title: HBDJKDAT01_N701_S503

value: midbrain

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: sequencing run id

tag: lane

tag: c1 chip size

tag: c1 machine id


title: Input_Female_1

status: Public on May 31 2018

type: SRA

city: Cold Spring Harbor

first: Jessica

last: Tollkuhn

address: 1 Bungtown Rd

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
Reads were base trimmed to 76bp, adapter trimmed, and quality filtered at Q > 30 using an internal Fast-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit/ (Galaxy Version 1.0.1)).
Filtered reads were mapped to the mm10 reference genome using STAR (Galaxy Version 0.0.1) (Dobin et al., 2013; Yue et al., 2014).
The number of reads mapped to each gene was calculated using featureCounts (Galaxy Version 2.4.5-p1)(Liao et al., 2014).
Differential expression between IP and input samples was determined using DESeq2 with an FDR of 0.1 (Galaxy Version 1.0.0)(Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: tab-delimited file with differential expression data between IP and input samples as derived from DESeq2
Supplementary_files_format_and_content: Normalized Counts: tab-delimited file with normalized count values for each sample as derived from DESeq2

molecule: total RNA

organism: Mus musculus

source_name: Central Amygdala-lateral division

extract_protocol:
Microdissected tissue from 8-12 mice was pooled and frozen at -80oC for each sample. Tissue homogenization, immunoprecipitation of polysomes from SOM+ neurons, and mRNA extraction was performed as previously described (Heiman et al., 2014; Sanz et al., 2009).
Libraries were prepared according to instructions provided by NuGEN Ovation RNA-Seq kits (7102 and0344)

tag: tissue

value: Central Amygdala-lateral division

tag: cell type

value: SOM+ neurons

value: Female

tag: pulldown

value: Input


title: Input_Female_2


title: HBDJKDAT01_N701_S502

city: Berkeley

first: Daniel

middle: J

last: Kramer

state: Ca

address: 291 Life Sciences Addition #3200

institute: UC Berkeley

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3).
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content: tab-delimited text files include gene level count values for each sample derived from Cufflinks and featureCounts
Supplementary_files_format_and_content: ExpressionSet and matrix that include all metadata and the appropriate count data
Supplementary_files_format_and_content: Files:
Supplementary_files_format_and_content: KramerDAT_eSet_phenoData.txt: metadata on samples including experimental condition and batch
Supplementary_files_format_and_content: KramerDAT_eSet_counts_table.txt: abundance measurements (featureCounts) prior to filtering, text file
Supplementary_files_format_and_content: KramerDAT_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: KramerDAT_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: KramerDAT_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data, prior to filtering
Supplementary_files_format_and_content: KramerDAT_imageAfterFiltering.RData: R data object containing expressionSet of filtered count data and vector for gene filtering

molecule: polyA RNA

extract_protocol:
single cell isolation, lysis, RT, amplification: Cells were brought to a concentration of 200,000/ml. The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
sequencing library synthesis: The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
sequencing library synthesis: RNA libraries were prepared for sequencing using standard Illumina protocols.
sequencing strategy: Single-cell RNA-sequencing.  scRNA-Seq was performed on an Illumina HISEQ 2500 sequencer; up to 192 samples were sequenced per lane, often in Rapid Run mode.

treatment_protocol:
dissociation protocol: Postnatal day 26 (P26) to P34 male and female DATIRESCre;Ai9 mice were briefly anesthetized with isoflurane and decapitated, and brains were removed and placed in ice-cold, oxygenated artificial CSF. The brain was cut coronally into 275-m sections on a vibratome (Leica VT1000 S) in oxygenated ice-cold choline cutting solution.
dissociation protocol: Midbrain sections were incubated for 15 min in ACSF at 34˚C. Midbrain (including the hypothalamus) was dissected in ACSF using forceps under a dissection microscope.
dissociation protocol: Midbrain sections were incubated in 10 ml oxygenated papain solution in ACSF for 25 min at 34˚C. Following papain digestion, tissue was placed into 9 ml oxygenated STOPovomucoid inhibitor solution and bubbled gently at 34˚C. 8 ml of the supernatant solution was removed, and the tissue was triturated serially in the remaining 2 ml of solution with polished 3-, 2-, and 1-mm glass pipettes to create a single-cell suspension. The 2-mL single-cell suspension was spun down in a 20% Percoll solution at 430 g for 6 min at room temperature (RT). The supernatant was aspirated, leaving 50 l of solution and the cell pellet. The pellet was resuspended in 1 ml HEPES-ACSF with 1 mM kynurenic acid and 5% FBS. This single-cell suspension was sorted on a BD Influx cell sorter in the Flow Cytometry Facility at UC Berkeley.
dissociation protocol: Cells were gated for PI-/tdTomato and sorted into a PCR tube. Based on the number of neurons sorted and cell viability count, neurons were brought to 200,000 neurons/ml.

tag: strain

value: dopamine neuron

value: F

tag: number of animals

tag: facs selection

value: TdTomato+ (PI -)

tag: c1 batch id

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

value: MEDIUM

value: SMEAGOL

tag: ercc spike-in dilution


title: 5_CS_ctrl

type: RNA

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

hyb_protocol: Standard Affymetrix hybridization protocol for GeneChipÂ® Exon 1.0 ST arrays

scan_protocol: Standard Affymetrix scanning protocol for GeneChipÂ® Exon 1.0 ST arrays

data_processing:
Probeset summarization was done by RMA and normalization by sketch quantile method (Affymetrix APT tools)
huex-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

label: biotin

organism: Homo sapiens

source_name: control tissue sample

label_protocol: Whole transcriptome Affymetrix protocol with rRNA depletion.

growth_protocol: 5 patients affected by nonsynodromic sagittal synostosis or nonsyndromic metopic synostosis were enrolled in this study.

extract_protocol: Total RNA was extracted from snap-frozen calvarial tissue specimens using pestel and TRIzol Reagent (Invitrogen), and subsequently purified using silica membrane spin columns from RNeasy Mini kit (Qiagen). The yield, quality and integrity of RNA were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue specimens were collected, from each patients, both from patent and fused calvarial sutures and cryopreservated in liquid nitrogen

tag: gender

value: M

tag: diagnosis

value: Craniosynostosis (CS)

value: patent coronal suture


title: Input_Male_2

tag: Sex

value: Male


title: 6_CS_crs

source_name: pathologic tissue sample

value: synostotic sagittal suture


title: 4_CS_crs


title: 7_CS_ctrl


title: Input_Male_1


title: IP_Female_3

value: IP


title: IP_Male_4


title: 3_CS_ctrl


title: IP_Male_1


title: 1_CS_ctrl

value: patent pericoronal frontal bone


title: 2_CS_crs


title: Full-Length IL-33 Clone 4 No Dox

city: Cincinnati

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

data_processing:
Data analysis was performed in BioWardrobe [PMID:26248465]
Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.2a PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2” (for the full manual see https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf?raw=true). RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for hg19 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors. All reads from produced .bam files were split for related isoform with respect to RefSeq annotation. Then EM algorithm was used to estimate appropriate number of reads for each isoform (details). To estimate difference between experiments DESeq (PMID: 20979621) or DESeq2 package were used (for experiments without replicates DESeq and blind method was forced).
RPKM values were calculated by BioWardrobe
Genome_build: hg19
Supplementary_files_format_and_content: The columns are RefSeqIDs, Read numbers, RPKM values

source_name: Esophagus

growth_protocol: TE-7 cells were grown in RPMI medium supplemented with 5% FCS

extract_protocol:
RNA was harvested using Tripure reagent and isolated by RNeasy kit with on-column DNaseI treatment
Libraries were prepared for sequencing using standard Illumina nonstranded polyA RNA-Seq protocols

treatment_protocol: Cells were treated with Doxycycline at 100 ng/ml for 48 hours

tag: cell line

tag: treatment

value: no dox

tag: biowardrobe id


title: Full-Length IL-33 Clone 2 No Dox


title: 112-270 IL-33 Clone 2 Dox

value: dox


title: 112-270 IL-33 Clone 3 Dox


title: Full-Length IL-33 Clone 2 Dox


title: Full-Length IL-33 Clone 7 No Dox


title: 112-270 IL-33 Clone 1 Dox


title: Full-Length IL-33 Clone 4 Dox


title: Full-Length IL-33 Clone 7 Dox


title: Empty Vector Clone 3 Dox


title: 112-270 IL-33 Clone 1 No Dox


title: Empty Vector Clone 4 Dox


title: 112-270 IL-33 Clone 2 No Dox


title: 112-270 IL-33 Clone 3 No Dox


title: Empty Vector Clone 2 Dox


title: Empty Vector Clone 3 No Dox


title: Empty Vector Clone 2 No Dox


title: p_S_01: Pregnant stromal cells

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: R2: UMI sequences to recognize PCR duplicates

data_processing:
The obtained sequence reads (Fastq files) were analyzed with a locally installed version of Galaxy
The adapter sequence was clipped (for shorter fragments where sequencing runs into the adapter) and 5 bp were removed from the start of the reads
Reads were filtered by CPM cutoff after removing the PCR duplicates with NUGEN nudup
The resulting read count table was used for statistical analysis in EdgeR to identify differentially expressed genes
Genome_build: Sscrofa 11.1

organism: Sus scrofa

source_name: Pregnant stromal cells

extract_protocol:
PicoPure RNA Isolation Kit
Ovation SoLo Single Cell RNA-Seq System

treatment_protocol: frozen endometrium samples were cut in 10 µm thick sections cryostat, mounted onto membrane slides, and stained using a modified, rapid Cresyl violet staining protocol to identify LE, GE, and stromal cells.  The target cells from the sections were captured using a laser capture microdissection (LCM)

tag: tissue

value: endometria

tag: cell type

value: stromal cells

tag: age

value: pregnant pig on Day 12 of gestation


title: p_S_05: Pregnant stromal cells


title: p_S_14: Pregnant stromal cells


title: siSA1_REP1

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Digested/Ligated genomic DNA

library_source: genomic

data_processing:
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks).
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw counts at 40kb and 100Kb resolution are stored as tab-separated files with bin in first column,  second bin as second column, and number of contacts as third column.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw interaction matrices per chromosome are included in the abc format, which has commented lines (start with a “#” character) and the actual interaction counts (one per line) as three column with left-bin, rigth-bin and raw-counts.

