title: TN2A-C55


title: TN2A-C66

status: Public on Jan 02 2019

type: SRA

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description:
Single cell fibroblast
ASE_gene_cell_ind.csv

library_source: transcriptomic

data_processing:
Genome sequencing: For each individual,we used the Burrows- Wheeler Aligner (BWA mem v.0.7.10) to align the sequencing reads (fastq) to the human reference genome (GRCh37/hg19). We used SAMtools v.1.4 to remove paired-end duplicates and pile up the remaining reads. BCFtools v.1.4 was used to call the SNVs and Annovar (2016Feb01) for the annotation. SNVs with quality score <100 where excluded from the analysis.
Single cell RNA-seq: RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis
Allele specific expression: For each gene on the X chromosome, the aggregate monoallelic ratio (AR) per cell was calculated by averaging the allelic ratio of the reads covering the respective heterozygous sites (AR = sum of number of reads from the active X allele / total SNV reads; 0≤AR≤1). Since we do not have the availability of parental genotype for all the individuals, we designed an algorithm to estimate the active X allele per site based on the assumption that the active X allele is, on average, more transcribed than the inactive X. We validated this assumption comparing the prediction of our algorithm with the phasing of twins’ X alleles based on parental information (more details in Methods S1). According to this metric, inactivated genes cluster around AR=1 while known escapees appear as been uniformly distributed between 0.5≤AR≤0.95 (linear phase of the cumulative distribution, Figure S12). As support of this observation, AR distribution of autosomal genes clearly indicates AR=0.95 as the threshold separating biallelically expressed genes from monoallelic expressed genes (Figure S13). Therefore, we consider a gene as escapee in the relaxed set when the aggregate AR is ≤ 0.95 in at least 1 individual and as escapee in the robust set when the aggregate AR is ≤ 0.95 in at least 2 individuals. To reduce the effect of allele dropout, we only consider for the analysis SNV sites covered by at least 5 reads in at least three cells. To reduce sampling bias effects a gene is included in the analysis if detectable in more than 5 different cells and/or SNVs per sample.
Genome_build: GRCh37/hg19

molecule: total RNA

organism: Homo sapiens

source_name: Dahoun et al 2008

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis.

tag: cell culture

tag: cell type

value: primary skin fibroblast

tag: individual id

value: Individual 4


title: TN2A-C43


title: TN2A-C74


title: TN2A-C41


title: TN2A-C71


title: TN2A-C39


title: TN2A-C46


title: TN2A-C40


title: TN2A-C67


title: TN2A-C63


title: TN2A-C57


title: TN2A-C47


title: TN2A-C59


title: TN2A-C38


title: TN2A-C75


title: TN2A-C61


title: TN2A-C78


title: TN2A-C58


title: CAP36-C80


title: CAP36-C79


title: CAP36-C78


title: CAP36-C94


title: CAP36-C84


title: TN2A-C33


title: CAP36-C86


title: CAP36-C96


title: CAP36-C91


title: TN2A-C37


title: CAP36-C92


title: CAP36-C90


title: TN2A-C27


title: CAP36-C77


title: CAP36-C75


title: CAP36-C76


title: CAP36-C81


title: TN2A-C28


title: TN2A-C26


title: CAP36-C93


title: CAP36-C89


title: TN2A-C34


title: CAP36-C82


title: CAP36-C87


title: CAP36-C85


title: TN2A-C31


title: CAP36-C88


title: CAP36-C74


title: CAP31-C45

description:
Single cell lymphoblastoid
ASE_gene_cell_ind.csv

source_name: Gencord collection (Borel et al 2015)

