title: KD6 - 934inh - Pool 3

city: Boston

description:
HUES6-derived NPCs (15 DIV) transduced with an anti-miR-934 lentivirus or the scrambled control virus at DIV 10 of neural induction and collected 5 days later.
Counts.GRCh38.89.merged.tsv

data_processing:
Raw RNA-Seq reads were quality checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminants were detected and removed utilizing a combination of an in-house-developed algorithm and already available tools such as Minion and Cutadapt.
Pre-processing was performed using cutadapt
microRNA expression was quantified using miRDeep2 (Mackowiak 2011) with miRBase v21 annotation (Kozomara and Griffiths-Jones 2014).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Read counts (tsv format)

source_name: iPSC-derived NPCs

growth_protocol: HUES6 cell line as maintained in HUES medium as described in Kouroupi et al, PNAS, 2017

extract_protocol:
Illumina Tru-Seq RNA-Seq
Total RNA was extracted from cell pellets using the TRIzol® Reagent (Life Technologies).
Total cellular RNA was extracted from the following samples and sequenced on an Illumina HiSeq sequencer. RNA libraries were prepared with the TruSeq RNA Sample Preparation Kit V2 (Illumina).
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina.

treatment_protocol: Sustained inhibition of miR-934 during neural induction was achieved with the miRZip lentivector-based anti-microRNA system (Systems Biosciences). Cultures were transduced with the anti-miR-934 lentivirus or the scrambled control virus at DIV10 of neural induction and were collected for analysis 5 days later at DIV15.

value: neural progenitor cell

tag: pool

value: anti-miR-934 lentivirus


title: Liver_Control 6

status: Public on Jun 06 2020

type: RNA

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station FS450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000 7G. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver Control

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The four-week feeding trial was approved by the local Animal Care and Use Committee (Regierungspräsidium Giessen; permission no: JLU 648_M). All experimental procedures described followed established guidelines for the care and handling of laboratory animals. This study used 24 male, 5-6-week-old, homozygous (fa/fa) obese Zucker rats (Crl:ZUC-Leprfa). The rats were randomly assigned to two groups of 12 rats each [obese control (OC), obese 5% PSC (OPSC)], with similar initial body weights (BW) (OC: 277 ± 23 g; OPSC: 279 ± 23 g; mean ± SD; n = 12/group). The rats were kept in groups of two per cage under controlled conditions (22 ± 1°C room temperature, 50-60 % relative humidity, light from 07.00 a.m. to 07.00 p.m.).

extract_protocol: Total RNA from aliquots of liver (≈ 20 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. Transcript profiling in liver was carried out for 6 randomly selected rats per group. Following an RNA quality check using an Agilent 2100 Bioanalyzer (Agilent technologies, Böblingen, Germany), the total RNA samples were processed at the Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany) using an  Affymetrix Rat Gene 2.0 ST array, which represents 19,212 porcine genes, according to the manufacturer´s instructions. A260:A280 ratios and RNA integrity number values (mean ± SD) for all samples (n = 12) were 1.90 ± 0.01 and 8.01 ± 0.38, respectively.

treatment_protocol: Two different diets - one with 5% PSC supplementation and the other with no supplementation (control) but with comparable levels of gross energy and crude nutrients were fed. Nutrient concentrations in the diets were sufficient to meet requirements of the rats for maintenance according to National Research Council (NRC). PSC was produced biotechnologically using a side stream from the agricultural industry as the sole carbon source. The diets were offered ad libitum and feed consumption was recorded weekly. BWs were recorded once per week. Water was constantly available ad libitum from a nipple drinker system. At day 29, the rats were killed by decapitation under CO2 anesthesia. Aliquots of the liver were excised, washed in ice-cold NaCl solution (0.9 %) and snap-frozen in liquid nitrogen.

tag: condition

value: control

tag: gender

value: male

tag: tissue

value: liver

tag: strain

value: obese Zucker rats


title: infantile hemangioama tumor tissue microRNA 2

city: Jinan

first: Cong

last: Fu

state: Shandong

address: No. 324, jingwu Road, Huaiyin Dist

country: China

institute: Shandong provincial hospital

description: microRNA expression data from infantile hemangioma (IH) tumor tissue

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

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

label: biotin

organism: Homo sapiens

source_name: infantile hemangioma (IH) tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: IH and matched non-tumor skin tissues

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

treatment_protocol: Tissues from IH surgury were immersed overnight in RNAlater at 4 ℃ and preserved at -80 ℃.

tag: age

value: 4 months

value: female


title: Δdgeo_0257

type: SRA

city: Seoul

first: Sung-Jae

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

department: Department of Biology

country: South Korea

institute: Kyung Hee University

description: Deinococcus geothermalis strain KACC12208 (from the Korean Agricultural Strains Collection Certer, http://www.genebank.go.kr) is derived from Deinococcus geothermalis strain DSM11300.

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to Deinococcus geothermalis whole genome using Bowtie2.
Read count extraction and normalization were performed using edgeR.
Genome_build: Deinococcus geothermalis DSM11300 (NC_008025.1, NC_008010.2, NC_009939.1).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read count values for each Sample.

organism: Deinococcus geothermalis DSM 11300

growth_protocol: D. geothermalis of wild-type (WT) and the mutant strains were cultured on TGY medium containing 1% tryptone, 0.5% yeast extract, and 0.1% glucose at 48°C.

extract_protocol:
The total RNA was extracted by the RIDOEx reagent (GeneAll, Korea). The extracted total RNA was purified using an RNeasy Mini Purification Kit (Qiagen, Germany) and RNase-Free DNase I Set (Qiagen, Germany).
We commissioned D. geothermalis bacterial RNA-Seq, and data analysis was performed using the ExDEGA analysis tool of e-biogen Co. (Seoul, Korea).

treatment_protocol: The WT and mutant strains of D. geothermalis were grown to an OD600 4.0 for late exponential phase in TGY broth at 48°C.

tag: genotype/variation


title: Δdgeo_1986-1987


title: Healthy donor 2

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

data_processing:
The raw data was processed with cellanger from 10XGenomics company.
Paired-end reads were mapped to the hg19 genome with STAR for read counts of genes annotated in ENSEMBL.
Genome_build: hg19

source_name: human bone marrow

extract_protocol: Libraries were generted using Genomics Chromium Single Cell ‘3 Solution Kit V2 from 10XGenomics.

tag: markers

tag: Sex

value: F

tag: subject

value: healthy donor


title: infantile hemangioama tumor tissue microRNA 1

value: 5 months


title: N2- L1 neural cells rep2

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

department: Biology

institute: Indiana University, Bloomington

description:
poly-A selected RNA
WT.adultvsL1.counts.txt

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v2.5.2b)
Differential gene expression analysis was performed using Feature counts and DeSeq2
A-to-I editing sites were de novo identified using SAILOR program
Variant calling was performed to quantify editing levels throughout C. elegans neural development.
Genome_build: C. elegans WS269
Supplementary_files_format_and_content: tab-delimited text files include the counts for each gene in L1 and adult neural RNA in WT and adr-2(-) backgrounds
Supplementary_files_format_and_content: .bed files from the de novo identification of SAILOR output include all the predicted sites and the confidence score for each predicted site

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Neural cells

growth_protocol: After hatching L1 was plated to grow upto 50 hr to obtain adults.

extract_protocol:
Worms were digested into single cell suspension and GFP positive neural cells were isolated using FACS.
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit

treatment_protocol: Worms were grown under optimum conditions.

tag: sample type

value: Rab-3 driven GFP expressed neural cells

value: 6 hr after hatching


title: N2- L1 neural cells rep1


title: GATA2 deficiency patient 8

value: M

value: patient


title: KD5 - Control - Pool 3

first: Ioannis

middle: S

last: Vlachos

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

tag: cell type

tag: transduction

value: scrambled control


title: GFP-FRH alone or co-cultured with vCAFs then sorted the GFP ICC cells

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

description: Gene expression of total RNAs in GFP-FRH alone or co-cultured with vCAFs for 7 days and then sorted the GFP ICC cells

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7. Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7.

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images. The signal ratio of Cy5 intensity and Cy3 intensity on the same array was subjected to quantile normalization followed by log2-scale transformation. After obtaining the normalized expression value of the probes, we first re-annotated the probes by mapping the probe sequences to gene sequences from the Gencode database (GencodeV19) using the Blat software with the parameter –minIdentity = 100. Only probes mapping to the unique gene sequence without mismatch were retained. If more than one probe was mapped to a gene, the median expression values of these probes would be used to represent the expression value of this gene. The eBayes moderated t statistic was used to obtain the differentially expressed genes (DEGs) using a Limma package in R. p value ≤ 0.05 and 2-fold change in its expression level were chosen as the cut-off criteria.

source_name: GFP-FRH alone

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: GFP-RBE or GFP-FRH cells alone or co-cultured with vCAF were cultured in H-DMEM supplemented with 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.

tag: cell line

value: FRH

source_name: GFP-FRH co-cultured with vCAFs for 7 days and FACS sorted the GFP cells


title: Δdgeo_2840


title: GATA2 deficiency patient 7


title: KD4 - 934inh - Pool 2

value: neural progenitor cell


title: GFP-RBE alone or co-cultured with vCAFs then sorted the GFP ICC cells

description: Gene expression of total RNAs in GFP-RBE alone or co-cultured with vCAFs for 7 days and then sorted the GFP ICC cells

source_name: GFP-RBE alone

value: REB

source_name: GFP-RBE co-cultured with vCAFs for 7 days and FACS sorted the GFP cells

value: RBE


title: KD3 - Control - Pool 2


title: GATA2 deficiency patient 6


title: Healthy donor 1


title: adr-1-adult neural cells rep3

description:
poly-A selected RNA
adr1.adult.merged.sailoroutput.csv

value: 50 hr after hatching


title: adr-1-adult neural cells rep4


title: GATA2 deficiency patient 5


title: KD1 - Control - Pool 1


title: KD2 - 934inh - Pool 1

value: anti-miR-934 lentivirus


title: CH1 + DMSO in FMC Cy5 - CH1 + heptamer in FMC Cy3, BioRep 2

city: Buffalo

first: M

middle: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Periodontics and Endodontics

institute: University at Buffalo

hyb_protocol: cDNA probes were hybridized to aminosilane-coated glass slides spotted with unique 70-mers representing each open reading frame from the S. gordonii strain CH1 genome sequence (Genbank number CP000725.1) in replicates of six (obtained from the Pathogen Functional Genomics Resource Center; NIDCR Oral Microbe Microarray Initiative; GPL10584); each slide contained a total of 500 Arabidopsis thaliana 70-mers as controls. Slides were blocked during prehybridization at 42°C in blocking buffer (5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7.4), 0.1% w/v SDS, 1% w/v bovine serum albumen (BSA), then washed successively with water and isopropanol before drying via centrifugation prior to hybridization. To account for biases during the labeling process, flip-dyes, in which the fluorescent labeling is reversed for each sample, were used. Cy3-labeled CH1 + DMSO cDNA was combined with Cy5-labeled CH1 + heptamer cDNA in appropriate ratios; similarly, Cy5-labeled CH1 + DMSO and Cy3-labeled CH1 + heptamer cDNA were combined. The dye-labeled cDNA mixtures were dried, resuspended in 50 µl of hybridization buffer (40% v/v formamide, 5x SSC, 0.1% SDS, 0.6 µg/µL Salmon Sperm DNA), heated at 95°C for 10 min, placed on ice, and individual mixtures added to each microarray slide under a Lifterslip (Erie Scientific Company, Portsmouth, NH, USA). Each slide was incubated at 42°C for 16 h in a sealed hybridization chamber (Corning Life Sciences, Tewksbury, MA, USA), then washed successively in 0.1% w/v SDS-2x SSC, 0.1% SDS-0.1x SSC, and 0.1x SSC and dried by centrifugation.

