after vehicle tranplantation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Regent Kit Manual Target Pretaration for GeneChip Whole Transcript Expression Arrays_user guide, 2017, Affymetrix).

growth_protocol: Rats were housed in an atmosphere of 50% humidity at a temperature of 24°C.All rats were injected daily with cyclosporine A.

extract_protocol: Motor cortex was extracted under anesthesia, and total RNA was purified using Rneasy Plus mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: MSC or vehicle intravenous infusion via femoral vein

tag: treatment

value: day3 after vehicle tranplantation

tag: phenotype

value: SCI

tag: Sex

value: male


title: Cerebellum of the brain from mice with Thr-Dio2 gene 13

description:
Gene expression data from the cerebellum of Thr92D2 mice
Thr Cerebellum 13

tag: tissue


title: Cerebellum of the brain from mice with Thr-Dio2 gene 16

description:
Gene expression data from the cerebellum of Thr92D2 mice
Thr Cerebellum 16


title: Vehicle7


title: Vehicle5


title: 0min_2RP


title: 60min_1RP


title: Vehicle4


title: 0min_1RP


title: Cerebellum of the brain from mice with Ala-Dio2 gene 11

description:
Gene expression data from the cerebellum of Ala92D2 mice
Ala Cerebellum 11


title: Cerebellum of the brain from mice with Ala-Dio2 gene 10

description:
Gene expression data from the cerebellum of Ala92D2 mice
Ala Cerebellum 10


title: Vehicle3


title: ATCC 31280 day 5

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the  Actinosynnema pretiosum ATCC 31280 genome assembly using bowtie2（version: 2-2.0.5）.
Gene abundance measurements were generationed and normalized  using BEDTools（version:2.16.1） ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Genome_build: Actinosynnema pretiosum ATCC 31280 (CP029607, not released yet)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample

organism: Actinosynnema pretiosum

source_name: bacteria

growth_protocol: For fermentation, the first seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract, and 5.0% sucrose (w/v), pH 7.5) was inoculated with agar-grown mycelia and cultivated at 30 °C, 220 rpm for 24 h. Subsequently, the second seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract and 2.5% sucrose, 1.0% soluble starch (w/v), 0.05% isobutanol, and 0.05% isopropanol (v/v), pH 7.5) was inoculated with 1 mL of the first seed culture, incubated for another 24 h at 30 °C. Fermentation medium (yeast extract 0.8%, malt extract 1.0%, sucrose 1.5%, soluble starch 2.5% (w/v), isobutanol 0.5% and isopropanol 1.2% (v/v), pH 7.5) was inoculated with the second seed culture at 10% (v/v) and incubated at 25 °C and 220 rpm for 7 days

extract_protocol:
One mililiter culture was collected at 72 h during fermentation process. The total RNA was extracted with Redzol reagent according to the procedures recommended by the manufacturer (SBS Genetech, China). Total DNA was removed by DNase I (Thermo Fisher, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 5-day old

value: wildtype


title: 30min_1RP


title: Amygdala of the brain from mice with Thr-Dio2 gene 7

description:
Gene expression data from the amygdala of Thr92D2 mice
Thr Amygdala 7

value: Amygdala


title: Amygdala of the brain from mice with Thr-Dio2 gene 8

description:
Gene expression data from the amygdala of Thr92D2 mice
Thr Amygdala 8


title: Cerebellum of the brain from mice with Ala-Dio2 gene 12

description:
Gene expression data from the cerebellum of Ala92D2 mice
Ala Cerebellum 12


title: NXJ-24 day 5

value: ansmitocin high producer


title: Vehicle1


title: MSC7

source_name: brain of SCI rat at day3 after MSC tranplantation

value: day3 after MSC tranplantation


title: Cerebellum of the brain from mice with Ala-Dio2 gene 9

description:
Gene expression data from the cerebellum of Ala92D2 mice
Ala Cerebellum 9


title: Cortex Naive 3mo, rep1

city: Northbrook

first: Michael

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

source_name: Cortex Naive 3mo, rep1

value: Sprague-Dawley


title: Amygdala of the brain from mice with Ala-Dio2 gene 4

description:
Gene expression data from the amygdala of Ala92D2 mice
Ala Amygdala 4