value: LCL

value: Individual 5


title: CAP36-C73


title: CAP36-C72


title: CAP36-C70


title: CAP36-C69


title: CAP36-C71


title: TN2A-C72


title: CAP36-C54


title: CAP36-C59


title: CAP36-C68


title: CAP36-C52


title: CAP36-C56


title: CAP36-C57


title: CAP36-C63


title: CAP36-C67


title: CAP36-C64


title: CAP36-C53


title: CAP36-C60


title: CAP36-C47


title: CAP36-C51


title: CAP36-C50


title: CAP36-C61


title: CAP36-C48


title: CAP36-C66


title: CAP36-C55


title: CAP36-C65


title: CAP36-C43


title: CAP36-C46


title: CAP36-C44


title: CAP36-C42


title: CAP36-C35


title: CAP36-C62


title: CAP36-C34


title: CAP36-C28


title: CAP36-C32


title: CAP36-C30


title: CAP36-C27


title: CAP36-C24


title: CAP36-C19


title: CAP36-C16


title: CAP36-C17


title: CAP36-C15


title: CAP36-C13


title: CAP36-C12


title: CAP36-C21


title: CAP36-C23


title: CAP36-C14


title: CAP36-C06


title: CAP36-C04


title: CAP24-C87


title: CAP36-C05


title: CAP36-C08


title: CAP36-C02


title: CAP24-C86


title: CAP36-C03


title: CAP24-C82


title: CAP24-C81


title: CAP36-C18


title: CAP24-C84


title: CAP36-C09


title: CAP24-C85


title: CAP24-C83


title: CAP24-C80


title: CAP24-C78


title: CAP24-C77


title: CAP24-C75


title: CAP24-C38


title: CAP24-C36


title: CAP24-C37


title: CAP24-C30


title: CAP24-C28


title: CAP24-C29


title: CAP24-C35


title: CAP24-C67


title: CAP24-C68


title: CAP24-C70


title: CAP24-C65


title: CAP24-C71


title: CAP24-C62


title: CAP24-C63


title: CAP24-C34


title: CAP24-C60


title: CAP24-C64


title: CAP24-C58


title: CAP24-C66


title: CAP24-C57


title: CAP24-C55


title: CAP24-C73


title: CAP24-C59


title: CAP24-C33


title: CAP24-C54


title: CAP24-C72


title: CAP24-C79


title: CAP24-C69


title: CAP24-C49


title: CAP24-C52


title: CAP24-C26


title: CAP24-C23


title: CAP24-C21


title: CAP24-C27


title: CAP24-C25


title: CAP24-C20


title: CAP24-C19


title: CAP24-C18


title: CAP24-C16


title: CAP24-C24


title: CAP24-C56


title: CAP24-C12


title: CAP24-C53


title: CAP24-C51


title: CAP24-C50


title: CAP24-C07


title: CAP24-C10


title: CAP24-C08


title: CAP24-C05


title: CAP24-C09


title: CAP24-C03


title: CAP24-C22


title: CAP24-C02


title: CAP24-C04


title: CAP23-C95

value: Individual 3


title: CAP24-C14


title: CAP24-C13


title: CAP24-C11


title: CAP23-C82


title: CAP23-C83


title: CAP23-C84


title: CAP23-C65


title: CAP23-C78


title: CAP23-C70


title: CAP23-C88


title: CAP23-C72


title: CAP23-C58


title: CAP24-C01


title: CAP23-C54


title: CAP23-C16


title: CAP23-C52


title: CAP23-C35


title: CAP23-C96


title: CAP23-C94


title: CAP23-C89


title: CAP23-C10


title: CAP23-C92


title: CAP23-C22


title: CAP23-C93


title: CAP23-C53


title: CAP23-C64


title: CAP23-C87


title: CAP23-C86


title: CAP23-C81


title: CAP23-C48


title: CAP23-C73


title: CAP23-C75


title: CAP23-C69


title: CAP23-C67


title: CAP23-C68


title: CAP23-C80


title: CAP23-C23


title: CAP23-C56


title: CAP23-C55


title: CAP23-C57


title: CAP23-C39


title: CAP23-C49


title: CAP23-C40


title: CAP23-C34


title: CAP23-C45


title: CAP23-C33


title: CAP23-C44


title: CAP23-C51


title: CAP23-C37


title: CAP23-C91


title: CAP23-C32


title: CAP23-C63


title: CAP23-C28


title: CAP23-C31


title: CAP23-C62


title: CAP23-C43


title: CAP23-C27


title: CAP23-C25


title: CAP23-C24


title: CAP23-C20


title: CAP23-C17


title: CAP23-C15


title: CAP23-C61


title: CAP23-C14


title: CAP23-C12


title: CAP23-C11


title: CAP23-C08


title: CAP23-C09


title: CAP23-C19


title: CAP35-C91


title: CAP35-C92


title: CAP35-C90


title: CAP23-C07


title: CAP35-C88


title: CAP23-C03


title: CAP23-C05


title: CAP35-C86


title: CAP35-C96


title: CAP35-C84


title: CAP35-C83


title: CAP23-C06


title: CAP23-C01


title: CAP35-C85


title: CAP35-C89


title: CAP35-C77


title: CAP35-C87


title: CAP35-C75


title: CAP35-C73


title: CAP35-C81


title: CAP35-C76


title: CAP35-C71


title: CAP35-C68


title: CAP35-C70


title: CAP35-C66


title: CAP35-C62


title: CAP35-C63


title: CAP35-C61


title: CAP35-C59


title: CAP35-C57


title: CAP35-C56


title: CAP35-C50


title: CAP35-C53


title: CAP35-C49


title: CAP35-C43


title: CAP35-C44


title: CAP35-C42


title: CAP35-C55


title: CAP35-C54


title: CAP35-C35


title: CAP35-C38


title: CAP35-C74


title: CAP35-C40


title: CAP35-C34


title: CAP35-C33


title: CAP35-C30


title: CAP35-C27


title: CAP35-C24


title: CAP35-C28


title: CAP35-C23


title: CAP35-C22


title: CAP35-C21


title: CAP35-C20


title: CAP35-C19


title: CAP24-C61


title: CAP35-C17


title: CAP35-C15


title: CAP35-C13


title: CAP35-C11


title: CAP35-C10


title: CAP35-C32


title: CAP35-C09


title: CAP35-C06


title: CAP35-C03


title: CAPSC-C90


title: CAP35-C46


title: CAP35-C05


title: CAPSC-C94


title: CAP35-C31


title: CAP35-C02


title: CAP35-C04


title: CAP35-C01


title: CAP35-C29


title: CAPSC-C71


title: CAPSC-C89


title: CAPSC-C17


title: CAPSC-C47


title: CAPSC-C18


title: CAPSC-C10


title: TS1B-C81


title: TS1B-C76


title: TS1B-C75


title: TS1B-C73


title: TS1B-C72


title: TS1B-C85


title: TS1B-C61


title: TS1B-C68


title: TS1B-C57


title: TS1B-C51


title: TS1B-C55


title: TS1B-C56


title: TS1B-C44


title: TS1B-C63


title: TS1B-C66


title: TS1B-C41


title: TS1B-C45


title: TS1B-C50


title: TS1B-C40


title: TS1B-C80


title: TS1B-C39


title: TS1B-C32


title: TS1B-C30


title: TS1B-C38


title: TS1B-C35


title: TS1B-C33


title: TS1B-C34


title: TS1B-C31


title: TS1B-C27


title: TS1B-C29


title: TS1B-C37


title: TS1B-C24


title: TS1B-C23


title: TS1B-C22


title: TS1B-C21


title: TS1B-C20


title: TS1B-C19


title: TS1B-C16


title: TS1B-C12


title: TS1B-C14


title: TS1B-C11


title: TS1B-C04


title: TS1B-C05


title: TS1B-C13


title: TS1B-C03


title: TS1B-C02


title: TS1B-C01


title: TS1B-C06


title: Temporal lobe epilepsy EpiB_16 Marburg

type: RNA

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

description:
Post-seizure
Temporal lobe epilepsy
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates

data_processing:
Filtering and statistical analysis of the OA miRNA profiling data were performed in R/Bioconductor. Data were first filtered according to cycle threshold (Ct< 25), amplification score (AmpScore >/= 1.24) and quantification cycle confidence (Cqconf >/= 0.8) provided by the ExpressionSuite software (ThermoFisher Scientific). Only miRNAs expressed in >80% of samples were included in the study. Missing data points were imputed. Next, we performed deltaCt normalization using miRNAs (miR-19b, miR-26a and miR-26b) that were identified by the geNorm method as being the most stable miRNAs. Differential expression analysis was then performed by applying a Student’s t-test to the normalized Ct values between each two conditions (C/EpiA, C/EpiB and EpiA/EpiB). The p-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg.
Matrix normalized worksheet reports DeltaCt normalized signal.
Fold Change worksheet reports log2FC, p.value and adj.p.value. FC was calculated as 2^-ΔΔCt, where -ΔΔCt = -[ΔCt_test -Δct_control]. Differential expression analysis was performed using the limma package (Ritchie et al., 2015). P-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995).

label: FAM

source_name: plasma

label_protocol: 3 µl of total RNA was processed by reverse transcriptase and pre-amplification steps following the manufacturer’s protocol (Applied Biosystems). The pre-amplification reaction was mixed with TaqMan OpenArray Real-Time PCR Master mix (1:1). The mix was loaded onto the OpenArray human panel (755 human miRNAs) using the Accufill System and ran using a QuantStudio 12K Flex PCR (Life Technologies).

extract_protocol: Total RNA was extracted from 200 μl of plasma using the miRCURY RNA isolation kit-biofluid (Exiqon) according to the manufacturer’s protocol

tag: center

value: Marburg


title: Temporal lobe epilepsy EpiB_15 Marburg


title: Temporal lobe epilepsy EpiB_13 Marburg


title: Temporal lobe epilepsy EpiB_14 Marburg


title: Temporal lobe epilepsy EpiB_11 Marburg


title: Temporal lobe epilepsy EpiB_12 Marburg


title: Temporal lobe epilepsy EpiB_9 Marburg


title: Temporal lobe epilepsy EpiB_8 Marburg


title: Temporal lobe epilepsy EpiB_10 Marburg


title: ECC-1 cells un-treated; M410

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner according to the instruction manual.

data_processing: RNA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6)).

label: biotin

source_name: ECC-1 cell line (type I endometroid endometrial carcinoma)

label_protocol: Samples were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol and Affymetrix WT Terminal Labeling Kit from 100 ng total RNA starting material

growth_protocol: ECC-1 cells were grown in DMEM and USPC-1 cells in RPM-1640 media (Biological Industries, Beit Haemek, Israel). Media were supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 50 µg/ml gentamicin sulfate and 5.6 mg/l amphotericin B.

extract_protocol: Total RNA was extracted using 108 the TRIzol® Reagent (Life Technologies, Carlsbad, CA, USA). RNA was quantitated by measuring absorption at 260/280 and 260/230 nm using a NanoDrop 2000 spectrophotometer  110 (Thermo Fisher Scientific, Wilmington, DE, USA).

treatment_protocol: Cells were treated with the following hormones: regular insulin (Humulin R®, Lilly Pharma, Germany), insulin glargine (Lantus®, Sanofi Aventis, Germany), insulin detemir (Levemir®, Novo Nordisk, Denmark) and IGF1 (PeproTech Ltd, Rocky Hill, NJ, USA). Cells were serum-starved for 24 hr and treated with insulin, IGF1, glargine or detemir, at a dose of 8.6 nM, for 8 hr.

tag: treatment

value: un-treated

tag: cell line


title: ECC-1 cells treated with insulin-like growth factor-1 ; M407


title: USPC-1 cells treated with insulin-like growth factor-1 ; M400

source_name: USPC-1 (type II uterine serous papillary endometrial carcinoma)


title: ECC-1 cells treated with insulin glargine ; M402

value: treated with insulin glargine


title: ECC-1 cells treated with insulin; M401

value: treated with insulin


title: ECC-1 cells treated with insulin; M398


title: ECC-1 cells treated with detemir; M399

value: treated with detemir


title: ECC-1 cells treated with detemir; M406


title: ECC-1 cells treated with insulin glargine ; M411


title: USPC-1 cells un-treated; M420


title: USPC-1 cells treated with insulin glargine ; M408


title: ECC-1 cells treated with insulin-like growth factor-1 ; M418


title: ECC-1 cells treated with detemir; M409


title: ECC-1 cells un-treated; M403


title: ECC-1 cells treated with insulin; M419


title: Temporal lobe epilepsy EpiB_7 Marburg


title: USPC-1 cells treated with detemir; M412


title: Temporal lobe epilepsy EpiB_5 Marburg


title: ECC-1 cells un-treated; M417


title: Temporal lobe epilepsy EpiB_3 Marburg


title: Temporal lobe epilepsy EpiB_4 Marburg


title: ECC-1 cells treated with insulin-like growth factor-1 ; M397


title: USPC-1 cells treated with insulin; M404


title: Temporal lobe epilepsy EpiB_1 Marburg


title: Temporal lobe epilepsy EpiA_15 Marburg

description:
Pre-seizure
Temporal lobe epilepsy
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates


title: Temporal lobe epilepsy EpiA_16 Marburg


title: Temporal lobe epilepsy EpiB_2 Marburg


title: ECC-1 cells treated with insulin glargine ; M405


title: Temporal lobe epilepsy EpiA_14 Marburg


title: Temporal lobe epilepsy EpiA_10 Marburg


title: 170712_T_E16

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

institute: UNIGE

data_processing:
Libraries were sequenced on illumina hiseq 4000, fastqs were generated using Cellranger v2.1.0, reads were aligned using cellranger count command with gencode reference genome GRCm38.p5 genome and its associated annotation. We added to this genome a Z chromosome containing the GFP sequence to obtain counts for the GFP transgene. (sequence in supplementary file)
Count matrix for all barcodes were outputed by cellranger count command. We made use of a homemade program based on the local minimum of the UMI number distribution across barcodes to assess which barcodes are associated to a cell or to an empty droplet. Selected barcodes are the one listed in processed expression files.
Data was then analyzed using R 3.5 and the Seurat v2.3 package. Counts were lognormalized using LogNormalize Seurat  function with a 10,000 scale factor for further analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content:
testis_E16_5_170712_umi_counts.csv: umi counts of all cells (columns) and genes (rows)
testis_E16_5_170712_lognormalized_counts.csv: lognormalized counts of all cells (columns) and genes (rows)

organism: Mus musculus

source_name: Testis

extract_protocol:
E16.5 testes from wild type mice were enzymatically dissociated 10 minutes at 37ºC using Trypsin-EDTA 0.05% (Gibco). After centrifugation and counting, 3000 to 7000 single cells were loaded on a 10x Chromium instrument (10x Genomics).
Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Each stage was performed in two independent replicates. Library quantification was performed using the Qubit fluorometric assay with dsDNA HS Assay Kit (Invitrogen). Library quality assessment was performed using a Bioanalyzer Agilent 2100 with a High Sensitivity DNA chip (Agilent Genomics). Libraries were diluted, pooled and sequenced on an Illumina HiSeq4000 using paired-end 26 x 98 bp as sequencing mode. Libraries were sequenced at a targeted depth of 100 000 to 150 000 reads per cell. Libraries of the two replicates were sequenced on two different runs.

tag: strain

tag: developmental stage

tag: tissue

value: testis

tag: transgene


title: Temporal lobe epilepsy EpiA_11 Marburg


title: Temporal lobe epilepsy EpiA_9 Marburg


title: Temporal lobe epilepsy EpiA_6 Marburg


title: Temporal lobe epilepsy EpiA_8 Marburg


title: Temporal lobe epilepsy EpiA_7 Marburg


title: Temporal lobe epilepsy EpiA_4 Marburg


title: Temporal lobe epilepsy EpiA_5 Marburg


title: 170313_T_E16

data_processing:
Libraries were sequenced on illumina hiseq 4000, fastqs were generated using Cellranger v2.1.0, reads were aligned using cellranger count command with gencode reference genome GRCm38.p5 genome and its associated annotation. We added to this genome a Z chromosome containing the GFP sequence to obtain counts for the GFP transgene. (sequence in supplementary file)
Count matrix for all barcodes were outputed by cellranger count command. We made use of a homemade program based on the local minimum of the UMI number distribution across barcodes to assess which barcodes are associated to a cell or to an empty droplet. Selected barcodes are the one listed in processed expression files.
Data was then analyzed using R 3.5 and the Seurat v2.3 package. Counts were lognormalized using LogNormalize Seurat  function with a 10,000 scale factor for further analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content:
testis_E16_5_170313_umi_counts.csv: umi counts of all cells (columns) and genes (rows)
testis_E16_5_170313_lognormalized_counts.csv: lognormalized counts of all cells (columns) and genes (rows)


title: Temporal lobe epilepsy EpiA_3 Marburg


title: Temporal lobe epilepsy EpiA_13 Marburg


title: Temporal lobe epilepsy EpiB_6 Marburg


title: V9_Nucleus accumbens

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

country: USA

institute: University of Illinois at Urbana

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 19
migraineNTG_TranscrptCounts.xlsx

