title: mads-box mutant seeds, T3h of 5μM ABA, biological rep1

city: Salamanca

first: Oscar

last: Lorenzo

address: C/ Río Duero, 12 Campus de Villamayor. Parque Científico

department: Dpt. Fisiologia Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE)

institute: Universidad de Salamanca

description: Gene expression data from water-stratified mads-box mutant seeds, subsequently treated with 5μM ABA, before seed germination.

hyb_protocol: If the quality control was correct, then 10 µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, Santa Clara, CA), containing 22500 transcript variants from 24000 well-characterized Arabidopsis thaliana genes. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix). Three biological replicates for each condition were independently hybridized.

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip Scanner 3000 7G System (Affymetrix).

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, Bioinformatics (2006), 22, 897-899). The Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al. (2003) Biostatistics, 4, 249-264). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini, Y and Hochberg, Y (1995) J.Roy.Stat.Soc, 57, 289-300, Reiner et al. (2003) Bioinformatics, 19, 368-375). Genes were considered to be differentially expressed if the corrected P values were <0.05. In addition, only genes with a signal log2 ratio ≥1 for induction or ≤-1 for repression were considered for further analysis.

organism: Arabidopsis thaliana

source_name: Water-stratified Arabidopsis seeds, mads-box mutant

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin-labeled cRNA. The cRNA preparation (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 (Col-0) and mads-box mutant seeds were stratified in water (4ºC, dark) for 3 days.

extract_protocol: RNA was isolated after Oñate-Sánchez and Vicente-Carbajosa (2008). Briefly, 30 - 50 mg ground seed powder was vortexed in 550 μl extraction buffer [0.4 M lithium chloride, 0.2 M Tris (hydroxymethyl)-methylamine (Tris base, pH = 8), 25 mM EDTA and 1% (w/v) sodium dodecyl sulphate] and 550 μl chloroform, and centrifuged (13,000 rpm) at room temperature for 3 min. Equal amounts of carbolic acid (phenol) and 1/6 of total volume of chloroform were added to the aqueous layer.  Eight M LiCl was used to precipitate nucleic acids on ice for 3h. After centrifugation at 4 °C for 30 min (13,000 rpm) the pellet was resuspended in 470 μl diethylpyrocarbonate (DEPC)-treated water with 7 μl sodium acetate (3M, pH = 5.2) and 250 μl of 100 % ethanol to precipitate carbohydrates. To precipitate and further separate RNA from carbohydrates and proteins, the supernatant was transferred to a new tube and 43 μl sodium acetate (3 M, pH = 5.2) were added. After mixing, 750 μl of 100 % ethanol were added and kept at -20 °C for at least 1 h. The pellet was washed with 500 μl of 70 % ethanol and resuspended in 30 μl DEPC water. All the samples were purified using the RNeasy Mini Kit (Qiagen, Crawley, UK). RNA quantity and integrity were tested using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) together with an Agilent RNA 6000 Nano Labchip kit (Copois et al., 2007), generating an electropherogram and a gel-like image.

treatment_protocol: Water-stratified seeds were transferred to light (22ºC, percival) in the presence of 5μM ABA for 3 hours.

tag: ecotype

value: Columbia-0 (Col-0)

tag: genotype

value: mads-box mutant

value: seeds

value: water stratification, then abscisic acid (ABA) treatment


title: Wild-type Col-0 seeds, T3h of 5μM ABA, biological rep2

status: Public on Dec 31 2019

type: RNA

country: Spain

description: Gene expression data from water-stratified Col-0 seeds, subsequently treated with 5μM ABA, before seed germination.

label: biotin

molecule: total RNA

source_name: Water-stratified Arabidopsis seeds, wild-type

value: wild-type

tag: tissue

tag: treatment


title: AS_A1_2102_1_(miRNA-1_0_2Xgain)

city: Sydney

first: Alen

last: Faiz

state: NSW

address: 431 Glebe Point Rd

country: Australia

institute: Woolcock Institute of Medical Research

hyb_protocol: The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The data were normalized with R using the affy package RMA() function

organism: Homo sapiens

source_name: Bronchial biopsy

label_protocol: Total RNA was labelled using the FlashTag™ Biotin HSR RNA Labeling Kit

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

treatment_protocol: Patients included in this study were treated with 1) Placebo twice daily for 30 months; 2) fluticasone 500µg twice daily with or without salmeterol 50µg twice daily for 30 months.

tag: time

value: 0 months

value: Fluticasone

tag: smoking status

value: ex-smoker

tag: copd severity

value: GOLD Stage II

value: Bronchial biopsy


title: Wild-type Col-0 seeds, T3h of 5μM ABA, biological rep3


title: Mouse Control1

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

institute: CABIMER

description: Gene expression data from human pancreatic islets isolated from healthy donors

hyb_protocol: Following fragmentation, 3.8 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on GeneChip® Human Gene 2,0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

organism: Mus musculus

source_name: Mouse Control1 pancreatic islets from healthy donor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

growth_protocol: Pancreatic iselts from healthy donors were isolated, cultured and processed

extract_protocol: Total RNA was extracted using the RNAeasy plus micro kit (Qiagen) following the instructions of the manufacturer.

treatment_protocol: Islet preparations were washed, handpicked and subsequently maintained in CMRL-1066 (Gibco) containing 5.6 mM glucose supplemented with 10% FCS, 100 Units/ml penicillin, 100 μg/ml streptomycin and 100 μg/ml gentamycin. At 16 hours upon reception islets  were invected with a control P SIN Dual-GFP lentiviral vector. Islets were processed for RNA exptraction at 96 hours post infection.

value: Murine pancreatic islets

tag: lentivirus

value: control


title: LSK_WT-C

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description:
LSK_WT replicate 3
Gene expression data from sorted LSK 14 days after administration of pIpC in wt mice

hyb_protocol: Fragmented and labeled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST Array (Affymetrix) for 16 hr at 45°C and 60rpm in an Hybridization oven 645. Chips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007.

scan_protocol: Affymetrix GeneChip Scanner GS3000

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: Lin- Sca 1+c kit+hematopoietic progenitors

label_protocol: RNA was amplified using the Nugen WT-Ovation Pico RNA Amplification System (Nugen). cDNA was fragmented and biotin-labeled using the Ambion WT Expression Kit (ThermoFisher) according to manufacturer’s protocol.

growth_protocol: LSK (Lin- Sca1+c kit+; Granulocyte-Macrophage-Progitors GMP) and GMP (Lin-Sca1-c-kit+CD34+FcγR+) were sorted from bone marrow of three wildtype Mx-Cre C57BL/6J and three C57BL/6J Mx-Cre Lamtor2f/f mice 14 days after administration of pIpC i.p.

extract_protocol: Qiagen Rneasy Micro Kit according to manufacturers instructions

treatment_protocol: Deletion of Lamtor2f/f alleles was induced by i.p. injection of pIpC

tag: strain

value: C57BL6 Mx1-Cre wt/wt;Lamtor2 wt/wt


title: Mouse PAX8 2

source_name: Mouse PAX8 2 pancreatic islets from healthy donor

value: over-expression of the PAX8 gene


title: Mouse PAX8 1

source_name: Mouse PAX8 1 pancreatic islets from healthy donor


title: LSK_WT-B

description:
LSK_WT replicate 2
Gene expression data from sorted LSK 14 days after administration of pIpC in wt mice

value: Lin- Sca 1+c kit+hematopoietic progenitors


title: LSK_WT-A

description:
LSK_WT replicate 1
Gene expression data from sorted LSK 14 days after administration of pIpC in wt mice


title: LSK_KO-C

description:
LSK_KO replicate 3
Gene expression data from sorted LSK 14 days after conditional deletion of Lamtor2 via pIpC

value: C57BL6 Mx1-Cre wt/wt;Lamtor2f/f


title: SP4_H3K9ac

type: SRA

city: Wuhan

first: jin

last: jing

state: Hubei

address: Wuhan, Hubei Province, P.R.China

department: College of Life Sciences

country: China

institute: Wuhan University

library_source: genomic

data_processing:
Raw reads of ATAC-seq, ChIP-seq and RNA-seq were separately aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using Bowtie2, SOAP2 aligner and HISAT2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks of ATAC-seq and ChIP-seq were identified using the MACS and SICER
Genome_build: MSU7
Supplementary_files_format_and_content: bed file were generated by MACS, scores represent -10*log10(pvalue); wig files were generated using SICER, Scores represent probability；tab-delimited text files include RPKM values for each sample.

molecule: genomic DNA

organism: Oryza sativa

source_name: Sterility male of WXS at uninucleate period

growth_protocol: The rice PTGMS line WXS (O. sativa ssp. indica) were grown in the paddy field of Wuhan University (30.35°N, 114.33°E), Wuhan, China, in summer. From 20 July to 30 August 2016, the average temperatures were? , with a 14h light/10 h dark photoperiod, which caused WXS male sterility (WXS(S)). When panicle length reached ~ 1 cm (before the stages of early premeiosis), half of the plants were transferred to growth chamber at an average temperature of 22°C with a 14h light/10h dark photoperiod and 77% relative humidity, ensuring the illumination, humidity values and other environment factors in the growth chamber close to the natural condition as far as possible, which could make WXS convert into male fertility (WXS(F))

extract_protocol:
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on the intact nuclei isolated by Plant Nuclei Isolation/Extraction Kit (CELLYTPN1, sigma) from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit. Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers. Total RNA of WXS was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Chromatin from panicle of WXS was immunoprecipitated with antibodies against H3K4me2 and H3K9ac. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
The genomic fragments of Tn5, RNA libraries and ChIP-ed DNA were separately prepared for sequencing using standard Illumina protocols

treatment_protocol: Young panicles were collected and were immediately frozen in liquid nitrogen. All collected samples were ground into fine powder for ChIP-seq, ATAC-seq and RNA-seq experiments.

tag: line

value: Wuxiang S (WXS)

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle

tag: period

value: uninucleate

tag: chip antibody


title: FP4_H3K9ac

source_name: Fertility male of WXS at uninucleate period


title: mads-box mutant seeds, T3h of 5μM ABA, biological rep2

value: Columbia-0 (Col-0)

value: mads-box mutant

value: seeds

value: water stratification, then abscisic acid (ABA) treatment


title: LSK_KO-A

description:
LSK_KO replicate 1
Gene expression data from sorted LSK 14 days after conditional deletion of Lamtor2 via pIpC


title: GMP_WT-B

description:
GMP_WT replicate 2
Gene expression data from sorted GMP 14 days after administration of pIpC in wt mice


title: anac089-2 mutant seeds at T3h of 5μM ABA, biological rep3

description: Gene expression data from water-stratified anac089-2 mutant seeds, subsequently treated with 5μM ABA, before seed germination.

hyb_protocol: If the quality control was correct, then 10 µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, Santa Clara, CA), containing 22500 transcript variants from 24000 well -characterized Arabidopsis thaliana genes. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix). Three biological replicates for each condition were independently hybridized.