scan_protocol: The Axon 4200A (Axon Instruments, Foster City, CA, USA) was used to obtain digital images of the microarrays.

data_processing: Data were analyzed using the TM4 Microarray Software Suite, consisting of Spotfinder, Midas, and MeV (http://www.tm4.org/). The fluorescence signals from the flip-dye hybridizations were measured using Spotfinder. Normalization and regularization of the data were performed using Midas (Lowess normalization, block mode, smooth parameter of 0.33, Cy3 reference; standard deviation regularization, block mode, Cy3 reference; flip-dye consistency checking and combination, using the data trim option of the standard deviation mode and keeping all data within 2.0 standard deviations; replicate spots were averaged to be used in the determination of the final ratio for each spot). Using MeV, with 100 permutations and a P value cutoff of 0.05, the final expression ratios were generated and used to determine the fold change for hybridization of each probe; fold changes were ranked. Experimental cDNA probes from CH1 cells incubated with 1 µM of the heptamer that hybridized to the oligonucleotide spots with average fold changes 1.6-times greater than or 1.6-times less than fold changes of CH1-DMSO controls were considered to be potentially up- or down- regulated, respectively.

organism: Streptococcus gordonii

source_name: CH1 + DMSO

label_protocol: cDNA was reverse transcribed using Superscript III (Life Technologies, Grand Island, NY, USA), end-labeled via amino-allyl-labeling (Life Technologies, Grand Island, NY, USA) and Cye-dye coupled (GE Healthcare/Amersham, Piscataway, NY, USA) to make microarray probes as previously described (Vickerman, M. M., Iobst, S., Jesionowski, A., M., and S. R. Gill. 2007. Genome-Wide Transcriptional Changes in Streptococcus gordonii in Response to Competence Signaling Peptide. JBac 189(21):7799-7807.) Probes were purified over QIAgen PCR purification columns (QIAgen) to remove excess dye before use.

growth_protocol: S. gordonii CH1 cells were grown in either TH or FMC to mid-log phase (approximately 108 cells/ml) and then incubated with either AFYWWFY (Genscript, Piscataway, NJ) or solvent alone added directly to the cultures.

extract_protocol: RNA was prepared from the pelleted CH1 cells (incubated with 1 µM heptamer or an equivalent volume of DMSO) with a FastPrep120 Instrument (MP Biomedicals, Santa Ana, CA, USA) and RNAPro Blue RNA Extraction Kit (MP Biomedicals) for prokaryotic cells according to the manufacturer's directions. The extracted RNA was digested with DNase (Roche Applied Science, Indianapolis, IN, USA) and purified with QIAgen RNA mini spin columns (QIAgen, Germantown, MD, USA) according to the manufacturer's directions. RNA integrity was confirmed by comparison of the ratios of absorbance at 260/280 nm and 260/230 nm as quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA).

treatment_protocol: The experimental samples were treated with 1 µM of heptamer, for 30 minutes statically at 36ºC with 5% CO2. The control samples were treated with an equivalent volume of solvent.

value: Challis CH1

tag: treatment

value: DMSO

tag: media

value: FMC

source_name: CH1 + heptamer

value: heptamer


title: GATA2 deficiency patient 4_2

value: F


title: HCT116 shNC.

type: genomic

first: Ja Young

last: Hahm

address: 84, Heukseok-ro, Dongjak-gu

institute: Chung-Ang University

description: modified HCT116 cell line

hyb_protocol: The whole-genome amplification process requires 250ng of input bisulfite-converted DNA , MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, then placed in a humidified container for a minimum of 16 h at 48°C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: colorectal cancer cell, lentiviral_shNC (puro selection), lentiviral_GFP_EV (FACS sorting)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from each samples using Promega Wizard® Genomic DNA Purification Kit were used to DNA samples were checked the quality using NanoDrop® ND-2000 UV-Vis Spectrophotometer.   Then samples were electrophoresed on agarose gels and samples with intact genomic DNA showing no smearing on agarose gel electrophoresis were selected for experiment. Intact genomic DNA was diluted to 50 ng/㎕ concentration based  on Quant-iT Picogreen (Invitrogen) quantitation. Concentrations were adjusted based on these results. All prepared samples were bisulfite-converted according to the Zymo EZ DNA methylation kit protocols.

tag: genotype


title: adr-1-adult neural cells rep2


title: HCT116 shUHRF1.

description: modified HCT116 cell line

source_name: colorectal cancer cell, lentiviral_shUHRF1 (puro selection), lentiviral_GFP_EV (FACS sorting)


title: adr-2- adult neural cells rep3

description:
poly-A selected RNA
adr-2.adultvsL1.txt
adr2.adult.merged.sailoroutput.csv


title: CH1 + DMSO in FMC Cy3 - CH1 + heptamer in FMC Cy5, BioRep 2


title: KD11 - Control - Pool 3

description:
HUES6-derived NPCs (15 DIV) transduced with an anti-miR-934 lentivirus or the scrambled control virus at DIV 10 of neural induction and collected 5 days later.
miRNA_expression_1516058454.csv

extract_protocol:
NEBNext Multiplex Small RNA
Total RNA was extracted from cell pellets using the TRIzol® Reagent (Life Technologies).
Total cellular RNA was extracted from the following samples and sequenced on an Illumina HiSeq sequencer. RNA libraries were prepared with the TruSeq RNA Sample Preparation Kit V2 (Illumina).
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: pool


title: GATA2 deficiency patient 3


title: adr-2- adult neural cells rep2


title: GATA2 deficiency patient 4_1


title: KD12 - 934inh - Pool 3


title: GATA2 deficiency patient 2


title: adr-1-adult neural cells rep1


title: adr-2- adult neural cells rep1


title: GATA2 deficiency patient 1


title: HCT116 shUHRF1+UHRF1 K490R

description: modified HCT116 cell line

source_name: colorectal cancer cell, lentiviral_shUHRF1 (puro selection), lentiviral_GFP_UHRF1 K490R (FACS sorting)


title: KD9 - Control - Pool 2


title: HCT116 shUHRF1+UHRF1 K490Q

description: modified HCT116 cell line

source_name: colorectal cancer cell, lentiviral_shUHRF1 (puro selection), lentiviral_GFP_UHRF1 K490Q (FACS sorting)


title: KD10 - 934inh - Pool 2


title: KD8 - 934inh - Pool 1


title: N2- adult neural cells rep4

description:
poly-A selected RNA
WT.adultvsL1.counts.txt
wt.adult.merged.sailoroutput.csv


title: N2- adult neural cells rep3


title: Line20

city: Nanjing

first: Ru-feng

last: Xu

state: Jiangsu Province

address: Longmian Avenue 101 number

department: Nanjing Medical University

institute: Rufeng Xu

data_processing:
Differential expression analysis of two conditions/groups (twobiologicalreplicatespercondition) was performed using the DESeq2 R package(1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.There sulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.Genes with an adjusted P-value<0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: pancretic islets_Brsk2 over-expression

growth_protocol: 8-10 week male mice drank water containing doxycycline for 4 days

extract_protocol:
Pancreatic islets were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

value: Brsk2 transgene

value: 10-12 weeks

value: male


title: CH1 + DMSO in FMC Cy5 - CH1 + heptamer in FMC Cy3, BioRep 1


title: Brain, P14

city: Kent

first: Colleen

last: Novak

state: Ohio

address: 222 Cunningham Hall, Biological Sciences, Kent State University

department: Biological Sciences

institute: Kent State University

data_processing:
Basecalling: sequenced on an Illumina Hiseq platform (CASAVA v1.8 software), and 150 bp paired-end reads were generated at sequencing depth of ~5 million reads
Filtering + Alignment: Clean reads were obtained by removing reads containing adapters, reads containing poly-N and low quality reads from raw data. Clean reads were mapped to the Ensembl Rattus norvegicus Rnor_5.0 version 79 reference genome using HISAT2.
Raw counts: HTSeq was used to count reads mapped to each gene
Normalization: FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Differential Expression: Differential expression analysis was performed using the DESeq R package. The p values were adjusted using the Benjamini and Hochberg’s method. Genes with an adjusted p value < 0.05 were considered as differentially expressed.
Genome_build: Ensembl Rattus norvegicus Rnor_5.0 version 79 reference genome
Supplementary_files_format_and_content: Tab-delimited .xls files include: 1 Quality Check Results, 2 Mapping Statistics, 3 Raw Read Counts, 4 Normalized (FPKM) Read Counts, 5 Differential Gene Expression Analysis Results, 6 Significantly Differentially Expressed Genes, 7 GO Enrichment Analysis Results, and 8 KEGG Enrichment Analysis Results expression analysis results, (4) Significantly differentially expressed genes, (5) Gene ontology enrichment analysis results

source_name: Ventromedial hypothalamic brain tissue

growth_protocol: Not applicable

extract_protocol:
We combined the use of TRIzol and silica-based columns. Tissue micropunches were sonicated in 250uL of TRIzol™ Reagent (Thermofisher Scientific, Waltham, MA). 50uL of chloroform was added to homogenate and incubated at room temperature for 5 minutes to facilitate phase separation. Samples were centrifuged at 12,000 x g for 15 minutes at 10°C. The aqueous layer (~100uL) was pipetted into a fresh microcentrifuge tube and mixed with an equal volume of ice-cold 70% ethanol to precipitate mRNA. The mixture was then pipetted onto a silica-based column membrane (Invitrogen™ PureLink™ RNA Mini Kit, Thermofisher Scientific, Waltham, MA). Samples were centrifuged at 12,000 x g for 30 seconds at 10°C and the supernatant was discarded. Samples were washed as directed by kit instructions. RNA was eluted into a fresh collection tube with 30uL of nuclease-free water. RNA concentration and quality were assessed using a spectrophotometer. All samples had 80-110 ng/uL, a 260/280 ratio of 2.0-2.1, and a 260/230 ratio of 1.8-2.0. Samples were stored in a freezer at -80°C until processing.
Novogene Corporation (Sacramento, CA) prepared our libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, 250-300 bp insert cDNA library, Illumina platform, paired-end 150 bp

treatment_protocol: Control odor (n=3) or predator odor (n=3) exposure was achieved by dropping a fragment (1-2” X 2”) of a clean towel or an identical towel that had been used as bedding for ferrets (Mustela putorius furo) for 2 weeks (Marshall BioResources, North Rose, NY) into the animal’s home cage. All animals were habituated to handling as well as daily exposure to control odor in their home cages for 2 weeks prior to experimental odor exposure. Animals were then anesthetized via 5% isoflurane inhalation and rapidly decapitated using a guillotine. Brains were dissected out then flash frozen in isopentane (2-methylbutane) chilled on dry ice.