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
100 nt paired-end reads were assembled into transcript isoforms and mapped to the C57Bl/6J mouse genome (version GRCm38) using Kallisto v0.43 (Bray et al., 2016)
Genome_build: C57Bl/6J mouse genome (version GRCm38)
Supplementary_files_format_and_content: csv format, comma-delimited file including transcripts per million (TPM) values for each sample, one column per sample

source_name: Nucleus accumbens

extract_protocol:
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000   using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Nucleus accumbens

value: Vehicle

tag: age

value: 9-12 weeks old

tag: Sex

value: male


title: V10_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 20
migraineNTG_TranscrptCounts.xlsx


title: Temporal lobe epilepsy EpiA_1 Marburg


title: Temporal lobe epilepsy EpiA_2 Marburg


title: primary endothelial cells extracted from muscle biopsies_sample11

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: 600 ng of labeled specimens were hybridized on Agilent Human Gene Expression v3 8x60K microarrays.

scan_protocol: After17 hours, slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7.3.1 (Agilent Technologies). Raw data elaboration was carried out with Bioconductor (www.bioconductor.org) (Gentleman et al., 2004), using The LIMMA (LInear Models for Microarray Analysis) R package. Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics (Smyth, 2004).

source_name: Endothelial cells

label_protocol: mRNA from 100 ng of totRNA was amplified, labeled with Cy3 and purified with columns.

growth_protocol: 3D vascularized muscle model: endothelial cells were co-cultured within 3D fibrin scaffolds in presence of muscle fibers and supporting cells (e.g. fibroblasts, mesenchymal stem cells). Scaffolds were incubated with EGM-2 medium (Lonza). Primary endothelial cells from muscle biopsies: cells were isolated from patients undergoing hip surgery and selected for the expression of CD31. Cells were cultured in EGM-2.

extract_protocol: RNA was extracted using the PureLink RNA Mini Kit (Ambion). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop.

tag: sample type

value: muscle biopsies


title: primary endothelial cells extracted from muscle biopsies_sample3


title: primary endothelial cells extracted from muscle biopsies_sample8


title: endothelial cells from the 3D vascularized muscle model_rep2

value: 3D vascularized muscle model


title: V8_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 18
migraineNTG_TranscrptCounts.xlsx


title: Control_16 Marburg

description:
Control
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates


title: V7_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 17
migraineNTG_TranscrptCounts.xlsx


title: Control_15 Marburg


title: V6_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 16
migraineNTG_TranscrptCounts.xlsx


title: Control_14 Marburg


title: Control_12 Marburg


title: Temporal lobe epilepsy EpiA_12 Marburg


title: Control_9 Marburg


title: Control_8 Marburg


title: endothelial cells from the 3D vascularized muscle model_rep1


title: Control_10 Marburg


title: N4_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 14
migraineNTG_TranscrptCounts.xlsx

value: Nitroglycerin


title: N5_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 15
migraineNTG_TranscrptCounts.xlsx


title: Control_6 Marburg


title: N2_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 12
migraineNTG_TranscrptCounts.xlsx


title: Control_7 Marburg


title: Control_5 Marburg


title: N3_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 13
migraineNTG_TranscrptCounts.xlsx


title: Control_1 Marburg


title: Control_3 Marburg


title: V10_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 10
migraineNTG_TranscrptCounts.xlsx

source_name: Trigeminal ganglia

value: Trigeminal ganglia


title: Control_4 Marburg


title: N1_Nucleus accumbens

description:
Nucleus Accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 11
migraineNTG_TranscrptCounts.xlsx


title: V9_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 9
migraineNTG_TranscrptCounts.xlsx


title: Temporal lobe epilepsy EpiB_14 Beaumont

value: Beaumont

tag: gender

value: M


title: Temporal lobe epilepsy EpiB_15 Beaumont


title: V8_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 8
migraineNTG_TranscrptCounts.xlsx


title: Control_13 Marburg


title: Temporal lobe epilepsy EpiB_12 Beaumont


title: V7_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 7
migraineNTG_TranscrptCounts.xlsx


title: Temporal lobe epilepsy EpiB_11 Beaumont

description:
Post-seizure
Temporal lobe epilepsy
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates


title: Temporal lobe epilepsy EpiB_10 Beaumont


title: Control_11 Marburg


title: Temporal lobe epilepsy EpiB_9 Beaumont


title: N5_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 5
migraineNTG_TranscrptCounts.xlsx


title: Temporal lobe epilepsy EpiB_7 Beaumont

value: F


title: Temporal lobe epilepsy EpiB_3 Beaumont


title: N3_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 3
migraineNTG_TranscrptCounts.xlsx


title: Control_2 Marburg

value: Marburg


title: Temporal lobe epilepsy EpiB_8 Beaumont


title: Temporal lobe epilepsy EpiB_4 Beaumont


title: Temporal lobe epilepsy EpiB_16 Beaumont


title: ΔIEC-tumor 2

city: Shanghai

first: Luoyan

last: Ai

state: Shanghai

address: 145 Middle Shandong Road

department: Division of Gastroenterology and Hepatology

country: China

institute: Shanghai Jiao Tong University

data_processing:
The raw data was checked by FastQC.
Clean reads were aligned to the mouse genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 FPKM values for each Sample

source_name: colon tumor

extract_protocol:
Colon tumors and adjacent tissues were dissected and immediately maintained in RNA stabilization solution. RNA was isolated with TRIzol. Samples were used with 1 ug of total RNA for the construction of sequencing libraries.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

value: colon

tag: tumor stage

value: tumor

tag: genotype/variation

value: SynbindindeltaIEC


title: N1_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 1
migraineNTG_TranscrptCounts.xlsx


title: N4_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 4
migraineNTG_TranscrptCounts.xlsx


title: Temporal lobe epilepsy EpiB_2 Beaumont


title: Temporal lobe epilepsy EpiA_16 Beaumont

description:
Pre-seizure
Temporal lobe epilepsy
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates


title: Temporal lobe epilepsy EpiB_13 Beaumont


title: Donor3_R848

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description:
Donor3_R848_S16
processed data file:
limma_DEG_R848-Control_all_genes.txt

data_processing:
Samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: hg19
Supplementary_files_format_and_content: Quantile-normalized differential expression values from limma-voom.

source_name: DCs treated with R848 for 4 hr

growth_protocol: DCs were generated by culturing purified monocytes at 5 x 105 cells/ml in complete RPMI 1640 medium (RPMI 1640 medium [Mediatech Inc] supplemented with 10% FBS [GemCell], 2 mM glutamine [Lonza], 25 mM HEPES [Quality Biological], 100 U/ml penicillin [Lonza], 100 mg/ml streptomycin [Lonza], and 50 mM of 2-Mercaptoethanol [Sigma]) containing 50 ng/ml human GM-CSF and IL-4 at 37°C in a humidified CO2 (5%) incubator for 5 days with 50% of the culture medium replaced with prewarmed fresh complete RPMI 1640 medium containing human GM-CSF and IL-4 at the same concentration on days 3.

extract_protocol:
Total RNA of stimulated DCs from three donors was isolated using the QIAGEN RNeasy kit according to manufacturer’s instructions. RNA quantity was measured using the Nanodrop.The integrity was checked by the RNA integrity number (RIN) value and samples that passed the quality control check were used for sequencing at the NCI, CCR sequencing facility.
12 mRNA-seq samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201 and paired-end sequencing.

treatment_protocol: DCs from 5-days culture were treated with or without N1, R848, or N1 plus R848 for 4 hours.

tag: subject id

tag: source type

value: Healthy individuals

value: Peripheral Blood

value: MACS sorted CD14+ cells

tag: cell stage

value: Monocyte derived DCs

value: R848 for 4 hr


title: flox-tumor 3

value: Synbindinflox


title: Temporal lobe epilepsy EpiB_1 Beaumont


title: Donor3_N1plus_R848

description:
Donor3_N1plus_R848_S17
processed data file:
limma_DEG_Both-Control_all_genes.txt

source_name: DCs treated with N1 plus R848 for 4 hr

tag: cell type

value: N1 plus R848 for 4 hr


title: V6_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 6
migraineNTG_TranscrptCounts.xlsx

value: Vehicle

value: 9-12 weeks old

value: male


title: Temporal lobe epilepsy EpiB_5 Beaumont

tag: center

value: Beaumont


title: N2_Trigeminal ganglia

description:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New  York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
Sample 2
migraineNTG_TranscrptCounts.xlsx

value: Trigeminal ganglia

tag: treatment

value: Nitroglycerin


title: Temporal lobe epilepsy EpiA_13 Beaumont

value: M


title: Donor3_Control

description:
Donor3_Control_S14
processed data file:
limma_DEG_Both-Control_all_genes.txt
limma_DEG_N1-Control_all_genes.txt
limma_DEG_R848-Control_all_genes.txt

source_name: DCs sham-treated

value: sham control


title: flox-tumor 1

value: colon

value: tumor


title: Donor2_N1

description:
Donor2_N1_S11
processed data file:
limma_DEG_N1-Control_all_genes.txt

source_name: DCs treated with N1 for 4 hr

value: Healthy individuals

value: N1 for 4 hr


title: Donor2_R848

description:
Donor2_R848_S12
processed data file:
limma_DEG_R848-Control_all_genes.txt

value: Peripheral Blood

value: MACS sorted CD14+ cells


title: ΔIEC-adjacent 3

source_name: adjacent colon epithelium

value: control

value: SynbindindeltaIEC


title: ΔIEC-tumor 3


title: ΔIEC-adjacent 2


title: ΔIEC-tumor 1


title: Donor3_N1

description:
Donor3_N1_S15
processed data file:
limma_DEG_N1-Control_all_genes.txt

value: Monocyte derived DCs


title: Temporal lobe epilepsy EpiB_6 Beaumont


title: Temporal lobe epilepsy EpiA_15 Beaumont


title: Donor2_N1plus_R848

description:
Donor2_N1plus_R848_S13
processed data file:
limma_DEG_Both-Control_all_genes.txt

value: N1 plus R848 for 4 hr


title: ΔIEC-adjacent 1


title: CN23

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition

hyb_protocol: OneArray Plus hybridization program

scan_protocol: Agilent 0.1 XDR program

data_processing: The GPR document is loaded into the Rosetta Resolver ® System (Rosetta Biosoftware) software for data operations.