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, Bioinformatics (2006), 22, 897-899). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al (2003) Biostatistics, 4, 249-264). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini, Y and Hochberg, Y (1995) J.Roy.Stat.Soc, 57, 289-300, Reiner et al (2003) Bioinformatics, 19, 368-375).  Genes were considered to be differentially expressed if the corrected P values were <0.05. In addition, only genes with a signal log2 ratio ≥1 for induction or ≤-1 for repression were considered for further analysis.

source_name: Water-stratified Arabidopsis seeds

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

treatment_protocol: Seeds of Arabidopsis thaliana ecotype Columbia-0 (Col-0) were stratified in water (4ºC, dark) during 3 days, and then transfered to light (22ºC, percival) in presence of 5μM ABA for 3 hours.

tag: genotype/variation

value: anac089-2 mutant

value: Seeds


title: anac089-2 mutant seeds at T3h of 5μM ABA, biological rep1

growth_protocol: Seeds of Arabidopsis thaliana ecotype Columbia-0 (Col-0) were stratified in water (4ºC, dark) during 3 days


title: anac089-2 mutant seeds at T3h of 5μM ABA, biological rep2


title: FP3_H3K9ac

source_name: Fertility male of WXS at meiosis period

value: meiosis


title: Wild-type Col-0 seeds at T3h of 5μM ABA, biological rep2

value: wild type


title: mads-box mutant seeds, T3h of 5μM ABA, biological rep3


title: LSK_KO-B

description:
LSK_KO replicate 2
Gene expression data from sorted LSK 14 days after conditional deletion of Lamtor2 via pIpC


title: Wild-type Col-0 seeds at T3h of 5μM ABA, biological rep3


title: GMP_KO-B

description:
GMP_KO replicate 2
Gene expression data from sorted GMP 14 days after conditional deletion of Lamtor2 via pIpC


title: GMP_WT-C

description:
GMP_WT replicate 3
Gene expression data from sorted GMP 14 days after administration of pIpC in wt mice


title: Wild-type Col-0 seeds at T3h of 5μM ABA, biological rep1


title: SP4_H3K4me2


title: GMP_KO-C

description:
GMP_KO replicate 3
Gene expression data from sorted GMP 14 days after conditional deletion of Lamtor2 via pIpC


title: GMP_KO-A

description:
GMP_KO replicate 1
Gene expression data from sorted GMP 14 days after conditional deletion of Lamtor2 via pIpC


title: GMP_WT-A

description:
GMP_WT replicate 1
Gene expression data from sorted GMP 14 days after administration of pIpC in wt mice


title: Wild-type Col-0 seeds, T3h of 5μM ABA, biological rep1

value: wild-type


title: SP3_H3K4me2

source_name: Sterility male of WXS at meiosis period


title: FP3_H3K4me2


title: CM2

city: Guangzhou

first: wang

middle: yi

last: qing

institute: South Medical University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 2.2ul containing 25X Fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) for 17 hours at 65Â°C . After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: colorectal tumor tissue with metastasis, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human colorectal tumor tissues are obtained from  Department of pathology , Nanfang Hospital (Guangzhou, China).

extract_protocol: RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  The protocol includes lysis of cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Tissues are keep in liquid nitrogen.

value: colorectal tumor tissue with metastasis


title: CM3

source_name: colorectal tumor tissue with metastasis, replicate 3


title: D1168_OP_24h_rep3

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

description:
BT_counts_table.txt
sample name:
D1168

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample ...

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were exposed to OP50 and BT at the stage L4. The experiments with BT were performed at 20°C.

value: whole body

value: Wild type (N2)

value: E. coli OP50

tag: timepoint

tag: medium

value: mNGM

tag: temperature

value: 20 degrees Celsius


title: D1167_OP_24h_rep2

description:
BT_counts_table.txt
sample name:
D1167


title: D1166_OP_24h_rep1

description:
BT_counts_table.txt
sample name:
D1166


title: D1169_OP_24h_rep4

description:
BT_counts_table.txt
sample name:
D1169


title: D1165_BT407_24h_rep4

description:
BT_counts_table.txt
sample name:
D1165


title: FP4_H3K4me2

value: Wuxiang S (WXS)

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle


title: D1164_BT407_24h_rep3

description:
BT_counts_table.txt
sample name:
D1164


title: C3

source_name: colorectal tumor tissue without metastasis, replicate 3


title: FAP organoid, HCT14-2_SNP

type: genomic

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: The JFCR-Cancer Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: GeneCHips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Chromosome Analysis Suite  (Affymetrix) using default analysis setting.

label: Biotin

source_name: FAP organoid, HCT14-2

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Organoids were embedded in Matrigel and cultured in ENR medium.

extract_protocol: Total DNA was isolated using a QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Organoids were recovered from Matrigel using Cell Recovery Sollution (Corning), washed with PBS once and collected by centrifugation.

tag: patient id

tag: gender

value: female

tag: diagnosis

value: AFAP

value: FAP organoid


title: FAP organoid, HCT23-7_SNP

source_name: FAP organoid, HCT23-7

value: male

tag: tissue


title: ChIP-seq_GRKO DexLPS rep2

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

description: MEFs_GRKO_aGR_DexLPS_merged_mm10_subsampled_mm10.ucsc.bedGraph.gz

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Due to high variation of peaks called between replicates, replicates were merged before mapping, downsampled to 64mio reads per genotype and one peak file generated from the merged replicates.
Peaks  were  called  using  MACS2 version  2.1.0 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) and peaks detected in GRKO MEFs were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files contain annotated peaks called with MACS2 version 2.1.0 and cleared from blacklisted regions and peaks called in GRKO MEFs. The .bedGraph.gz files contain tracks for visualization.

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: MEFs generation: C57BL/6 male mouse embryos from either wild-type, GR Zn/Zn or GRKO were harvested at 13.5 days after vaginal plug formation. Internal organs (mainly heart and liver) and head were removed and embryos were minced and digested with Trypsin 10-15min at 37°C. MEFs were cultured for 7 days in high glucose DMEM incl. 10% FBS and 1% Pen/Strep.

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al., 2013) with the addition of a chromatin pre-clearing step. Briefly, cells were fixed with 30min DSG and 10min 1% formaldehyde. Crosslink was quenced with 0.2M glycine for 5min. Cells were lysed with Fast IP buffer (150mM NaCl, 5mM EDTA, 5mM Tris, 1% Triton X-100 and 0.5% NP40). Chromatin was sheared in shearing buffer (1% SDS, 10µM EDTA and 0.05% Tris) until majority of chromatin fragments were between 200-500bp. Chromatin pre-clearing was done by incubation with Dynabeads at 4°C rotating before IP set-up overnight. Next day, Dynabeads were added to IPs and 6h incubated at 4°C rotating. IPs were washed 6 times with Fast IP buffer. DNA was eluted with ChIP elution buffer (100mM NaHCO3 and 1%SDS).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: 16h 1uM Dex in EtOH + 3h 100ng/ul LPS (Dex+LPS)

tag: antibody

value: Glucocorticoid Receptor - Proteintech 24050-1-AP

tag: Sex

tag: genotype

value: GRKO/KO

tag: treatment

value: 16h 1 uM Dex in EtOH + 3 100ng/ul LPS in PBS


title: D1163_BT407_24h_rep2

description:
BT_counts_table.txt
sample name:
D1163


title: CM1

source_name: colorectal tumor tissue with metastasis, replicate 1


title: ChIP-seq_GRKO DexLPS rep1


title: FAP organoid, HCT24-14_SNP

source_name: FAP organoid, HCT24-14

value: CFAP


title: C1

source_name: colorectal tumor tissue without metastasis, replicate 1


title: Sample Kidney Pair 2 with DOT1-knockout NPC

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

country: USA

institute: Tulane University School of Medicine

description: KO2 vs. WT1

hyb_protocol: Manufacturer's protocol (Agilent)

scan_protocol: Scan Protocol: GE2_1200_Jun14 Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: KO2: Kidneys with DOT1-knockout NPC at embryonic day 16.5