value: Sprague Dawley

tag: condition

value: Experimental (predator odor)

value: 10 months (approx.)

value: Ventromedial hypothalamic brain tissue


title: CH1 + DMSO in TH Cy5 - CH1 + heptamer in TH Cy3

value: TH


title: CH1 + DMSO in FMC Cy3 - CH1 + heptamer in FMC Cy5, BioRep 1


title: CH1 + DMSO in TH Cy3 - CH1 + heptamer in TH Cy5


title: Brain, P8


title: Brain, P13


title: KD7 - Control - Pool 1

source_name: iPSC-derived NPCs

value: neural progenitor cell

value: scrambled control


title: N2- adult neural cells rep2

value: Rab-3 driven GFP expressed neural cells

value: 50 hr after hatching


title: WT

source_name: pancretic islets_WT

value: Wild type


title: RIPK1 ASO B

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Raw sequencing reads were processed using CellRanger v2.2.0 using default parameters
Genome_build: mm10 (mouse) and GRCh38 (human)
Supplementary_files_format_and_content: UMI count matrix: Cellranger count output from filtered_gene_bc directory. Contains UMI counts for each cell. Gene identifiers: Cellranger count output from filtered_gene_bc directory. Contains gene identifiers for the count matrix. Cell barcode list: Cellranger count output from filtered_gene_bc directory. Contains cell barcodes for the count matrix.

source_name: Adipose tissue

extract_protocol:
Single-cell suspensions from omental adipose tissue from mouse or human were prepared as follows: for mouse, CD45+ cells were sorted using BD FACSAria III (n=3 mice/group pooled); human CD45+ cells (from n=3 bariatric surgery subjects, as above) were isolated using the Miltenyi Human CD45 MicroBead MS selection kit (Miltenyi, 130-045-801) according the manufacturer’s instructions.  Cells were processed using the 10X Genomics Chromium v2 Single Cell 3’ RNA-seq (10X Genomics, Pleasanton, CA) and Illumina next generation sequencing technologies (Illumina NextSeq 500 Sequencer) and carried out by the uOttawa StemCore Laboratories (mouse) or the UNGC Sequencing Core at UCLA (human). Input cells were quantified and checked for viability using the Countess II (Thermo Fisher). Suspended cells were loaded on a Chromium controller Single-Cell instrument to generate barcoded single-cell Gel Bead-In-Emulsions (GEMs). GEMs were broken and the barcoded cDNA were amplified using the C1000 Touch Thermal cycler with 96- Well Reaction Module. The amplified barcoded cDNA was then fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3′ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32854) and the fragment size distribution of the libraries were determined using the AATI Fragment analyzer High Sensitivity NGS kit (DNF-486-0500). Pooled libraries were then sequenced using Illumina Nextseq. All samples were sequenced to an average of >50,000 reads per cell, as per 10x Genomics recommendation.
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit (v2)

value: Adipose tissue

value: CD45+ cells


title: HCT116 shUHRF1+UHRF1 WT

description: modified HCT116 cell line

source_name: colorectal cancer cell, lentiviral_shUHRF1 (puro selection), lentiviral_GFP_UHRF1 WT (FACS sorting)


title: Brain, C4

value: Control


title: glycinelowCO2_2

city: Wageningen

first: Nico

middle: J

last: Claassens

address: Stippeneng 4

department: Laboratory of Microbiology

country: Netherlands

institute: Wageningen University

data_processing:
Sequence data of all samples were mapped with STAR v2.5.4b using default parameters. Ensembl version 38 genome reference in FASTA format and Ensembl version 38 cDNA Annotation in GTF format were used for genome indexing with adapted parameters for genome size (--genomeSAindexNbases 10) and read length (--sjdbOverhang 150).
Genome_build: Bacteria ensembl version 38 of Ralstonia eutropha H16 (synonymous species name)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Cupriavidus necator

source_name: Bacterial cells

growth_protocol: Pre-cultures of Cupriavidus necator were inoculated at a starting OD600 of 0.01 on 10 mL minimal medium supplemented with 40 mM glycine (JMM medium, Li et al., Science, 2012 doi: 10.1126/science.1217643) in 50 mL erlenmeyer flasks. Cultures were incubated at 30C while shaking at 180 rpm with ambient air.

extract_protocol:
RNA was extracted after stabilization of 1 mL samples using RNA Protect Bacteria Kit (Qiagen). Total RNA was isolated using RNeasy mini-kit QIAGEN, including enzymatic (15 mg/mL lysozyme) and phsyical lysis (Retschmill, 5 min, 30Hz). An on-column DNAase step was performed to digest all DNA (RNase-Free DNAse Set Qiagen).
cDNA libraties were made at after rRNA depletion using the Ribozero Bacteria kit (Illumina ) at the Max Planck-Genome-centre Cologne, Germany , sequencing was performed using 150 bp single read sequencing in Illuminqa HiSeq3000

tag: replicate


title: RIPK1 ASO A

tag: tissue


title: N2- adult neural cells rep1

source_name: Neural cells

tag: strain


title: glycinelowCO2_3


title: glycinelowCO2_1


title: HCT116 shNC

description: modified HCT116 cell line

value: lentiviral_shNC (puro selection), lentiviral_GFP_EV (FACS sorting)


title: ICC_25_Adjacent: CCA25N

city: Beijing

first: Min

last: Zhang

state: Beijing

address: No. 8 East Road, Fengtai District

department: The Fifth Medical Center of Chinese PLA General Hospital

institute: Academy of Military Medical Sciences

data_processing:
Illumina CASAVA version 1.8 used for basecalling.
Sequencing data from 10x was aligned and quantified using the CellRanger version 2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: adjacent

extract_protocol:
Single-cell suspensions were stained for 7AAD (Invitrogen) per the manufacturer’s recommendations, washed with cold PBS, and re-suspended for flow cytometric analyses.
Fluorescence-activated cell sorting (FACS) -sorted viable cells (7-AAD-negative) were loaded into a well of a microfluidic chip to generate a cDNA library using a commercial 10x Genomics platform. Single-cell transcriptomic amplification and library preparation was performed using single-cell 3′ v2 chemistry (10X Genomics) according to manufacturer’s instructions.
The libraries were then pooled and sequenced across six lanes on an Illumina Xten or NovaSeq 6000 system.

treatment_protocol: All the freshly resected surgical specimens were immediately washed with phosphate-buffered saline (PBS) and divided into two equal parts. One part was processed to generate single-cell suspensions, while the second part was used for other experiments, including pathology examination.Tissue digestion was performed in a 15 ml centrifuge tube containing 10 ml pre-warmed RPMI 1640 (ThermoFisher Scientific), 2 mg/ml dispase (Roche), 1 mg/ml type IV collagenase (Sigma) and 10 U/µl DNase I (Roche) for 60 minutes at 37°C. The reaction was deactivated by 10% FBS. Cell suspensions were filtered using a 70 μm filter and then centrifuged at 500 rpm for 6 min at 4°C to pellet dead cells and red blood cells. The cells were washed twice and suspended in PBS with 0.5% bovine serum albumin (BSA, Sigma).

value: human intrahepatic cholangiocarcinoma adjacent


title: Brain, C3

tag: age


title: CC32S

data_processing:
10X Genomics CellRanger version 2.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments.  Reads with adapter contaminants or low-quality bases (N > 20%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human  intrahepatic cholangiocarcinoma

extract_protocol:
We used a negative selection strategy removing EpCAM+CD31+CD45+ cells to enrich fibroblast population in two tumor samples (ICC32S and STROMA24T)
Fluorescence-activated cell sorting (FACS)-sorted viable cells (7-AAD-negative) and negative enriched fibroblasts (7-AAD/CD45/CD31/EpCAM-negative), respectively, were loaded into a well of a microfluidic chip to generate a cDNA library using a commercial 10x Genomics platform. Single-cell transcriptomic amplification and library preparation was performed by Capitalbio Technology Corporation (Beijing, China) using single-cell 3′ v2 or v3 chemistry (10x Genomics) according to manufacturer’s instructions. The libraries were then pooled and sequenced across six lanes on an Illumina Xten or NovaSeq 6000 system.

value: tumor


title: Brain, C2


title: Control ASO


title: KMT2A_MLLT1_Runx2ko_rep3

status: Public on Jun 05 2020

city: Ghent

first: Filip

last: Matthijssens

state: België

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Sequencing of the cDNA library with 75 bp single end reads was performed using an Illumina NextSeq 500 system
Quality control of fastq files was done with FastQC and reads were aligned  using STARv2.42 and gencode as guide gtf
Counts were generated on the fly by STAR using GTF GRCm38 version 91 from Ensembl
Differential expression analysis was performed using DESeq2, which used Wald test statistic for p-value calculation
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files contain raw and DESeq2 normalized counts in txt format.

source_name: Runx2fl/flCreER T2tg Lin- BM cells

growth_protocol: lineage depleted (Runx2fl/fl CreErt2tg/+) BM cells  were transduced with KMT2A-MLLT1-eGFP expressing retrovirus and cultured for 24 hours in RPMI with 10% FBS, murine IL-3 (10ng/ml), IL-6 (10ng/ml), and stem cell factor (50 ng/ml, Peprotech). Clonal growth of transduced cells was performed on methylcellulose (M3534, STEMCELL Technologies) according to protocol instructions. Cells were harvested and replated every 7 days for 3 consecutive rounds. RNA was collected prior to the first replating (BM progenitors), and after the second replating, cells were grown in suspension and considered KMT2A-MLLT1 (MLL-ENL) transformed cells. For RNA sequencing experiments, RNA from BM progenitors was compared to transformed cells, with (Runx2 ko) or without (Runx2 wt) 4-OHT treatment. All samples originated from independent biological replicates

extract_protocol:
RNA was extracted from T-ALL cells using the miRNeasy mini kit (Qiagen)
Total RNA samples (500 ng) were purified using DNAse I kit according to the Rapid out removal DNA kit instructions (Thermoscientific) and converted into cDNA by using QuantSeq 3ʹ mRNA-seq reverse 4 Library Prep Kit (Lexogen) according to manufacturer’s instruction to generate compatible library for Illumina sequencing.