molecule: genomic DNA

source_name: Human Mammary Epithelial Cells

growth_protocol: MCF10A cells were grown in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol: Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).

value: MCF10A -Transformed nontumorigenic

tag: experiment

value: MCF10A cells were arrested in G1 by means of high confluency culture (150,000 cells per cm2). Hi-C was performed as described (Serra et al., 2017) using MboI enzyme. Two library replicates per condition were sequenced (>200 million reads each).

value: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG1 siRNAs at seeding in high confluency (Dharmacon L-010638)  using DharmaFECT reagent 1.


title: siControl_REP2

description: Digested/Ligated genomic DNA


title: p_L_14: Pregnant luminal epithelium

source_name: Pregnant luminal epithelium

value: luminal epithelium


title: p_L_05: Pregnant luminal epithelium


title: siControl_REP1

description: Digested/Ligated genomic DNA


title: siSA2_REP2

description: Digested/Ligated genomic DNA

value: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG2 siRNAs (Dharmacon L-021351) at seeding in high confluency  using DharmaFECT reagent 1.


title: p_L_03: Pregnant luminal epithelium


title: p_G_05: Pregnant glandular epithelium

source_name: Pregnant glandular epithelium

value: glandular epithelium


title: Empty Vector Clone 4 No Dox


title: c_L_06: Control luminal epithelium

source_name: Control luminal epithelium

value: nonpregnant pig on Day 12 after ovulation


title: p_L_01: Pregnant luminal epithelium


title: siSA1_REP2

description: Digested/Ligated genomic DNA


title: c_L_13: Control luminal epithelium


title: c_L_02: Control luminal epithelium


title: c_S_13: Control stromal cells

source_name: Control stromal cells


title: p_G_01: Pregnant glandular epithelium


title: c_S_02: Control stromal cells


title: c_L_04: Control luminal epithelium


title: siSA2_REP1

description: Digested/Ligated genomic DNA


title: HEp2 Kontrolle #2

city: Hannover

first: Ralf

last: Gerhard

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute of Toxicology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V6.7’, except that 1000ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) and of the red channel ,‘rProcessedSignal’ (rPS) to retrieve one resulting value per channel and unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 units. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: Hep-2 cell culture

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Low Input Quick Amp Labeling kit, two color’ (#5190-2944, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Cells were cultures in DMEM supplemented with 10% fetal calf serum, 100 µg/ml penicillin and 100 µM strptomycin.

extract_protocol: Total RNA was extracted by the RNeasy Mini Kit from Qiagen and cDNA was generated by Omniscript Reverse Transcription (RT) Kit from Qiagen according to the manufacturer’s recommendations.

treatment_protocol: Control cells were left untreated. TcdB 1101-1836-treatment of cells was done by repeated addition 2 µg/ml of toxin fragment every 24 hours.

value: control


title: HEp2 Kontrolle #1


title: c_G_13: Control glandular epithelium

source_name: Control glandular epithelium


title: p_G_14: Pregnant glandular epithelium


title: TcdB 1101-1836 VPI10463  #1

value: TcdB


title: c_G_06: Control glandular epithelium


title: p_G_03: Pregnant glandular epithelium


title: c_G_04: Control glandular epithelium


title: c_S_04: Control stromal cells


title: TcdB 1101-1836 VPI10463  #2


title: c_G_02: Control glandular epithelium


title: skin normal mice rep4

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

country: China

institute: hinese Academy of Medical Sciences and Peking Union Medical College

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO8

data_processing:
The NGS (Next Generation Sequencing) technology uses to sequence cDNA. The original image file firstly obtained is then base-recognized and error-filtered to finally obtain the original sequencing fragments that can be used for analysis. We call them Reads. The results are stored in fastq format
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Seqtk [1]
Using the spliced mapping algorithm of TopHat(version:2.0.9)[2] to perform Genome mapping on preprocessed reads.
HTSeq [4] was used to count the number of Fragments of each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) [5] method. Finally, the perl script was used to calculate the FPKM value of each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: normal mice

growth_protocol: Eight-week-old male Ncstn flx/flx; Krt14 CreER+/- mice were first administrated 20 mg/kg body weight of tamoxifen per day for 5 consecutive days, followed by treatment every 10 days by oral gavage. The Ncstn flx/flx; Krt14 CreER+/- mice received the same volume of corn oil and were used as controls.

extract_protocol:
Total RNA was extracted and purified using mirVana miRNA Isolation Kit, following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The NcstnΔKC and normal mice were sacrificed at the age of 16 weeks and skin lesions were excised for RNA isolation

value: skin

value: 16 weeks

tag: genotype

value: wildtype

value: male


title: skin NcstnΔKC mice rep1

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO1

source_name: NcstnΔKC mice


title: T24 cells_control siRNA_rep2

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

institute: Institute of Urology, Drum Tower hospital

description: human bladder cancer cells T24, transfected with control siRNA

hyb_protocol: Labeled miRNA was hybridized to the array for 16 hours at 48 “C and 60 rpm as described in the protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) algorithm as normalization method.

label_protocol: Per RNA sample, 1 ug were used as input into the procedure as recommended by protocol (Genisphere FlashTagTM Biotin RNA Labeling for Affymetrix GeneChip miRNA arrays).

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% FBS, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 “C.

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

treatment_protocol: T24 cells were transfected with 20μM siRNA control (siNC) or siRNA NF90 (siNF90) for 48 hours using Lipofectamine 3000. Then, cells were washed with PBS and placed on ice in the Trizol solution.

tag: transfection

value: control siRNA


title: T24 cells_control siRNA_rep1

source_name: human bladder cancer cells T24, transfected with control siRNA


title: T24 cells_NF90 SiRNA_rep1

description: human bladder cancer cells T24, transfected with NF90 siRNA

value: NF90 siRNA


title: T24 cells_NF90 SiRNA_rep2

source_name: human bladder cancer cells T24, transfected with NF90 siRNA


title: skin normal mice rep2

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO6


title: skin NcstnΔKC mice rep3

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO3


title: Whole Blood 16hr after 12Gy dose rep 3

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 Mouse Genome microarrays 8x60K v1 Design ID 028005 or v2 Design ID 074809 (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 G2505C 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). Only the 30,000+ probes that are printed on both arrays (Agilent-028005, Agilent-074809) are reported.

label: Alexa 555

source_name: Whole Blood 16hr after 12Gy dose

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA). After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. The quantity and quality of the cRNA were assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation.

treatment_protocol: Whole body irradiation done with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 0-12 Gy with a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same plastic container as the irradiated mice and sham irradiated. 3 animals/dose/time-point have been included in the study.

tag: strain/background

value: female

value: six to eight weeks

value: whole blood

value: 12Gy gamma rays

tag: time point


title: Whole Blood 16hr after 8Gy dose rep 2

source_name: Whole Blood 16hr after 8Gy dose

value: 8Gy gamma rays


title: No. 15 (FGFRL1-KO)

city: Kyoto

first: Yoshinori

last: Takei

address: 29-46 Shimoadachicho Yoshida

department: Graduate school of pharmaceutical science

country: Japan

institute: Kyoto University

description: The microarray chip used in this project, TORAY 3D gene mRNA Oligo chip, contains 24,460 probes including ACTB gene as a positive control and non-human derived sequences as negative controls.

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

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

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

source_name: cultured cells derived from oesophageal squamous cell carcinomas

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

growth_protocol: cells were cultured in a fumidified chamber at 37°C and condition under 10% CO2 and 90% air, with DMEM/F12 medium containing 5% FBS.

extract_protocol: Cells (approximately 2x10e7) were harvested with Trizol (Thermo) as manufacture's protocole.

value: KYSE 520

value: esophageal squamous cell carcinoma

tag: genotype of fgfrl1 gene


title: No. 1(FGFRL1-wild type)


title: No. 21 (FGFRL1-KO)


title: Whole Blood 16hr after 12Gy dose rep 2


title: parent KYSE520


title: skin NcstnΔKC mice rep2

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO2


title: skin NcstnΔKC mice rep4

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO4


title: skin normal mice rep1

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO5


title: B1-6-F24

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: Sample name: SAMPLE 17

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was converted to log2, quantile median-normalized using Genespring v12.1

source_name: Fallopian tube epithelium

label_protocol: Labelled using Illumina TotoalPrep-96 Human HT-12 v4.0 beadchip arrays

growth_protocol: Surgical fallopian tube samples were dissociated and epithelial cells were cultured in a transwell system atop a collagen type IV layer until confluent.  At this point cultures from each patient were treated.

extract_protocol: total RNA was extracted from FTE using TRIzol reagent according to manufacturer's instructions and further purified using an Rneasy MiniELute cleanup kit

treatment_protocol: Cultures from each patient were treated with periovulatory follicular fluid for 24 hours in the upper well of the transwell, afterwhich the follicular fluid was removed for an additional 24 hours.  Parallel cultures were treated identically but with culture media changes instead of follicular fluid.  Cells were harvested and RNA extracted 24 hours after follicular fluid addition (F24) or 24 hours after follicular fluid replacement with culture medium (FC).  Treatment control (baseline) cultures treated with culture medium only (not exposed to follicular fluid) were harvested at the same time as F24 samples and are referred to as C24.