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

extract_protocol: Total RNA was isolated from kidneys using RNAlater (ThermoFisher Scientific) and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: age

value: embryonic day 16.5

value: Mouse Kidneys

source_name: WT1: Kidneys at embryonic day 16.5

value: control


title: C2

source_name: colorectal tumor tissue without metastasis, replicate 2


title: Sample Kidney Pair 4 with DOT1-knockout NPC

description: KO4 vs. WT1

source_name: KO4: Kidneys with DOT1-knockout NPC at embryonic day 16.5

tag: strain


title: FAP organoid, HCT20-3_SNP

source_name: FAP organoid, HCT20-3


title: Sample Kidney Pair 3 with DOT1-knockout NPC

description: KO3 vs. WT1

source_name: KO3: Kidneys with DOT1-knockout NPC at embryonic day 16.5


title: Sample Kidney Pair 1 with DOT1-knockout NPC

description: KO1 vs. WT1

source_name: KO1: Kidneys with DOT1-knockout NPC at embryonic day 16.5


title: Control wildtype Kidney Pair 4

description: WT4 vs. WT1

source_name: WT4: Kidneys at embryonic day 16.5


title: D1162_BT407_24h_rep1

description:
BT_counts_table.txt
sample name:
D1162

value: whole body

value: Wild type (N2)


title: ChIP-seq_GR MUT DexLPS rep4

description:
MEFs_GRC437G_aGR_DexLPS_merged_mm10_subsampled_mm10.ucsc.bedGraph.gz
MEFs_mutantSpecific_aGR_merged_Kopeaksremoved_annotated.txt

value: GR Zn / Zn


title: FAP organoid, HCT23-8_SNP

source_name: FAP organoid, HCT23-8


title: D1161_BT679_24h_rep4

description:
BT_counts_table.txt
sample name:
D1161

source_name: whole body

value: mNGM

value: 20 degrees Celsius


title: D1160_BT679_24h_rep3

description:
BT_counts_table.txt
sample name:
D1160


title: ChIP-seq_GR MUT DexLPS rep3


title: D1159_BT679_24h_rep2

description:
BT_counts_table.txt
sample name:
D1159


title: ChIP-seq_GR MUT DexLPS rep1


title: Control wildtype Kidney Pair 2

description: WT2 vs. WT1

source_name: WT2: Kidneys at embryonic day 16.5


title: ChIP-seq_GR MUT DexLPS rep2


title: FAP organoid, HCT24-8_SNP

source_name: FAP organoid, HCT24-8


title: ChIP-seq_GR WT DexLPS rep3

description:
MEFs_Grwt_aGR_DexLPS_merged_mm10_subsampled_mm10.ucsc.bedGraph.gz
MEFs_wtSpecific_aGR_merged_Kopeaksremoved_annotated.txt

value: GR wt / wt


title: D1158_BT679_24h_rep1

description:
BT_counts_table.txt
sample name:
D1158


title: SP3_H3K9ac

source_name: Sterility male of WXS at meiosis period

tag: line

value: Wuxiang S (WXS)

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle

value: meiosis


title: D1157_BT247_24h_rep4

description:
BT_counts_table.txt
sample name:
D1157


title: ChIP-seq_GR WT DexLPS rep1

source_name: mouse embryonic fibroblasts (MEFs)

value: Glucocorticoid Receptor - Proteintech 24050-1-AP

value: male


title: D1156_BT247_24h_rep3

description:
BT_counts_table.txt
sample name:
D1156


title: ChIP-seq_GR WT DexLPS rep2

value: 16h 1 uM Dex in EtOH + 3 100ng/ul LPS in PBS


title: FAP organoid, HCT14-9_SNP

source_name: FAP organoid, HCT14-9

value: female

value: AFAP

value: FAP organoid


title: D1155_BT247_24h_rep2

description:
BT_counts_table.txt
sample name:
D1155


title: Control wildtype Kidney Pair 3

description: WT3 vs. WT1

source_name: WT3: Kidneys at embryonic day 16.5

value: embryonic day 16.5

value: Mouse Kidneys

value: control


title: Sample DOT1-null UB cells 4

description: KO4 vs. WT3

scan_protocol: Scan Protocol: GE2_107_Sep09 Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: KO4: DOT1-null UB cells at P0

extract_protocol: Total RNA was isolated from FACS-sorted GFP-positive UB cells and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: Postnatal day 0

tag: cell type

value: UB cells

source_name: WT3: Wildtype UB cells at P0


title: D1154_BT247_24h_rep1

description:
BT_counts_table.txt
sample name:
D1154

value: whole body

value: Wild type (N2)

value: mNGM

value: 20 degrees Celsius


title: Control wildtype Kidney Pair 1

description: WT1 vs. WT1

source_name: WT1: Kidneys at embryonic day 16.5


title: D1153_OP_12h_rep4

description:
BT_counts_table.txt
sample name:
D1153

value: E. coli OP50


title: D1152_OP_12h_rep3

description:
BT_counts_table.txt
sample name:
D1152


title: Sample DOT1-null UB cells 1

description: KO1 vs. WT3

source_name: KO1: DOT1-null UB cells at P0


title: Sample DOT1-null UB cells 3

description: KO3 vs. WT3

source_name: KO3: DOT1-null UB cells at P0


title: D1149_BT407_12h_rep4

description:
BT_counts_table.txt
sample name:
D1149


title: D1151_OP_12h_rep2

description:
BT_counts_table.txt
sample name:
D1151


title: CCl4-Fibroblasts rep3

city: Tokyo

first: Michiko

last: Itoh

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the mm10 genome using STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: activated fibroblasts

growth_protocol: Collagen α2(I) promoter–driven green fluorescent protein transgenic (Col1a2-GFP Tg) mice were crossed with melanocortin 4 receptor–deficient (MC4R-KO) mice (MC-COL).

extract_protocol:
The fibroblasts were FACS-sorted as CD45-GFP+ positive cells from fibrotic livers, and hepatic stellate cells were isolated from normal livers by density gradient–based separation method. Total RNA purified from sorted fibroblasts was amplified using SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech).
RNA-seq libraries were prepared according to the manufacturer's protocol (Illumina).

treatment_protocol: MC-COL mice were fed Western diet for 20 weeks (NASH model), and Col1a2-GFP Tg were received carbon tetrachloride twice a week for 8 weeks (CCl4 model).

value: liver

tag: status

value: fibrosis


title: FAP organoid, HCT20-6_SNP

source_name: FAP organoid, HCT20-6

value: CFAP


title: D1150_OP_12h_rep1

description:
BT_counts_table.txt
sample name:
D1150


title: NASH-fibroblasts rep3


title: CCl4-Fibroblasts rep1


title: 35S::FDPi replicate 4

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: After fragmentation, 7.5 ug of ds-cDNA was hybridized for 16 hr at 45C on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained with Fluidics Script FS450_0001 in the Affymetrix Fluidics Station 450.

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

data_processing: Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Probe-level data were pre-processed using the RMA algorithm (Irizarry et al., 2003), which involves three steps: (i) background correction – where an error component of the intensities is estimated and eliminated; (ii) quantile normalization – where every slide is normalized to have the same cumulative frequency distribution; and (iii) summarization, using the median polish algorithm – where the median values per probe set, adjusted for slide differences, are calculated. RMA ignores the MM probes. On the basis of an empirical Bayes moderated t-statistic for the contrasts (Smyth, 2004), as implemented in the Bioconductor package limma, P values were calculated and then transformed into false-discovery rates, or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue.

source_name: 35S::FDPi, Arabidopsis seedlings

label_protocol: 1 μg of total RNA was reverse transcribed into cDNA using an oligo(dT)-T7 primer, and was then converted into cRNA and linearly amplified by T7 in vitro transcription reaction using the standard Ambion protocol (MessageAmp aRNA Kit, Ambion). cRNA was then reverse transcribed with random primers to dUTP-containing ds cDNA (WT ds cDNA Synthesis Kit, catalog no. 900813; Affymetrix). Fragmentation and labeling was performed with the GeneChip WT double-stranded DNA Terminal Labeling Kit (catalog no. 900812, Affymetrix)

growth_protocol:
Plants were grown under under long day conditions for 9 days and aerial parts were harvested at ZT16.
Plants were grown under under long day conditions for 9 days and aerial parts were harvested at ZT16.

extract_protocol: RNA was extracted using the RNA Plant Mini kit, QIAGEN (www1.qiagen.com/). (The amount of total RNA was quantified by NanoDrop).

tag: ecotype

tag: genotype/variation

value: 35S::FDP dsRNA

value: seedlings-aerial part

value: 9 days old


title: 35S::FDPi replicate 6


title: 35S::FDPi replicate 5


title: wt replicate 6

source_name: wt, Arabidopsis seedlings

value: wt


title: Sample DOT1-null UB cells 2

description: KO2 vs. WT3

source_name: KO2: DOT1-null UB cells at P0


title: D1147_BT407_12h_rep2

description:
BT_counts_table.txt
sample name:
D1147

source_name: whole body

tag: timepoint

tag: medium


title: D1148_BT407_12h_rep3

description:
BT_counts_table.txt
sample name:
D1148

tag: temperature


title: NASH-fibroblasts rep2


title: wt replicate 4


title: Control wildtype UB cells 2

description: WT2 vs. WT3

source_name: WT2: Wildtype UB cells at P0


title: D1146_BT407_12h_rep1

description:
BT_counts_table.txt
sample name:
D1146


title: D1145_BT679_12h_rep4

description:
BT_counts_table.txt
sample name:
D1145


title: CCl4-Fibroblasts rep2


title: hepatic stellate cells rep3

source_name: hepatic stellate cell

value: normal


title: hepatic stellate cells rep2


title: D1144_BT679_12h_rep3

description:
BT_counts_table.txt
sample name:
D1144


title: Il18+/+ mice

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

institute: Hyogo College of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low input Quick Amp Labeling Kit (Agilent) according to the manufacture’s instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was purified from prefrontal cortex using a Sepasol-RNA I Super (Nacalai Tesque, Kyoto, Japan) according to the manufacturer’s instructions, and treated with five units of RNase free DNase I at 37°C for 30 min to remove genomic DNA contamination. After phenol/chloroform extraction and ethanol precipitation, total RNA was dissolved in de-ionized distilled water. RNA concentrations determined by spectrophotometry.

tag: gender

value: male

tag: background strain

value: C57Bl/6 N

value: hippocampus


title: Control wildtype UB cells 4

description: WT4 vs. WT3

source_name: WT4: Wildtype UB cells at P0

value: Postnatal day 0

tag: tissue

value: Mouse Kidneys

value: UB cells

value: control


title: NASH-fibroblasts rep1


title: Control wildtype UB cells 3

description: WT3 vs. WT3


title: D1143_BT679_12h_rep2

description:
BT_counts_table.txt
sample name:
D1143

value: whole body

value: Wild type (N2)

value: mNGM

value: 20 degrees Celsius


title: Control wildtype UB cells 1

description: WT1 vs. WT3

source_name: WT1: Wildtype UB cells at P0


title: hepatic stellate cells rep1

value: liver


title: wt replicate 5


title: HUVEC_TNF_rep3

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description:
SAMPLE 14
HUVEC cells treated with TNFalpha.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip using standard Illumina protocol.