label_protocol: 5 micrograms Cy5 labeled Arna

extract_protocol: extraction of total RNA from tumor cell

treatment_protocol: HEP3B cells transaffected with vector and CCN2

value: hepatocellular carcinoma Cells


title: flox-adjacent 3

value: Synbindinflox


title: Donor2_Control

description:
Donor2_Control_S10
processed data file:
limma_DEG_Both-Control_all_genes.txt
limma_DEG_N1-Control_all_genes.txt
limma_DEG_R848-Control_all_genes.txt


title: Temporal lobe epilepsy EpiA_9 Beaumont

value: Beaumont


title: Temporal lobe epilepsy EpiA_14 Beaumont


title: Donor1_R848

description:
Donor1_R848_S8
processed data file:
limma_DEG_R848-Control_all_genes.txt

value: R848 for 4 hr


title: flox-adjacent 2


title: Temporal lobe epilepsy EpiA_8 Beaumont


title: Temporal lobe epilepsy EpiA_12 Beaumont


title: CN22


title: Donor1_N1

description:
Donor1_N1_S7
processed data file:
limma_DEG_N1-Control_all_genes.txt


title: flox-tumor 2


title: Temporal lobe epilepsy EpiA_6 Beaumont


title: Temporal lobe epilepsy EpiA_11 Beaumont


title: CN21


title: Donor1_N1plus_R848

description:
Donor1_N1plus_R848_S9
processed data file:
limma_DEG_Both-Control_all_genes.txt


title: 3B2


title: Temporal lobe epilepsy EpiA_10 Beaumont


title: Temporal lobe epilepsy EpiA_5 Beaumont

value: F


title: Temporal lobe epilepsy EpiA_4 Beaumont


title: 18-22h_elav-neg_1

city: Berlin

first: Peter

last: Menzel

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Adapter trimming using AdapterRemoval v2.1.7: AdapterRemoval --threads 2 --trimns --trimqualities --minlength 15 --gzip --minadapteroverlap 3 --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --file1 6-8h_repo-pos_1_S5_L007_R1_001.fastq.gz --basename 6-8h_repo-pos_1_S5_L007_R1_001
Mappnig to Drosophila genome using bowtie v1.1.2 for mapping: bowtie -m 10 -a --strata --best -p 2 -S -l 10 bowtie_index <(zcat 6-8h_repo-pos_2_S7_L007_R1_001.truncated.gz) glia_06-08h_rep1_pos.sam
Sorting reads using samtools v1.8: samtools sort -m 38G -@ 3 -o glia_06-08h_rep1_pos.bam glia_06-08h_rep1_pos.sam
Counting reads per gene using featureCounts v1.5.1: featureCounts -M --fraction -O -T 3 -s 1 -t exon -g gene_id -a ensembl85/gtf/Drosophila_melanogaster.BDGP6.85.gtf -o glia_06-08h_rep1_pos_counts.txt -i glia_06-08h_rep1_pos.bam
Differential expression analysis of microRNAs and protein-coding genes was done with DESeq2 on those genes that have more than 1000 reads across all samples
Genome_build: genome build: dm6, gene annotation: ENSEMBL85 Drosophila_melanogaster.BDGP6.85.gtf
Supplementary_files_format_and_content:
processed data files contain the output of featureCounts, which has Ensembl gene id in the first and the read count in the last column.
The files DE_genes_miRNAS_*.tsv are specific for each of the 11 differential expression comparisons and contain all differentially expressed microRNAs paired with their target genes that are differentially expressed in the opposite direction of the microRNA. The columns include miRNA/gene IDs and names as well as fold changes and adjusted P-values.

organism: Drosophila melanogaster

source_name: enriched neurons

extract_protocol:
Drosophila embryos were collected at time points 6-8h and 18-22h after egg laying.  Embryos were dissociated into single-cell suspensions, cells were fixed in 4% formaldehyde.  Fixed cell suspensions were immunostained under RNase-free conditions and FACS-purified using a FACSAria II cell sorter (BD Biosciences).  Marker-positive and marker-negative cell populations were collected in biological duplicates.  FACS-purified cells were subjected to cross-linking reversal and Proteinase K digestion prior to RNA isolation.  From both FACS fractions, RNA was extracted and prepared for strand-specific Illumina sequencing.
NEBNext Small RNA (New England Biolabs)
smallRNA-Seq, 1x51bp

tag: marker

value: elav

tag: sorting

value: negative


title: 18-22h_elav-neg_2

tag: developmental stage


title: Temporal lobe epilepsy EpiA_3 Beaumont


title: Donor1_Control

description:
Donor1_Control_S6
processed data file:
limma_DEG_Both-Control_all_genes.txt
limma_DEG_N1-Control_all_genes.txt
limma_DEG_R848-Control_all_genes.txt

tag: tissue

value: sham control


title: Temporal lobe epilepsy EpiA_2 Beaumont

value: M


title: Temporal lobe epilepsy EpiA_1 Beaumont


title: S6-NL-2

city: Boston

first: Julio

middle: C

last: Mantero

state: MA

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: processed using affy package for R, using RMA normalization. Brainarray custom CDF for HGU133A2 (version 21.0.0, ENTREZG) was utilized for this data set. Http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/entrezg.asp

source_name: human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Skin biopsies placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was exrtacted by homogenization in RLT Buffe and purifying over Rneasy columns

tag: skin phenotype

value: Non Lesional

value: skin

tag: disease state

value: discoid lupus erythematosus


title: S7-L

value: Lesional


title: flox-adjacent 1

tag: strain

value: colon

value: control


title: 18-22h_elav-pos_1

value: positive


title: 3B12


title: S7-NL


title: 18-22h_elav-pos_2


title: 3B1


title: Temporal lobe epilepsy EpiA_7 Beaumont

tag: age


title: 18-22h_repo-neg_2

source_name: enriched glia

value: repo


title: Control_15 Beaumont

description:
Control
TaqMan OpenArray Human MicroRNA Panel and individual TaqMan Assays 96 well plate qPCR plates

tag: gender


title: S6-NL


title: 18-22h_repo-neg_1


title: 18-22h_repo-pos_1


title: Control_13 Beaumont


title: S5-NL-2


title: Control_12 Beaumont


title: Control_14 Beaumont


title: 6-8h_pros-neg_2

source_name: enriched neuroblasts

value: prospero


title: S6-L


title: S5-NL


title: Control_11 Beaumont

source_name: plasma


title: Control_16 Beaumont


title: Control_10 Beaumont


title: Control_9 Beaumont


title: 6-8h_pros-neg_1


title: 6-8h_pros-pos_2


title: Control_8 Beaumont


title: 18-22h_repo-pos_2


title: 6-8h_pros-pos_1


title: S3-NL


title: 6-8h_elav-neg_1


title: S5-L


title: S4-L


title: 6-8h_elav-neg_2


title: S4-NL


title: S3-L


title: S1-NL


title: Control_7 Beaumont


title: 6-8h_elav-pos_2


title: Control_6 Beaumont


title: S2-L


title: S2-NL


title: Control_5 Beaumont


title: Control_4 Beaumont


title: 6-8h_repo-neg_2


title: Control_3 Beaumont


title: 6-8h_elav-pos_1


title: 6-8h_repo-pos_2


title: Control_2 Beaumont


title: 6-8h_repo-neg_1


title: Control_1 Beaumont


title: SK_P8_2_Xeno_2

city: ORLANDO

first: Anupama

last: Sahoo

state: Florida

address: 6400 SANGER ROAD

institute: SBPMRI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped using tophat2 v2.1.1, with --b2-sensitive --no-novel-juncs options, mapped reads were filtered by quality >10.
Reads Per Kilobase of transcript per Megabase of library size (RPKM) were calculated in Partek GenomicSuite 6.0.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: SKMEL28(ATCC® HTB-72™) and SK-P8-2  cells were cultured  in RPMI (#M254500, Life Technologies, Carlsbad, CA) supplemented with 10% FBS, penicillin, and streptomycin and grown in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
Tumor xenografts  were removed, flash frozen in liquid nitrogen and stored in dry ice.Total RNA was harvested from cell pellets or tissues using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001; Illumina Inc., San Diego, CA)  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: SK-P8-2 xenograft tissue from SCID mice

tag: genotype

value: SK


title: 6-8h_repo-pos_1


title: SK_P8_2_Xeno_1


title: S1-L


title: epiWAT Gipr-/- /S100a9-/- BM; TF59

description: C57BL/6J mice (Envigo)

scan_protocol: GeneChips were scanned using the Affymetrix   3000 7G scanner according to the instruction manual.