value: Fallopian tube epithelium

tag: brca1/2 mutation status

value: BRCA1 mutation carrier


title: Whole Blood 16hr after 8Gy dose rep 1


title: Whole Blood 16hr after 12Gy dose rep 1


title: Whole Blood 16hr after 2Gy dose rep 3

source_name: Whole Blood 16hr after 2Gy dose

value: 2Gy gamma rays


title: Whole Blood 16hr after 4Gy dose rep 2

source_name: Whole Blood 16hr after 4Gy dose

value: 4Gy gamma rays


title: Whole Blood 16hr after 1Gy dose rep 3

source_name: Whole Blood 16hr after 1Gy dose

value: 1Gy gamma rays


title: Whole Blood 16hr after 8Gy dose rep 3


title: Whole Blood 16hr after 2Gy dose rep 2


title: skin normal mice rep3

description:
differentially expressed genes of the skin tissue of Ncstn ΔKC mice and normal mice
NO7

value: skin

value: 16 weeks


title: Whole Blood 16hr after 1Gy dose rep 2


title: Whole Blood 16hr after 4Gy dose rep 1


title: Whole Blood 16hr after 4Gy dose rep 3


title: Whole Blood 16hr after 0Gy dose rep 3

source_name: Whole Blood 16hr after 0Gy dose

value: 0Gy gamma rays


title: Whole Blood 16hr after 2Gy dose rep 1


title: Whole Blood 16hr after 0Gy dose rep 2


title: Whole Blood 16hr after 0Gy dose rep 1


title: skin NCSTN 2

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
14

data_processing:
The NGS (Next Generation Sequencing) technology uses to sequence cDNA. The original image file firstly obtained is then base-recognized and error-filtered to finally obtain the original sequencing fragments that can be used for analysis. We call them Reads. The results are stored in fastq format
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Seqtk [1]
Using the spliced mapping algorithm of TopHat(version:2.0.9)[2] to perform Genome mapping on preprocessed reads.
HTSeq [4] was used to count the number of Fragments of each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) [5] method. Finally, the perl script was used to calculate the FPKM value of each gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count and  RPKM values for each Sample

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: This study was performed according to the principles of the Declaration of Helsinki. Written informed consent was provided by all the individuals participating in the experiments.Skin biopsies of AI patients with NCSTN mutations were obtained from surgical excision.Control skin tissues were obtained from healthy individuals undergoing cosmetic surgery procedures.

value: acne inversa (AI)


title: skin NCSTN 3

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
LLG

source_name: Skin biopsies of AI patients with NCSTN mutations


title: Whole Blood 6hr after 4Gy dose rep 2

source_name: Whole Blood 6hr after 4Gy dose


title: skin NCSTN 4

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
15


title: WT_mature stem [WT]

city: beijing

first: zhang

middle: yong

last: zhuo

address: Beijing Forestry University

institute: Beijing Forestry University

description: HDT1 vs WT stem.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: NCBI
Supplementary_files_format_and_content: Tab-delimited text file includes RPKMs (log2-transformed with an offset value of 1.0) for each sample

organism: Arabidopsis thaliana

source_name: WT_mature stem

growth_protocol: All the plants grew in greenhouse at 20 oC (16h light, 8h dark).

extract_protocol:
Total RNA was isolated from the main stem of different developmental stage of Arabidopsis plant, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genotype/variation

value: wild type

tag: Stage

value: 35 days after flowering

value: stem


title: skin NCSTN 1

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
10

tag: diagnosis


title: hdt1 mutant_mature stem [H1]

description: HDT1 vs WT stem.txt

source_name: hdt1 mutant_mature stem

value: hdt1 mutant


title: skin control 3

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
E

source_name: skin tissues of healthy individuals

value: healthy


title: Whole Blood 6hr after 0Gy dose rep 1

source_name: Whole Blood 6hr after 0Gy dose

tag: gender

value: female

value: six to eight weeks

value: whole blood


title: Whole Blood 6hr after 0Gy dose rep 2


title: skin control 2

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
8


title: skin control 1

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
3


title: Whole Blood 6hr after 4Gy dose rep 1


title: skin control 4

description:
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
F


title: Whole Blood 6hr after 4Gy dose rep 3


title: Whole Blood 16hr after 1Gy dose rep 1


title: leave_NA_toxic [PC3]

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

hyb_protocol: Samples labelled with Cy3 (825 ng) were hybridized using the Gene Expression Hybridization kit (Agilent Technologies) for 17 hours at 65°C and 10 rpm in the hybridization oven.

scan_protocol: The arrays were washed according to supplier´s instructions and scanned on an Agilent G2505C scanner at 3 µm resolution.

data_processing: Data were acquired using Agilent Feature Extraction software version 10.5.1.1. Raw data was background corrected and quantile normalized (Bioconductor / limma)

organism: Jatropha curcas

label_protocol: RNA labeling, hybridization onto Agilent 8x60K oligonucleotide microarrays as well as scanning and raw data analysis was performed according to the One-Color Microarray-Based Gene Expression Analysis Protocol from Agilent Technologies. Total RNA (200 ng) from each sample was used to synthesize cyanine-3 labeled cRNA using the QuickAmp Labeling kit, one Color and RNA Spike-In kit one Color (Agilent Technologies). The cyanine labeled cRNA was in vitro transcribed using T7 polymerase and purified using RNeasy mini kits (Qiagen).

extract_protocol: Total RNA was extracted from six developmental stages of seeds of J. curcas using plant RNA purification reagents (Invitrogen) according to the supplier’s instructions. The quality and concentration of total RNAs were determined using NanoVue Spectrophotometer (GE Healthcare Life Sciences) and gel electrophoresis. All RNA samples showing A260/280 ratios between 2.0 and 2.15 were selected and analyzed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an integrity number above 7.0 were used for further analyses.

tag: toxicity

value: toxic


title: Whole Blood 6hr after 0Gy dose rep 3

tag: treatment


title: MEFdKO_AICAR_24h_rep2

city: Bordeaux

first: Michel

last: Moenner

address: 1, rue Camille Saint-Saens

department: IBGC CNRS UMR5095

country: France

institute: CNRS

description: Gene expression data from cells at (t=24h) in the presence of 1mM AICAR

hyb_protocol: cRNAs were hybridized to Mouse MG-430 PM Array Strip Kit.

scan_protocol: Fluorescence intensities were quantified and analyzed using the Expression Console v 1.2 software.

data_processing: The digital intensity values were then converted into cell intensity files using the Affymetrix GeneAtlas Software. Initial cut-offs for differential expression were set to a fold change threshold of ± 2 or above and a maximum adjusted p-value of 0.05.

source_name: MEFdKO, AICAR, 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: MEFs were grown at low density in 10 cm dishes at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen). The quality of samples was assessed on a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Cells were stimulated at different times with 1 mM AICAR.

value: Murine Embryonic Fibroblasts

value: Ampk{alpha}1/{alpha}2 double knockout

tag: culture

tag: agent

value: AICAR

tag: time


title: MEFdKO_AICAR_24h_rep3

tag: cell type


title: seed_green-half_NA [H-Green]

description: H-Green

value: green-half


title: MEFdKO_AICAR_8h_rep1

description: Gene expression data from cells at (t=8h) in the presence of 1mM AICAR

source_name: MEFdKO, AICAR, 8h


title: MEFdKO_AICAR_4h_rep3

description: Gene expression data from cells at (t=4h) in the presence of 1mM AICAR

source_name: MEFdKO, AICAR, 4h


title: MEFdKO_AICAR_4h_rep1


title: MEFdKO_AICAR_12h_rep3

description: Gene expression data from cells at (t=12h) in the presence of 1mM AICAR

source_name: MEFdKO, AICAR, 12h


title: seed_dry_NA [Dry_A_2013]

value: dry


title: MEFdKO_AICAR_24h_rep1


title: MEFdKO_AICAR_12h_rep2


title: leave_NA_non-toxic [MA2]

value: non-toxic


title: MEFdKO_AICAR_12h_rep1


title: seed_dry_NA [Dry]

description: Dry


title: leave_NA_non-toxic [MA1]


title: MEFdKO_AICAR_4h_rep2


title: seed_green-white_NA [GW 2B]

description: GW 2B

value: green-white


title: leave_NA_non-toxic [MMA-1A]


title: seed_brown_NA [Brown]

description: Brown

value: brown


title: leave_NA_toxic [PC4]


title: leave_NA_toxic [MPC-3B]


title: seed_green-half_NA [GH 1A]

description: GH 1A


title: MEFdKO_AICAR_2h_rep1

description: Gene expression data from cells at (t=2h) in the presence of 1mM AICAR

source_name: MEFdKO, AICAR, 2h


title: MEFdKO_AICAR_1h_rep1

description: Gene expression data from cells at (t=1h) in the presence of 1mM AICAR

source_name: MEFdKO, AICAR, 1h


title: MEFdKO_AICAR_1h_rep2


title: seed_yellow_NA [YellowA]

description: YellowA

value: yellow


title: MEFdKO_Ctrl_0h_rep3

description: Gene expression data from cells at (t=0h) in the absence of AICAR

source_name: MEFdKO, Ctrl, 0h

value: control


title: seed_green-black_NA [GB_1A]

value: green-black


title: seed_brown_NA [BrownB klein ]

description: BrownB klein


title: MEFdKO_AICAR_1h_rep3


title: MEFdKO_AICAR_2h_rep2


title: leave_NA_toxic [MPC-4A]


title: leave_NA_non-toxic [MMA-3B]


title: seed_dry_NA [Dry_B_2013]


title: E2

city: ChengDu

first: Yong

last: Lv

state: SiChuan

department: Department of pediatric surgery

institute: West China hospital of Sichuan university

description: Gene expression in paired adjacent normal tissue

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: EGFR negative paired adjacent normal tissue