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

data_processing:
CpG-probes were filtered before normalization based on following criteria: probes containing a SNP within 3 bp of the analyzed CpG site, bad quality probes based on an iterative greedycut algorithm with a detection p-value threshold of 0.01, and probes with missing values in at least one sample. After filtering these CpG-probes, methylation values were within-array normalized using the beta mixture quantile dilation (BMIQ) method. Another filtering step was performed after normalization based on following criteria: probes measuring methylation not at CpG sites (CC, CAG, CAH, …) and probes on sex chromosomes.
processed.matrix.txt: BMIQ normalized beta-values.
signal.matrix.txt: Unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: HUVEC, TNF, replicate3

label_protocol: Standard Illumina Protocol.

growth_protocol: Human umbilical vein endothelial cells (HUVEC) (Lonza, Walkersville, MD, USA), a pool from four donors, at passage 3 were cultured in a phenol-free endothelial growth medium (EGM) supplemented with 2% fetal bovine serum (FBS), 0.4% fibroblast growth factor, 0.1% vascular endothelial growth factor, 0.1% heparin, 0.1% insulin-like growth factor, 0.1% ascorbic acid, 0.1% epidermal growth factor and 0.04% hydrocortisone (all from Lonza).

extract_protocol: DNeasy Blood & Tissue kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: HUVECs, at passage 4, were seeded into the 24-well plates (BD-Falcon, Le Pont-De-Claix, France) and grown to reach 60-70% confluence. The medium was then replaced to expose the cells for 3 h to the culture medium containing either solvent alone (ethanol 0.5‰, control wells, vehicle) or different metabolites: 3′-O-methyl(-)-epicatechin, 4′-O-methyl(-)-epicatechin-7-β-D-glucuronide or (-)-epicatechin-4′-sulfate at 1µM. At the end of the incubation period, the medium was replaced with flavanol free medium and left for further 18 hours until confluence. The confluent monolayer was stimulated for 4 hours with TNFα (R&D Systems Lille, France) at 0.1 ng/mL or only incubated with PBS/BSA (0,01‰, negative control).

tag: cell line

value: HUVEC

value: Human umbilical vein endothelial cells

value: TNF


title: Il18-/- mice


title: HUVEC_MIX_rep2

description:
SAMPLE 12
HUVEC cells treated with mixture of epicatechin metabolites followed by TNFalpha stimulus.

source_name: HUVEC, MIX, replicate2

value: MIX+TNF


title: D1141_BT247_12h_rep4

description:
BT_counts_table.txt
sample name:
D1141


title: D1139_BT247_12h_rep2

description:
BT_counts_table.txt
sample name:
D1139


title: HUVEC_MIX_rep1

description:
SAMPLE 11
HUVEC cells treated with mixture of epicatechin metabolites followed by TNFalpha stimulus.

source_name: HUVEC, MIX, replicate1


title: HUVEC_EC4S_rep1

description:
SAMPLE 9
HUVEC cells treated with 1 µM EC4'S epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, EC4S, replicate1


title: HUVEC_EC4S_rep2

description:
SAMPLE 10
HUVEC cells treated with 1 µM EC4'S epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, EC4S, replicate2


title: D1140_BT247_12h_rep3

description:
BT_counts_table.txt
sample name:
D1140


title: D1137_OP_6h_rep4

description:
BT_counts_table.txt
sample name:
D1137

value: E. coli OP50

value: 6 h


title: HUVEC_4MEC7G_rep2

description:
SAMPLE 8
HUVEC cells treated with 1 µM 4'MEC7G epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, 4MEC7G, replicate2


title: D1136_OP_6h_rep3

description:
BT_counts_table.txt
sample name:
D1136


title: D1135_OP_6h_rep2

description:
BT_counts_table.txt
sample name:
D1135


title: HUVEC_3MEC_rep2

description:
SAMPLE 6
HUVEC cells treated with 1 µM 3'MEC epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, 3MEC, replicate2


title: D1134_OP_6h_rep1

description:
BT_counts_table.txt
sample name:
D1134


title: HUVEC_3MEC_rep1

description:
SAMPLE 5
HUVEC cells treated with 1 µM 3'MEC epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, 3MEC, replicate1


title: HUVEC_TNF_rep2

description:
SAMPLE 4
HUVEC cells treated with TNFalpha.

source_name: HUVEC, TNF, replicate2


title: HUVEC_TNF_rep1

description:
SAMPLE 3
HUVEC cells treated with TNFalpha.

source_name: HUVEC, TNF, replicate1


title: D1132_BT407_6h_rep3

description:
BT_counts_table.txt
sample name:
D1132


title: D1131_BT407_6h_rep2

description:
BT_counts_table.txt
sample name:
D1131


title: HUVEC_control_rep2

description:
SAMPLE 2
HUVEC cells treated with solvent control.

source_name: HUVEC, control, replicate2

value: Solvent


title: D1130_BT407_6h_rep1

description:
BT_counts_table.txt
sample name:
D1130

source_name: whole body


title: D1138_BT247_12h_rep1

description:
BT_counts_table.txt
sample name:
D1138


title: HUVEC_control_rep3

description:
SAMPLE 13
HUVEC cells treated with solvent control.

source_name: HUVEC, control, replicate3


title: mutant oligodendrocyte rep2 [RNA-Seq]

city: Chicago

first: Huan

last: Xu

state: Illinois

address: 5841 S. Maryland Ave MC2030, Ab514

department: Neurology

institute: University of Chicago

data_processing:
Quality Control: fastQC V0.11.8
Gapped mapping to reference genome: STAR V2.6.1
Ungapped mapping to reference genome: Kallisto V0.44.0
Expression Quantification: Subread V1.6.3
Data visualization: R v3.5.1
Genome_build: UCSC mouse genome mm10
Supplementary_files_format_and_content: count

source_name: Brain

growth_protocol: Using an immunopanning approach, we purified OPCs from neonatal mouse pups. These cells were maintained under proliferating conditions with the addition of the OPC mitogen PDGFα. We obtained mature oligodendrocytes by promoting OPC differentiation via removal of PDGFα and addition of the T3 hormone to the culture media

extract_protocol:
Lysis buffer (Bio-Rad Aurum total RNA Mini Kit , Cat# 732-6820) was added to culture dishes, cells were then removed by cell scrapers, and flash frozen on dry ice. RNA was extracted using the Bio-Rad Aurum total RNA Mini Kit (Cat# 732-6820) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: Mettl14 fl/fl; Olig2-Cre

value: C57BL/6 background


title: HUVEC_control_rep1

description:
SAMPLE 1
HUVEC cells treated with solvent control.

source_name: HUVEC, control, replicate1


title: mutant oligodendrocyte rep3 [RNA-Seq]


title: control oligodendrocyte rep3 [RNA-Seq]


title: D1127_BT679_6h_rep2

description:
BT_counts_table.txt
sample name:
D1127


title: D1142_BT679_12h_rep1

description:
BT_counts_table.txt
sample name:
D1142


title: D1129_BT679_6h_rep4

description:
BT_counts_table.txt
sample name:
D1129


title: control oligodendrocyte rep1 [RNA-Seq]


title: D1133_BT407_6h_rep4

description:
BT_counts_table.txt
sample name:
D1133


title: D1126_BT679_6h_rep1

description:
BT_counts_table.txt
sample name:
D1126


title: mutant oligodendrocyte rep1 [RNA-Seq]


title: HUVEC_4MEC7G_rep1

description:
SAMPLE 7
HUVEC cells treated with 1 µM 4'MEC7G epicatechin metabolite followed by TNFalpha stimulus.

source_name: HUVEC, 4MEC7G, replicate1


title: D1124_BT247_6h_rep3

description:
BT_counts_table.txt
sample name:
D1124


title: TAMs 4

city: Charlottesville

first: Hui

last: Zong

state: VA

address: 7046 Jordan Hall, 7th Floor, 1340 JPA

department: Microbiology, immunology and cancer biology

institute: University of Virginia

data_processing:
Adaptor Trimming by bioconductor
Initial quality assessment of sequencing reads using FastQC
Transcript abundance was estimated with Sailfish
Counts of reads mapping to GENCODE genes using the tximport package
Differential gene expression by Deseq2 Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: TAMs 4

extract_protocol: Tumor associated microglia and normal microglia was purified from tumor and cerebral cortex separately. In briefly, tumor mice were anaesthetized (60mg/kg ketamine; 12 mg/kg xylazine). Tumor tissue or cerebral cortex was dissected. After cutting into pieces, tissue was dissociated in enzyme solution (100 U papain, 4mg L-cysteine and 200U DNase I) for 45 minutes. Digested tumor pieces were triturated in enzyme inhibitor solution. After depletion of myelin, the microglia was incubated and captured with CD11b magnetic beads for one hour on ice. The cell suspension was added into purification column. After washing three times with washing buffer, the microglia was eluted into suspension buffer. Cells were spin down at 1000g for 5 minutes.

tag: mouse age

value: postnatal  day 66

tag: rna extraction methods

value: Trizol method

value: tumor-associated microglia/macrophage


title: mutant OPC rep3 [RNA-Seq]

tag: genotype


title: mutant OPC rep2 [RNA-Seq]


title: D1123_BT247_6h_rep2

description:
BT_counts_table.txt
sample name:
D1123

value: whole body

tag: treatment


title: D1122_BT247_6h_rep1

description:
BT_counts_table.txt
sample name:
D1122

tag: strain

value: Wild type (N2)


title: mutant OPC rep1 [RNA-Seq]


title: control OPC rep3 [RNA-Seq]


title: D1128_BT679_6h_rep3

description:
BT_counts_table.txt
sample name:
D1128

value: mNGM


title: control OPC rep2 [RNA-Seq]


title: control oligodendrocyte rep2 [RNA-Seq]


title: control OPC rep1 [RNA-Seq]


title: no UV tdTomato+ rep 1

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

description:
R_r1
RvsG_expression.csv

data_processing:
Paired-end sequencing reads were trimmed of adapter sequences, analyzed for quality using the Fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned to the mouse reference genome version mm10 using the Tophat alignment software (version 2.0.12) (Trapnell, Pachter, & Salzberg, 2009)
Fragments and exons were quantified using the Cufflinks program (version 2.2.1) (Trapnell et al., 2013).
DEseq2 (version 1.14.1) (Love, Huber, & Anders, 2014) was utilized to distinquish differentially expressed genes from GFP+ and tdTomato+ populations in R (3.3.2).
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values files include base mean, log2 fold change, log fold change standard error (lfcSE), stat (Wald statistic), pvalue, padj (Benjamini-Hochberg).