title: MSC6

description: gene expression data in brain after infused MSC in SCI rat


title: Amygdala of the brain from mice with Thr-Dio2 gene 6

description:
Gene expression data from the amygdala of Thr92D2 mice
Thr Amygdala 6


title: MSC5


title: Amygdala of the brain from mice with Thr-Dio2 gene 5

description:
Gene expression data from the amygdala of Thr92D2 mice
Thr Amygdala 5


title: NXJ-24 day 3

value: 3-day old


title: MSC4


title: Vehicle2


title: NXJ-24 day 2

value: 2-day old


title: NXJ-24 day 1

value: 1-day old


title: Amygdala of the brain from mice with Ala-Dio2 gene 3

description:
Gene expression data from the amygdala of Ala92D2 mice
Ala Amygdala 3

value: brain


title: MSC3


title: wt_3_H4Ac

status: Public on Aug 31 2018

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Raw reads were aligned to the Arabidopsis TAIR10 genome using Bowtie2 with default parameters
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks were identified in ChIP-seq datasets using the Findpeaks function of the Homer package, using the parameter "-region" and the matched input dataset as the reference. Peaks were called on each replicate H2A.Z ChIP-seq dataset from wild-type and mbd9 mutants, and on H4Ac ChIP-seq datasets from wild-type. Bed files of the peaks are included for these specific datasets they were called in.
Datasets not used for peak calling were also analyzed by examining normalized reads (in bigwig files) across gene bodies or at the regions identified as peaks in other datasets.
To produce bigwig files (.bw), all the filtered ChIP-seq bam files generated with a given antibody (H2A.Z or H4Ac) were first scaled to the same number of reads. These scaled bam files were converted to the bigwig format using a bin size of 1 base pair.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: .bed files containing peaks for the specific histone mark as defined using the findPeaks function of the Homer software package.

source_name: wild type_H4Ac

growth_protocol: All plants were grown under 16hr light/8 hr dark cycles at 20C on 1/2 MS plates for seedling collection.

extract_protocol:
Chromatin immunoprecipitation was performed as described (in Gendrel at al. (2005) Nature Methods 2), followed by isolation of immunoprecipitated DNA using the QIagen PCR purification kit
Antibody-specific immunoprecipitated DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.

treatment_protocol: Six-day-old seedlings, not including roots, were collected and cross-linked with 1% formaldehyde under vacuum for 15 minutes.

tag: ecotype background

tag: genotype/variation

value: wild type

value: 6 day old seedling

tag: chromatin immunopurification


title: wt_2_H4Ac


title: wt_1_H4Ac


title: mbd_3_H4Ac

source_name: mbd9-1 mutant_H4Ac

value: mbd9-1 mutant


title: mbd_2_H4Ac


title: mbd_1_H4Ac


title: arp_3_H4Ac

source_name: arp6-1 mutant_H4Ac

value: arp6-1 mutant


title: arp_2_H4Ac


title: Amygdala of the brain from mice with Ala-Dio2 gene 1

description:
Gene expression data from the amygdala of Ala92D2 mice
Ala Amygdala 1

value: 8-10 weeks-old


title: arp_1_H4Ac


title: Amygdala of the brain from mice with Ala-Dio2 gene 2

description:
Gene expression data from the amygdala of Ala92D2 mice
Ala Amygdala 2


title: arp_3_H2AZ

source_name: arp6-1 mutant_H2AZ


title: mbd_1_H2AZ

source_name: mbd9-1 mutant_H2AZ


title: mbd_2_H2AZ


title: wt_1_H2AZ

source_name: wild type_H2AZ


title: mbd_3_H2AZ


title: MSC1

value: SCI


title: MSC2

value: male


title: arp_1_H2AZ


title: arp_2_H2AZ


title: Rbm7-EBd3-rep-1 [CAGE-Seq]

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Cells with a shRNA against RBM7 differentiated into embryoid bodies for three days in medium with FBS and without LIF or 2i.

data_processing:
Library strategy: CAGE-seq
The CAGE data was trimmed and quality controlled using FASTX Toolkit.
The trimmed reads were mapped using Bowtie against mm10.
Uniquely mapped reads were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: Rbm7 EBd3 total RNA replicate 1

extract_protocol:
TRIzol
CAGE libraries were prepared using the protocol by Takahashi et al. (doi: 10.1038/nprot.2012.005) with an input of 3 μg of total RNA.
CAGE. Sequencing of the libraries was performed on a HiSeq2000 instrument from Illumina.