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. Careful attention was paid to the mi

tag: tissue

tag: age

value: 61 years

tag: Sex

value: Male


title: F1

description: Gene expression in colorectal cancer

source_name: EGFR positive colorectal cancer

value: EGFR positive colorectal cancer

value: 68 years


title: F2

source_name: EGFR positive paired adjacent normal tissue


title: MEFdKO_Ctrl_0h_rep2

tag: genotype


title: MEFdKO_AICAR_2h_rep3


title: MEFdKO_Ctrl_0h_rep1


title: seed_green-black_NA [green Black B]

description: green Black B


title: E1

description: Gene expression in colorectal cancer

source_name: EGFR negative colorectal cancer

value: EGFR negative colorectal cancer


title: Harumi_60_DAF

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

description: Gene expression 60 day after flowering in whole young fruit of polyembryonic citrus cultivar 'Harumi'

hyb_protocol: The labelled cRNAs were subsequently hybridized on the custom oligo-DNA microarray using a Gene Expression Hybridization kit (Agilent Technologies) according to the manufacturer’s directions.

scan_protocol: After washing in GE washing buffer (Agilent Technologies), the glass slides were scanned with an Agilent Microarray Scanner (G2505C, Agilent Technologies).

data_processing: The Feature Extraction software (version 10.5.1.1), employing defaults for all parameters, was used to convert the images into gene expression data.

organism: (Citrus unshiu x Citrus sinensis) x Citrus reticulata

source_name: Harumi, 60 day after flowering, polyembryonic

label_protocol: RNA samples were labelled with cyanine-3-labelled cytosine triphosphate using a Low Input Quick-Amp Labelling Kit (Agilent Technologies) according to the manufacturer’s directions.

growth_protocol: ‘Kiyomi’ and ‘Harumi’, cultivated at NARO Institute of Fruit and Tea Tree Science (NIFTS), Department of Citrus Research (Shizuoka, Japan), were used as materials for monoembryonic and polyembryonic varieties, respectively.

extract_protocol: Total RNA was extracted following Ikoma et al. (1996) J. Jpn. Soc. Hort. Sci. 64: 809-814.

treatment_protocol: Whole young fruits at 15, 30, 45 and 60 DAF were collected for microarray analysis, immediately frozen in liquid nitrogen, and stored at −80°C for RNA isolation.

tag: cultivar

value: Harumi

value: whole young fruit

tag: embryonic

value: polyembryonic


title: seed_brown_NA [BrownA_2013]


title: Harumi_45_DAF

description: Gene expression 45 day after flowering in whole young fruit of polyembryonic citrus cultivar 'Harumi'

source_name: Harumi, 45 day after flowering, polyembryonic


title: seed_yellow_NA [Y1]


title: Harumi_30_DAF

description: Gene expression 30 day after flowering in whole young fruit of polyembryonic citrus cultivar 'Harumi'

source_name: Harumi, 30 day after flowering, polyembryonic


title: seed_green-half_NA [greenhalfB]

description: greenhalfB


title: seed_green-white_NA [Green White B]

description: Green White B


title: Nematostella ELAV negative cells ATACseq_rep2

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

data_processing:
Read_1 files were mapped into Nematostella genome assembly v1.0 (http://genome.jgi.doe.gov/Nemve1/Nemve1.download.html) using bowtie2, using default parameters.
Duplicate reads were removed using samtools.
The starting position of each read was moved +4 (in positive strand) or -5 (negative strand) to compensate for the 9bp insertion of Tn5 transposase.
deepTools bamCoverage was used to generate bigWig coverage files, using a total extension of 50bps from the read start position, and a scaleFactor parameter of 0.1

organism: Nematostella vectensis

source_name: Adult polyps

extract_protocol: ATAC-seq experiments were performed starting from 200,000 fresh cells, following the ATAC protocol originally described in Buenrostro et al. 2013 (10.1038/nmeth.2688)

tag: stage/cell type

value: Polyps

tag: strain

value: ELAV::mOrange reporter transgenic line


title: seed_green-black_NA [GB_2B]

tag: Stage


title: leave_NA_toxic [MPC-5A]

value: toxic


title: Nematostella ELAV positive cells ATACseq_rep1


title: Nematostella ELAV negative cells ATACseq_rep1


title: Nematostella adult stage ATACseq_rep2

value: Wild type


title: Nematostella_Larva_scRNAseq

data_processing:
Read_1 files were mapped into Nematostella genome assembly v1.0 (http://genome.jgi.doe.gov/Nemve1/Nemve1.download.html) using bowtie2, using default parameters.
Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651)
Additional details in: Readme_MARSseq.xlsx

source_name: Larva

extract_protocol: 1. RNA extraction: cells were lysed in a water-based hypotonic buffer, containing 0.2% Triton X-100 and RNAse inhibitors. 2. polyadenylated RNAs were Reverse Transcribed, with a polyT oligonucleotide, containing a Unique Moleculer Identifier and a cell barcode. 3. cDNA was subject to In Vitro Transcription amplification, prior to adaptor ligation (that included a batch barcode) and library preparation (through 16 cycles of PCR amplification). 4. Libraries were sequenced in a NextSeq 500 machine, using a v2 mid-ouput 75 cycles kit (Illumina).

value: Planula larva


title: Nematostella ELAV positive cells ATACseq_rep2


title: Pi-replete

city: Dalian

first: Wang

middle: Ya

address: 457 Zhongshan Road

institute: Dalian Institute of Chemical Physics

data_processing:
Illumina HiSeq™ 2000 platform  software used for basecalling.
As the raw reads which were transferred from base calling may contain low quality reads and/or adaptor sequences, preprocessing is necessary before starting further analysis. Clean reads were mapped to R. toruloides NP11 and R. toruloides ATCC 204091 combined reference gene sequences and to R. toruloides reference genome sequences set using SOAPaligner/SOAP2.
The gene expression level was then calculated using the reads per kilobases per million reads (RPKM) method, which quantified transcript levels in reads per kilobase of exon model per million mapped reads and computed RPKM by software package Cufflinks. The statistical significance of the differential expression of each gene was determined using the P value. The FDR (false discovery rate) ≤ 0.001 and |log2Ratio| ≥ 1 were used to identify differentially expressed genes (DEGs). The P value and FDR were acquired by a more commonly used software package DEseq.
Genome_build: R. toruloides NP11 and R. toruloides ATCC 204091 combined reference gene sequences
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

organism: Rhodotorula toruloides

source_name: Pi-replete

growth_protocol: The red yeast R. toruloides AS 2.1389 (China General Microbiological Culture Collection Center) was grown in 3-l stirred tank reactor (Baoxing Bio-Engineering Equipment, Shanghai, China) with a constant working volume of 2.0 liter. The bioreactor was equipped with a 405-DPAS-SC-K8S/225 pH electrode and an InPro 6800 O2 sensor (Mettler Toledo).

extract_protocol:
Samples for RNA isolation from chemostat cultivations were taken by rapidly sampling 40 ml of culture into a tube with ice to decrease the sample temperature. Cells were then centrifuged (8000 rpm at 4°C for 2 min), instantly stored at −80°C until further use. Total RNA was extracted from samples using RNAiso Plus (Takara, Dalian, China) in accordance with the manufacturer's instructions and samples were stored at −80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: Pi-replete


title: Harumi_15_DAF

description: Gene expression 15 day after flowering in whole young fruit of polyembryonic citrus cultivar 'Harumi'

source_name: Harumi, 15 day after flowering, polyembryonic


title: Nematostella adult stage ATACseq_rep1


title: Pi-limited

source_name: Pi-limited

value: Pi-limited


title: Nematostella_Adult_scRNAseq


title: Kiyomi_60_DAF

description: Gene expression 60 day after flowering in whole young fruit of monoembryonic citrus cultivar 'Kiyomi'

organism: Citrus unshiu x Citrus sinensis

source_name: Kiyomi, 60 day after flowering, monoembryonic

value: Kiyomi

value: monoembryonic


title: CanS testes

status: Public on May 30 2018

city: Cold Spring Harbor

first: Yixin

last: Zhao

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Small RNAs

data_processing:
For RNA seq, raw data from RNA-seq were mapped to the D. melanogaster genome (r6.04), and normalized using Tophat (Trapnell, et al. 2009) and SeqMonk version 1.36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). The expression level of each gene was calculated in Reads Per Kilobase per Million (RPKM) and log2 transformed.
For small RNA seq, sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format. The expression of mature miRNA was then measured using the Mapper and Quantifier modules of miRDeep2 version 2.0.0.7 (Friedlander, et al. 2012) with default parameters, normalized by the total reads matching all the miRNA precursors per library, and scaled as Reads Per Million (RPM).
Genome_build: FlyBase Drosophila melanogaster r6.04
Supplementary_files_format_and_content: gene expression, miRNA expression and fasta files include clean reads and raw read count;

organism: Drosophila melanogaster

source_name: CanS testes

growth_protocol: Fruit flies were cultured under 25℃

extract_protocol:
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions

tag: genotype/variation

value: Canton-S

value: 3-5d adult

value: testes

tag: molecule subtype

value: Small RNAs


title: MEFdKO_AICAR_8h_rep2

source_name: MEFdKO, AICAR, 8h

value: Murine Embryonic Fibroblasts

value: Ampk{alpha}1/{alpha}2 double knockout

value: AICAR


title: leave_NA_non-toxic [MMA-2B]

tag: toxicity

value: non-toxic


title: seed_yellow_NA [YellowB]

description: YellowB

value: yellow


title: seed_green-white_NA [GW-1A]

value: green-white


title: seed_brown_NA [BrownB-2013]

value: brown


title: Kiyomi_45_DAF

description: Gene expression 45 day after flowering in whole young fruit of monoembryonic citurs cultivar 'Kiyomi'

source_name: Kiyomi, 45 day after flowering, monoembryonic

value: whole young fruit


title: Kiyomi_30_DAF

description: Gene expression 30 day after flowering in whole young fruit of monoembryonic citrus cultivar 'Kiyomi'