source_name: mouse skin

extract_protocol:
Total RNA from GFP+ and tdTomato+ cells from mice 1-4 was monitored for quality control using the Agilent Bioanalyzer Nano RNA chip.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol.  The input quantity for total RNA was 1µg, and mRNA was enriched using oligo dT magnetic beads.  The enriched mRNA was chemically fragmented for four minutes.  First strand cDNA synthesis was performed using random primers, dNTPs, and reverse transcriptase to make cDNA.  After second strand synthesis the cDNA was cleaned using AMPure XP beads, the cDNA was end repaired, and then the 3’ ends were adenylated.  Illumina barcoded adapters were ligated on the ends, and the adapter ligated fragments were enriched through nine cycles of PCR.  The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.

treatment_protocol: Mice were injected once daily for 10 days with tamoxifen starting at P21.  At P50 mice were shaved and depilated.  Mice were either treated with 150mJ/cm2 UVB or mock treated (normal light) for 3 days. Back skin was collected at P54 and dissociated into single cells for FACs analysis.  Sorted EGFP+ and tdTomato+ cells from each mouse were used for total RNA extractions

value: ROSA<mTmG> +; Cre+

tag: mouse #

tag: uv treatment

value: mock

tag: flourescent marker

value: tdTomato


title: UV EGFP+ rep 1

description:
G_r3
RvsG_expression.csv

value: EGFP


title: UV tdTomato+ rep 2

description:
R_r4
RvsG_expression.csv


title: UV EGFP+ rep 2

description:
G_r4
RvsG_expression.csv


title: UV tdTomato+ rep 1

description:
R_r3
RvsG_expression.csv


title: Hdac2-3

city: Sherbrooke

first: Alexis

last: Gonneaud

state: QC

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

country: Canada

institute: Université de Sherbrooke

description:
mutant HDAC2-/-
O23

data_processing:
The mapping is performed with “Star 2.4.0f1”.
The basecalling is performed directly with the HiSeq instrument and run with the tool “Illumina RTA”
The “Illumina bcl2fastq 1.8.4” tool is used to generate the FASTQ prior to the alignment
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files contain gene counts for each Sample

source_name: Jejunum

growth_protocol: Enteroid were grown in ENR media for 5 days.

extract_protocol:
Total RNAs from wild-type, Hdac1- or Hdac2-deleted enteroids were purified with the RNeasy mini kit (Qiagen), and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.
RNA-seq - Illumina HiSeq4000 PE100 Sequencing

tag: cell type

value: Enteroid in culture


title: MAVSKO-Veh-4_2

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-4_ACGCACCT-GGTGAAGG_AH25YVBCX3_L002_001

data_processing:
Basecalling was performed using RTA 2.4.11
bcl files were converted to fastq using CASAVA 1.8.2
For protein coding genes, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Count tables were generated using featureCounts v1.6.2.
For Transposable elements, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files of raw counts

extract_protocol:
bulk RNA extracted from the whole tissue: RNA was extracted from hippocampal lysates using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
for WT and MAVS-KO ICV-Veh and ICV-STZ mice: Total RNA library preparation and sequencing (500ng 2x125bp). RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (kapabiosystems) in accordance with the manufacturer’s instructions. Briefly, 500ng of total RNA was used for ribosomal depletion and fragmentation. Depleted RNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 9 cycles). Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent 2100), and were sequenced on an Illumina HiSeq2500 sequencer (v2 chemistry for Rapid Run) using 2 x 125bp cycles.
muMT and WT mice: Library preparation and RNAseq for WT and muMT mice were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina NextSeq 500 System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit – Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).

tag: genotype/variation

value: intracerebroventricular injection of vehicle (ICVI-Veh)

value: hippocampus


title: Hdac2-2

description:
mutant HDAC2-/-
O22


title: Hdac2-4

description:
mutant HDAC2-/-
O24


title: no UV tdTomato+ rep 2

description:
R_r2
RvsG_expression.csv


title: Hdac2-1

description:
mutant HDAC2-/-
O21


title: Hdac1-4

description:
mutant HDAC1-/-
O14


title: P70 K14Cre-cKO bulge CD34(+)CD49f(+)_rep2

city: Zhunan

first: Liang-Tung

last: Yang

state: Miaoli County

address: 35, Keyan Rd.

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from FACS sorted hair follicle stem cells using cell surface markers

hyb_protocol: Samples were hybridized with GeneChipTM Mouse gene 2.0 ST Arrays (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Affymetrix GeneChip Command Console software (version4.1.2, Affymetrix) was used to analyze array images to get raw data and then Affymetrix Expression Console 1.4.1. for normalization (RMA); Partek Genomics Suite software (PGS, v6.6, Partek, Inc.) for statistical analysis

source_name: FACS sorted CD34+CD49f+ cells from postnatal day 70 K14Cre_cKO replica#2

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT pico cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Keratinocytes were isolated enzymatically from mouse skin and FACS sorted, no expansion

extract_protocol: Total RNA was isolated from FACS-purified cells directly sorted into TRIzol (Invitrogen), followed by purification using RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. The RNA quality and concentrations were determined by an Agilent 2100 Bioanalyzer using the RNA 6000 Pico Assay (Agilent Technologies).

value: back skin

value: bulge stem cells

tag: hair stage

value: telogen


title: no UV EGFP+ rep 1

description:
G_r1
RvsG_expression.csv


title: MAVSKO-Veh-4_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-4_ACGCACCT-GGTGAAGG_AH25YVBCX3_L001_001


title: Hdac1-3

description:
mutant HDAC1-/-
O13


title: Hdac1-2

description:
mutant HDAC1-/-
O12


title: D1117_BT407_2h_rep4

description:
BT_counts_table.txt
sample name:
D1117

tag: timepoint

value: 2 h

tag: medium

value: 20 degrees Celsius


title: D1115_BT407_2h_rep2

description:
BT_counts_table.txt
sample name:
D1115

tag: temperature


title: D1114_BT407_2h_rep1

description:
BT_counts_table.txt
sample name:
D1114


title: D1121_OP_2h_rep4

description:
BT_counts_table.txt
sample name:
D1121

value: E. coli OP50


title: D1119_OP_2h_rep2

description:
BT_counts_table.txt
sample name:
D1119


title: D1120_OP_2h_rep3

description:
BT_counts_table.txt
sample name:
D1120


title: D1118_OP_2h_rep1

description:
BT_counts_table.txt
sample name:
D1118


title: D1116_BT407_2h_rep3

description:
BT_counts_table.txt
sample name:
D1116


title: MAVSKO-Veh-3_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-3_GTATGTTC-AACAGGAA_AH25YVBCX3_L001_001


title: D1112_BT679_2h_rep3

description:
BT_counts_table.txt
sample name:
D1112


title: D1113_BT679_2h_rep4

description:
BT_counts_table.txt
sample name:
D1113


title: Hdac1-1

description:
mutant HDAC1-/-
O11


title: D1111_BT679_2h_rep2

description:
BT_counts_table.txt
sample name:
D1111


title: MAVSKO-Veh-2_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-2_CGCTATGT-TCCGACAC_AH25YVBCX3_L002_001


title: Ctrl4

description:
Ctr
O4


title: no UV EGFP+ rep 2

description:
G_r2
RvsG_expression.csv


title: MAVSKO-Veh-2_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-2_CGCTATGT-TCCGACAC_AH25YVBCX3_L001_001


title: D1110_BT679_2h_rep1

description:
BT_counts_table.txt
sample name:
D1110


title: Ctrl3

description:
Ctr
O3


title: D1109_BT247_2h_rep4

description:
BT_counts_table.txt
sample name:
D1109


title: MAVSKO-Veh-3_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-3_GTATGTTC-AACAGGAA_AH25YVBCX3_L002_001


title: MAVSKO-Veh-1_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-1_TATCGCAC-CTTAGTGT_AH25YVBCX3_L002_001


title: Ctrl2

description:
Ctr
O2


title: MAVSKO-Veh-1_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-Veh-1_TATCGCAC-CTTAGTGT_AH25YVBCX3_L001_001


title: D1125_BT247_6h_rep4

description:
BT_counts_table.txt
sample name:
D1125

value: 6 h


title: Ctrl1

description:
Ctr
O1


title: MAVSKO-STZ-2_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKo-STZ-2_CGTCTGCG-TTCACAAT_AH25YVBCX3_L002_001

value: intracerebroventricular injection of streptozotocin (ICVI-STZ)


title: MAVSKO-STZ-3_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-STZ-3_TCGATATC-ACACGAGT_AH25YVBCX3_L001_001


title: D1107_BT247_2h_rep2

description:
BT_counts_table.txt
sample name:
D1107

value: whole body

value: Wild type (N2)


title: Empty_vector_BT407_12h_rep2

treatment_protocol: Worms were exposed to OP50 and BT at the stage L4. The BT strains were diluted in varied concentration (1:100 for B-18679, 1:10 for B-18247 and 1:2 for B-18407 by Standard lab food E. coli OP50). The experiments with BT were performed at 20°C. mNGM medium.

