title: ATAC-NK-Day06

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

description: PBMC_ATAC_NK_d6_AFC_16_03_25_GCTACG_S111_L008

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads were aligned to the GRCh38/hg38 assembly of the human genome using STAR (version 2.5.2a) using default parameters [23]. Gene expression values were calculated as fragments per kilobase per million mapped reads (FPKM) across GENCODE transcript exons (release 24) [24] using HOMER [25]. To remove possible contamination from genomic DNA in the RNA-seq samples, FPKM measurements were calculated for long introns (>10 kb) and the median intron FPKM per experiment was subtracted from each exon FPKM values to remove background signal. Gene expression FPKM values across all samples set to a minimum of zero and then quantile normalized. Only GENCODE transcripts with length greater than 300 bp were considered. Log2 fold change ratios were calculated using a pseudo count by adding a FPKM of 4 to both numerator (i.e. day 3, 6, 17) and denominator (i.e. day 48/convalescent) to reduce the impact of low expression noise and contamination on the lists of regulated genes.
For ATAC-seq, fastq files were trimmed and aligned to hg38 using bowtie2. Mitochondrial reads were removed and tag directories made while removing all PCR duplicates. Peaks were called using a standardized peak size using HOMER.
ATAC-Seq: Tab-delimited Peak files containing peak positions for each ATAC-seq experiment (one peak file per sample, hg38) Columns: 1:peak ID, 2:chromosome,3:start,4:end,5:strand,6:Normalized Tag Count,7:focus ratio,8:findPeaks Score,9:Fold change,10:p-value vs. Local,11:Clonal Fold Change.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:copies, 8:gene_type, 9:gene_name, 10:Annotation/Divergence, 11-45: FPKM for each experiment.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq tab-delimited text files include FPKM values for each Sample at each time point, Tab-delimited Peak files containing peak positions for each ATAC-seq experiment