source_name: epiWAT  Gipr-/- /Protein S100-A9 (S100 Calcium Binding Protein A9) -/- bone marrow

growth_protocol: Epididymal fat pads or inguinal subcutaneous fat were surgically removed from the following BM chimera mice after 6 weeks of BM reconstitution and additional 14 weeks of HFD (60% cal from fat):WT into WT, Gipr-/- into WT, Gipr-/-S100a9-/-.Fat tissues were frozen in liquid nitrogen and kept at -80 degree C until RNA extraction.

extract_protocol: RNA was prepared using QIAzol Lysis Reagent and Lipid RNA extraction RNeasy Mini Kit. RNA purity was assessed with NanoDrop™ (2000/2000c Spectrophotometers; Thermo, Fisher Scientific) and TapeStation Analysis (Software A.02.01, Agilent Technologies). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: The fat tissue were isolated from chimeric mice reconstituted with bone marrow from Gipr-/-, S100a9-/- and Gipr-/-/ S100a9-/- mice.

value: Epididymal fat pads

value: male


title: SKMEL28_Xeno_1

value: SKMEL28 xenograft tissue from SCID mice

value: Wild-type (xenograft)


title: SKMEL28_Xeno_2


title: Pooled_S2FOV vs S2F-PW4EA9-OV9

city: Khlong Luang

first: Wananit

last: Wimuttisuk

state: PATHUM THANI

address: 113 Thailand Science Park

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 8

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than 1.3 standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the print-tip group loess normalization method, and across arrays by the scale normalization method using the LimmaGUI package (Smyth & Wettenhall 2004) with the statistics software R (http://www.r-project.org/). Data from replicated spots were averaged before clustering.  Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: pooled ovary samples from 10 P. monodon broodstock pre-treatment with stage 1 ovaries

label_protocol: RNA samples were extracted from both hepatopancreases and ovaries of P. monodon collected before feeding experiment began (week 0, pooled from N=9 for hepatopancreases and N=10 for ovaries) and labeled with Cy3 dye as a reference. The hepatopancreases and ovaries samples collected after four weeks of eyestalk ablation at different ovarian maturation stages (individual, N = 2 for each maturation stage, 4 stages total) were labeled with Cy5 dye.  The Cy3- and Cy5-samples were mixed together and hybridized onto the arrays overnight. The hybridized slides were washed according to Corning’s instruction.

growth_protocol: 11 month old P. monodon were raised in the earthen ponds and fed with food pellets

extract_protocol: RNA samples were extracted from both hepatopancreases and ovaries of the 11-month-old broodstock. Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

treatment_protocol: Shrimp were acclimatized in cement pond and fed with polychaetes for 4 weeks. Eyestalk ablation was performed and shrimp were collected over the next 9 days post-ablation.

value: pre-treatment

tag: maturation stage

value: stage 1 ovaries

source_name: individual ovary from P. monodon broodstock post-treatment with stage 4 ovary

value: 4 weeks of feeding with polychaetes and unilateral eyestalk ablation

value: stage 4 ovary


title: epiWAT Gipr-/- /S100a9-/- BM; TF58

description: C57BL/6J mice (Envigo)


title: SK-P8-2

tag: cell

value: pigmented melanoma cell line

value: miR-211 deletion (cell line)


title: epiWAT Gipr-/- /S100a9-/- BM; TF60

description: C57BL/6J mice (Envigo)


title: epiWAT Gipr-/- BM; TF54

description: C57BL/6J mice (Envigo)

source_name: epiWAT glucose-dependent insulinotropic   polypeptide (GIP) receptor -/- bone marrow

value: Gipr-/-


title: Pooled_S2FOV vs S2F-PW4EA9-OV10

value: pooled ovary samples from 10 P. monodon broodstock

source_name: individual ovary from P. monodon broodstock post-treatment with stage 3 ovary

value: stage 3 ovary


title: Pooled_S2FOV vs S2F-PW4EA8-OV2

value: individual ovary from P. monodon broodstock


title: epiWAT Gipr-/- BM; TF55

description: C57BL/6J mice (Envigo)


title: Pooled_S2FOV vs S2F-PW4EA9-OV8


title: epiWAT WT BM; TF52

description: C57BL/6J mice (Envigo)

source_name: epiWAT wild-type bone marrow

value: wild type


title: epiWAT Gipr-/- /S100a9-/- BM; TF57

description: C57BL/6J mice (Envigo)


title: epiWAT Gipr-/- BM; TF53

description: C57BL/6J mice (Envigo)


title: SKMEL28

value: Wild type (cell line)


title: epiWAT WT BM; TF51

description: C57BL/6J mice (Envigo)


title: Pooled_S2FOV vs S2F-PW4EA9-OV6

source_name: individual ovary from P. monodon broodstock post-treatment with stage 2 ovary

value: stage 2 ovary


title: epiWAT Gipr-/- BM; TF56

description: C57BL/6J mice (Envigo)

value: Epididymal fat pads


title: epiWAT WT BM; TF50

description: C57BL/6J mice (Envigo)

value: male


title: Pooled_S2FOV vs S2F-PW4EA8-OV6

source_name: individual ovary from P. monodon broodstock post-treatment with stage 1 ovary

value: stage 1 ovary


title: Pooled_S2FOV vs S2F-PW4EA8-OV5


title: ingWAT Gipr-/- /S100a9-/- BM; TF75

description: C57BL/6J mice (Envigo)

source_name: ingWAT Gipr-/- /Protein S100-A9 (S100 Calcium Binding Protein A9) -/- bone marrow

value: Inguinal subcutaneous fat


title: ingWAT Gipr-/- /S100a9-/- BM; TF74

description: C57BL/6J mice (Envigo)


title: epiWAT WT BM; TF49

description: C57BL/6J mice (Envigo)


title: Pooled_S2FOV vs S2F-PW4-EA7-OV10

value: pre-treatment


title: CON_NEU_90

type: genomic

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The R software package minfi was used to perform quantile normalization and extract beta (β) values for each methylation site which represents the fraction of methylated cytosines at a given site.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Neutrophil DNA

label_protocol: standard Illumina protocol

extract_protocol: Peripheral blood samples were collected from each participant, and Ficoll density gradient centrifugation was used to isolate peripheral blood mononuclear cells (PBMCs). Neutrophils were further isolated from the granulocyte layer through sedimentation by mixing a dextran solution with the red blood cell layer. Red blood cells were lysed using a hypotonic solution leaving a neutrophil population with ~95% purity. DNA was extracted immediately from the neutrophils using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) then bisulfite converted for DNA methylation studies using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA) using the provided protocol and thermocycler settings recommended by Zymo for Illumina DNA methylation array samples included in the product literature.

value: Neutrophil

tag: disease status

value: healthy

tag: Sex

value: M


title: Pooled_S2FHP vs S2F-PW4EA9-HP9

source_name: pooled hepatopancreas samples from 9 P. monodon broodstock pre-treatment with stage 1 ovaries

value: stage 1 ovaries

source_name: individual hepatopancreas from P. monodonbroodstock post-treatment with stage 4 ovary

value: 4 weeks of feeding with polychaetes and unilateral eyestalk ablation

value: stage 4 ovary


title: CON_NEU_94

tag: cell type

value: F


title: Pooled_S2FHP vs S2F-PW4EA9-HP8

value: pooled hepatopancreas samples from 9 P. monodon broodstock

value: individual hepatopancreas from P. monodonbroodstock


title: ingWAT Gipr-/- /S100a9-/- BM; TF73

description: C57BL/6J mice (Envigo)


title: ingWAT Gipr-/- BM; TF92

description: C57BL/6J mice (Envigo)

source_name: ingWAT glucose-dependent insulinotropic   polypeptide (GIP) receptor -/- bone marrow

value: Gipr-/-


title: S4-NL-2

source_name: human skin

value: Non Lesional

value: skin

value: discoid lupus erythematosus


title: ingWAT Gipr-/- BM; TF71

description: C57BL/6J mice (Envigo)

value: male


title: CON_NEU_91


title: CON_NEU_72


title: CON_NEU_89


title: CON_NEU_88


title: CON_NEU_85


title: Pooled_S2FHP vs S2F-PW4-EA9-HP6

source_name: individual hepatopancreas from P. monodonbroodstock post-treatment with stage 2 ovary

value: stage 2 ovary


title: Pooled_S2FHP vs S2F-PW4EA8-HP2

source_name: individual hepatopancreas from P. monodonbroodstock post-treatment with stage 3 ovary

value: stage 3 ovary


title: Pooled_S2FHP vs S2F-PW4EA7-HP10

value: pre-treatment


title: ingWAT WT BM; TF66

description: C57BL/6J mice (Envigo)

source_name: ingWAT wild-type bone marrow

value: wild type

value: Inguinal subcutaneous fat


title: ingWAT WT BM; TF65

description: C57BL/6J mice (Envigo)


title: SL2_HMR_induced_2

status: Public on Jan 01 2019

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

library_source: genomic

data_processing:
The raw reads were aligned to the D. melanogaster genome assembly (UCSC dm6) using Bowtie2 (2.2.9) and filtered for uniquely mapped reads using samtools (1.3.1) (Li et al., 2009). Input and sequencing depth normalized tracks were generated by Homer (4.9) on the pooled replicates. Peak calling was performed using HOMER 4.9 with parameters –style factor –F 2 –size 200
Genome_build: dm6
Supplementary_files_format_and_content: Peak list in bed format and input normalized tracks in bedgraph format

source_name: SL2 cells

extract_protocol:
Drosophila SL2 cells stably transfected with FLAG-HA-HMR under a CuSO4 inducible promoter (pMT) were grown at 26˚C in Schneider Drosophila medium (Invitrogen) supplemented with 10% fetal calf serum and antibiotics (100 units/mL penicillin and 100 μg/mL streptomycin). Transfected cells were selected with 20 ug/mL Hygromycin B. Cells were grown to confluence in 550 mL flasks and induced for 20-24h with 250 uM CuSO4 before harvesting for chromatin immunoprecipitation.Chromatin immunoprecipitation was essentially performed as in Gerland et al., 2017. For each ChIP reaction, chromatin isolated from 1–2 x 106 cells was incubated with rat anti-HMR 2C10 antibody pre-coupled to Protein A/G Sepharose through a rabbit IgG anti-rat.
ChIP-seq Library