tag: transfection

value: empty vector

tag: treatment (bacillus thuringiensis)


title: Empty_vector_BT407_12h_rep1


title: D1108_BT247_2h_rep3

description:
BT_counts_table.txt
sample name:
D1108

tag: tissue

value: mNGM


title: D1106_BT247_2h_rep1

description:
BT_counts_table.txt
sample name:
D1106


title: P70 control bulge CD34(+)CD49f(+)_rep1

source_name: FACS sorted CD34+CD49f+ cells from postnatal day 70 control littermate replica#1


title: P70 control bulge CD34(+)CD49f(+)_rep2

source_name: FACS sorted CD34+CD49f+ cells from postnatal day 70 control littermate replica#2


title: elt-2_RNAi_BT407_12h_rep3

value: elt-2 RNAi


title: P70 K14Cre_cKO bulge CD34(+)CD49f(+)_rep1

source_name: FACS sorted CD34+CD49f+ cells from postnatal day 70 K14Cre_cKO replica#1


title: WT-STZ-2

description:
processed data file:
wt-veh-vs-stz-genomic-counts.csv
wt-veh-vs-stz-genomic+transposable-elements-counts.csv
WT-STZ-2_TGGAACAA_BC7NCLANXX_L002_001

tag: strain background

value: wild type


title: WT-STZ-3

description:
processed data file:
wt-veh-vs-stz-genomic-counts.csv
wt-veh-vs-stz-genomic+transposable-elements-counts.csv
WT-STZ-3_AGCACCTC_BC7NCLANXX_L002_001


title: MAVSKO-STZ-2_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKo-STZ-2_CGTCTGCG-TTCACAAT_AH25YVBCX3_L001_001


title: MAVSKO-STZ-1_1

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-STZ-1_TACTCATA-CCTGTGGC_AH25YVBCX3_L001_001


title: MAVSKO-STZ-1_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-STZ-1_TACTCATA-CCTGTGGC_AH25YVBCX3_L002_001


title: WT-C-2_2

description:
processed data file:
wt-veh-vs-stz-genomic-counts.csv
wt-veh-vs-stz-genomic+transposable-elements-counts.csv
WT-C-2_ATTGAGGA_BC7FHHANXX_L002_001


title: WT-STZ-1

description:
processed data file:
wt-veh-vs-stz-genomic-counts.csv
wt-veh-vs-stz-genomic+transposable-elements-counts.csv
WT-STZ-1_GCTCGGTA_BC7NCLANXX_L001_001


title: WT-C-2_1

description:
processed data file:
wt-veh-vs-stz-genomic-counts.csv
wt-veh-vs-stz-genomic+transposable-elements-counts.csv
WT-C-2_ATTGAGGA_BC7NCLANXX_L001_001


title: Empty_vector_BT407_6h_rep3


title: Empty_vector_BT407_6h_rep2


title: elt-2_RNAi_BT407_12h_rep1


title: WT-C-1

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
WT-C-1_AAGGTACA_BC7NCLANXX_L002_001

value: untreated


title: Empty_vector_BT407_12h_rep3


title: elt-2_RNAi_BT407_6h_rep3


title: C35 Treated

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Illumina RTA was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
Read counts for each refseq gene were summarized using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: Tab Delimited file containing raw gene expression counts

source_name: TET inhibition

extract_protocol: Kapa mRNA HyperPrep

treatment_protocol: Mouse Embryonic Fibroblasts are treated with C35 for 7 days

value: Mouse Embryonic Fibroblasts


title: elt-2_RNAi_BT407_12h_rep2


title: Empty_vector_BT407_6h_rep1


title: elt-2_RNAi_BT407_6h_rep2


title: 4615 KO m6A-IP

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
Read count of connected bins was quantified by R package RADAR.
Differential methylation sites detection by RADAR
Genome_build: mm10
Supplementary_files_format_and_content: differential methylation sites in BED12 file.

source_name: liver

extract_protocol:
TRIzol (Invitrogen) + polyT beads(thermo fisher)
Kapa hyper RNA library kit

value: METTL14 knockout

value: liver

tag: molecule subtype

value: m6A enriched mRNA


title: 4616 KO m6A-IP

tag: genotype


title: miRNA AD2_9m

city: BEIJING

first: MA

address: haidian

institute: peking university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The details of mRNA-seq, miRNA-seq, and circRNA-seq methods are described in Supplementary files.

value: brain

tag: age


title: miRNA AD3_9m

tag: strain


title: 4612 WT m6A-IP

value: Wild Type


title: MAVSKO-STZ-3_2

description:
processed data file:
4veh-vs-3stz-mavsko-genomic-counts.csv
4veh-vs-3stz-mavsko-genomic+transposable-elements-counts.csv
MAVSKO-STZ-3_TCGATATC-ACACGAGT_AH25YVBCX3_L002_001

tag: treatment

value: hippocampus


title: Empty_vector_BT247_12h_rep2

city: Kiel

first: Hinrich

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 4587 WT m6A-IP


title: 4586 KO m6A-IP


title: Empty_vector_BT247_12h_rep1


title: miRNA WT3_9m


title: miRNA AD1_9m


title: Empty_vector_BT247_12h_rep3


title: elt-2_RNAi_BT407_6h_rep1


title: miRNA WT2_9m


title: 4584 WT m6A-IP


title: miRNA WT1_9m


title: 4583 KO m6A-IP


title: elt-2_RNAi_BT247_12h_rep1


title: elt-2_RNAi_BT247_12h_rep2


title: miRNA AD3_6m


title: miRNA AD2_6m


title: Empty_vector_BT247_6h_rep3


title: 4616 KO INPUT

value: mRNA


title: Empty_vector_BT247_6h_rep2

value: 6 h


title: 4615 KO INPUT


title: Empty_vector_BT247_6h_rep1


title: miRNA AD1_6m


title: miRNA WT3_6m


title: 4612 WT INPUT


title: miRNA WT2_6m


title: elt-2_RNAi_BT247_6h_rep2


title: 4584 WT INPUT


title: elt-2_RNAi_BT247_6h_rep3


title: elt-2_RNAi_BT247_6h_rep1


title: elt-2_RNAi_BT247_12h_rep3


title: 4582 WT m6A-IP


title: 5xFAD-21

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

data_processing:
The quality of the sequence reads was checked and low-quality sequences were trimmed using the Trimmomatic (Bolger et al, 2014).
The trimmed sequences were aligned into the mouse genome using the STAR aligner (Dobin et al, 2013), and the Cuffnorm (Trapnell et al, 2012) was used to calculate normalized values of fragments per kilobase of transcript per million mapped reads (FPKM) based on GENCODE annotation (Release M17, GRCm38.p6).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each transcript were calculated.

source_name: Pineal gland

extract_protocol:
Total RNA from the pineal gland was extracted using TRIzol reagent (Thermo Fisher), and their integrity was checked using the Agilent 2100 BioAnalyzer (Agilent).
Total RNA was treated with a Ribo-Zero Gold rRNA Removal Kit (Illumina) to remove ribosomal RNAs, and RNA sequencing libraries were constructed using a TruSeq Stranded Total RNA Kit (Illumina). The libraries were paired-end sequenced with 100 sequencing cycles on a HiSeq 2500 system (Illumina).

value: Pineal gland

tag: biological replicate

value: Replicate 4


title: 4587 WT INPUT


title: 4586 KO INPUT


title: Empty_vector_BT679_12h_rep3

last: Schulenburg

address: Am Botanischen Garten 1-9


title: 5xFAD-3

value: Replicate 3


title: 4583 KO INPUT


title: 5xFAD-2

value: Replicate 2


title: 4582 WT INPUT


title: 5xFAD-1

value: Replicate 1


title: Empty_vector_BT679_12h_rep1

value: empty vector


title: miRNA WT1_6m

value: wild type


title: Normal-23


title: elt-2_RNAi_BT679_12h_rep3

value: elt-2 RNAi


title: Normal-22


title: Mock control

description: VC

source_name: Control

value: Mouse Embryonic Fibroblasts


title: Normal-21


title: elt-2_RNAi_BT679_12h_rep2

source_name: whole body


title: Empty_vector_BT679_12h_rep2


title: elt-2_RNAi_BT679_12h_rep1


title: Empty_vector_BT679_6h_rep3


title: E57-lung  SCC

city: Seattle

first: Laura

last: Riolobos

state: WA

address: 850 Republican St

institute: University of Washington

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 generating 50 base pair paired end reads
Reads of low quality were filtered, and adapters trimmed using Cutadapt v1.9.1.
Alignment to the reference genome (UCSC mm10) was performed using TopHat v2.0.1
RNA counts were generated for each gene using the Python package HTSeq v0.6.1, employing the “intersection-strict” overlap mode
DESeq2 was used to normalize and transform the data, examine the relationship between samples (by plotting the first two principal components) and to test for differential expression

source_name: lung

extract_protocol:
RNA was extracted using the RNeasy FFPE kit (Qiagen, Hilden, Germany)
Libraries were prepared from using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (Clontech Laboratories, Inc., Mountain View, CA, USA).

treatment_protocol: FFPE sections were subjected to laser capture microdisection (LCM) before RNA extraction

value: NIH Swiss

value: lung squamous cell carcinoma

value: NTCU

value: wt


title: D44-lung  SCC


title: elt-2_RNAi_BT679_6h_rep3


title: elt-2_RNAi_BT679_6h_rep2


title: Empty_vector_BT679_6h_rep1


title: Normal-11


title: Pancreatic islet-derived exosome, HI-Cyto-SAMN08769397

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

institute: Indiana University School of Medicine

description: Raw counts and variance stabilized normalized counts of mRNAs and lncRNAs for all the samples are provided in two tabs in the same excel sheet

data_processing:
Sequencing reads were aligned to the human genome hg19 using STAR aligner v 2.5.3a
Gencode v29 was used for annotating the reads to mRNA and long non-coding RNAs.
DESeq2 was used to analyze the raw counts and perform differential expression analysis step
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx files for raw counts and variance stabilized normalized counts

source_name: Pancreatic islet-derived exosome

extract_protocol:
After 24 hours of cytokine treatment, the islet culture media was collected and centrifuged for 30 minutes at 3000 x g to remove cellular debris. The supernatant was recovered and exosomes were isolated using ExoQuick-TC (SBI Biosciences), according to manufacturer’s protocol. Total RNA was isolated using the SeraMir RNA isolation kit (SBI Biosciences).
Total RNA sequencing utilized 1 – 10 ng of RNA as input. Libraries for total RNA sequencing were prepared using Clontech SMARTer RNA Pico Kit v2, 96 rxns (Takara). Sequencing was performed using Illumina HiSeq 4000 (75 bp paired-end reads), generating 30 million reads per library

treatment_protocol: Cadaveric islets were cultured overnight in standard Prodo medium (Prodo Labs, CA) that had been depleted for exosomes. In order to mimic the pro-inflammatory conditions of T1D, islets were treated with or without 50 U/ml IL-1β and 1000 U/ml IFN-γ for 24 hours.