value: KMT2A-MLLT1 transformed BM progenitor

tag: biological replicate

value: biological replicate 3

value: 400 nM 4-hydorxytamoxifen treated


title: KMT2A_MLLT1_Runx2wt_rep1

value: biological replicate 1

value: EtOH control treated


title: BM_progenitor_rep2

value: BM progenitor

value: biological replicate 2

value: untreated


title: KMT2A_MLLT1_Runx2wt_rep2


title: KMT2A_MLLT1_Runx2wt_rep3


title: BM_progenitor_rep3


title: HCT116 shUHRF1

description: modified HCT116 cell line

value: lentiviral_shUHRF1 (puro selection), lentiviral_GFP_EV (FACS sorting)


title: splenic monocytes from BALB mice at 4wk post immunization rep1

city: Pittsburgh

first: Wei

last: Chen

state: PA

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

description: scRNA data from tumor

data_processing:
Standard 10X Genomics CellRanger pipeline
Genome_build: mm10
Supplementary_files_format_and_content: for each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

source_name: spleen

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

value: spleen

value: 4 weeks

value: BALB/cJ (BALB/c, H-2d)


title: splenic monocytes from C3H mice at 4wk post immunization rep1

description: scRNA data from tumor


title: BM_progenitor_rep1


title: splenic monocytes from BALB mice at 4wk post immunization rep2

description: scRNA data from tumor


title: splenic monocytes from C3H mice at 4wk post immunization rep2

description: scRNA data from tumor


title: KMT2A_MLLT1_Runx2ko_rep1


title: splenic monocytes from B6 mice at 4wk post immunization rep3

description: scRNA data from tumor


title: splenic monocytes from BALB mice at 4wk post immunization rep3

description: scRNA data from tumor


title: splenic monocytes from B6 mice at 4wk post immunization rep2

description: scRNA data from tumor


title: KMT2A_MLLT1_Runx2ko_rep2


title: splenic monocytes from B6 mice at 4wk post immunization rep1

description: scRNA data from tumor


title: splenic monocytes from C3H mice at 1wk post immunization rep2

description: scRNA data from lymph node

value: 1 week


title: splenic monocytes from BALB mice at 1wk post immunization rep2

description: scRNA data from lymph node


title: splenic monocytes from C3H mice at 1wk post immunization rep1

description: scRNA data from lymph node


title: splenic monocytes from B6 mice at 1wk post immunization rep2

description: scRNA data from lymph node


title: Extracted RNA 11.5-day old mouse slice #2 from dorsal-to-ventral axis

city: Utrecht

first: Catherine

last: Robin

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
CEL-seq were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Genome_build: mouse: mm10; chicken: galGal4, with improved 3’UTR annotations (see Junker et al., Cell, 2014); zebrafish: Zv9, with improved 3’UTR annotations (see Junker et al., Cell, 2014); human: hg19
Supplementary_files_format_and_content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the number of sections/primers, separated by an underscore. For 'ggcells2.coutc.csv' Tab, which belongs to the chicken IAHC sorted cells, the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 (primer#95 and primer#96, respectively). The order of the columns/primers follows the description of the sample from the title.  For instance: "Extracted RNA 3-day old chicken embryo from posterior-to-anterior axis":  the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed.

source_name: transversal slice

growth_protocol: Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo-seq at both 28hpf and 40hpf. Fertilized chicken eggs (Bovans Brown) were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo-seq. C57BL/6 mouse strain was housed according to institutional guidelines, and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo-seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory (LUMC, Leiden, Netherlands). The Medical Ethical Committee of the Leiden University Medical Center (P08.087) approved all procedures regarding the collection and use of human embryonic material.

extract_protocol:
Total RNA was isolated from individual cryosection using TRIzol reagent (Ambion), according to the manufacturer’s manual. RNA extraction, amplification and sequencing libraries were performed as described in {Junker et al., 2014}. Briefly, RNA samples were treated according to the CEL-seq protocol {Hashimshony, 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit (Illumina).
Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing.

value: embryo

tag: tissue preparation

value: transversal slice

tag: developmental stage

value: 11.5 days old


title: Extracted RNA 11.5-day old mouse slice #3 from dorsal-to-ventral axis


title: splenic monocytes from BALB mice at 1wk post immunization rep1

description: scRNA data from lymph node


title: WT

tag: genotype/variation

value: WT


title: ZFX-E10-1119-23

city: Philadelphia

first: Eduardo

middle: A

last: Torre

department: Bioengineering

institute: University of Pennsylvania

data_processing:
We aligned reads to hg19 and quantified reads per gene using STAR and HTSeq
Note that we sequenced the same libraries multiple times. Thus, each fastq file is a concatenation of all runs.
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files conain reads per gene (unnormalized)

source_name: WM989-A6-G3-Cas9 5a3 melanoma cells with the indicated gene knocked out

growth_protocol: We grew these cells at 37°C in Tu2% media (78% MCDB, 20% Leibovitz’s L-15 media, 2% FBS, and 1.68mM CaCl2)

extract_protocol:
For each sample, we isolated mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module
We built the RNA sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina
We sequenced the libraries via paired-end sequencing (36x2 cycles) on a NextSeq 500