value: SL2 cells

value: pMT - HMR-FLAG-HA

value: induced (CuSO4 250 uM)

tag: chip antibody

value: ChIP anti-HMR


title: CON_NEU_84

value: Neutrophil

value: healthy

value: F


title: CON_NEU_96

value: M


title: ingWAT WT BM; TF87

description: C57BL/6J mice (Envigo)


title: SL2_Input_induced_2

tag: treatment

value: input


title: Pooled_S2FHP vs S2F-PW4EA9-HP10

value: pooled hepatopancreas samples from 9 P. monodon broodstock

value: stage 1 ovaries

value: individual hepatopancreas from P. monodonbroodstock

value: 4 weeks of feeding with polychaetes and unilateral eyestalk ablation


title: Pooled_S2FHP vs S2FW4EA8-5HP

source_name: individual hepatopancreas from P. monodonbroodstock post-treatment with stage 1 ovary

value: stage 1 ovary


title: SL2_HMR_uninduced_1

value: uninduced


title: ingWAT Gipr-/- BM; TF91

description: C57BL/6J mice (Envigo)

value: Gipr-/-

value: male


title: CON_NEU_87


title: SL2_Input_uninduced_1

value: SL2 cells


title: SL2_HMR_induced_1

value: pMT - HMR-FLAG-HA


title: SL2_Input_induced_1

value: induced (CuSO4 250 uM)


title: APS_NEU_6

value: APS


title: Pooled_S2FHP vs S2FW4EA8-6HP

value: pre-treatment


title: APS_NEU_8

value: Neutrophil


title: C3

city: Harbin

first: Zhiguo

last: Lin

state: Heilongjiang

address: No.23 Youzheng street

department: Neurosugery

institute: First affiliated hospital of Harbin medical university

description:
total miRNA
no-HS type

data_processing:
Quality control: Raw data(raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N,with 5’adaptercontaminants, without 3’adapteror the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
Reads mapping to the reference sequence: The small RNA tags were mapped to reference sequence by Bowtie (Langmeadet al.,2009) without mismatch to analyze their expression and distribution on the reference.
Known miRNA alignment: Mapped small RNA tags were used to looking for known miRNA. miRBase20.0was used as reference, modified software mirdeep2 (Friedlander et al., 2011)and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
Remove tags from these sources: To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Small RNA annotation summary: Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was useda markeras sample quality indicator.Usually it should be less than 60% in plant samples and 40% in animal samples as high quality.
miRNA editing analysis: Position 2~8 of a mature miRNA were called seed region which were highly conserved. The target of a miRNA might be different with the changing of nucleotides in this region. In our analysis pipeline, miRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch.
Quantification of miRNA: miRNA expression levels were estimated by TPM (transcript per million) through the following criteria(Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited text files include Readcount values and TPM values for each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the frozen hippocampal tissues using Trizol Reagent (Thermo Fisher Scientific, Waltham, MA, USA). RNA purity and concentration were assessed using the NanoPhotometer® spectrophotometer (Implen GmbH, Munich, Germany) and the Qubit® RNA Assay Kit in the Qubit® 2.0 Flurometer (Thermo Fisher Scientific). The RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA) was used to measure RNA integrity.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAsare not substrates for ligation mediated by T4 RNA Ligase 1 and therefore donot ligate to the 5´SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X)primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessedon the Agilent Bioanalyzer 2100 systemusing DNA High Sensitivity Chips.

value: brain

value: female


title: I_3

description:
total miRNA
HS ILAE type 1


title: C1

description:
total miRNA
no-HS type


title: I_2

description:
total miRNA
HS ILAE type 1


title: APS_NEU_10

value: F


title: IMR90 fNSF 6 h + tBHP 1 h + 5 h rep 3

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Graduate School of Medicine

country: Japan

institute: Osaka Metropolitan University

data_processing:
Sequenced reads were cleaned with Trimmomatic-0.32 before mapping them to the human genome (GRCh38.p7 primary assembly + gencode 25 annotation) with STAR-2.5.2b.
Raw read counts were obtained using featureCounts from the Subread-1.5.0-p3 package and gencode 25 annotation.
Only uniquely aligned reads were used. Normalization and differential expression analysis were carried out using DESeq2.
Genome_build: GRCh38.p7 primary assembly + gencode 25 annotation
Supplementary_files_format_and_content: A .txt file reporting Normalized_Counts.

molecule: polyA RNA

source_name: IMR90 fNSF 6 h + tBHP 1 h + 5 h

growth_protocol: Cells were cultured in EMEM suplmeneted with 15% FBS.

extract_protocol:
The RNA samples were extracted using Trizol reagent.
RNA samples were sent to the Genomics Research Center of the University of Rochester for RNA-Seq. The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used for library construction. The libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. Single end reads of 100 nt were generated for each sample. The sequencing was performed using the Illumina high-throughput HiSeqTM 2500.

treatment_protocol: Cells were pretreated for 6 h with PBS, cNSF, or fNSF (20ug/ml), and then exposed to tBHP (200uM) for 1 h. Cells were collected after the pretreatment or 6 h after starting the tBHP treatment.

tag: cell line

value: fNSF 6 h + tBHP 1 h + 5 h


title: IMR90 fNSF 6 h + tBHP 1 h + 5 h rep 2


title: BJAB, siRNA-mediated knockdown of TBL1XR1

city: Seoul

first: Sung-Yeon

last: Hwang

address: School of Biological Sciences, Seoul National University

country: South Korea

hyb_protocol: cRNA was fragmented for hybridization on the Agilent’s Gene Expression Hybridization Kit

scan_protocol: It's scanned through Agilent’s DNA microarray scanner.

data_processing: Data was extracted by Feature Extraction Software and normalized using Agilent's GeneSpring Software.

source_name: siRNA-mediated knockdown of TBL1XR1

label_protocol: Total RNA was converted into Cy3 labeled cRNA using Agilent’s Low RNA Input Linear Amplification kit PLUS .

extract_protocol: Total RNA  (300 ng each sample) was isolated using RNeasy Mini kit (Qiagen) according to manufacturer's instruction.

treatment_protocol: Plasmids expressing N terminal GFP- tagged wild-type TBL1XR1 and TBL1XR1 mutants (Leu282Pro and His348Glu) were transfected into cells using the Nucleofector I device (Amaxa) with Nucleofector solution V and program O-017. One million cells were transfected with 3 μg of plasmid. A siRNA duplex specific for the TBLR1 was transfected into cells by electroporation. The efficiency of TBLR1 silencing was determined by immunoblotting cell extracts collected 48 h after transfection.

value: BJAB


title: I_1

description:
total miRNA
HS ILAE type 1


title: BJAB, control

institute: School of Biological Sciences, Seoul National University

source_name: control


title: IMR90 fNSF 6 h + tBHP 1 h + 5 h rep 1


title: APS_NEU_4

value: M


title: IMR90 cNSF 6 h + tBHP 1 h + 5 h rep 3

source_name: IMR90 cNSF 6 h + tBHP 1 h + 5 h

value: cNSF 6 h + tBHP 1 h + 5 h


title: IMR90 cNSF 6 h + tBHP 1 h + 5 h rep 2


title: IMR90 cNSF 6 h + tBHP 1 h + 5 h rep 1


title: CON_NEU_86

value: healthy


title: BJAB, mutant TBL1XR1 (H348Q)

source_name: mutant TBL1XR1 (H348Q)


title: IMR90 PBS 6 h + tBHP 1 h + 5 h rep 3

source_name: IMR90 PBS 6 h + tBHP 1 h + 5 h

value: PBS 6 h + tBHP 1 h + 5 h


title: CON_NEU_81

source_name: Neutrophil DNA


title: APS_NEU_5


title: BJAB, wild-type TBL1XR1

source_name: wild-type TBL1XR1


title: BJAB, mutant TBL1XR1 (L282P)

source_name: mutant TBL1XR1 (L282P)


title: IMR90 PBS 6 h + tBHP 1 h + 5 h rep 1


title: IMR90 fNSF 6 h rep 1

source_name: IMR90 fNSF 6 h

value: fNSF 6 h


title: IMR90 fNSF 6 h rep 3


title: APS_NEU_3


title: APS_NEU_9


title: IMR90 fNSF 6 h rep 2


title: APS_NEU_1


title: C2

description:
total miRNA
no-HS type

value: male


title: IMR90 cNSF 6 h rep 1

source_name: IMR90 cNSF 6 h

value: cNSF 6 h


title: IMR90 PBS 6 h + tBHP 1 h + 5 h rep 2


title: IMR90 PBS 6 h rep 3

source_name: IMR90 PBS 6 h

value: PBS 6 h


title: IMR90 PBS 6 h rep 2


title: HBV_2_IP

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

institute: University of Zurich

data_processing:
Basecalls performed using CASAVA version 1.8.2
STAR version 2.5.0 alignment to combined hg38 and viral genome reference
Reads aligning to viral genomes were extracted for peak calling
Peaks identified using macs2
Viral genome coverage was normalized by the total number of reads aligned to the HBV genome in input and IP samples to identify most plausible peak
Genome_build: hg38
Supplementary_files_format_and_content: macs2 peak files (bed)

source_name: HepG2 liver cell line

growth_protocol: HepG2 cells were cultured in DMEM + 10% FBS. Post-infection, 2x10^8 cells were distributed into 100mm plates.