treatment_protocol: E14 mESC were transduced with lentiviral particles. After selection with puromycin, the cells were grown in 2i media without puromycin and differentiated as follows: 1.5 million cells in 30 ml differentiation media were hung in 20 microliters drops from the lids of p15 plates with PBS in the plate for humidity. After two days, they were taken off the lid with PBS, let fall down in a falcon tube for 5 minutes. Then the liquid was removed and 26 ml of new differentiation media were added and the embryoid bodies and this media were split into two petri dishes for bacterial culture. 24 hours later, the embryoid bodies were harvested and lysed with TRIzol.

tag: cell line

tag: shRNA

value: Embryonic stem cells differentiated for 3 days as embryoid bodies


title: Rbm7-ESC-rep-2 [CAGE-Seq]

description: ES cells grown in 2i medium and transduced with a pLKO lentiviral vector carrying a shRNA against RBM7 (NM_144948.2-1021s1c1).

source_name: Rbm7 mESC total RNA replicate 2

tag: cell type

value: Embryonic stem cells


title: wt_2_H2AZ


title: Rbm7-EBd3-rep-2 [CAGE-Seq]

source_name: Rbm7 EBd3 total RNA replicate 2


title: Rbm7-ESC-rep-1 [CAGE-Seq]

source_name: Rbm7 mESC total RNA replicate 1


title: wt_3_H2AZ


title: Rrp40 EBd3 total RNA replicate 2 [CAGE-Seq]

description: ES-E14TG2a differentiated for 3 days as embryoid bodies

data_processing:
The CAGE data was trimmed and quality controlled using FASTX Toolkit.
The trimmed reads were mapped using Bowtie against mm10.
Uniquely mapped reads were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: Rrp40 EBd3 total RNA replicate 2

extract_protocol:
TRIzol
CAGE libraries were prepared using the protocol by Takahashi et al. (doi: 10.1038/nprot.2012.005) with an input of 3 μg of total RNA.

treatment_protocol: E14 mESC were transduced with lentiviral particles.     After selection with puromycin, the cells were grown in 2i media without puromycin and differentiated as follows:  1.5 million cells in 30 ml differentiation media were hung in 20 microliters drops from the lids of p15 plates with PBS in the plate fro humidity.   After two days, they were taken off the lid with PBS, let fall down in a falcon tube for 5 minutes. Then the liquid was removed and 26 ml of new differentiation media were added and the embryoid bodies and this media were split into two petri dishes for bacterial culture. 24 hours later, the embryoid bodies were harvested and lysed with TRIzol.


title: Rrp40 EBd3 total RNA replicate 1 [CAGE-Seq]

source_name: Rrp40 EBd3 total RNA replicate 1


title: Rrp40 mESC total RNA replicate 1 [CAGE-Seq]

source_name: Rrp40 mESC total RNA replicate 1


title: Scr(control) EBd3 total RNA replicate 2 [CAGE-Seq]

source_name: Scr(control) EBd3 total RNA replicate 2

value: scrambled (control)


title: Rrp40 mESC total RNA replicate 2 [CAGE-Seq]

source_name: Rrp40 mESC total RNA replicate 2


title: Scr(control) mESC total RNA replicate 1 [CAGE-Seq]

source_name: Scr(control) mESC total RNA replicate 1


title: Scr(control) mESC total RNA replicate 2 [CAGE-Seq]

source_name: Scr(control) mESC total RNA replicate 2


title: Scr(control) EBd3 total RNA replicate 1 [CAGE-Seq]

source_name: Scr(control) EBd3 total RNA replicate 1


title: SKBR3_shCTR_rep1_RNA-seq

city: Miami

first: Ho Lam

last: Chan

state: FL

address: 1501 NW 10th Ave. BRB 742A

department: Human Genetics

institute: University of Miami

data_processing:
FASTQ data  were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.
RNA-seq reads were aligned to the hg19 human genome using STAR aligner (version 2.5.3a) with default parameters  and RSEM (version 1.2.31) to obtain expected gene counts against the human RefSeq (release  76).
Duplicate reads were removed using Picard tools (version 1.126 -  http://broadinstitute.github.io/picard).
RNA-seq differential expression was determined using DESeq2 and R (version 3.2.3) with q-value <0.05.
Homer annotatePeaks v4.8.3 was used for peak  annotation.
Bedtools v2.26.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in text format containing the genelist and enrichment values.