tag: cell line background

value: WM989-A6-G3-Cas9 5a3 melanoma cells

tag: genotype/ko gene


title: WT-19


title: DEAF1-E11-84-0


title: ZFP57-E4-768-120


title: MAPKAPK2-PKc-E6-76-6


title: NFYA-E8-105-2


title: MTF1-E3-215-9


title: FGFR1-PKc-E13-191-13


title: MAPK1-PKc-E2-183-3


title: IRF7-E2-189-20


title: MAP2K7-PKc-E10-143-8


title: NFATC2-E4-203-6


title: FOXC2-E1-234-31


title: MYBL1-E5-221-13


title: WT-18


title: EP300-e29-162-9


title: Extracted RNA 10.5-day old mouse slice #2 from dorsal-to-ventral axis

value: 10.5 days old


title: Extracted RNA 11.5-day old mouse slice #1 from dorsal-to-ventral axis


title: TADA2B-E2-73-10


title: splenic monocytes from B6 mice at 1wk post immunization rep1

description: scRNA data from lymph node


title: CLK1-PKc-E5-67


title: TGIF1-E2-138-5


title: Extracted RNA 10.5-day old mouse slice #1 from dorsal-to-ventral axis


title: SP1-E5-200-13


title: RUNX3-E2-126-1


title: SRC-PKc-E10-180-27


title: neg03


title: FEZF2-E3-117-3


title: CHD7-H-e12-244-14


title: MAPK1-PKc-E1-65-1


title: PRKRIR-E1-80-2


title: RPL9-e4-2


title: RAF1-PKc-E10-103-1


title: DYRK1A-PKc-E8-141-1


title: MAPK1-PKc-E6-132-9


title: TLK2-PKc-E23-144-8


title: PLK2-PKc-E4-130-5


title: KDM1A-e19-147-2


title: PKN2-PKc-E15-92


title: INO80-H-e29-73-0


title: PLK1-PKc-E5-111-2


title: WT-17


title: MAPK1-PKc-E3-190-8


title: NFAT5-E6-114-1


title: TGIF1-E3-36-0


title: VEZF1-E2-78-4


title: STK11-PKc-E2-84-3


title: WT-16


title: PRPF4B-PKc-E14-87


title: CSNK2A2-PKc-E1-41


title: GFI1-E7-155-17


title: YBX1-E2-50-0


title: SETD1B-e17-118-1


title: WT-15


title: BRD8-BD-e17-77-2


title: BUB1B-PKc-E19-150-8


title: SRC-PKc-E12-154


title: DOT1L-e9-80-7


title: RIPK2-PKc-E2-154-5


title: MAP3K1-PKc-E20-138-6


title: STK11-PKc-E4-133-16


title: JUNB-E1-162-21


title: neg01


title: MYBL1-E5-221-15


title: KLF6-E3-65-5


title: ZFX-E10-1119-67


title: BRD2-BD1-e4-60-1


title: WT-14


title: NFYA-E9-66-5


title: SOX5-E13-109-0


title: DSTYK-PKc-E12-135


title: PRKCE-PKc-E13-189-18


title: ZFP57-E4-768-6


title: SOX5-E14-107-5


title: CHEK1-PKc-E2-65-4


title: PLK2-PKc-E3-117


title: MITF-E8-76-1


title: CBFB-E2-87-6


title: THAP11-E1-234-8


title: neg10


title: MAFA-E1-273-31


title: FGFR1-PKc-E15-71-2


title: VEZF1-E2-78-5


title: STK11-PKc-E3-90-3


title: CSK-PKc-E12-87


title: ZFP57-E4-768-119


title: CHD7-D-e16-118-9


title: CSK-PKc-E9-91


title: WT-13


title: BRD2-BD2-e7-129-0


title: MAPK1-PKc-E5-115


title: DEAF1-E4-88-1


title: EGFR-PKc-E20-186-28


title: KDM2A-E9-154-1


title: LHX1-E4-42-0


title: KMT2D-e52-109-3


title: PKN2-PKc-E19-143-9


title: SIX5-E1-156-8


title: neg06


title: MAFA-E1-273-33


title: NR1I2-E4-50-1


title: DYRK1A-PKc-E7-147-1


title: TLK2-PKc-E18-90-4


title: KDM2A-E8-93-6


title: MAPKAPK2-PKc-E5-127-3


title: FOSL1-E3-63-3


title: CHD7-H-e13-177-11


title: PRKAA1-PKc-E6-88-3


title: PRKRIR-E1-80-9


title: GLI4-E4-489-33


title: MTF1-E3-215-12


title: CBFB-E2-87-3


title: neg08


title: DEAF1-E4-88-0


title: WT-12


title: THAP11-E1-234-5


title: ADCK3-PKc-E8-141-23


title: WT-10


title: NR1I2-E3-134-23


title: WT-11


title: EP300-e25-147-10


title: CHEK1-PKc-E4-65-6


title: NFATC2-E4-203-5


title: PRKCE-PKc-E10-174-13


title: MAP3K1-PKc-E15-96-4


title: PLK1-PKc-E2-169-19


title: TP73-E5-187-11


title: NFATC2-E5-173-0


title: VDR-E3-101-2


title: SIX5-E1-156-15


title: KDM1A-e9-95-4


title: BRD8-BD-e19-178-3


title: ZEB2-E8-1970-33


title: WT-9


title: WT-8


title: DOT1L-e9-80-5


title: GFI1-E5-138-6


title: ZEB2-E10-131-7


title: JUNB-E1-162-11


title: SIX5-E1-156-17


title: JUNB-E1-162-14


title: LATS2-PKc-E5-487-68


title: JUN-E1-162-8


title: CLK1-PKc-E4-40


title: NFYA-E8-105-10


title: PTK2-PKc-E18-101-4


title: RELB-E4-132-15


title: MAP2K7-PKc-E6-120


title: HOXB6-E4-177-0


title: RUNX3-E2-126-11


title: PRPF4B-PKc-E11-154-2


title: TP73-E5-187-12


title: THAP11-E1-234-14


title: WT-7


title: PRKAA1-PKc-E1-58-5


title: PLK2-PKc-E5-88-5


title: TGIF1-E2-138-11


title: HOXB6-E4-177-12


title: PBRM1-E26-202-13


title: SUV420H1-e9-105-0


title: KDM2A-E10-56-4


title: PTK2-PKc-E17-85-1


title: NR1I2-E4-50-0


title: JUN-E1-162-9


title: SOX10-E3-91-0


title: VDR-E3-101-1


title: MAP3K1-PKc-E17-132-1


title: TADA2B-E2-73-9


title: FEZF2-E5-80-4


title: MAFA-E1-273-36


title: neg02


title: MITF-E9-76-3


title: BUB1B-PKc-E17-37


title: PTK2-PKc-E19-116-3


title: YBX1-E2-50-2


title: TLK2-PKc-E20-139


title: JUN-E1-162-4


title: ADCK3-PKc-E12-108-8


title: VDR-E3-101-13


title: LHX1-E3-135-9


title: SOX10-E3-91-1


title: ZBTB17-E12-121-8


title: POLR2A-e2-1


title: KMT2D-e50-153-15


title: BRD2-BD2-e7-129-7


title: KDM1A-e17-115-1


title: PKN2-PKc-E16-177-5


title: PRKCE-PKc-E11-155-2


title: CSK-PKc-E10-74-8


title: SUV420H1-e9-105-1


title: YBX1-E4-90-5


title: THAP11-E1-234-6


title: RPL9-e3-2


title: GLI4-E4-489-32


title: RAF1-PKc-E15-132-9


title: CSNK2A2-PKc-E2-112-4


title: PBRM1-E26-202-18


title: EGFR-PKc-E22-76-2


title: SP1-E5-200-12


title: FOSL1-E3-63-5


title: SOX5-E14-107-2


title: ADCK3-PKc-E13-66-1


title: MYBL1-E5-221-14


title: BRD2-BD2-e6-145-6


title: SRF-E1-90-0


title: KMT2D-e52-109-8


title: SETD1B-e16-138-9


title: MTF1-E3-215-13


title: PLK1-PKc-E3-145-19


title: RIPK2-PKc-E1-116-3


title: BRD8-BD-e18-69-2


title: ZEB2-E8-1970-34


title: KLF6-E3-65-0


title: PBRM1-E26-202-8


title: SRC-PKc-E14-206


title: SP1-E5-200-7


title: BRD2-BD1-e4-60-3


title: EGFR-PKc-E21-156


title: FEZF2-E3-117-8


title: PRKAA1-PKc-E2-142-3


title: NFAT5-E7-191-2


title: GATA4-E4-126-1


title: GATA4-E3-167-7


title: CSNK2A2-PKc-E3-102-5


title: RIPK2-PKc-E6-162-6


title: CDK11B-PKc-E15-122-1


title: RAF1-PKc-E12-177-12


title: SUV420H1-e7-167-5


title: FOXC2-E1-234-18


title: INO80-D-e14-96-3


title: SRF-E2-156-19


title: WT-4


title: WT-6


title: GFI1-E5-138-9


title: CDK11B-PKc-E16-108-16


title: IRF7-E1-153-12


title: MAP2K7-PKc-E5-114-12


title: DSTYK-PKc-E10-114-7


title: ZBTB17-E12-121-7


title: NFAT5-E6-114-2


title: INO80-D-e13-81-3


title: ZBTB17-E8-143-17


title: WT-5


title: HOXB6-E4-177-18


title: CLK1-PKc-E6-117-1


title: neg04


title: MITF-E8-76-0


title: GATA4-E4-126-2


title: DOT1L-e6-95-2


title: LATS2-PKc-E8-366-32


title: BUB1B-PKc-E22-107-9


title: CDK11B-PKc-E14-106-1


title: KLF6-E3-65-2


title: SRF-E2-156-0


title: WT-2


title: neg07


title: FOSL1-E3-63-4


title: NSD1-e20-142-13


title: GLI4-E4-489-5


title: LATS2-PKc-E5-487-64


title: IRF7-E2-189-16


title: CHEK1-PKc-E7-105-1


title: WT-1


title: RELB-E4-132-16


title: CBFB-E2-87-9


title: ZFX-E10-1119-45


title: RELB-E7-132-6


title: VEZF1-E2-78-0


title: SOX10-E3-91-6


title: neg09


title: FOXC2-E1-234-17


title: WT-3


title: SETD1B-e15-95-7


title: NSD1-e21-41-1


title: DYRK1A-PKc-E9-213-21


title: RUNX3-E4-105-12


title: neg05


title: KPS_ctrl_rep3

data_processing:
Sequencing of the cDNA library with 75 bp single end reads was performed using an Illumina NextSeq 500 system
Quality control of fastq files was done with FastQC and reads were aligned GRCh38 using STARv2.42 and gencode v25 as guide gtf
Counts were generated on the fly by STAR
Differential expression analysis was performed using DESeq2, which used Wald test statistic for p-value calculation
Genome_build: hg38

growth_protocol: T-ALL cell were cultured in RPMI-1640 medium supplemented with 20% FBS (KARPAS-45), 2mM L-glutamine and 100 U/ml penicillin G- streptomycin in  5% CO2 at 37°C

tag: cell type

value: T-ALL cell line

value: biological replicate 3

value: DMSO


title: KPS_AI-10-104_rep3

tag: cell line


title: KPS_AI-10-104_rep4

value: biological replicate 4

tag: treatment


title: KPS_AI-10-104_rep2

value: biological replicate 2


title: KPS_ctrl_rep4


title: KPS_rep5_shCTRL_72h

value: biological replicate 5

value: shCTRL (plko_shc002)

tag: time

value: 72 hours


title: KPS_rep5_sh55_72h


title: KPS_rep5_sh55_48h

value: 48 hours


title: KPS_ctrl_rep2


title: KPS_AI-10-104_rep1

value: biological replicate 1


title: KPS_rep5_sh53_72h


title: KPS_rep5_shCTRL_48h


title: KPS_rep5_sh53_48h


title: KPS_rep4_sh55_72h


title: KPS_rep4_shCTRL_72h


title: KPS_rep4_sh55_48h


title: KPS_rep4_sh53_48h


title: PRPF4B-PKc-E13-152-11


title: KPS_rep4_sh53_72h


title: KPS_rep3_sh53_72h


title: KPS_rep3_shCTRL_72h


title: KPS_rep3_shCTRL_48h


title: KPS_rep3_sh53_48h


title: KPS_rep2_sh55_72h


title: KPS_rep3_sh55_72h


title: KPS_rep4_shCTRL_48h


title: KPS_rep3_sh55_48h


title: KPS_rep2_sh55_48h


title: KPS_rep1_sh55_72h


title: KPS_rep2_shCTRL_48h


title: KPS_rep1_sh53_72h


title: KPS_rep2_shCTRL_72h


title: KPS_rep1_shCTRL_72h


title: KPS_rep2_sh53_48h


title: KPS_rep1_sh53_48h


title: KPS_ctrl_rep1


title: KPS_rep2_sh53_72h


title: PER_H3K27ac

library_source: genomic

data_processing:
Raw sequencing data were mapped to the human reference genome (hg38) using STAR v2.4.2a with --outFilterMultimapNmax 1 and --alignIntronMax 1
Peak calling was performed using MACS2 with default settings and using input DNA as control. For histone marks, --broad option was turned on
Genome_build: hg38
Supplementary_files_format_and_content: bed/narrowPeak MACS2 output containing histone marks/ RUNX2 peaks

growth_protocol: T-ALL cell were cultured in RPMI-1640 medium supplemented with 10% (PER-117) or 20% FBS (KARPAS-45), 2mM L-glutamine and 100 U/ml penicillin G- streptomycin in  5% CO2 at 37°C

extract_protocol:
107 cells were cross-linked for each ChIP experiment with 1.1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. The purified chromatin was fragmented to 200–300 bp fragments by sonication (Covaris, Woburn, MA, USA; S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 μl of protein-A coated beads (Thermo-Scientific, Waltham, MA, USA; catalog number 53139) and 10 μg of the specified antibodies. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65 °C overnight. DNA was subsequently purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime
DNA obtained from the ChIP assays was adaptor ligated, amplified and analyzed by Illumina sequencing

tag: chip antibody

value: H3K27Ac (ab4729, Abcam)


title: PER_RUNX2_ChipSeq

value: RUNX2 (D1H7, Cell Signalling Technology)


title: KPS_rep1_shCTRL_48h


title: PER_input


title: PER_H3K27ac_input


title: KPS_rep1_sh55_48h


title: KPS_RUNX2_ChipSeq


title: KPS_H3K27ac


title: KPS_input


title: Extracted RNA 35-day old human slice #1 from dorsal-to-ventral axis

value: embryo

value: transversal slice

value: 35 days old


title: Superior Cervical Ganglia

city: Seattle

first: Pavitra

last: Roychoudhury

state: Washington

address: 1100 Fairview Ave N, PO Box 19024, E5-110

institute: University of Washington

data_processing:
Sequencing reads were processed using Cell Ranger v 2.1 (10X Genomics) and cell by gene matrices further analyzed using Seurat v 2.3.4.
Reads were also filtered using bbduk to look for HSV and AAV
Analysis scripts available at https://github.com/proychou/HSV_10X
Genome_build: mm10

source_name: primary murine SCG neurons

extract_protocol:
Three weeks after AAV treatment, TG and SCG from animals were collected and each tissue (TG or SCG) was pooled from all animals for neuron isolation via enzymatic tissue digest with papain and with collagenase/dispase, followed by density gradient centrifugation and enrichment using the Neuron Isolation Kit (Miltenyi BioTech.), which allows untouched neurons to flow through the column while non-neuronal cells remain bound. 3 animals from each AAV treatment except only 2 AAV8-mEGFP  animals were used for cell preparations or analyses. Tissue and isolated neurons were maintained in ice cold Neurobasal A medium supplemented with 2% B27 supplement, 1% PenStrep, L-glutamine (500 μM) or PBS throughout the procedure except during the enzymatic tissue digestion steps. Cells were encapsulated, lysed and the mRNA captured/barcoded in the Genomics Core Facility at the FHCRC using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 from 10X Genomics according to manufacturer instructions.
Libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 from 10X Genomics according to manufacturer instructions. 10X Genomics Single Cell 3’ expression libraries were sequenced on an Illumina HiSeq 2500 running in High-Output mode with a paired end (26 bp x 8 bp x 98 bp) sequencing strategy. The SCG and TG libraries were pooled and distributed over 4 sequencing lanes.
single cell RNA-seq

treatment_protocol: Swiss-Webster mice were latently infected with 105 PFU HSV-1 syn 17+ via the ocular route, and after 60 days injected with one of 4 different AAV serotypes : 1, 8, PHP.S, and Rh10, each carrying a unique fluorescent protein transgene: mScarlet, mEGFP, DsRed.Express2, and TagBFP2 respectively under the CBh promoter. For each serotype three mice were independently injected with 1012 AAV genomes subcutaneously in the whisker pad (AAV1) or intravenously in the retro-orbital vein (AAV8, PHP.S, and Rh10).