source_name: Natural Killer Cell

extract_protocol:
This research study was approved by the UCSD IRB with Human Research Protections Program # 161060. Written informed consent was obtained from the adult human subject described in this report. After obtaining written informed consent, blood was collected on five occasions d3, d6, d17, d48, and d240 post-onset of symptoms (POS). Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Histopaque-1077 per manufacturers instructions and subjected to flow activated cell sorting (FACS). For innate immune cell sorting ten million PBMCs were stained with antibodies against CD3 PE-Cy7, CD19 PE-Cy7 CD20 PE-Cy7, HLADR BV421, CD11c AF700, CD123 PE, CD14 AF488, CD16 APC, CD56 APC-Cy7, and Zombie Aqua Fixable viability dye and separated. For T cell sorting, five million cryopreserved PBMCs were stained with CD16 BV510, CD56 BV510, CD4 APC-eFluor780, CD3 AF700, CD8 BV785, CD45RA BV570, CCR7 PE-Cy7, CXCR5 BV421, CXCR3 BV605, TCR V_24-J_18 BV711, CD226 BB515, CCR6 PerCP-Cy5.5, CCR4 PE, CD25 PE-Dazzle 594, and CD127 AF647 and sorted into CD3+ T cell CD4+ and CD8+ populations. Stained PBMCs were sorted in the La Jolla Institute (LJI) Flow Cytometry Core Facility on a FACSAria Fusion sorter.
RNA-seq library preparation: sequencing libraries were prepared using a low input RNA-seq prepared according to the Smart-seq2 method [22] with some modifications. 5000-15,000 PBMCs (pre-sort) or FACS isolated cell populations were lysed in TRIzol and RNA extracted using Direct-zol RNA Microprep (Zymo) with on-column DNAseI treatment. 10 µL purified RNA was mixed with 5.5 µL of SMARTScribe 5X First-Strand Buffer (Clontech), 1 µL polyT-RT primer (2.5 µM, 5’-AAGCAGTGGTATCAACGCAGAGTAC(T30)VN, 0.5 µL SUPERase-IN (Ambion), 4 µL dNTP mix (10 mM, Invitrogen), 0.5 µL DTT (20 mM, Clontech) and 2 µL Betaine solution (5 M, Sigma), incubated 50°C 3 min. 3.9 µL of first strand mix, containing 0.2 µL 1% Tween-20, 0.32 µL MgCl2 (500 mM), 0.88 µL Betaine solution (5 M, Sigma), 0.5 µL (5 M, Sigma) SUPERase-IN (Ambion) and 2 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) was added and incubated one cycle 25°C 3 min., 42°C 60 min. 1.62 µL template switch (TS) reaction mix containing 0.8 µL biotin-TS oligo (10 µM, Biotin-5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 0.5 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) and 0.32 µL SMARTScribe 5X First-Strand Buffer (Clontech) was added, then incubated at 50°C 2 min., 42°C 80 min., 70°C 10 min. 14.8 µL second strand synthesis, pre-amplification mix containing 1 µL pre-amp oligo (10 µM, 5’AAGCAGTGGTATCAACGCAGAGT-3’), 8.8 µL KAPA HiFi Fidelity Buffer (5X, KAPA Biosystems), 3.5 µL dNTP mix (10 mM, Invitrogen) and 1.5 µL KAPA HiFi HotStart DNA Polymerase (1U/µL, KAPA Biosystems), was added,  then amplified by PCR: 95°C 3 min., 5 cycles 98°C 20 sec, 67°C 15 sec and 72°C 6 min, final extension 72°C 5 min.  The synthesized dsDNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 8.4% PEG8000, 1.1M NaCl, then eluted with 13 µL UltraPure water (Invitrogen). The product was quantified by Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and libraries were prepared using the Nextera DNA Sample Preparation kit (Illumina). Tagmentation mix containing 11 µL 2X Tagment DNA Buffer and 1 µL Tagment DNA Enzyme was added to 10 µL purified DNA, then incubated at 55°C 15 min. 6 µL Nextera Resuspension Buffer (Illumina) was added and incubated at room temperature for 5 min. Tagmented DNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 7.8% PEG8000, 0.98M NaCl, then eluted with 25 µL UltraPure water (Invitrogen). Final enrichment amplification was performed with Nextera primers, adding 1 µL Index 1 primers (100 µM, N7xx), 1 µL Index 2 primers (100 µM, N5xx) and 27 µL NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs), then amplified by PCR: 72°C 5 min., 98°C 30 sec., 6-12 cycles 98°C 10 seconds, 63°C 30 sec., and 72°C 1 min. Libraries were size selected, quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), pooled and sequenced on a HiSeq 2000 sequencer using single-end 50bp reads. Assay for Transposase-Accessible Chromatin-sequencing (ATAC-seq): 50,000 FACS isolated classical monocytes or NK cells were lysed in 50 μl lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water) on ice and nuclei were pelleted by centrifugation at 500 RCF for 10 min. Nuclei were then resuspended in 50 μl transposase reaction mix (1x Tagment DNA buffer (Illumina 15027866), 2.5 μl Tagment DNA enzyme I (Illumina 15027865), in water) and incubated at 37°C for 30 min on a PCR cycler. DNA was then purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205) and eluted with 10 μl of elution buffer. DNA was then amplified with PCR mix (1.25 μM Nextera primer 1, 1.25 μM Nextera index primer 2-bar code, 0.6x SYBR Green I (Life Technologies, S7563), 1x NEBNext High-Fidelity 2x PCR MasterMix, (NEBM0541)) for 8-12 cycles, size selected for fragments (160-290 bp) by gel extraction (10% TBE gels, Life Technologies EC62752BOX) and single-end sequenced for 51 cycles on a HiSeq 4000 or NextSeq 500.
RNA-seq and ATAC-seq single-end sequenced for 51 cycles on an Illumina HiSeq 2000