source_name: Kiyomi, 30 day after flowering, monoembryonic


title: seed_dry_NA [dryA-klein ]

description: dryA-klein

value: dry


title: seed_green-half_NA [greenhalfA]

description: greenhalfA

value: green-half


title: Kiyomi_15_DAF

description: Gene expression 15 day after flowering in whole young fruit of monoembryonic citurs cultivar 'Kiyomi'

source_name: Kiyomi, 15 day after flowering, monoembryonic


title: ΔsigT untreated 2-BS

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
FastQ files from Illumina HiSeq were processed using CLC genomics workbench (Qiagen), RNA-seq data analysis pipeline. Reads were mapped to the Caulobacter crescentus NA1000 genome (accession CP001340)
Genome_build: GenBank accession CP001340
Supplementary_files_format_and_content: processed data files report results of expression analysis in CLC genomics workbench, and are in .txt format

organism: Caulobacter vibrioides

source_name: ΔsigT untreated BS

growth_protocol: Cultures of Caulobacter crescentus in M2-xylose defined medium (OD660=0.05) were prepared by diluting a saturated overnight culture (OD ~0.85-0.90). The diluted culture was grown to OD660=0.075 and split into two 4 mL cultures; one split culture was treated with sucrose to a final concentration of 150 mM to induce hyperosmotic stress. Both cultures were grown for an additional 5 hours (MT samples) or 6 hours (BS samples) in a 30 degree rolling incubator, pelleted, and then treated with TRIzol for total RNA purification.

extract_protocol:
Total RNA was extracted from pelleted Caulobacter crescentus cells using Trizol, per manufacturer protocol.
TruSeq stranded total RNA kit was used to prepare RNA-seq library, per manufacturer (Illumina) protocol

treatment_protocol: Culture conditions are described in the field above. Split samples were either treated with 150 mM sucrose (final concentration) to induce hyperosmotic shock for 5-6 hours, or remained untreated.

value: sigT deletion

tag: treated with

value: none (untreated control)


title: tonsil dendritic cells

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

institute: Institut Curie

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: GRCh38

source_name: tonsil dendritic cells

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

value: tonsil dendritic cells

tag: donor number

value: donor 1


title: wild type hyperosmotic treated 4-BS

source_name: wild type hyperosmotic treated BS

value: wild type

value: osmotic upshock (150 mM sucrose)


title: ΔsigT hyperosmotic treated 3-BS

source_name: ΔsigT hyperosmotic treated BS


title: ΔsigT untreated 1-BS


title: tumor ascites macrophages

source_name: tumor ascites macrophages

value: tumor ascites macrophages


title: tumor ascites dendritic cells

source_name: tumor ascites dendritic cells

value: tumor ascites dendritic cells


title: ΔsigT hyperosmotic treated 1-BS


title: ΔsigT untreated 3-BS


title: ΔsigT untreated 4-BS


title: wild type hyperosmotic treated 3-BS


title: wild type hyperosmotic treated 2-BS


title: wild type hyperosmotic treated 1-BS


title: wild type untreated 2-BS

source_name: wild type untreated BS


title: 3T3; control; replicate 2

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: RMA expression value derived from Expression Console software

hyb_protocol: According to manufacturers instructions without modifications.

data_processing: CEL files were processed using the Aroma.Affymetrix package with RMA background subtraction and quantile normalization

source_name: mouse fibroblast cells

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

growth_protocol: Stable CTCFL-inducible p19 clone was grown in DMEM supplemented with 2 µg/ml Doxycyclin to repress CTCFL expression (Tet-Off)

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

treatment_protocol: Overexpression of CTCFL was achieved by growing the cells in medium lacking Doxycyline for 48h.

tag: cell line

tag: stable integrate

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

tag: treatment

value: 2 ug/ml  Doxycycline


title: 3T3; Ctcfl overexpression replicate 2

scan_protocol: According to manufacturers instructions without modifications.


title: 3T3; control; replicate 1


title: 3T3; Ctcfl overexpression replicate 1


title: wild type untreated 4-BS


title: wild type untreated 3-BS


title: wild type untreated 1-BS


title: gsrN++ hyperosmotic treated 2-MT

source_name: gsrN++ hyperosmotic treated MT

value: gsrN overexpression (gsrN++)


title: gsrN++ hyperosmotic treated 3-MT


title: gsrN++ hyperosmotic treated 4-MT


title: gsrN++ hyperosmotic treated 1-MT


title: ΔsigT hyperosmotic treated 2-BS


title: gsrN++ untreated 2-MT

source_name: gsrN++ untreated MT


title: gsrN++ untreated 3-MT


title: wild type hyperosmotic treated 3-MT

source_name: wild type hyperosmotic treated MT


title: BMM-HdAg-rep3

city: Calgary

first: Jose

middle: L

last: Reyes

state: Alberta

address: 3330 Hospital Dr. NW

department: Physiology and Pharmacology

institute: The University of Calgary

data_processing: Analysis of the nanostring data was done in R 3.3.1. Raw nanostring data was imported into R using NanoStringQCPro and normalized using NanoStringNorm. Samples were adjusted for technical variation (sum of positive controls), followed by subtraction of background (mean negative controls) and RNA content normalization using the geometric mean of the housekeeping genes.  An additional variance stabilizing transform was applied to improve downstream analysis.

label: nanostring fluorescence barcode

source_name: bone-marrow derived macrophages

extract_protocol: After a period of 20 hr incubation with aforementioned treatments, 500 ul of Trizol reagent (invitrogen) was added into the wells and upon 15 gently shaking at 4°C samples were centrifuged (12,000 rpm 15 min) and supernatants transferred into new tubes with fresh cold chloroform (300 ul) gently mixed and left additional 10 min at 4°C. After another round of centrifugation (12,000 rpm 15 min), supernatants were mixed with 500 ul of ice cold isopropil alcohol and a final round of centrifugation conducted (12,000 rpm 5 min) pellets were left to dry, quantified by using nanodrop and normalized to 20 ng each sample.

value: H. diminuta extract


title: BMM-HdAg_aIL10-rep1

value: H. diminuta extract and anti-IL-10 antibodies


title: BMM-IL_4-rep3


title: gsrN++ untreated 4-MT


title: BMM-HdAg-rep2


title: BMM-HdAg_aIL10-rep3


title: BMM-HdAg-rep1


title: BMM-HdAg_aIL10-rep2


title: gsrN++ untreated 1-MT


title: BMM-IL_4-rep2


title: BMM-Unst-rep1

value: Unstimulated


title: BMM-Unst-rep3


title: BMM-IL_4-rep1


title: BMM-Unst-rep2


title: wild type hyperosmotic treated 2-MT


title: wild type hyperosmotic treated 1-MT


title: ex-vivo_patient_ID:_SQ038_2007_Gedaref_Sudan

type: genomic

first: Margaret

middle: Jane

last: Mackinnon

country: Australia

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

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

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

organism: Plasmodium falciparum

source_name: P. falciparum (ex vivo), Gedaref, Sudan

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

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

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

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

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

value: ex-vivo, SQ038, 2007, Gedaref, Sudan

source_name: P. falciparum lab-adapted strain P4

value: strain P4


title: wild type hyperosmotic treated 4-MT


title: ex-vivo_patient_ID:_SQ035_2007_Gedaref_Sudan

value: ex-vivo, SQ035, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_SQ034_2007_Gedaref_Sudan

value: ex-vivo, SQ034, 2007, Gedaref, Sudan


title: wild type untreated 2-MT

source_name: wild type untreated MT

value: none (untreated control)


title: wild type untreated 1-MT


title: wild type untreated 3-MT


title: wild type untreated 4-MT


title: ex-vivo_patient_ID:_SQ032_2007_Gedaref_Sudan

value: ex-vivo, SQ032, 2007, Gedaref, Sudan


title: LCM-3

city: Philadelphia

first: Kim

last: Kridsada

state: PA

address: 3610 Hamilton Walk 145 Johnson Pavilion UNIVERSITY OF PA/CLINICAL

department: Neuroscience

institute: University of Pennsylvania

description: Laser capture microdissection (LCM)

data_processing:
Sequencing was performed with HiSeq control software version 2.0.12.0, and HiSeq real time analysis software version 1.17.21.3
Sequences were aligned to mm9 whole genome.
Differentially expressed genes were called using a custom pipeline from the Next-Generation Sequencing Core at UPenn: reads were aligned to ribosomal sequences, repeats removed to assess level of ribosomal sequence in the libraries; RUM is used to generate files to be used in the TessLA browser and other down-stream analyses.
Quantile normalized reads were calculated as described (Bolstad et al., 2003, Bullard et al., 2009)
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes quantile normalized reads (Bolstad et al., 2003; Bullard et al., 2009) for all samples to match read count distribution of all samples ("Compare" sheet, columns R-W), comparison tests between midline cell replicates and RA mechanoreceptor replicates (MvA, EdgeR, SAMR)

source_name: spinal cord dorsal column

extract_protocol:
For FACS isolated replicates, DRG from E14.5 embryos were harvested and dissociated with Trypsin-EDTA, resuspended in HBSS, and isolated using Diva or Aria TMII cell sorter. For LCM isolated replicates, spinal cords from E14.5 embryos were harvested and flash frozen on dry ice, stained with hematoxylin, dessicated, and microdissected with a Zeiss PALM system. All RNA was extracted using GeneJet RNA Purification Kit (K0731, Fermentas).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For Ret-Tdt replicates, 1.5 and 2mg of 4-hydroxytamoxifen were administered via oral gavage to pregnant mothers in order to label specifically the Ret+ RA mechanoreceptor populations in the embryos.