value: Superior Cervical Ganglia

value: Swiss-Webster

value: purified neurons

value: HSV-1 infected/~1/4 AAV1 transduced/~1/4 AAV8 transduced/~1/4 AAV-PhP.s transduced/~1/4 AAV-Rh10 transduced

tag: gender

value: female


title: Trigeminal Ganglia

source_name: primary murine TG neurons

value: Trigeminal Ganglia


title: J-O12: TESS rep3

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia

description: 10x v2

data_processing:
Reads were aligned using Cellranger v.2.2.0
Exon and intron counts were tabulated using Velocyto
Data were analyzed using Seurat v3
Genome_build: mm10-1.2.0 (GRCm38.93)
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell with tab delimeters

source_name: Lumbar spinal cord

extract_protocol:
Single nucleus dissociation was completed with a modified protocol based on our previous work64. Briefly, animals were euthanized by isoflurane inhalation and cervical dislocation. The thoracic SCI site was rapidly dissected and frozen on dry ice. Spinal cords were dounced in 500 µl sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg-acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was added and filtered through a µm cell strainer. The lysate was subsequently centrifuged at 3200 g for 10 min at 4°C. The supernatant was decanted, and 3 mL of sucrose buffer added to the pellet and incubated for 1 min. The pellet was homogenized using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg-acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant immediately poured off. The nuclei on the bottom half of the tube wall were collected with 100 µl PBS with 0.04% BSA and 0.2 U/µl RNase inhibitor. Resuspended nuclei were filtered through a 30 µm strainer. The nuclei suspension was finally adjusted to 1000 nuclei/µl.
Library preparation was carried out with 10X Genomics Chromium Single Cell Kit Version 2. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 5000. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed.

value: spinal cord

tag: condition

value: TESS

tag: genotype

value: wild type


title: J-32: TESS rep1

description: 10x v2

tag: tissue


title: J-36: TESS rep2

description: 10x v2

tag: strain


title: F-14: CON rep3

description: 10x v2

value: paralyzed


title: F-13: CON rep2

description: 10x v2


title: F-12: CON rep1

description: 10x v2


title: Extracted RNA 10.5-day old mouse slice #3 from dorsal-to-ventral axis

value: 10.5 days old


title: To rep2

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
Basecalls and Demultiplexing were performed using Illumina CASAVA version 1.8.2 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC version 0.11.2, then mapped to mm10 whole genome using bowtie2 v2.2.0.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Bioconductor package DEGSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include raw counts and RPKM values for each sample.

source_name: Caput epididymis

extract_protocol:
Caput, coupus, and cauda epididymis were removed, flash frozen on dry ice, and RNA was harvested using Trizol.
Sequence libraries were generated using the KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA Biosystems).  The resulting libraries were sequenced on the Illumina GAIIx (single end 36 base reads with TruSeq SBS kit v5 for GA., Illumina).

value: Caput epididymis

tag: age

value: 9 month old


title: The prefrontal cortex from a control mouse (without chronic mild stress treatments), biological rep1.

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from 6-23 week-old wild-type male mice prefrontal cortex without chronic mild stress treatments.

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

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

data_processing:
The data were analyzed by GeneSpring GX software (Agilent Technologies, Inc.) with GC-RMA as normalization algorithm.
Genespring GX signal intensity.

source_name: Prefrontal cortex from wild-type mice without chronic mild stress treatments.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Six to eight week-old wild-type mice were housed in the animal center at temperature 22±1℃ with 50±2 % humidity with 12 h light/ 12 h dark schedule and had free access to food and water before experiments. The chromic mild stress treatment: mice were randomly divided into two groups including the CMS group and the control group. The CMS experimental group underwent unpredicted unique or combined stressors exposure 6 days a week for 4 weeks. All CMS treated mice experienced the same sequence of stressors.

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

treatment_protocol: Mice were sacrified and brain parts including amygdala, hippocampus, prefrontal cortex, and cerebral cortex were isolated and collected. After 1xPBS washing, all were assessed for total RNA extraction.

value: Brains (Prefrontal cortex)

value: wild-type

value: 6-8 weeks

tag: Sex

value: male


title: To rep1


title: The cerebral cortex from a control mouse (without chronic mild stress treatments), biological rep2.

description: Gene expression data from 6-30 week-old wild-type male mice cerebral cortex without chronic mild stress treatments.

source_name: Cerebral cortex from wild-type mice without chronic mild stress treatments.

value: Brains (Cerebral cortex)


title: The cerebral cortex from a control mouse (without chronic mild stress treatments), biological rep1.

description: Gene expression data from 6-29 week-old wild-type male mice cerebral cortex without chronic mild stress treatments.


title: The prefrontal cortex from a control mouse (without chronic mild stress treatments), biological rep3.

description: Gene expression data from 6-25 week-old wild-type male mice prefrontal cortex without chronic mild stress treatments.


title: The hippocampus from a control mouse (without chronic mild stress treatments), biological rep3.

description: Gene expression data from 6-19 week-old wild-type male mice hippocampus without chronic mild stress treatments.

source_name: Hippocampus from wild-type mice without chronic mild stress treatments.

value: Brains (Hippocampus)


title: The cerebral cortex from a chronic mild stress treated mouse, biological rep1.

description: Gene expression data from 6-26 week-old wild-type male mice cerebral cortex with chronic mild stress treatments.

source_name: Cerebral cortex from wild-type mice with chronic mild stress treatments.


title: The amygdala from a control mouse (without chronic mild stress treatments), biological rep1.

description: Gene expression data from 6-11 week-old wild-type male mice amygdala without chronic mild stress treatments.

source_name: Amygdala from wild-type mice without chronic mild stress treatments.

value: Brains (Amygdala)


title: The hippocampus from a control mouse (without chronic mild stress treatments), biological rep1.

description: Gene expression data from 6-17 week-old wild-type male mice hippocampus without chronic mild stress treatments.


title: The cerebral cortex from a chronic mild stress treated mouse, biological rep3.

description: Gene expression data from 6-28 week-old wild-type male mice cerebral cortex with chronic mild stress treatments.


title: The prefrontal cortex from a chronic mild stress treated mouse, biological rep3.

description: Gene expression data from 6-22 week-old wild-type male mice prefrontal cortex with chronic mild stress treatments.

source_name: Prefrontal cortex from wild-type mice with chronic mild stress treatments.


title: The cerebral cortex from a control mouse (without chronic mild stress treatments), biological rep3.

description: Gene expression data from 6-31 week-old wild-type male mice cerebral cortex without chronic mild stress treatments.


title: The prefrontal cortex from a chronic mild stress treated mouse, biological rep1.

description: Gene expression data from 6-20 week-old wild-type male mice prefrontal cortex with chronic mild stress treatments.


title: The prefrontal cortex from a chronic mild stress treated mouse, biological rep2.

description: Gene expression data from 6-21 week-old wild-type male mice prefrontal cortex with chronic mild stress treatments.


title: The hippocampus from a control mouse (without chronic mild stress treatments), biological rep2.

description: Gene expression data from 6-18 week-old wild-type male mice hippocampus without chronic mild stress treatments.


title: The hippocampus from a chronic mild stress treated mouse, biological rep1.

description: Gene expression data from 6-14 week-old wild-type male mice hippocampus with chronic mild stress treatments.

source_name: Hippocampus from wild-type mice with chronic mild stress treatments.


title: The cerebral cortex from a chronic mild stress treated mouse, biological rep2.

description: Gene expression data from 6-27 week-old wild-type male mice cerebral cortex with chronic mild stress treatments.


title: Ta rep1

source_name: Corpus epididymis

value: Corpus epididymis


title: The amygdala from a control mouse (without chronic mild stress treatments), biological rep2.

description: Gene expression data from 6-12 week-old wild-type male mice amygdala without chronic mild stress treatments.


title: The prefrontal cortex from a control mouse (without chronic mild stress treatments), biological rep2.

description: Gene expression data from 6-24 week-old wild-type male mice prefrontal cortex without chronic mild stress treatments.


title: The amygdala from a control mouse (without chronic mild stress treatments), biological rep3.

description: Gene expression data from 6-13 week-old wild-type male mice amygdala without chronic mild stress treatments.


title: To rep3


title: The amygdala from a chronic mild stress treated mouse, biological rep3.

description: Gene expression data from 6-10 week-old wild-type male mice amygdala with chronic mild stress treatments.

source_name: Amygdala from wild-type mice with chronic mild stress treatments.


title: Bi rep3

source_name: Cauda epididymis

value: Cauda epididymis


title: The hippocampus from a chronic mild stress treated mouse, biological rep2.

description: Gene expression data from 6-15 week-old wild-type male mice hippocampus with chronic mild stress treatments.


title: The amygdala from a chronic mild stress treated mouse, biological rep2.

description: Gene expression data from 6-9 week-old wild-type male mice amygdala with chronic mild stress treatments.


title: Ta rep3


title: Bi rep1


title: Ta rep2


title: Bi rep2


title: WT rep2

data_processing:
Basecalls and Demultiplexing were performed using Illumina CASAVA version 1.8.2 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC version 0.11.2, then mapped to mm10 whole genome using bowtie2 v2.2.0.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Bioconductor package DEGSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include raw counts and RPKM values for each sample and fold change and t-test results compared between WT and Nell2-KO.

extract_protocol:
Caput epididymis were removed, flash frozen on dry ice, and RNA was harvested using Rneasy Mini kit. RNAs were amplified by using TargetAmp 1-Round aRNA Amplification Kit 103 (Epicentre).
Sequence libraries were generated using the KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA Biosystems).  The resulting libraries were sequenced on the Illumina GAIIx (single end 36 base reads with TruSeq SBS kit v5 for GA., Illumina).