growth_protocol: SKBR3 were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of McCoy's 5a Medium Modified that was supplemented with 10% FBS, 1x penicillin/streptomycin, and 1x glutamax.

extract_protocol:
RNA was isolated from fresh or frozen cell pellets using TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions.
Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit (New England Biolabs cat# E6310) starting with 1µg total RNA and following the manufacturer’s instructions. Ribo-depleted RNA was then further processed with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs cat# E7420) for library preparation following the manufacturer’s instructions.

value: Mammary gland adenocarcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-30

tag: modifications

value: pLKO_shCTR stable cells


title: SKBR3_shRING1B_rep1_RNA-seq

value: pLKO_shRING1B stable cells


title: SKBR3_shRING1B_rep2_RNA-seq


title: SKBR3_shCTR_rep2_RNA-seq


title: Fasted HMZ 1030 3

city: Riverside

first: Jonathan

middle: Robert

last: Deans

address: 3111 BSB, University of California Riverside

department: Molecular, Cell and Systems Biology

institute: University of California Riverside

data_processing:
Reads were de-multiplexed and had adapters trimmed by Genomics Core at UCR. Fastq files representing each adapter from each of the 4 lanes within the same flowcell of NextSeq500 were merged before alignment.
Reads were aligned to the mouse reference genome, mm10, with Illumina’s iGenome genes.gtf file using TopHat v2.1.1 using default parameters with the exception of allowing only 1 unique alignment for a given read
Raw read counts were calculated at the gene level for each sample using HTSeq v0.6.1
Library normalization was performed with EDASeq; within-lane normalization on GC content was performed with the LOESS method and between-lane normalization was performed with non-linear full quantile method
Normalization factors from EDASeq were used for differential expression analysis with DESeq2. Normalized read counts, FPKM (fragments per kilobase per million), and rlog (regularized log transformation) results were generated for downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: FPKM output from DESeq2 split into each sample.

molecule: polyA RNA

source_name: Fasted HMZ 1030_fasted

extract_protocol:
Three mice were harvested in succession within a 30-min time frame for each time point. Two ~25 mg pieces from each liver were immediately frozen in liquid nitrogen and stored at -4°C. The miRNeasy Mini Kit (Qiagen, #74104) was used to extract and purify total RNA
4 µg of each sample was used to prepare a poly(A)+ RNA library using TruSeq RNA Sample Prep v2 Kit (Illumina, Cat# RS-122-2001). Libraries submitted for 75-bp single-end sequencing with Illumina NextSeq 500 at the UCR IIGB Genomics Core

tag: strain background

value: mixed 129/Sv plus C57BL/6

tag: gender

value: exon swap a7HMZ (P2-HNF4a only)

value: 16 to 20 weeks

tag: diet

value: fasted (12 hr)

value: liver

tag: flowcell


title: HMZ 1330 3

source_name: HMZ 1330_fed ad libitum

tag: age

value: fed ad libitum (LabDiet, #5001)


title: Fasted WT 1030 2

source_name: Fasted WT 1030_fasted

value: WT


title: Fasted HMZ 1030 2


title: HMZ 2030 1

source_name: HMZ 2030_fed ad libitum


title: HMZ 1330 1


title: Fasted WT 1030 3


title: HMZ 1030 3

source_name: HMZ 1030_fed ad libitum


title: RBM7_EBd3_2 [PRO-Seq]

data_processing:
Library strategy: PRO-Seq
Adapter sequences were trimmed with FASTX-Toolkit and filtered for a minimum of 15 bases. All reads were then trimmed to a maximum of 36 bases and then reverse complimented.
Reads were first mapped with Bowtie to a copy of the mouse rDNA repeat (GenBank: BK000964.1) with the -K1 option, and unaligned reads were then mapped to the mouse genome (mm10) filtering for unique matches.
Uniquely mapped reads were used for downstream analysis.
Only the final 3’-base representing position of the polymerase was reported to output files used in all analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: RBM7 EBd3 total RNA replicate 2

extract_protocol:
Around 1 million cells were permeabilised and incubated with biotin-labeled NTPs. The RNA was then hydrolyzed with NaOH and biotin containing fragments were enriched by affinity purification using streptavidin-coated magnetic beads.
A 3′ sequencing adaptor was ligated to the hydroxyl (OH) group at the 3′ end of nascent RNA, the 5'cap was removed, then a 5'OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase. Then, a 5′ sequencing adaptor was ligated to the nascent RNA. RNA was purified to enrich for fragments with adaptor at both ends and reverse transcribed.
PROseq. Libraries were sequenced on an Illumina NextSeq 500 (75 bp – high throughput kit).