extract_protocol:
TRIZOL
Illumina Tru-seq PolyA RNA, 1 x 50

treatment_protocol: HBV infection, 120 hours

tag: viral strain

value: pHBV 1.3mer (subtype agw)


title: IMR90 PBS 6 h rep 1


title: IMR90 cNSF 6 h rep 3


title: HBV_3_Input


title: APS_NEU_7

value: APS


title: HBV_1_Input


title: HBV_1_IP


title: IMR90 cNSF 6 h rep 2


title: LY19Y646F_H3K27me3_rep1

city: Lausanne

first: Giovanni

last: Ciriello

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

description:
LY19Y646F_H3K27me3_mergedReplicates_filtered.bedGraph
LY19Y646F_H3K27me3_vs_input_SICERpeaks_FDR0.001.bed

data_processing:
Reads were aligned to hg19 using Bowtie2 (v2.2.9, parameters: --local, --very-sensitive, others were default)
Bam files were filtered for MAPQ>0 and sorted with Samtools (v1.3.1). Biological replicates were merged into a single .bam file. PCR duplicates were removed with custom bash scripts.
In the merged .bam file, peaks of H3K27me3 enrichment compared to the corresponding input control were identified using the peak calling software SICER with the wrapper SICERpy (v1.1, flags -F 3972 -q 1)
Peaks were filtered for FDR<0.001
bedGraph files were generated with bedtools genomecov (v2.26.0)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files are tracks showing coverage of aligned reads along the genome. Peak files are .bed lists containing peak location, fold change, p-value and FDR

source_name: Lymphoma B-cell immortalized cell line

growth_protocol: Cell lines were propagated in sterile incubators at 37°C, 5% CO2, grown in RPMI (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% antibiotic.

extract_protocol:
10 x106 cells were fixed with 1% formaldehyde, lysed and sonicated leading to a DNA size of approximately 200bp. Tri-methyl histone H3 (Lys 27) (H3K27me3) monoclonal antibody (Cell Signaling, 9733) was added to the samples and incubated overnight at 4°C. The complex was purified using magnetic beads followed by elution from the beads and de-crosslinking. DNA was purified using PCR purification columns.
ChIP sequencing libraries on purified DNA were generated and sequenced by Genewiz (New Jersey, USA)

treatment_protocol: Cell lines were untreated

value: constitutive expression EZH2-Y646F (CMV promoter)

tag: cell line passages

value: H3K27me3 (Cell Signaling, 9733)


title: LY19Y646F_H3K27me3_rep2


title: APS_NEU_2

value: Neutrophil


title: ingWAT WT BM; TF64

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

institute: Tel Aviv University

description: C57BL/6J mice (Envigo)

data_processing: RNA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6)).

source_name: ingWAT wild-type bone marrow

value: wild type

tag: tissue

value: Inguinal subcutaneous fat


title: LY19WT_input

value: EZH2-wild type


title: HBV_3_IP


title: LY19Y646F_input


title: HBV_2_Input


title: LY19WT_H3K27me3_rep3


title: LY19WT_H3K27me3_rep2


title: LY19WT_H3K27me3_rep1

description:
LY19WT_H3K27me3_mergedReplicates_filtered.bedGraph
LY19WT_H3K27me3_vs_input_SICERpeaks_FDR0.001.bed


title: 30_DPL

city: Taian

first: Yuding

last: Wang

address: No. 61, Daizong Street

institute: Shandong Agricultural University

data_processing:
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
Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10.
Clean reads are mapped to a reference sequences using SOAPaligner/SOAP2. No more than 5 mismatches are allowed in the alignment.
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by PRKM value.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: DPL_longissimus dorsi muscle

growth_protocol: A total of 32  pigs (L, DPL, LDPL, DLDPL, n=8) reared were selected under similar environmental and feeding conditions.

extract_protocol:
RNA was extracted from longissimus dorsi muscle samples (stored at −80°C) according to the EZNA Tissue RNA Kit instruction manual. RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (Cat# E7420L).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Dapulian (DPL)

value: 6 months

value: longissimus dorsi muscle


title: 28_DLDPL

source_name: DLDPL_longissimus dorsi muscle

value: Duroc x Landrace x Dapulian (DLDPL)


title: 27_DLDPL


title: 29_DLDPL


title: 26_DPL


title: 24_LDPL

source_name: LDPL_longissimus dorsi muscle

value: Landrace x Dapulian (LDPL)


title: 23_DPL


title: 32_DLDPL


title: 19_DPL


title: 21_DPL


title: 18_DLDPL


title: 16_DPL


title: 11_DPL


title: 20_DLDPL


title: 14_LDPL


title: 15_LDPL


title: 10_LDPL


title: 7_DPL


title: 9_LDPL


title: 5_LDPL


title: LY19Y646F_H3K27me3_rep3


title: L10

source_name: L_longissimus dorsi muscle

value: Landrace (L)


title: 8_LDPL


title: 6_DLDPL


title: 4_LDPL


title: L8


title: L5


title: L9


title: 25_DLDPL


title: L7


title: L4


title: L1


title: L2


title: SBI615: Leaf Bio#2

city: Newark

first: Karl

last: Franke

state: Delaware

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: University of Delaware

data_processing:
Library strategy: PARE-seq
Adapters were trimmed from reads.
PARE reads were mapped to their appropriate genome using bowtie 0.12.7
PARE libraries were normalized to TP10M
RNAseq reads were mapped to the Brachypodium genome using STAR 2.5.3a with ENCODE standard settings.
RNAseq libraries were normalized using RSEM 1.2.31
Genome_build: Brachypodium distachyon JGI v3.1
Genome_build: Panicum virgatum JGI v4.1
Genome_build: Sorghum bicolor JGI v3.1.1
Supplementary_files_format_and_content: RNAseq proccessed data files are RSEM normalized gene counts. PARE processed data files indicate the prominence of PARE reads mapping to predicted miRNA target sites.

organism: Sorghum bicolor

source_name: Leaf

growth_protocol: Seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath. Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf. Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed.

extract_protocol:
RNAs were isolated using Trizol reagent (Molecular Research Center).
PARE libraries were constructed as described (German et al., 2008). RNA-seq libraries were constructed using the ScriptSeq RNA-Seq Library Preparation Kit from Illumina (Cat#SSV21124) and sequenced using Illumina HiSeq 2500.

tag: stress

value: Leaf


title: SBI618: Panicle Bio#2

source_name: Panicle

tag: strain

value: Panicle


title: SBI616: Panicle Bio#1


title: SBI619: Leaf Bio#1


title: SBI617: Root Bio#1

source_name: Root

value: Root


title: SBI520: Cold Bio#2

source_name: Above ground tissue

value: Cold

value: Above ground tissue


title: SBI519: Control for Cold Bio#2


title: SBI517: Control for Cold Bio#1


title: SBI620: Root Bio#2


title: 4G: replicate C, 10 minutes

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

description: replicate C, 10 minutes

data_processing:
Sequencing files were aligned to the chromsome (NC_010475), pAQ1 (NC_010476), pAQ3 (NC_010477), pAQ4 (NC_010478), pAQ5 (NC_010479), pAQ6 (NC_010480), pAQ7 (NC_010474), and phiX174 (NC_001422) using Bowtie2 (v 2.2.6) and samtools (v 1.2).
Counts for each feature in the general feature format (.gff) files were obtained with the htseq-count script using union mode and stranded set to reverse (HTseq v 0.6.1).
A linear relationship between log RNA spike-in copy number and read counts was only observed for spike-ins added at a ratio of 0.01 – 10 copies/cell, so only these were used for normalization. All PCC 7002 genes were within this range and all samples had a good correlation between log RNA spike-in copy number and read count with all R2 values were between 0.971 and 0.999. The sum of the reads that aligned to the spike-ins was calculated for each sample and used to create a normalization factor to keep the sum of reads that aligned to the spike-ins constant throughout the time course.
Counts for each feature were normalized with the normalization factor created using the sum of the RNA spike-in reads.
The number of reads that aligned to each position (and strand) in the chromosome and plasmids was counted using Integrated Genome Viewer count tool (window size set to 1 base) on the alignment files. These counts were normalized with the normalization factor determined by the RNA spike-in read counts.
Half lives of each gene were calculated by fitting gene read counts from all 21 samples to an exponential decay model. For most genes a poor fit was found when including all timepoints because the decay happened at the earlier part of the timecourse. The number of timepoints included that gave the best fit (highest R-squared value) was used on a per gene basis. The half life was only calculated if the best R-squard fit was > 0.6. If the gene still had at least 50% of the original read counts at the end timepoint it was classified as stable.
Genome_build: NC_010475, NC_010476, NC_010477, NC_010478, NC_010479, NC_010480, NC_010474, NC_001422
Supplementary_files_format_and_content: .csv files contain the number of reads (normalized for decay) that align to each position of the chromosome and plasmids (row number corresponds to position in chromosome/plasmid). The data is stranded so there are separate files for both the plus and minus strand.

organism: Picosynechococcus sp. PCC 7002

source_name: bacterial cells

growth_protocol: The WT strain was maintained on media A+ agar (1.5%) plates. Three pre-cultures of 20 mL A+ media were bubbled with air overnight. The OD730nm was measured and 1 1L pyrex bottles filled with 900 mL media A+ was inoculated with pre-culture for an OD730nm = 0.01. Cultures were bubbled with air for 24 hours before harvesting (OD ~0.1WT PCC 7002 (Pasteur collection) was grown on grown on media A+ (Stevens, 1973) 1.5% agar plates. All liquid cultures were grown at 37C and bubbled with air. A bubble tube containing 21 mL media A+ was inoculated and was grown for 24 hours. The OD730nm was measured and used to inoculate 3 separate bubble tubes containing 21 mL media A+ at an OD730nm = 0.1, which were grown for 24 hours. The OD730nm was measured and 3 separate 1 L bottles containing 900 mL of media A+ were inoculated with pre-culture to achieve an OD 730nm of 0.01. Cultures were bubbled with air at 37C for 22 hours before sampling.

extract_protocol:
RNA spike-ins were added to samples immediately before extraction with hot phenol and DNase-treatment as in RNA was extracted using the hot phenol method outlined in Khodursky A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. 2003. Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods Mol Biol 224:61–78.
RNA was submitted to the University of Wisconsin Biotechnology Gene Expression Center for RNA-sequencing. rRNA was removed with a Ribo-Zero Magnetic Kit and the library was created using a TruSeq Stranded Total RNA Library Kit. Samples were run on an Illumina HiSeq 2500.