value: post natal week 14


title: Nell2-KO rep2


title: The amygdala from a chronic mild stress treated mouse, biological rep1.

description: Gene expression data from 6-8 week-old wild-type male mice amygdala with chronic mild stress treatments.


title: Nell2-KO rep1


title: Nell2-KO rep3


title: WT rep3


title: WT rep4


title: Nell2-KO rep4


title: The hippocampus from a chronic mild stress treated mouse, biological rep3.

description: Gene expression data from 6-16 week-old wild-type male mice hippocampus with chronic mild stress treatments.


title: WT rep1


title: H3K4me3_IP1_st7_embryo

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

description:
ChIP-seq - single-end
macs2_st7_Ind15_19_H3K4me3_rep1_peaks.narrowPeak

data_processing:
Adatpert trimming (cutadapt)
duplicate marked with Picard(2.14 - markDupicates) and removed; removal of reads with quality below 20 (samtools view -q20)
BAM files sorted, unmapped reads and secondary alignment removed; properly paired reads were joined to have fragments information and stored as BEDPE
BED files extracted from BEDPE
Given the length of fragments, BED for each fragment group have been created (150 - 110 - 70)
Peak calling with MACS2 (-q 0.01) with default options for H3K4me3 in frog ,and H3K4me3 H3K27me3 in Human, with broad option in H3K27me3 frog.
HMD was estimated as reported in paper considering coverages in windows 50-bp wide across the genome.
Genome_build: Xenopus laevis 6.1
Genome_build: HG38
Supplementary_files_format_and_content: BED files for peaks, bigwig files for tracks

organism: Xenopus laevis

growth_protocol: no growth protocol

extract_protocol:
Preparation sperm and egg extract treated sperm chromatin for ChIP-seq: Chromatin fractionation and chromatin immunoprecipitation (ChIP) were performed as described before (Hisano et al., 2013 and Teperek et al., 2016) with slight modifications. Xenopus sperm were purified from their testes and permeabilised before ChIP. Sperm or egg extract treated sperm chromatin was resuspended in 50 l of Buffer 1 (0.3 M Sucrose, 15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM DTT) and added 50 l of Buffer 1 with detergent (Buffer 1 including 0.5% NP40 and 1% NaDOC). Samples were incubated for 10 min on ice. 100 l of MNase buffer (0.3 M Sucrose, 85 mM Tris, 3 mM MgCl2, 2　mM CaCl2, 2.5U of micrococcal nuclease: Roche 10107921001) was added in to each tube (0.5 million of cells per tube). Tubes were incubated at 37C for 30 min in pre-warmed water bath. Reaction was stopped by adding 2 l of 0.5 M EDTA pH8.0 in the same order as started. Tubes were vortexed and placed on ice for at least 5 min. Supernatant and pellet were separated by centrifugation at 13,000 rpm for 10 min at room temperature. Supernatant was transferred to new tube and stored on ice. For ICeChIP, semi-synthetic nucleosomes were spiked in as described (Grzybowski et al., 2015) before MNase digestion. Preparation Chromatin for embryo ChIP-seq: ChIP was performed as described previously (Gentsch and Smith, 2014) with the following modifications. Blastula (stage 7) embryos were generated by in vitro fertilization. For each ChIP experiment, 50 embryos were fixed in 2 mL of 1% Formaldehyde in 1x MMR for 25 min at room temperature, followed by 4 washes with 1 ml of 1xMMR and equilibration in 500 μl HEG solution (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 20% Glycerol) at 4°C, then excess buffer was removed and samples were frozen at −80°C. To extract chromatin, the samples were transferred to 2 ml tube or 15 ml Falcon tube and homogenized in 200-250 μl of sonication buffer (20 mM Tris-HCl pH 8.0, 70 mM KCl, 1 mM EDTA pH 8.0, 10% Glycerol, 5 mM DTT, 0.125% NP40, 1x complete protease inhibitors), by pipetting up and down in a 1 ml pipette tip. 250 μl of diagenode beads were transferred to diagenode falcon tube (Diagenode, C1020031). 750 μl of embryo lysates were added and diagnode falcons were transferred to the sonicator bath (diagnode bioruptor). Sonication is carried out in 30 cycles (with 30 s on/off cycles). Sonicated embryo extract was transferred into eppendorf tubes. Chromatin was collected by centrifugation for 5 min at top speed in tabletop centrifuge at 4°C. Chromatin extract was transferred to new tube and stored on ice.
ChIP-seq library preparation was performed using the TruSeq DNA kit (Illumina, FC-121-2001) according to the manufacturer’s protocol.

treatment_protocol: see extra column

value: st7 xenopus embryo

value: xenopus laevis


title: Input2_st7_embryo

description:
ChIP-seq input - single-end
macs2_st7_Ind18_12_H3K4me3_rep2_peaks.narrowPeak

source_name: input

value: input


title: H3K4me3_IP2_st7_embryo

description:
ChIP-seq - single-end
macs2_st7_Ind18_12_H3K4me3_rep2_peaks.narrowPeak


title: H3K27me3_Input_Sperm -geminin 3

description:
ChIP, single-ended
H3K27me3_sperm_EggTr_2rep_strict.bed

value: sperm


title: H3K27me3_IP_Sperm +geminin 1

description:
ChIP, single-ended
H3K27me3_sperm_EggTr_GMN_2rep_strict.bed


title: H3K27me3_IP_Sperm +geminin 2


title: H3K27me3_Input_Sperm -geminin 1


title: H3K27me3_Input_Sperm +geminin 2


title: H3K4me3_IP_Sperm -geminin 3

description:
ChIP, single-ended
H3K4me3_sperm_EggTr_2rep_strict.bed


title: H3K27me3_Input_Sperm +geminin 3


title: H3K27me3_IP_Sperm -geminin 1


title: H3K27me3_Input_Sperm -geminin 2


title: H3K27me3_IP_Sperm +geminin 3


title: H3K27me3_Input_Sperm +geminin 1


title: H3K4me3_IP_Sperm -geminin 2


title: H3K4me3_IP_Sperm -geminin 1


title: Input1_st7_embryo

description:
ChIP-seq input - single-end
macs2_st7_Ind15_19_H3K4me3_rep1_peaks.narrowPeak


title: H3K27me3_IP_Sperm -geminin 3


title: H3K27me3_IP_Sperm -geminin 2


title: H3K4me3_Input_Sperm -geminin 1


title: H3K4me3_Input_Sperm -geminin 2


title: H3K4me3_Input_Sperm -geminin 3


title: H3K4me3_IP_Sperm +geminin 2

description:
ChIP, single-ended
H3K4me3_sperm_EggTr_GMN_2rep_strict.bed


title: H3K4me3_Input_Sperm +geminin 3


title: H3K4me3_IP_Sperm +geminin 1


title: H3K27me3_IP_Sperm2 paired-end

description:
ICeChIP, paired-ended
macs2_nodup_190_H3K27me3_broad_common_rep1_rep2.broadPeak
macs2_nodup_190_H3K27me3_broad_common_rep1_rep2.broadPeak


title: H3K4me3_IP_Sperm1 paired-end

description:
ICeChIP, paired-ended
macs2_nodup_190_H3K4me3_common_rep1_rep2.narrowPeak
HMD_macs2_nodup_190_H3K4me3_common_rep1_rep2.narrowPeak.coverage.bed


title: Input_Sperm2 paired-end

description: ICeChIP, paired-ended


title: H3K4me3_IP_Sperm2 paired-end


title: H3K27me3_IP_Sperm1 paired-end


title: Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior-to-anterior axis

organism: Danio rerio

source_name: whole embryo

value: embryo

tag: tissue preparation

value: whole embryo

value: 28 hours post-fertilization


title: Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior-to-posterior axis

tag: developmental stage

value: 40 hours post-fertilization


title: Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior-to-posterior axis


title: Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal-to-ventral axis

source_name: Dissected trunk

value: Dissected trunk


title: Input_Sperm1 paired-end

description: ICeChIP, paired-ended


title: Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior-to-posterior axis


title: Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior-to-posterior axis


title: H3K4me3_IP_Sperm +geminin 3


title: Hela_NT_FANCM_ChIP_repl2

city: Baltimore

first: Marina

last: Bellani

state: Maryland

address: 251 Bayview Blvd

department: LMB

institute: NIA

data_processing:
ChIP-seq reads were aligned to the human genome assembly hg38 using BWA [version 0.7.17] using the following parameters
Picard [version 2.20.8] SamFormatConverter was used to convert SAM to BAM, SortSAM was used to sort the resulting BAM file [VALIDATION_STRINGENCY=Lenient], MarkDuplicates was used to mark duplicates
Deeptools [version 3.3.0] bamCoverage was used to generate BigWig files with the following parameters [-bs 150 -e  --normalizeUsing RPKM --ignoreDuplicates]
Deeptools [version 3.3.0] bigwigCompare was used to calculate log2 rations between bigwig files from each ChIP-seq and the corresponding Input [parameters: --skipZeroOverZero --operation log2 --skipNonCoveredRegions --outFileFormat bigwig --blackListFileName]
Genome_build: hg38

source_name: Hela/GFP-DONSON cells

growth_protocol: GFP-DONSON expressing HeLa cells 30 were cultured with L-Glutamine (Gibco), 200 ug/ml Hygromycin B (Invitrogen), and 5 ug/ml Blasticidin (Gibco). To induce GFP-DONSON expression, cells were incubated with 1 μg/ml Doxycycline for 48 hr.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture media for 8 min, followed by quenching the formaldehyde with 0.1 M glycine. Cells were washed with PBS, harvested by scraping, then suspended in lysis buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris-HCL pH 8.0) supplemented with protease and phosphatase inhibitors. Lysates were sonicated in a 4 ⁰C water bath ultrasonicator (Bioruptor, Diagenode). The time of sonication was adjusted to yield short DNA fragments <500 bp (total 8 minutes, 30 seconds sonication, then cool 30 seconds). In some experiments the time was adjusted to yield longer DNA fragments of 500-5000 bp (2 x 30 seconds with a 30 second cooling period). Diluted lysates were incubated overnight at 4 °C with antibodies as indicated. Immunoprecipitations were performed using Protein G magnetic beads (Pierce, 10% v/v), or GFP Trap (Chromotek, gta-20). Bead bound complexes were washed with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), LiCl immune complex buffer (0.25 M LiCl, 1% NP-40, 1% mM EDTA, 10 mM Tris-HCl pH 8.0) and TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0). DNA was eluted in elution buffer (1% SDS, 0.2 M NaCl) with Proteinase K (100 µg/ml) overnight at 65 °C. Eluted DNA was purified with DNA Clean & Concentrator PCR purification Kit (ZYMO Research, D4033) according to the manufacturer instructions.
Illumina sequencing adapters with a T-overhang were ligated to the precipitated ChIP DNA fragments or the input DNA, with a corresponding A-overhang, to construct a sequencing library according to the manufacturer’s protocol (Illumina, San Diego, CA). The fragments were purified using a magnetic bead protocol and eighteen cycles of PCR amplification were performed to enrich for fragments with an adapter on both ends. The products were purified again with size selection (approximately 200–600 bases) using a dual bead selection protocol with SPRIselect Beads (Beckman Coulter, Brea, CA). These libraries were sequenced on an Illumina Hi-Seq 2500 sequencer using on-board cluster generation on a rapid run paired end flow cell for 75 X 75 cycles (DONSON) and single end of 75 bp for 75 cycles (FANCM). Real-time analysis was performed using RTA v1.18.66.3 and base-calling was performed using bcl2fastq v2.18.0.12.