tag: subject status

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

tag: cell subtype

value: Natural Killer Cell

tag: time post onset of symptoms

value: 6 days


title: ATAC-NK-Day17

status: Public on Dec 19 2018

type: SRA

city: La Jolla

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: 17 days


title: ATAC-CD14posCD16neg-Day06

description: PBMC_ATAC_CD14pos_16neg_Mono_d6_AFC_16_03_25_GGACTC_S108_L008

source_name: CD14posCD16neg monocyte

value: CD14posCD16neg monocyte


title: ATAC-CD14posCD16neg-Day17

description: PBMC_ATAC_CD14pos_16neg_Mono_d17_AFC_16_04_04_S66_L004


title: Het_Z_Q175_(neo-)_KI_Cortex_male_rep4 [mRNA]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
Q175NM0010_04_Left_Cortex
mRNA
404238_Q175NM0010_04_Left_Cortex_L17
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Genome mapped via Omicsoft OSA 4.0.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming /Mode=TrimByQuality /ReadTrimQuality=2; Options /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.mm10, gene models version Ensembl.R78
Supplementary_files_format_and_content: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx: Excel file includes FPKM and Count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Cortex of left cerebral hemisphere

growth_protocol: Housed with Wild Type and Z_Q175 (neo-) KI mice.

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: background

tag: genotype/variation

value: Het Z_Q175 (neo-) KI

tag: Sex

value: male

tag: age

value: 6 months

tag: tissue

value: Cortex


title: Ctrl [A3]

type: RNA

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description: Gene expression in non-infected cells

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A

scan_protocol: A total of 2 µg RNA from each sample was then labeled with the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). After hybridization, the slides were scanned with the Agilent Microarray Scanner (Agilent p/n G2505C),

data_processing: Quantified signals were extracted and analyzed by using the Agilent Feature Extraction Software, in accordance with MIAME guidelines

source_name: IEC4.1 cells

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: Mouse intestinal epithelial cells (IEC4.1 cells) cultured in DMEM/F12 Medium 1:1 supplemented with 10 ng/ml epidermal growth factor (EGF), 5% fetal bovine serum and antibiotics (100 IU/ml of penicillin,100 µg/ml of streptomycin and 10ug/ml Gentamicin). Atmosphere: air, 95%; carbon dioxide (CO2), 5% ; Temperature: 37°C

treatment_protocol: The IEC4.1 cells  were grown to 80% confluence for two groups:  control (Group A, A1-A3) and C. parvum infection (Group B, B1-B3; cells exposed to C. parvum infection for 24h). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: intestinal epithelial cells

tag: agent

value: Ctrl

tag: cell line


title: genomic DNA from neuroblastoma 17

type: genomic

city: Heidelberg

first: Kai-Oliver

last: Henrich

address: INF 280

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Raw data files generated from the array usage were preprocessed using the minfi Bioconductor package (preprocessIllumina function).

label: Cy5 and Cy3

source_name: neuroblastoma 17

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from snap-frozen neuroblastoma tissue using standard procedures.

tag: tert status

value: TERT non-rearranged

tag: alt status

value: ALT negative

tag: mycn status

value: MYCN-non-amplified

tag: atrx status

value: ATRX non-mutated

value: TERT expression high

value: neuroblastoma


title: C. parvum infection [B1]

description: Gene expression in infected cells

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: Cryptosporidium parvum


title: Het_Z_Q175_(neo-)_KI_Cortex_male_rep3 [mRNA]

description:
Q175NM0010_03_Left_Cortex
mRNA
404263_Q175NM0010_03_Left_Cortex_L21
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc60

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Process of sciCOOL-seq data: Data quality was checked and reads were mapped according to our recent publication (Guo F, Yan L, Guo H et al. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 2015; 161:1437-1452). Briefly, raw reads were trimmed and QC filtered before aligned to mouse reference genome (mm9). Duplicated reads were removed and only those non-duplicated ones were retained for further analysis.
Process of single-cell RNA seq data:Raw reads were firstly classified by cell barcodes on read2, then read1 were trimmed and aligned to the mm9 mouse transcriptome. After de-duplicated by UMIs information, the transcript copy numbers of each gene were counted. Single cells with less than 3,000 detected genes and 20,000 transcripts were excluded. And the retained 275 single cells were used for downstream analysis. Genes with averaged counts above 0.1 among all the retained single cells were used.
Genome_build: mm9
Supplementary_files_format_and_content:
scRNA-seq: mOocy_rna_rawCounts.txt contains abundance measurements;mOocy_rna_barcodes.txt contains sequences of barcodes used to split RNA fastq files to single cells
sciCOOL-seq: bigWig; *.gch.bw are bigwig files which included the methylation level of covered GCH (GCA,GCC,GCT) sites to estimate chromatin accessibility; *.wcg.bw are bigwig files which included the methylation level of covered WCG (ACG, TCG) sites to estimate DNA methylation.