treatment_protocol: 2 mL of each culture was collected for cell counts via hemocytometer and OD measurements. 40 mL of culture was collected and deposited into a 50 mL conical tube containing 5.0 mL stop solution (10% phenol in ethanol) placed in ice. Rifampicin was added at a concentration of 50mg/mL (in DMSO) and samples were taken as described above at 0.5, 1, 2.5, 5, 7.5, and 10 minutes following addition. Samples were spun down in a Beckman Coulter Avanti J-E Centrifuge at 7,500xg for 10 minutes at 4C. The supernatant was removed and samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction (1 week). RNA spike-ins were used for normalization and to ensure read counts corresponded to RNA copy number. Six RNA spike-ins from bacteriophage phiX174 were used as in Chen, 2015. DNA templates for in vitro transcription were created by including the T7 promoter sequence in the primer sequence and amplifying phiX174 DNA (New England Biolabs, #N3023S). DNA templates were purified with ethanol precipitation and used to synthesize RNA with the T7 RiboMAX Express Large Scale RNA Production System (Promega, #P1320). RNA was purified with ethanol precipitation and quantified via Nanodrop. RNA spike-ins were combined to obtain a range of copy numbers per cell (gene H: 0.1 copies/cell; gene D: 1 copy/cell; genes F and G: 10 copies/cell; fragment 290: 100 copies/cell; and fragment 190: 1,000 copies/cell).

tag: timepoint

value: 10 minutes


title: 4F: replicate C, 7.5 minutes

description: replicate C, 7.5 minutes

value: 7.5 minutes


title: 4D: replicate C, 2.5 minutes

description: replicate C, 2.5 minutes

value: 2.5 minutes


title: 4E: replicate C, 5 minutes

description: replicate C, 5 minutes

value: 5 minutes


title: 4A: replicate C, 0 minutes

description: replicate C, 0 minutes

value: 0 minutes


title: 3G: replicate B, 10 minutes

description: replicate B, 10 minutes


title: 4C: replicate C, 1 minute

description: replicate C, 1 minute

value: 1 minute


title: 4B: replicate C, 0.5 minutes

description: replicate C, 0.5 minutes

value: 0.5 minutes


title: 3E: replicate B, 5 minutes

description: replicate B, 5 minutes


title: Huh7-shACOT12-rep2

city: Shanghai

first: Ming

last: Lu

address: No. 12, Middle Urumqi Road

department: Huashan hospital

institute: Fudan university

description: D

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: ACOT12 shRNA ovexpressed Huh7 cell

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: Cells were maintained in DMEM supplemented with 10% (v/v) FBS at 37 °C in 5% CO2

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: human hepatocellular carcinoma (HCC) cell line

tag: genotype/variation

value: overexpressing ACOT12 shRNA


title: 3F: replicate B, 7.5 minutes

description: replicate B, 7.5 minutes


title: MHCC97H-ACOT12m-rep1

description: E

value: overexpressing ACOT12 mutant


title: Huh7-scramble shRNA-rep1

description: A

source_name: scramble shRNA ovexpressed Huh7 cell

value: overexpressing scramble shRNA


title: Huh7-scramble shRNA-rep2

description: C


title: Huh7-shACOT12-rep1

description: B


title: MHCC97H-ACOT12-rep1

description: B

value: overexpressing ACOT12


title: MHCC97H-ACOT12-rep2

description: D


title: SBI518: Cold Bio#1


title: 3C: replicate B, 1 minute

description: replicate B, 1 minute


title: 3B: replicate B, 0.5 minutes

description: replicate B, 0.5 minutes


title: 3A: replicate B, 0 minutes

description: replicate B, 0 minutes


title: 2G: replicate A, 10 minutes

description: replicate A, 10 minutes


title: MHCC97H-empty vector-rep2

description: C

source_name: MHCC97H-empty vector

value: overexpressing empty vector


title: 2A: replicate A, 0 minutes

description: replicate A, 0 minutes


title: 2B: replicate A, 0.5 minutes

description: replicate A, 0.5 minutes


title: 2D: replicate A, 2.5 minutes

description: replicate A, 2.5 minutes


title: 2E: replicate A, 5 minutes

description: replicate A, 5 minutes


title: 2C: replicate A, 1 minute

description: replicate A, 1 minute


title: MHCC97H-empty vector-rep1

description: A


title: 2F: replicate A, 7.5 minutes

description: replicate A, 7.5 minutes


title: 6072 vs. 5074

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: polarity(-)

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.

extract_protocol: Total RNA was isolated according the manufacturer´s protocol.

treatment_protocol: Tamoxifen (Sigma) was injected intraperitoneally into mice either as single dose or on three consecutive days (4 mg/25 g bodyweight, diluted in 200 µl corn oil) at the indicated time points to deplete Rspo3 expression

tag: background strain

tag: genotype

value: Rspo3 KO

value: stomach

tag: stomach region

value: antrum

value: Rspo3 ++


title: 3D: replicate B, 2.5 minutes

description: replicate B, 2.5 minutes


title: 5073 vs. 6037

description: polarity(+)


title: Rsp3 Corpus 3 vs. Corpus 6

description: polarity(-)

value: corpus


title: 6037 vs. 5073

description: polarity(-)


title: CCR2-  SM

city: Beijing

first: xiaoqing

last: xu

address: No.5 Dongdan Santiao, Dongcheng District

department: Immunology

institute: Chinese Academy of Medical Sciences

description: Gene expression data from

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

source_name: C57BL6 mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: CCR2+ and CCR2- spenic macrophages (SM) sorted from  C57BL6 mouse infected with Listeria Monocytogenes in vivo on day3

extract_protocol: Total RNA of mouse PM was extracted with Trizol  according to the manufacturer's instructions.

treatment_protocol: the collected splenic macrophages were washed by PBS and centrifuged at 4 degree, and then the cells was put into 1.0ml Trizol (Sigmma)


title: Corpus 5 vs. Rsp3 Corpus 1

city: Berlin

description: polarity(+)


title: CCR2+ SM

description: Gene expression data from

value: CCR2+  spenic macrophages (SM) sorted from  C57BL6 mouse infected with Listeria Monocytogenes in vivo on day3


title: Shammed, ventral SCN, replicate 2, batch A

city: Rotterdam

last: Brand

address: Dr Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus Medical Center

hyb_protocol: Each batch of biotin labelled cDNA samples was fragmented and combined with hybridisation cocktail including DMSO according to the manufacturers protocol (Nugen Technologies) and hybridised to Affymetrix GeneChip 430_2.0 arrays for 18 hrs. Post-hybridisation washing, scanning and image analysis were performed according to the Affymetrix fluidics protocol FS450_0004.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression measures were exported using the MAS5.0 software suite (Affymetrix, Santa Clara, USA), and normalised per batch using the GeneChip Robust Multi-array Analysis method available as the BioConductor (v2.12) package, gcrma,v2.32.0, running in the R v3.0.2 environment.

source_name: Sham treated ventral suprachiasmatic nuclei

label_protocol: Amplification and cDNA labelling with biotin was accomplished using the Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 respectively according to the manufacturers protocols (Nugen Technologies, San Carlos, USA). Efficiency of the amplification was assayed quantitatively by 260/280 nm estimation of cDNA concentration, where a yield of at least 5 μg cDNA was deemed sufficient for specific amplification of the RNA template. Amplification and labelling was achieved batch wise.

growth_protocol: Eight week old C57BL/6 mice were obtained from Harlan (Horst, The Netherlands) and individually housed with conventional chow (Special Diets Services, Witham, UK) and tap water (acidified with HCl to pH 2.9, to prevent bacterial growth) ad libitum.

extract_protocol: Isolated SCN sub-regions were lysed in Lysis Buffer (Qiagen, Hilden, Germany) and stored at -80° C until RNA purification. RNA was purified with on-column DNase treatment using the RNeasy Micro kit (Qiagen) according to the manufacturers instructions, except that 20 ng of 16S/23S bacterial ribosomal RNA (Roche, Woerden, The Netherlands) was used as carrier species and an additional elution was performed in the final step to maximise RNA yield. RNA was eluted with DEPC treated water, vacuum evaporated and immediately amplified.

treatment_protocol: 25 μm thick coronal cryosections mounted on 1mm PALM pen-membrane slides (Carl Zeiss AG, Oberkochen, Germany) were rapidly thawed, fixed for 30sec in 70% ethanol and stained with haematoxylin for 3min. Following staining, sections were rinsed in diethylpyrocarbonate (DEPC) treated water and dehydrated by several rinses in 100% ethanol. Laser catapult microdissection of ventral, dorsal and central SCN subregions was accomplished using the PALM Micolaser system (Carl Zeiss AG, Oberkochen, Germany ) on freshly prepared sections.

value: 30m sham treatment

value: ventral core SCN

tag: batch

value: batch A


title: Pulsed, central SCN, replicate 3, batch B

source_name: Light pulsed central suprachiasmatic nuclei

value: 30m light pulsed

value: central middle SCN

value: batch B


title: Pulsed, dorsal SCN, replicate 1, batch A

source_name: Light pulsed dorsal suprachiasmatic nuclei

value: dorsal shell SCN


title: Pulsed, dorsal SCN, replicate 4, batch B


title: Shammed, central SCN, replicate 3, batch B

source_name: Sham treated central suprachiasmatic nuclei


title: Pulsed, ventral SCN, replicate 3, batch B

source_name: Light pulsed ventral suprachiasmatic nuclei


title: Shammed, central SCN, replicate 2, batch A


title: Shammed, ventral SCN, replicate 1, batch A


title: Pulsed, central SCN, replicate 2, batch A


title: Shammed, dorsal SCN, replicate 2, batch A

source_name: Sham treated dorsal suprachiasmatic nuclei


title: Shammed, dorsal SCN, replicate 3, batch B


title: Pulsed, central SCN, replicate 4, batch B


title: Shammed, ventral SCN, replicate 4, batch B


title: Pulsed, dorsal SCN, replicate 2, batch A