treatment_protocol: Non-treated cells

value: Hela/GFP-DONSON cells

value: Bethyl A302-637A, Rabbit anti FANCM


title: Tassel_MNase_seq_rep2_light_digest

city: St. Louis

first: Andrea

last: Eveland

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: The bed files for this sample contain information of the iSeg peak calls from small fragments (0-130bp) for tassel at the bc 2.0 and bc 3.0 threshold for replicate 2

data_processing:
Paired-end reads were first trimmed for adapter sequences using Cutadapt
Cleaned reads were mapped to maize AGPB73_v3 using Bowtie2
BAM files were seperated based on size. small fragments (<131bp). All fragments (0-500bp).
Peak calling with iSeg. Selection based on biological cutoff (bc) thresholds 2.0, 3.0 and 4.0 as described in Girimurugan et al., BMC Bioinformatics 2018.
AGP B73_v3
Supplementary_files_format_and_content: bed and bw files

organism: Zea mays

source_name: Tassel primordia nuclei

growth_protocol: B73 seeds were grown in climate controlled growth facility at 27°C/23°C day/night for 4-5 weeks for tassel and 6-7 weeks for ear and primordia were hand dissected

extract_protocol:
The nuclei were isolated with tissue disrupture and purified with a percol gradient.  Nuclei were digested with different concentrations of micrococcal nuclease and DNA was extracted with in house protocol.
The libraires were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following manufacturer instructions.
50 bp paired-end reads were generated using the Illumina Illumina HiSeq 2500 platform

treatment_protocol: The ground tissue was cross linked to fix nucleosome bound DNA in fixation buffer (15 mM Pipes·NaOH at pH 6.8, 0.32 M sorbitol, 80 mM KCl, 20 mM NaCl, 0.5 mM EGTA, 2mM EDTA, 1 mM DTT, 0.15 mM spermine, and 0.5 mM spermidine) with 1% formaldehyde

value: Tassel primordia 1-5 mm

value: pool ~ 170 hand-dissected  inflorescence primordia


title: H3K4me3_Input_Sperm +geminin 2


title: H3K4me3_Input_Sperm +geminin 1


title: Hela_NT_Input_F_repl2


title: Tassel_MNase_seq_rep1_heavy_digest

description: The bed files for this sample contain information of the iSeg peak calls differential nuclease sensitivity (DNS) (light - heavy digest) for tassel at bc 2.0 and bc 3.0 threshold for replicate 1


title: Tassel_MNase_seq_rep1_light_digest

description: The bed files for this sample contain information of the iSeg peak calls from small fragments (0-130bp) for tassel at the bc 2.0 and bc 3.0 threshold for replicate 1


title: Ear_MNase_seq_rep2_heavy_digest

description: The bed files for this sample contain information of the iSeg peak calls differential nuclease sensitivity (DNS) (light - heavy digest) for ear at bc 2.0 and bc 3.0 threshold for replicate 2

source_name: Ear primordia nuclei

value: Ear primordia 1-5 mm


title: Extracted RNA 35-day old human slice #2 from dorsal-to-ventral axis (2nd part)

source_name: transversal slice

value: transversal slice

value: 35 days old


title: Extracted RNA 35-day old human slice #2 from dorsal-to-ventral axis (1st part)


title: Ear_MNase_seq_rep1_heavy_digest

description: The bed files for this sample contain information of the iSeg peak calls differential nuclease sensitivity (DNS) (light - heavy digest) for ear at bc 2.0 and bc 3.0 threshold for replicate 1


title: Tassel_MNase_seq_rep2_heavy_digest

description: The bed files for this sample contain information of the iSeg peak calls differential nuclease sensitivity (DNS) (light - heavy digest) for tassel at bc 2.0 and bc 3.0 threshold for replicate 2


title: Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal-to-ventral axis


title: Ear_MNase_seq_rep2_light_digest

description: The bed files for this sample contain information of the iSeg peak calls from small fragments (0-130bp) for ear at the bc 2.0 and bc 3.0 threshold for replicate 2


title: Extracted RNA 3-day old chicken anterior slice #3 from dorsal-to-ventral axis

organism: Gallus gallus

value: bovans brown

value: 3 days old


title: Extracted RNA 3-day old chicken posterior slice #3 from dorsal-to-ventral axis


title: D42 injured B12

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

description: rpkm.txt

data_processing:
RNA sequencing reads were aligned to the mouse reference genome (mm10) using STAR (Dobin et al., 2013).
Raw expression levels were quantified for all annotated genes (Ensembl 86).
Raw expression levels were normalized to RPKM values using edgeR (Robinson et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all samples

source_name: heart

extract_protocol:
Injured and uninjured regions of the heart were harvested at different time points following injury
Total RNA extracted using RNeasy Mini kit (Qiagen); RNA-Seq libraries were generated using TrueSeq RNA Library Prep Kit (Illumina)

value: cardiac muscle

value: injured

tag: time point

value: day 42 after injury


title: Extracted RNA 3-day old chicken anterior slice #2 from dorsal-to-ventral axis

value: embryo


title: Ear_MNase_seq_rep1_light_digest

description: The bed files for this sample contain information of the iSeg peak calls from small fragments (0-130bp) for ear at the bc 2.0 and bc 3.0 threshold for replicate 1


title: D42 uninjured B3

description: rpkm.txt

value: uninjured


title: D42 injured B9

description: rpkm.txt


title: D42 uninjured B9

description: rpkm.txt


title: Phenylalanine-betaxanthin treated N2 animals, Independent Trial 3

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

description: Gene expression data from phenylalanine-betaxanthin treated animals

hyb_protocol: 3.75 µg of fragmented and biotinylated ss-cDNA were included in the hybridization mix, using the GenAtlas Hybridization, Wash and Stain kit for WT Array Strips (Affymetrix, P/N 901667) according to the recommendations of the manufacturer. The resulting preparations were hybridized to GeneChip® C. elegans Gene 1.1 ST Array Strip (Affymetrix, 902157) with 26 unique sequences of each transcript. After applying hybridization (spike controls) and labeling tests it was observed that the 20 chips had fulfilled the quality criteria.

scan_protocol: GeneAtlas Microarray System from Affymetrix

data_processing:
After scanning, microarrays data were processed using Affymetrix Expression Command Console (Affymetrix) and all samples were within bounds for hybridization and labeling tests. Three independent RNA samples were employed. Samples from worms treated with betalains were grouped as “treatment” and worms without betalains exposition were grouped as “control”. Data analysis was then performed with RMA (Robust Multiarray Average) allowing raw intensity values to be background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.
log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.

label: BIOTIN-STREPTAVIDIN

source_name: C. elegans treated with phenylalanine-betaxanthin (25 uM)

label_protocol: Ss-cDNA was synthetized from 3.5 ng of each sample using the GeneChip WT Pico Reagent kit (Affymetrix, P/N 703262). The amount and quality of ss-cDNA were checked by Nanodrop and Bioanalyzer. ss-cDNA targets were cleaned up, and after fragmentation and terminal labelling with biotin

growth_protocol: N2 worm were synchronized using the bleaching protocol, from adultworms maintained in standard NGM agar plates at 20 ºC

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions, followed by a purification using PureLink TM RNA Mini Kit from Invitrogen

treatment_protocol: 16-18 hours after haching L1 larvae were treated with 25 uM of each betalain in S. medium for 48 hours at 20 ºC

value: Whole animal

value: Wild-type N2

value: 3 days after hatching, young adults

value: phenylalanine-betaxanthin


title: Extracted RNA 3-day old chicken posterior slice #2 from dorsal-to-ventral axis


title: D42 uninjured B12

description: rpkm.txt


title: D42 injured B3

description: rpkm.txt


title: Indoline carboxylic acid-betacyanin treated N2 animals, Independent Trial 2

description: Gene expression data from indoline carboxylic acid-betacyanin treated animals

source_name: C. elegans treated with indoline carboxylic acid-betacyanin (25 uM)

value: indoline carboxylic acid-betacyanin


title: D42 uninjured B1

description: rpkm.txt


title: PCNSL44

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

institute: Kyoto Prefectural University of Medicine

description: PCNSL44_AF_9463_(miRNA-4_0).rma-dabg-Signal

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 17hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: PCNSL tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: subject age

value: Male

value: primary central nervous system lymphomas (PCNSL)

tag: molecule subtype

value: miRNA


title: Phenylalanine-betaxanthin treated N2 animals, Independent Trial 1


title: PCNSL47

description: PCNSL47_AF_9463_(miRNA-4_0).rma-dabg-Signal

value: Female


title: D42 injured B1

description: rpkm.txt


title: Indoline carboxylic acid-betacyanin treated N2 animals, Independent Trial 3


title: PCNSL45

description: PCNSL45_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: Indoline carboxylic acid-betacyanin treated N2 animals, Independent Trial 1


title: PCNSL43

description: PCNSL43_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: PCNSL42

description: PCNSL42_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: PCNSL46

description: PCNSL46_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: D21 uninjured A11

description: rpkm.txt

value: day 21 after injury


title: Phenylalanine-betaxanthin treated N2 animals, Independent Trial 2


title: PCNSL38

description: PCNSL38_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: Indicaxanthin treated N2 animals, Independent Trial 3

description: Gene expression data from indicaxanthin treated animals

source_name: C. elegans treated with indicaxanthin (25 uM)

value: indicaxanthin


title: PCNSL41

description: PCNSL41_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: PCNSL37

description: PCNSL37_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: PCNSL39

description: PCNSL39_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: PCNSL35

description: PCNSL35_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: D21 injured A11

description: rpkm.txt


title: PCNSL40

description: PCNSL40_AF_9463_(miRNA-4_0).rma-dabg-Signal


title: Indicaxanthin treated N2 animals, Independent Trial 2


title: PCNSL34

description: PCNSL34_AF_9463_(miRNA-4_0).rma-dabg-Signal