source_name: Non-Growing Oocyte

extract_protocol:
All the animal procedures were carried out according to the ethical guidelines of Laboratory Animal Center of the Sichuan University. None-growing oocytes (NGO) with diameters less than 20μm were collected from 3- to 4-day-old female ICR mice. Growing oocytes (GO) and fully-growing oocytes (FGO) were collected from 3- to 4-week-old female ICR mice, the diameters of oocytes for each stage were: GO1 (30μm< diameters <45μm), GO2 (50μm< diameters <55μm), GO3 (60μm< diameters <65μm), FGO (diameters >70μm). Excessive washes were performed to remove the contamination of somatic cells from oocytes. Individual oocyte was then picked for the downstream single-cell experiments.
Firstly, individual oocyte was in vitro methylated by GpC methylase (New England Biolabs), digested by protease and bisulfite converted26. Then, the single-cell genomic DNA was randomly primed and dC tailed. The oligos with anchor sequences were then introduced to fragmented genomic DNA and PCR amplified. Finally, libraries were checked, pooled together and sequenced with paired-end 150-bp reads on Illumina HiSeq 4000 platform (Novogene).

value: ICR

tag: genotype

value: wild type

value: Ovary

value: oocyte

tag: oocyte size

value: < 20 microns


title: NGO_sc61


title: C. parvum infection [B2]

description: Gene expression in infected cells


title: Het_Z_Q175_(neo-)_KI_Cortex_male_rep2 [mRNA]

description:
Q175NM0010_02_Left_Cortex
mRNA
404255_Q175NM0010_02_Left_Cortex_L59
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Het Z_Q175 (neo-) KI

value: male


title: Het_Z_Q175_(neo-)_KI_Cortex_male_rep1 [mRNA]

description:
Q175NM0010_01_Left_Cortex
mRNA
404247_Q175NM0010_01_Left_Cortex_L1
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months

value: Cortex


title: PlasmacytoidDC-Day48

description:
PBMC_RNA_plasmacytoidDC_d48_AFC_16_05_05_CTCTCT_S72_L004
PlasmacytoidDC-Day48/ FPKM

molecule: polyA RNA

source_name: Plasmacytoid Dendritic Cell

tag: subject status

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

tag: cell subtype

value: Plasmacytoid Dendritic Cell

value: 48 days


title: PlasmacytoidDC-Day06

description:
PBMC_RNA_plasmacytoidDC_d6_AFC_16_03_25_S74_L005
PlasmacytoidDC-Day06/ FPKM

tag: cell type

tag: time post onset of symptoms

value: 6 days


title: NGO_sc58

tag: strain


title: PlasmacytoidDC-Day03

description:
PBMC_RNA_plasmacytoidDC_d3_AFC_16_03_22_S73_L005
PlasmacytoidDC-Day03/ FPKM

value: 3 days


title: NGO_sc59


title: genomic DNA from neuroblastoma 391

source_name: neuroblastoma 391

value: TERT rearranged

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: TERT expression high

value: neuroblastoma


title: NGO_sc57

value: ICR

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: genomic DNA from neuroblastoma 383

source_name: neuroblastoma 383

value: TERT non-rearranged

value: TERT expression low


title: CTR Sample11 treated with compound2

city: Pavia

first: Stella

last: Gagliardi

state: Pavia

address: Via Mondino, 2

department: GPG center

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Counts files were obtained with the MiSeq reporter Targeted RNA Workflow
Genome_build: HG19
Supplementary_files_format_and_content: Count files (targeted transcriptome)