value: Islet derived exosomes

value: Cytokines IL-1β and IFN-γ

tag: Sex

value: Male

tag: ethnicity

value: White

tag: bmi


title: Pancreatic islet-derived exosome, HI-Cyto-SAMN08768738


title: D42-lung  SCC


title: Pancreatic islet-derived exosome, HI-Ctrl-SAMN08769397

value: Untreated


title: Pancreatic islet-derived exosome, HI-Ctrl-SAMN08768738


title: A08-normal lung

value: normal lung


title: Empty_vector_BT679_6h_rep2

value: 6 h


title: N2_BT679_12h-Rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text file includes Raw reads counts for each Sample

treatment_protocol: Worms were exposed to OP50 and BT at the stage L4. The BT strains were diluted in 1:10 (non-pathogenic BT strain BT407). The experiments with BT were performed at 20°C.

value: Wild type

tag: time

value: mNGM


title: A07-normal lung


title: N2_BT679_12h-Rep2


title: D39-lung  SCC


title: A06-normal lung


title: Serum_CT2_rep1

city: Weifang

first: Donghua

state: Shandong

address: Yuhe Road No.2428

department: Department of Rheumatology and Immunology

institute: Weifang Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Serum, CT2, replicate 1

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: All blood samples were separately collected and sequentially centrifuged at 2000 rpm for 10 min. The cell-free serum from the supernatant was stored at -80°C for further detection.

tag: disease

value: healthy control

value: serum

tag: gender

value: female


title: Pancreatic islet-derived exosome, HI-Cyto-SAMN08769129

value: Female


title: D36-lung  SCC

value: NIH Swiss


title: Serum_RA2_rep1

source_name: Serum, RA2, replicate 1

growth_protocol: The cell-free serum from the supernatant was stored at -80°C for further detection.

value: RA


title: Serum_CT1_rep1

source_name: Serum, CT1, replicate 1


title: A03-normal lung


title: elt-2_RNAi_BT679_6h_rep1

value: elt-2 RNAi

tag: timepoint


title: Serum_CT3_rep1

source_name: Serum, CT3, replicate 1


title: Serum_RA1_rep1

source_name: Serum, RA1, replicate 1


title: Serum_RA3_rep1

source_name: Serum, RA3, replicate 1


title: clec-4_BT679_12h-Rep2

tag: medium

tag: temperature


title: Pancreatic islet-derived exosome, HI-Ctrl-SAMN08769129

tag: tissue


title: A01-normal lung

value: wt


title: Pancreatic islet-derived exosome, HI-Cyto-SAMN08773446

value: Islet derived exosomes


title: clec-4_BT679_12h-Rep1


title: N2_BT247_12h-Rep3


title: Gabra6-cre;LSL-SmoM2_3

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

description:
ATAC-seq
LTGA1_Gabra6-SmoM2_TOTAL.NORM_peaks.bed

data_processing:
Sequenced reads from all independent sequenced libraries were quality assessed by using fastQC and trimmed with Trimmomatic. Reads from biological replicates were merged for all analysis. Total reads were aligned to either the mouse genome NCBI37/mm9 or the human genome GRCh37/hg19 using Bowtie2, using the parameters ‘--very-sensitive -k 1’, thus discarding ambiguous reads mapping at multiple sites. Duplicated reads and reads mapping on mitochondrial DNA were discarded for further analysis with SAMtools.
Normalized BigWig tracks of ATAC-seq signals were generated with BEDtools 2.24.0 and the bedGraphToBigWig program and visualized on the UCSC Genome Browser.
The HOMER software was further used to analyze ATAC-seq data. The command ‘findPeaks’ was used for peak calling with these parameters ‘-size 150 -minDist 1000’; the command ‘get-DifferentialPeaks’ was used to find peaks with differential ATAC-seq signals between two conditions (‘-F 2 -P 0.001’); the command ‘findMotifsGenome.pl’ was used for motifs enrichment analysis; the command ‘annotatePeaks.pl’ was used to annotate peaks to related genes and genomic regions and to count the number of normalized reads on specific regions.
Genome_build: mouse genome NCBI37/mm9 and the human genome GRCh37/hg19
Supplementary_files_format_and_content: BED files of peaks called with HOMER on normalized ATAC-seq data

source_name: mice cerebellum

growth_protocol: Human iPSC-derived neuroepithelial-like stem cells AF22 at passage 30, were cultured in a 1:1 ratio mixture of Neurobasal and DMEM/F12 media supplemented with N2 (1:100), B27 (1 µl/ml), 10 ng/ml EGF and 10 ng/ml FGF2. Cerebella were dissected from P7 mice.

extract_protocol:
Nuclei were isolated by transferring 400 ul of supernatant in a plastic tube and sequentially added 400 ul of 50% Iodixanol solution (homogenization buffer and 50% Iodixanol solution), 600 ul of 29% Iodixanol (homogenization buffer, 160 mM and 29% Iodixanol solution) and 600 ul of 35% Iodixanol solution (homogenization buffer, 160 mM and 35% Iodixanol solution) to the bottom of the tube, avoiding mixture of layers.   We centrifuged for 20 min at 3,000 RCF and we discarded upper layers of the gradient in order to collect 200 ul from the nuclei band. We counted nuclei and transferred 50.000 into a tube with 1 ml of ATAC-Resuspension Buffer (RSB) + 0.1% Tween-20 (10 mM  Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). We pelleted nuclei by centrifuging for 10 minutes at 500 RCF and resuspended in 50 ul cold ATAC-RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin,. We lysed for 3 minutes on ice and washed with 1 ml of cold ATAC-RSB + 0.1% Tween-20.
We transposed the samples by resuspending nuclei in 50 ul of transposition mix (25 ul 2x TD buffer, 100nM transposase, 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) and incubated at 37°C for 30 minutes. We purified the transposed DNA using the Qiagen MinElute PCR Purification Kit (cat. # 28004) and eluted in 10 μl elution buffer. Next we amplified the transposed DNA fragments in the PCR mix (10 μl transposed DNA, 10 μl nuclease-free H2O, 2.5 μl 25 μM PCR Primer 1, 2.5 μl 25 μM Barcoded PCR Primer 2 and 25 μl NEB Next High-Fidelity 2× PCR Master Mix cat. # M0541L). The final ATAC-seq libraries were purified using the Qiagen MinElute PCR Purification Kit, quantified at the Qubit Fluorometer (Invitrogen, cat. #Q33226) and quality controlled with the High Sensitivity DNA Assay at the 2100 Bioanalyzer (Agilent, cat. # G2939BA). Four and three independent biological replicates, sequenced as independent libraries, were performed for Gabra6-cre;LSL-SmoM2 and control Gabra6-cre, respectively. Two independent biological replicates, sequenced as independent libraries, were performed for hSynI-creER+LSL-tdTomato, hSynI-creER+LSL-BRPF1 TR, hSynI-creER+LSL-SmoM2 and hSynI-creER+LSL-SmoM2+LSL-BRPF1 TR cell lines.
All libraries were sequenced as single reads of 50 bp with the Illumina HiSeq2500.

treatment_protocol: Frozen cerebella were dounced in 2 ml cold homogenization buffer (0.017 mM PMSF, 0.17 mM β-mercaptoethanol, 320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8) and pelleted at 100 RCF for 1 min.

value: cerebellum


title: Pancreatic islet-derived exosome, HI-Cyto-SAMN08769390

value: Cytokines IL-1β and IFN-γ

value: Black/African


title: ECM2_1

city: Baltimore

first: Daniele

middle: Marie

last: Gilkes

state: MD

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

data_processing:
Preliminary analysis was performed by Quick Biology. The reads were then mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
Gene expression level was estimated using RSEM v1.2.15.
TMM (Trimmed Mean of M-values) was used to normalize gene expression.
Differentially expressed genes were identified using the edgeR program.
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

source_name: MCF7 cell culture

growth_protocol: MCF7 cells and fibroblasts were obtained from ATCC and cultured as recommended.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 14 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: We cultured MCF7 cells alone or in coculture with BJ fibroblasts to examine stromal signalling on ER+ breast cancer. Cocultured MCF7 were isolated by magnetically activated cell sorting. We also cultured MCF7 cells in decellularized ECM scaffolds generated by BJ fibroblasts or IMR90 fibroblasts or on an uncoated, plastic cell culture dish.

tag: cell line

tag: culture method

value: ECM from IMR90 fibroblasts


title: ECM2_2


title: Gabra6-cre;LSL-SmoM2_2


title: Pancreatic islet-derived exosome, HI-Ctrl-SAMN08769390

value: Untreated


title: N2_BT679_12h-Rep1

tag: genotype


title: Gabra6-cre;LSL-SmoM2_1


title: N2_BT247_12h-Rep2


title: Pancreatic islet-derived exosome, HI-Ctrl-SAMN08773446

tag: age

value: White


title: N2_BT247_12h-Rep1

tag: strain

value: Wild type


title: clec-4_BT247_12h-Rep3

tag: treatment

value: mNGM


title: Gabra6-cre_2

description:
ATAC-seq
84_alfa6-cre_TOTAL.NORM_peaks.bed


title: ECM1_1

value: ECM from BJ fibroblasts


title: clec-4_BT247_12h-Rep2


title: Gabra6-cre_3


title: Unc_2

value: Uncoated control


title: Gabra6-cre_1


title: Unc_1


title: N2_BT407_12h-Rep3


title: DO-1318

city: Bar Harbor

first: Yuka

last: Takemon

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

data_processing:
bclfastq v1.8.3 was used for base-calling
EMASE was used to align multi-parent allele specific expression and quantify gene expresison counts from fastq files
GBRS was used to quantify multiway allele specificity to account for DO generation.
EMASE raw counts were rank normalized
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing matrix of gene expression (raw and rank normalized) for all 188 samples.