tag: cell type

value: roof plate-derived dorsal column midline cells

value: mixed

value: wild-type

tag: age


title: LCM-5

description: Laser capture microdissection (LCM)

tag: genotype


title: ex-vivo_patient_ID:_SQ030_2007_Gedaref_Sudan

value: ex-vivo, SQ030, 2007, Gedaref, Sudan


title: LCM-2

description: Laser capture microdissection (LCM)


title: ex-vivo_patient_ID:_SQ012_2007_Gedaref_Sudan

value: ex-vivo, SQ012, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_SQ008_2007_Gedaref_Sudan

value: ex-vivo, SQ008, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_SQ031_2007_Gedaref_Sudan

value: ex-vivo, SQ031, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_M034_2007_Wad Madani_Sudan

source_name: P. falciparum (ex vivo), Wad Madani, Sudan

value: ex-vivo, M034, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SQ009_2007_Gedaref_Sudan

value: ex-vivo, SQ009, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_M035_2007_Wad Madani_Sudan

value: ex-vivo, M035, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M033_2007_Wad Madani_Sudan

value: ex-vivo, M033, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SQ004_2007_Gedaref_Sudan

value: ex-vivo, SQ004, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_SQ002_2007_Gedaref_Sudan

value: ex-vivo, SQ002, 2007, Gedaref, Sudan

value: strain P4


title: ex-vivo_patient_ID:_M031_2007_Wad Madani_Sudan

value: ex-vivo, M031, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M030_2007_Wad Madani_Sudan

value: ex-vivo, M030, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M026_2007_Wad Madani_Sudan

value: ex-vivo, M026, 2007, Wad Madani, Sudan


title: Ret-Tdt8

description: FACS isolated

source_name: dorsal root ganglia

value: Ret+ RA mechanoreceptors

value: Ret-CreERT2; Rosa26-Tdtomato


title: Ret-Tdt9

description: FACS isolated

value: mixed


title: ex-vivo_patient_ID:_M025_2007_Wad Madani_Sudan

value: ex-vivo, M025, 2007, Wad Madani, Sudan


title: parental (control)

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

description:
comparison of the binding of TgAP2XI-5 in presence of TgAP2X-5 (WT) or absence of TgAP2X-5 (iKD TgAP2X-5 / KI TgAP2XI-5)
RHΔhxgprtΔku80

hyb_protocol: The labeled ChIP DNA was mixed with a Hybridization Master Mix (260µL 2X HI-RPM Hybridization Buffer, 52µL 10X aCGH Blocking Agnet and 50µL Human Cot-1 DNA (Roche)). The labeled ChIP DNA was incubated 3min at 98°C and 30min at 37°C. Arrays were hybridized in an Agilent SureHyb chamber for 40h at 67°C into an oven rotator rack at 20rpm. Arrays were washed with Agilent Oligo aCGH/ChIP-on-chip Wash buffer 1 and 2 according to manufacturer's recommandation.

scan_protocol: Arrays were scanned on an SureScan C Agilent scanner per manufacturer's protocol

data_processing: The value is log2R normalized with the Feature Extraction Software

organism: Toxoplasma gondii

source_name: IgG ChIP DNA from parental strain

label_protocol: 2 µg ChIP DNA was directly labeled by SureTag DNA labeling kit (Agilent) per manufacturer's protocol

growth_protocol: Intracellular parasite grown 40h on HFF

extract_protocol: DNA were processed by sonication for 10min at 4°C with a 30sec on/off cycle. Protein-DNA complexes were then diluted in IP Dilution Buffer and incubated ON with IgG Agarose beads. The next day, beads were washed five times with ChIP wash buffer and eluted twice in 75µL of ChIP elution buffer. DNA was further subjected to a treatment with proteinase K for 2 h and then purified using the Qiagen PCR purification kit. Amplification of immunoprecipitated DNA and 10 ng input DNA was performed using the GenomePlex Complete Whole Amplification (WGA) kit.

treatment_protocol: Intracullular parasite were fixed for 10min at room temperature using 1% formaldehyde

tag: antibody

value: Rabbit IgG (Sigma)

source_name: INPUT DNA from parental strain


title: iKD TgAP2X-5 / TgAP2XI-5 +ATc_1

description:
comparison of the binding of TgAP2XI-5 in presence of TgAP2X-5 (WT) or absence of TgAP2X-5 (iKD TgAP2X-5 / KI TgAP2XI-5)
RHΔhxgprtΔku80 TATi; teto7SAG4:AP2X-5-3HA; DHFR-TS; AP2XI-5-TAP, DHFR-TS:CAT

source_name: IgG ChIP DNA from iKD TgAP2X-5 / TgAP2XI-5 tagged strain

growth_protocol: Intracellular parasite grown 40h with ATc on HFF

value: RHdeltahxgprtdeltaku80 TATi; teto7SAG4:AP2X-5-3HA; DHFR-TS; AP2XI-5-TAP, DHFR-TS:CAT

source_name: INPUT DNA from iKD TgAP2X-5 / TgAP2XI-5 tagged strain


title: TgAP2XI-5_2

description:
comparison of the binding of TgAP2XI-5 in presence of TgAP2X-5 (WT) or absence of TgAP2X-5 (iKD TgAP2X-5 / KI TgAP2XI-5)
RHΔhxgprtΔku80 ; AP2XI-5-TAP, DHFR-TS:CAT

source_name: IgG ChIP DNA from TgAP2XI-5 tagged strain

value: RHdeltahxgprtdeltaku80 ; AP2XI-5-TAP, DHFR-TS:CAT

source_name: INPUT DNA from TgAP2XI-5 tagged strain


title: iKD TgAP2X-5 / TgAP2XI-5 +ATc_2


title: Ret-Tdt2

description: FACS isolated


title: TgAP2XI-5_1


title: TgAP2X-5

description:
comparison of the binding of TgAP2XI-5 in presence of TgAP2X-5 (WT) or absence of TgAP2X-5 (iKD TgAP2X-5 / KI TgAP2XI-5)
RHΔhxgprtΔku80 ; AP2X-5-3xHA-TAP, HXGPRT:HXGPRT

source_name: IgG ChIP DNA from TgAP2X-5 tagged strain

value: RHdeltahxgprtdeltaku80 ; AP2X-5-3xHA-TAP, HXGPRT:HXGPRT

source_name: INPUT DNA from TgAP2X-5 tagged strain


title: ex-vivo_patient_ID:_M022_2007_Wad Madani_Sudan

value: ex-vivo, M022, 2007, Wad Madani, Sudan


title: E17_5_Mut_R1

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

data_processing:
The raw RNA-Seq results were mapped onto mm9 genome (NCBI37) using the default parameters in Tophat
Cufflinks (Trapnell et al., 2012) was used to generate gene expression FPKM (fragments per kilobase of exon per million)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene expression (FPKM) for each sample following columns: Gene symbol, NCBI accession number, FPKM of gene

source_name: Foxd1-mutant E17.5 hypothalamic tissues

growth_protocol: Hypothalamic tissue was dissected at E12.5 and E17.5 as previously described (Shimogori, et al. 2010) and stored -80°C prior to use

extract_protocol:
A total of 8a Foxd1-null and 10 control (either wild-type or Foxd1-mutant) embryos were harvested
After genotyping, the RNA was extracted using the RNeasy kit (Qiagen). A cDNA library was generated and barcoded for each pooled RNA sample, then sequenced to a paired-end read depth of 100 cycles using Illumina HiSeq 2500.

tag: mutant

tag: embryonic stage

tag: replicate


title: ex-vivo_patient_ID:_M020_2007_Wad Madani_Sudan

value: ex-vivo, M020, 2007, Wad Madani, Sudan

tag: strain


title: ex-vivo_patient_ID:_M023_2007_Wad Madani_Sudan

value: ex-vivo, M023, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M024_2007_Wad Madani_Sudan

value: ex-vivo, M024, 2007, Wad Madani, Sudan


title: E17_5_Cntl_R2

source_name: Wild-type E17.5 hypothalamic tissues

value: Wild-type


title: E12_5_Mut_S4

source_name: Foxd1-mutant E12.5 hypothalamic tissues


title: E17_5_Cntl_R1


title: E17_5_Mut_R2


title: E12_5_Cntl_S3

source_name: Wild-type E12.5 hypothalamic tissues


title: E12_Mut_S2

source_name: Foxd1-mutant E12.0 hypothalamic tissues


title: E12_Cntl_S1

source_name: Wild-type E12.0 hypothalamic tissues


title: ex-vivo_patient_ID:_M019_2007_Wad Madani_Sudan

value: ex-vivo, M019, 2007, Wad Madani, Sudan

source_name: P. falciparum lab-adapted strain P4

value: strain P4


title: ex-vivo_patient_ID:_M016_2007_Wad Madani_Sudan

source_name: P. falciparum (ex vivo), Wad Madani, Sudan

value: ex-vivo, M016, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M015_2007_Wad Madani_Sudan

value: ex-vivo, M015, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M018_2007_Wad Madani_Sudan

value: ex-vivo, M018, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0071_2008_Kisumu_Kenya