treatment_protocol: E14 mESC were transduced with lentiviral particles. After selection with puromycin, the cells were grown in 2i media without puromycin and differentiated as follows: 1.5 million cells in 30 ml differentiation media were hung in 20 microliters drops from the lids of p15 plates with PBS in the plate for humidity. After two days, they were taken off the lid with PBS, let fall down in a falcon tube for 5 minutes. Then the liquid was removed and 26 ml of new differentiation media were added and the embryoid bodies and this media were split into two petri dishes for bacterial culture. 24 hours later, the embryoid bodies were trypsinized by incubating them for 3 minutes in 0.5% trypsin-EDTA and pipetting up and down.


title: RBM7_ESC_1 [PRO-Seq]

source_name: RBM7 mESC total RNA replicate 1


title: HMZ 1330 2


title: HMZ 2030 2


title: Fasted WT 1030 1


title: RBM7_ESC_2 [PRO-Seq]

source_name: RBM7 mESC total RNA replicate 2


title: HMZ 1030 1


title: HMZ 2030 3


title: RBM7_EBd3_1 [PRO-Seq]

source_name: RBM7 EBd3 total RNA replicate 1


title: HMZ 1030 2


title: WT 2030 1

source_name: WT 2030_fed ad libitum


title: WT 2030 2


title: WT 1330 1

source_name: WT 1330_fed ad libitum


title: WT 1330 2


title: WT 1030 3

source_name: WT 1030_fed ad libitum


title: WT 1330 3


title: Fasted HMZ 1030 1


title: WT 1030 2


title: WT 1030 1


title: RRP40_EBd3_1 [PRO-Seq]

description: Cells with a shRNA against RRP40 differentiated into embryoid bodies for three days in medium with FBS and without LIF or 2i.

source_name: Rrp40 EBd3 total RNA replicate 1

extract_protocol:
Around  1 million cells were permeabilised and incubated with biotin-labeled NTPs. The RNA was then hydrolyzed with NaOH and biotin containing fragments were enriched by affinity purification using streptavidin-coated magnetic beads.
A 3′ sequencing adaptor was ligated to the hydroxyl (OH) group at the 3′ end of nascent RNA, the 5'cap was removed, then a 5'OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase. Then, a 5′ sequencing adaptor was ligated to the nascent RNA. RNA was purified to enrich for fragments with adaptor at both ends and reverse transcribed.

treatment_protocol: E14 mESC were transduced with lentiviral particles.     After selection with puromycin, the cells were grown in 2i media without puromycin and differentiated as follows:  1.5 million cells in 30 ml differentiation media were hung in 20 microliters drops from the lids of p15 plates with PBS in the plate fro humidity.   After two days, they were taken off the lid with PBS, let fall down in a falcon tube for 5 minutes. Then the liquid was removed and 26 ml of new differentiation media were added and the embryoid bodies and this media were split into two petri dishes for bacterial culture. 24 hours later, the embryoid bodies were trypsinized  by incubating them for 3 minutes in 0.5% trypsin-EDTA and pipeting up and down.


title: RRP40_EBd3_2 [PRO-Seq]

source_name: Rrp40 EBd3 total RNA replicate 2


title: RRP40_ESC_1 [PRO-Seq]

description: ES cells grown in 2i medium and transduced with a pLKO lentiviral vector carrying a shRNA against RRP40 (NM_025513.1-909s1c1)

source_name: Rrp40 mESC total RNA replicate 1


title: SCR_ESC_1 [PRO-Seq]

description: ES cells grown in 2i medium and transduced with a lentiviral vector carrying a scrambled shRNA (SHC002, sigma)

source_name: Scr(control) mESC total RNA replicate 1


title: RRP40_ESC_2 [PRO-Seq]

source_name: Rrp40 mESC total RNA replicate 2