source_name: Right kidney

extract_protocol:
Pulverized aliquots lysed and homogenized in TRIzol reagent (Ambion, cat#15596026). Total RNA was isolated using miRNeasy Mini kit (Qiagen, cat#217004) according to manufactures’ protocols, including the optional DNase digest step.
Poly(A) RNA-seq libraries were constructed using the TruSeq RNA Library Prep Kit v2 (Illumina), including the addition of unique barcode sequences. Library quality and quantity were assessed using the DNA 1000 LabChip assay (Agilent Technologies) and quantitative PCR (Kapa Biosystems). Libraries were randomized and pool in batches for sequencing at 100 bp single-end on the HiSeq 2500 (Illumina) using TruSeq SBS Kit v4 reagents (Illumina).

treatment_protocol: Whole right kidneys were flash frozen and pulverized.

value: Kidney

tag: generation

value: M


title: clec-4_BT679_12h-Rep3


title: ECM1_2


title: Co_3

value: Cocultured with BJ fibroblasts then magnetically separated


title: Co_2


title: clec-4_BT247_12h-Rep1


title: DO-1316

tag: Sex


title: DO-1312


title: N2_BT407_12h-Rep2


title: N2_BT407_12h-Rep1


title: DO-1311


title: DO-1309


title: Unc_2_Mono

value: Monoculture control


title: clec-4_BT407_12h-Rep2


title: Unc_3_Mono


title: clec-4_BT407_12h-Rep3


title: DO-1307


title: DO-1306


title: clec-4_BT407_12h-Rep1


title: N2_OP_12h-Rep3


title: N2_OP_12h-Rep2


title: DO-1300


title: N2_OP_12h-Rep1


title: DO-1297


title: DO-1299


title: DO-1290


title: DO-1285


title: DO-1279


title: DO-1268


title: clec-4_OP_12h-Rep2


title: N2_BT679_6h-Rep2

value: 6 h


title: clec-4_BT679_6h-Rep3


title: clec-4_OP_12h-Rep1


title: clec-4_BT679_6h-Rep2


title: DO-1267


title: DO-1265


title: DO-1254

value: F


title: N2_BT679_6h-Rep1


title: clec-4_BT679_6h-Rep1


title: N2_BT679_6h-Rep3


title: DO-1252


title: DO-1263


title: N2_BT247_6h-Rep3


title: DO-1251


title: N2_BT247_6h-Rep2


title: clec-4_OP_12h-Rep3


title: Skin fibroblasts, unaffected individual 3

city: Rotterdam

first: Maarten

last: Fornerod

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: ErasmusMC

data_processing:
[Mapping of reads]  Reads were mapped using the STAR_2.4.2a aligner
[Counting reads per gene]  Counts per gene were determined by the featureCounts program (version 1.6.3) under Linux.
[Differential gene expression]  Differential gene expression was determined by the edgeR (version 3.20.9) package in R (version 3.4.3)
Genome_build: hg38.86
Supplementary_files_format_and_content: Counts.txt contains counts per gene
TMX2_DGE_annotated_201780319.txt contains columns for ENSMBL GeneID, log2FC, logCPM, PValue, FDR, Gene Start (bp), Gene End (bp), Chromosome Name, Strand, Associated Gene Name, Gene type, Transcript type, Status gene and Status transcript.

source_name: skin fibroblasts

growth_protocol: Fibroblasts from skin biopsies of  affected individuals P1 and P2 and and four sex- and age-matched healthy individuals were grown in Dulbecco Modified Eagle Medium medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine (v/v) and 1% penicillin/streptomycin (v/v) (DMEM+/+) at 37°C and 5% CO2. Cells were enzymatically detached from T75 confluent flasks by using 1 mL trypsin/EDTA (0.25 %).

extract_protocol:
Skin fibroblasts from individuals P1 and P2 and four different healthy age matched controls were cultured to 80% confluence in T175 flasks, before lysis with TRIzol™ Reagent (Invitrogen®, 15596026) and RNA isolation with RNeasy mini kit (Qiagen®, 74106).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples. The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L).

tag: individual

value: unaffected individual 3

tag: condition

value: unaffected

tag: passage

value: skin

tag: cell type

value: skin fibroblasts


title: Skin fibroblasts, unaffected individual 4

value: unaffected individual 4


title: Skin fibroblasts, unaffected individual 2

value: unaffected individual 2


title: DO-1250


title: Skin fibroblasts, P2

value: affected (neurological disorder)


title: clec-4_BT247_6h-Rep3

department: Evolutionary Ecology and Genetics, Zoological Institute

tag: time


title: DO-1249


title: Skin fibroblasts, P1


title: N2_BT247_6h-Rep1

value: Wild type


title: unaffected individual 2

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
82E0101

data_processing:
Mapping of reads: Reads were mapped using the STAR_2.4.2a aligner
Counting reads per gene: Counts per gene were determined by the HTSeq program (version 0.6.1) under Python.
Differential gene expression: Differential gene expression was determined by the egdeR (version 3.0.2) package in R (version 2.15.2)
Genome_build: hg38.86
Supplementary_files_format_and_content: Processed data file contains columns for ENSMBL GeneID, log2FC, logCPM, PValue, FDR, Gene Start (bp), Gene End (bp), Chromosome Name, Strand, Associated Gene Name, Gene type, Transcript type, Status gene and Status transcript.

growth_protocol: Fibroblasts from skin biopsies of  affected individuals V-3 and VI-1 from family 1 and and four sex- and age-matched healthy individuals were grown in Dulbecco Modified Eagle Medium medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine (v/v) and 1% penicillin/streptomycin (v/v) (DMEM+/+) at 37°C and 5% CO2. Cells were enzymatically detached from T75 confluent flasks by using 1 mL trypsin/EDTA (0.25 %).

extract_protocol:
Skin fibroblasts from individuals V-3 and VI-1 from family 1 and four different healthy age matched controls were cultured to 80% confluence in T175 flasks, before lysis with TRIzol™ Reagent (Invitrogen®, 15596026) and RNA isolation with RNeasy mini kit (Qiagen®, 74106).
Strand-specific mRNA-seq libraries for the Illumina platform were generated with a poly-A selection and sequenced at GenomeScan (GenomeScan, Leiden, The Netherlands). Fastq files from forward and reverse reads were aligned to reference genome hg38 with the STAR aligner tool (v.2.4.2a) (https://www.ncbi.nlm.nih.gov/pubmed/23104886) and quantified per gene with HTSeq using hg38 exon coordinates (release 86). Count data were used for differential gene expression using the edgeR package in R.

tag: disease state


title: DO-1248


title: unaffected individual 1

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
80E0279


title: clec-4_BT247_6h-Rep1

tag: medium

value: mNGM


title: N2_BT407_6h-Rep3

tag: temperature


title: DO-1247

tag: tissue


title: DO-1243


title: unaffected individual 4

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
76E0145


title: fam 1 VI-1

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
13E0745

value: affected


title: DO-1242


title: unaffected individual 3

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
80E0062


title: DO-1237


title: N2_BT407_6h-Rep1


title: DO-1224


title: Skin fibroblasts, unaffected individual 1

value: unaffected individual 1


title: clec-4_BT407_6h-Rep2


title: DO-1222

value: Kidney


title: DO-1218


title: N2_OP_6h-Rep3


title: clec-4_BT407_6h-Rep3


title: N2_OP_6h-Rep2


title: clec-4_BT247_6h-Rep2


title: clec-4_BT407_6h-Rep1


title: N2_OP_6h-Rep1


title: DO-1213


title: fam 1 V-3

description:
SMPD4_Fam01_DGE_annotated_20170116.txt
06E0239


title: Gabra6-cre;LSL-SmoM2_4

value: cerebellum


title: N2_BT407_6h-Rep2


title: DO-1209


title: DO-1208


title: DO-1201


title: clec-4_OP_6h-Rep3


title: DO-1200

value: M


title: DO-1199


title: clec-4_OP_6h-Rep2


title: DO-1197


title: S178

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

data_processing:
Raw fastq data were aligned to mouse transcriptome by Salmon v0.91
Salmon counts were imported through Tximport to get unnormalized gene expressions
Normalized counts were extracted from DESeq2
Genome_build: Mouse ensembl release 95
Supplementary_files_format_and_content: csv file with unnormalized gene counts from Tximport

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: Male


title: DO-1215

value: F


title: 180K GFP neg

city: Cleveland

first: Martin

middle: L

last: Basch

state: Ohio

address: 10900 Euclid Ave

department: Otolaryngology

institute: Case Western Reserve University

data_processing:
Pair end sequencing for both populations of cells was done in HiSeq2000 sequencing platform (Illumina)
Reads were aligned to thee Mus musculus Ensemble mm9 iGenome using bothtopHat 1.4.1 software and STAR software. Both libraries were compared in terms of gene expression level,
A significant DEG was considered to have an RPKM >3000. Th level of DEG significance between libraries for each gene was established with a FC >2 and a p value and FDR< 0.01
Genome_build: mm9

source_name: cochlea lateral wall

extract_protocol:
Inner ears from P0 wnt1CRE::EYFP mice were dissected and the lateral wall of the cochlea was isolated in eppendorf tubes. Cells were dissociated in 0.1% trypsin/EDTA. After 10 minutes incubation at 37 C cells were washed in DMEM+ FBS and triturated with a yellow tip. After filtering,  the cells  were sorted and colected in 2 fractions: GFP positive and GFP negative. Total mRNA was extracted form the samples using a modified trizol method (IRB functionsl genomics core, www.dnaarrays.com).
Libraries were made using the Illumuna TruSeq kit V2

value: cochlea lateral wall

tag: cell population

value: FACS sorted GFP negative


title: 68K GFP pos

value: FACS sorted GFP positive


title: S177