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

value: ex-vivo, K0071, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_M014_2007_Wad Madani_Sudan

value: ex-vivo, M014, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0070_2008_Kisumu_Kenya

value: ex-vivo, K0070, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0072_2008_Kisumu_Kenya

value: ex-vivo, K0072, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_SQ013_2007_Gedaref_Sudan

source_name: P. falciparum (ex vivo), Gedaref, Sudan

value: ex-vivo, SQ013, 2007, Gedaref, Sudan


title: ex-vivo_patient_ID:_K0073_2008_Kisumu_Kenya

value: ex-vivo, K0073, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_M003_2007_Wad Madani_Sudan

value: ex-vivo, M003, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M013_2007_Wad Madani_Sudan

value: ex-vivo, M013, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M011_2007_Wad Madani_Sudan

value: ex-vivo, M011, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M012_2007_Wad Madani_Sudan

value: ex-vivo, M012, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0068_2008_Kisumu_Kenya

value: ex-vivo, K0068, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0067_2008_Kisumu_Kenya

value: ex-vivo, K0067, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_M004_2007_Wad Madani_Sudan

value: ex-vivo, M004, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_M005_2007_Wad Madani_Sudan

value: ex-vivo, M005, 2007, Wad Madani, Sudan

value: strain P4


title: ex-vivo_patient_ID:_M008_2007_Wad Madani_Sudan

value: ex-vivo, M008, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0065_2008_Kisumu_Kenya

value: ex-vivo, K0065, 2008, Kisumu, Kenya


title: LPM027b_T

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

description: Gene expression analysis of tumor infiltrating T-cells

hyb_protocol: Overnight hybridization according to Affymetrix Protocol

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 and GCOS software

data_processing: CEL files were RMA normalized using GenePattern ExpressionFileCreator module

label: Biotin

source_name: Follicular lymphoma tumor

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

growth_protocol: Cells were not cultured

extract_protocol: Qiagen AllPrep Mini Kit

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

tag: disease state

value: follicular lymphoma

value: T-cells

tag: condition

value: Relapse 1


title: ex-vivo_patient_ID:_M007_2007_Wad Madani_Sudan

value: ex-vivo, M007, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0066_2008_Kisumu_Kenya

value: ex-vivo, K0066, 2008, Kisumu, Kenya


title: LPM029b_T


title: LPM027a_T

value: Diagnosis


title: LPM029c_T

value: Relapse 2


title: LPM029a1_T

value: Diagnosis 1


title: LPM029a2_T

value: Diagnosis 2


title: LPM024a_T


title: LPM024b_T


title: MCF7PTHrP BR3

city: Nashville

first: Rachelle

last: Johnson

address: 2215B Garland Ave

institute: Vanderbilt University Medical Center

description: biological replicate 3

data_processing:
Sequenced reads were mapped to hg38 genome by STAR (2.5.2a)
Mapped reads were assigned to Ensembl genes (v86) by HTSeq-Count with option -q -m intersection-nonempty -s no -i gene_id
Differential expression analaysis was performed by MultiRankSeq which was described in Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y. MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control. Biomed Res Int. 2014;2014:248090. doi: 10.1155/2014/248090.
Genome_build: hg38
Supplementary_files_format_and_content: One excel file named MultiRankSeq_456_vs_123.html.diff contains all of the analyses for these data. The processed data file provides relative gene expression values for DESeq, edgeR, and baySeq with adjusted p-values and Rank. The gene expression values provided indicate the fold change in gene expression in MCF7 PTHrP overexpressing cells relative to the MCF7 pcDNA control cells.

source_name: Human MCF7 breast cancer cells

extract_protocol:
Cells were harvested in TRIzol and extracted per the manufacturer's instructions using phenol/chloroform.
The library was generated for at the Stanford Functional Genomics Facility using the KAPA Stranded mRNA-Seq kit according to manufacturer's instructions.

treatment_protocol: The cells were grown in DMEM+10%FBS with no additional treatments. 16 hours prior to collection the cells were switched to DMEM+2%FBS containing approximately 15-30ul PBS.

tag: genotype/variation

value: PTHrP over-expression


title: MCF7PTHrP BR2

description: biological replicate 2


title: ex-vivo_patient_ID:_K0064_2008_Kisumu_Kenya

value: ex-vivo, K0064, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0063_2008_Kisumu_Kenya

value: ex-vivo, K0063, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0058_2008_Kisumu_Kenya

value: ex-vivo, K0058, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0056_2008_Kisumu_Kenya

value: ex-vivo, K0056, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0059_2008_Kisumu_Kenya

value: ex-vivo, K0059, 2008, Kisumu, Kenya

value: strain P4


title: MCF7pcDNA BR3

description: biological replicate 3

value: control pcDNA


title: MCF7PTHrP BR1

description: biological replicate 1


title: MCF7pcDNA BR2

description: biological replicate 2


title: LPM022b_T

value: follicular lymphoma


title: ex-vivo_patient_ID:_K0054_2008_Kisumu_Kenya

value: ex-vivo, K0054, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0060_2008_Kisumu_Kenya

value: ex-vivo, K0060, 2008, Kisumu, Kenya


title: LPM023a_T

value: T-cells


title: LPM022a_T


title: LPM019c_T


title: ex-vivo_patient_ID:_K0047_2008_Kisumu_Kenya

value: ex-vivo, K0047, 2008, Kisumu, Kenya


title: CD8αβ+ SPLs, replicate 1

city: Hefei

first: Banru

last: Chen

address: 443 Huangshan Road

institute: School of Life Sciences, University of Science & Technology of China

hyb_protocol: Indocarbocyanine-labeled cDNA was assessed with the NanoDrop ND-2000 (Thermo Scientific), and equal amounts of indocarbocyanine-labeled target were hybridized to Agilent SurePrint G3 Mouse Gene Expression (8x60K) microarrays（Design ID：74809）.

scan_protocol: Arrays were scanned with the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Raw signal intensities were extracted with Feature Extraction v10.7.1.1 software(Agilent Technologies).

label: indocarbocyanine

source_name: CD8αβ+ SPLs, replicate 1

label_protocol: RNA was amplified and abeling of CTP with indocarbocyanine was done with Agilent one-color labeling kits (Agilent Technologies).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.Total RNA quality was assessed with a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: CD8αβ+ IELs and CD8αβ+ SPLs were sorted from intraepithelium of small intestines and spleens of WT mice (8–12w), and we lysed the cells in TRIzol (Invitrogen) and freezed them in refrigerator (-80°C).

tag: tissue

value: spleen

tag: gender

value: male


title: LPM020a_T

value: Diagnosis


title: MCF7pcDNA BR1

description: biological replicate 1

tag: cell line


title: CD8αβ+ IELs, replicate 2

source_name: CD8αβ+ IELs, replicate 2

value: epithelium of small intestine


title: ex-vivo_patient_ID:_K0049_2008_Kisumu_Kenya

value: ex-vivo, K0049, 2008, Kisumu, Kenya


title: LPM021a_T

value: Relapse 1


title: CD8αβ+ SPLs, replicate 2

source_name: CD8αβ+ SPLs, replicate 2


title: ex-vivo_patient_ID:_K0044_2008_Kisumu_Kenya

value: ex-vivo, K0044, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0046_2008_Kisumu_Kenya

value: ex-vivo, K0046, 2008, Kisumu, Kenya


title: LPM019b_T


title: Beta-estradiol/5-ALA-treated double mutant cells for 48 h, replicate 2

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 4009 WIMR 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

description: double mutant

data_processing:
Sequencing reads were aligned to mouse genome assembly (mm9) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1.
Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the windows was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: G1E-ER-GATA1 cells

growth_protocol: G1E-ER-GATA-1 cells were cultured in IMDM (Gibco) containing 15% FBS (Gemini), 1% penicillin-streptomycin (Gemini), 2 U/ml erythropoietin, 120 nM monothioglycerol (Sigma), 0.6% conditioned medium from a Kit ligand-producing CHO cell line, and 1ug/ml puromycin (Gemini).

extract_protocol:
For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Libraries were generated using standard Nextera DNA library kit protocol.

treatment_protocol: ER-GATA-1 activity was induced by addition of 1 uM beta-estradiol (Steraloids) to the media. To rescue heme biosynthesis, 1 mM 5-aminolevulinic acid hydrochloride (5-ALA; Sigma) was added to the media.

value: 48 h beta-estradiol and 48 h 5-ALA


title: Beta-estradiol/5-ALA-treated double mutant cells for 48 h, replicate 1

description: double mutant


title: Beta-estradiol/5-ALA-treated double mutant cells for 12 h, replicate 3

description: double mutant

value: 48 h beta-estradiol and 12 h 5-ALA


title: Beta-estradiol/5-ALA-treated double mutant cells for 48 h, replicate 3

description: double mutant


title: ex-vivo_patient_ID:_K0043_2008_Kisumu_Kenya

value: ex-vivo, K0043, 2008, Kisumu, Kenya

value: strain P4


title: ex-vivo_patient_ID:_K0041_2008_Kisumu_Kenya

value: ex-vivo, K0041, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0042_2008_Kisumu_Kenya

value: ex-vivo, K0042, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0039_2008_Kisumu_Kenya

value: ex-vivo, K0039, 2008, Kisumu, Kenya


title: LPM018c_T

value: follicular lymphoma

value: T-cells

value: Relapse 2


title: ex-vivo_patient_ID:_K0040_2008_Kisumu_Kenya

value: ex-vivo, K0040, 2008, Kisumu, Kenya


title: LPM019a_T

value: Diagnosis


title: LPM018d_T

value: Relapse 3


title: CD8αβ+ IELs, replicate 1

source_name: CD8αβ+ IELs, replicate 1

value: epithelium of small intestine

value: male


title: LPM018b_T

value: Relapse 1


title: LPM018a_T


title: Beta-estradiol-treated double mutant cells, replicate 3

description: double mutant

value: 48 h beta-estradiol


title: Beta-estradiol/5-ALA-treated double mutant cells for 12 h, replicate 1

description: double mutant


title: Beta-estradiol/5-ALA-treated double mutant cells for 12 h, replicate 2

description: double mutant


title: LPM016a_T


title: ex-vivo_patient_ID:_K0038_2008_Kisumu_Kenya

value: ex-vivo, K0038, 2008, Kisumu, Kenya


title: LPM016b_T


title: LPM017a_T


title: LPM011a_T


title: ex-vivo_patient_ID:_K0036_2008_Kisumu_Kenya

value: ex-vivo, K0036, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0035_2008_Kisumu_Kenya

value: ex-vivo, K0035, 2008, Kisumu, Kenya


title: LPM011b_T


title: Beta-estradiol-treated double mutant cells, replicate 1

description: double mutant


title: Untreated double mutant cells, replicate 3

description: WT

value: Untreated


title: Untreated double mutant cells, replicate 2

description: WT


title: Untreated double mutant cells, replicate 1

description: WT


title: Beta-estradiol-treated double mutant cells, replicate 2

description: double mutant


title: Beta-estradiol-treated WT cells, replicate 1

description: double mutant


title: ex-vivo_patient_ID:_K0034_2008_Kisumu_Kenya

value: ex-vivo, K0034, 2008, Kisumu, Kenya

value: strain P4


title: Beta-estradiol-treated WT cells, replicate 3

description: double mutant


title: ex-vivo_patient_ID:_K0030_2008_Kisumu_Kenya

value: ex-vivo, K0030, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0031_2008_Kisumu_Kenya

value: ex-vivo, K0031, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0033_2008_Kisumu_Kenya

value: ex-vivo, K0033, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0028_2008_Kisumu_Kenya

value: ex-vivo, K0028, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0027_2008_Kisumu_Kenya

value: ex-vivo, K0027, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0026_2008_Kisumu_Kenya

value: ex-vivo, K0026, 2008, Kisumu, Kenya


title: Untreated WT cells, replicate 3

description: WT


title: ex-vivo_patient_ID:_K0025_2008_Kisumu_Kenya

value: ex-vivo, K0025, 2008, Kisumu, Kenya


title: LPM001b_T

value: follicular lymphoma

value: T-cells


title: LPM001c_T

value: Relapse 2


title: LPJ128a_T

value: Diagnosis


title: LPM005a_T


title: LPM001a_T


title: Beta-estradiol-treated WT cells, replicate 2

description: double mutant

value: 48 h beta-estradiol


title: Untreated WT cells, replicate 2

description: WT


title: LPJ040a2_T


title: Untreated WT cells, replicate 1

description: WT


title: ex-vivo_patient_ID:_K0024_2008_Kisumu_Kenya

value: ex-vivo, K0024, 2008, Kisumu, Kenya


title: LPM029b_B

description: Gene expression analysis of follicular lymphoma B-cells

value: B-cells

value: Relapse 1


title: ex-vivo_patient_ID:_K0023_2008_Kisumu_Kenya

value: ex-vivo, K0023, 2008, Kisumu, Kenya


title: LPM029a2_B

value: Diagnosis 2


title: LPJ040b_T


title: miRNA_human-paracancerous normal tissues-biological rep12

city: Nanning

first: Guangqiang

last: Ye

address: NO.22 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Following fragmentation,  50µl 2X hybridization mix (from GeneChip Hyb, Wash and Stain Kit, Affymetrix cat. no. 900720)  were hybridized for 16 hr at  48°C and 60 rpm  on Hybridization Oven 640(Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.Scan using the Library file at the link below.(http://www.affymetrix.com/products_services/arrays/specific/mi_rna.affx#1_4)  The instructions for using the scanner and scanning arrays can be found in the Affymetrix Command Console Software in Chapter 6 (page 141).(http://www.affymetrix.com/support/downloads/manuals/agcc_command_console_user_guide.pdf)

data_processing: Use AGCC software（Affymetrix® GeneChip® Command Console® Software) to save the scanned image of the chip as a .DAT file for analysis. Then the data were analyzed with RMA using  the free miRNA QC Tool software for data summarization, normalization, and quality contro. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: paracancerous normal tissues

label_protocol: 1 ug of total RNA was labeled with Biotin using the FlashTag™ Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays.

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

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

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

value: liver

value: paracancerous normal tissues

tag: patient id

tag: sample id


title: miRNA_human-paracancerous normal tissues-biological rep10


title: miRNA_human-paracancerous normal tissues-biological rep9


title: LPM029a1_B

value: Diagnosis 1


title: miRNA_human-paracancerous normal tissues-biological rep11


title: miRNA_human-paracancerous normal tissues-biological rep8


title: ex-vivo_patient_ID:_K0018_2008_Kisumu_Kenya

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

value: ex-vivo, K0018, 2008, Kisumu, Kenya

value: strain P4


title: LPM027b_B

tag: cell type


title: LPM005b_T


title: miRNA_human-paracancerous normal tissues-biological rep7


title: ex-vivo_patient_ID:_K0022_2008_Kisumu_Kenya

value: ex-vivo, K0022, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0020_2008_Kisumu_Kenya

value: ex-vivo, K0020, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0014_2008_Kisumu_Kenya

value: ex-vivo, K0014, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_SK02_2007_Wad Madani_Sudan

value: ex-vivo, SK02, 2007, Wad Madani, Sudan


title: miRNA_human-paracancerous normal tissues-biological rep4


title: LPM027a_B

value: follicular lymphoma


title: LPM024a_B

value: Diagnosis


title: ex-vivo_patient_ID:_K0019_2008_Kisumu_Kenya

value: ex-vivo, K0019, 2008, Kisumu, Kenya


title: miRNA_human-paracancerous normal tissues-biological rep6


title: miRNA_human-paracancerous normal tissues-biological rep5


title: LPM022a_B


title: LPM024b_B


title: miRNA_human-paracancerous normal tissues-biological rep2


title: ex-vivo_patient_ID:_K0011_2008_Kisumu_Kenya

value: ex-vivo, K0011, 2008, Kisumu, Kenya


title: LPM023a_B

value: B-cells


title: ex-vivo_patient_ID:_K0013_2008_Kisumu_Kenya

value: ex-vivo, K0013, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_K0010_2008_Kisumu_Kenya

value: ex-vivo, K0010, 2008, Kisumu, Kenya


title: LPM021a_B


title: miRNA_human-paracancerous normal tissues-biological rep3


title: miRNA_human-paracancerous normal tissues-biological rep1


title: LPM022b_B

value: Relapse 1


title: LPM021b_B


title: ex-vivo_patient_ID:_K0008_2008_Kisumu_Kenya

value: ex-vivo, K0008, 2008, Kisumu, Kenya


title: miRNA_human-HCC-biological rep11

source_name: hepatocellular carcinoma

value: liver

value: hepatocellular carcinoma


title: miRNA_human-HCC-biological rep12


title: ex-vivo_patient_ID:_K0005_2008_Kisumu_Kenya

value: ex-vivo, K0005, 2008, Kisumu, Kenya


title: LPM020b_B


title: ex-vivo_patient_ID:_K0007_2008_Kisumu_Kenya

value: ex-vivo, K0007, 2008, Kisumu, Kenya

value: strain P4


title: miRNA_human-HCC-biological rep10


title: miRNA_human-HCC-biological rep9


title: LPM029c_B

value: Relapse 2


title: LPM020a_B


title: miRNA_human-HCC-biological rep8


title: ex-vivo_patient_ID:_SK01_2007_Wad Madani_Sudan

value: ex-vivo, SK01, 2007, Wad Madani, Sudan


title: miRNA_human-HCC-biological rep7


title: ex-vivo_patient_ID:_SH09_2007_Wad Madani_Sudan

value: ex-vivo, SH09, 2007, Wad Madani, Sudan


title: LPM019b_B

value: follicular lymphoma


title: LPM020c_B


title: LPM019c_B


title: ex-vivo_patient_ID:_SH06_2007_Wad Madani_Sudan

value: ex-vivo, SH06, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_K0002_2008_Kisumu_Kenya

value: ex-vivo, K0002, 2008, Kisumu, Kenya


title: ex-vivo_patient_ID:_SH05_2007_Wad Madani_Sudan

value: ex-vivo, SH05, 2007, Wad Madani, Sudan


title: miRNA_human-HCC-biological rep6


title: ex-vivo_patient_ID:_SH03_2007_Wad Madani_Sudan

value: ex-vivo, SH03, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SH04_2007_Wad Madani_Sudan

value: ex-vivo, SH04, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SH01_2007_Wad Madani_Sudan

value: ex-vivo, SH01, 2007, Wad Madani, Sudan


title: LPM018c_B

value: B-cells


title: LPM019a_B

value: Diagnosis


title: LPM018d_B

value: Relapse 3


title: miRNA_human-HCC-biological rep5

value: liver

value: hepatocellular carcinoma


title: miRNA_human-HCC-biological rep3


title: miRNA_human-HCC-biological rep4


title: ex-vivo_patient_ID:_SG013_2007_Wad Madani_Sudan

value: ex-vivo, SG013, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SG08_2007_Wad Madani_Sudan

value: ex-vivo, SG08, 2007, Wad Madani, Sudan

value: strain P4


title: ex-vivo_patient_ID:_SG015_2007_Wad Madani_Sudan

value: ex-vivo, SG015, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SG037_2007_Wad Madani_Sudan

value: ex-vivo, SG037, 2007, Wad Madani, Sudan


title: LPM017b_B

value: follicular lymphoma

value: Relapse 1


title: miRNA_human-HCC-biological rep2


title: LPM017a_B


title: LPM016b_B


title: LPM018b_B


title: miRNA_human-HCC-biological rep1


title: LPM018a_B


title: LPM016a_B


title: Rhesus_WGBS

city: Portland

first: Lucia

last: Carbone

state: Oregon

address: 3303 SW Bond Ave.

institute: Oregon Health & Science University

description: Rhesus macaque

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

organism: Macaca mulatta

source_name: Blood

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

value: White blood cells

tag: age

value: adult


title: ex-vivo_patient_ID:_SG010_2007_Wad Madani_Sudan

value: ex-vivo, SG010, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SG009_2007_Wad Madani_Sudan

value: ex-vivo, SG009, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SG005_2007_Wad Madani_Sudan

value: ex-vivo, SG005, 2007, Wad Madani, Sudan


title: ex-vivo_patient_ID:_SG002_2007_Wad Madani_Sudan

value: ex-vivo, SG002, 2007, Wad Madani, Sudan