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction. PBMCs have be grown with RPMI containing 10% FBS.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Targeted RNA Expression NF-kB Panel integrated with BACE1, VDR and MGAT3 genes, using XX-ng total RNA (Illumina). The qualities of the libraries were assessed by 2100 Bioanalyzer with a DNA1000 assay. Libraries were quantified by qPCR using the KAPA Library Quantification kit for Illumina sequencing platforms (KAPA Biosystems); RNA processing has been carried out using Illumina MiSeq Sequencing.

treatment_protocol: About 5*106 PBMCs were treated for 24 hours at 0.1 µM of curcuminoids and then with Aβ 1-42  at 1 µM for an additional 24 hours.

tag: diagnosis

value: Helathy Control

tag: treatment

value: untreated


title: CTR Sample12

value: Peripheral blood mononuclear cells (PBMCs)


title: PBMC-Day17

description:
PBMC_RNA_PBMC_d17_AFC_16_04_04_CGAGGC_S75_L004
PBMC-Day17/ FPKM

source_name: PBMC

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: 17 days


title: PBMC-Day48

description:
PBMC_RNA_PBMC_d48_AFC_16_05_05_S70_L005
PBMC-Day48/ FPKM

value: 48 days


title: CTR Sample13


title: NGO_sc55


title: NGO_sc56


title: genomic DNA from neuroblastoma 277

source_name: neuroblastoma 277

value: ALT positive

value: MYCN-non-amplified

value: ATRX non-mutated


title: genomic DNA from neuroblastoma 339

source_name: neuroblastoma 339

value: ALT negative

value: neuroblastoma


title: PBMC-Day06

description:
PBMC_RNA_PBMC_d6_AFC_16_03_25_GCTACG_S74_L004
PBMC-Day06/ FPKM

value: 6 days


title: NGO_sc54

value: ICR

value: wild type

value: Ovary

value: oocyte


title: genomic DNA from neuroblastoma 351

source_name: neuroblastoma 351

value: TERT non-rearranged

value: TERT expression high


title: CTR Sample11

value: Helathy Control

value: untreated

value: Peripheral blood mononuclear cells (PBMCs)


title: genomic DNA from neuroblastoma 282

source_name: neuroblastoma 282

value: TERT expression low


title: NGO_sc53

value: < 20 microns


title: genomic DNA from neuroblastoma 54

source_name: neuroblastoma 54

value: MYCN-amplified


title: PBMC-Day03

description:
PBMC_RNA_PBMC_d3_AFC_16_03_22_CAGAGA_S73_L004
PBMC-Day03/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: 3 days


title: NK-Day17

description:
PBMC_RNA_NK_d17_2_AFC_16_04_04_S68_L005
NK-Day17/ FPKM

value: Natural Killer Cell

value: 17 days


title: CTR Sample10


title: NGO_sc51

value: ICR


title: genomic DNA from neuroblastoma 253

source_name: neuroblastoma 253

value: TERT rearranged

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: neuroblastoma


title: APLNR+ MES

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: APLNR+ MES samples collected from day 2 after hematopoietic differentiation through FACS.

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 2 days. Finally, cells were feeded with Custom mTeSR1 medium supplemented with  40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) and SB-431542 (Sellleck) for 3 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: APLNR+ MES


title: genomic DNA from neuroblastoma 48

source_name: neuroblastoma 48

value: TERT expression high


title: genomic DNA from neuroblastoma 263

source_name: neuroblastoma 263


title: genomic DNA from neuroblastoma 259

source_name: neuroblastoma 259

value: TERT non-rearranged


title: genomic DNA from neuroblastoma 60

source_name: neuroblastoma 60

value: ALT positive

value: ATRX mutated

value: TERT expression low


title: genomic DNA from neuroblastoma 275

source_name: neuroblastoma 275


title: CTR Sample9

value: Helathy Control

value: untreated

value: Peripheral blood mononuclear cells (PBMCs)


title: MyeloidDC-Day48

description:
PBMC_RNA_myeloidDC_d48_AFC_16_05_05_TAGGCA_S71_L004
MyeloidDC-Day48/ FPKM

source_name: Myeloid Dendritic Cell

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: Myeloid Dendritic Cell

value: 48 days


title: CTR Sample9 treated with compound1


title: NGO_sc50

source_name: Non-Growing Oocyte

value: ICR

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: NK-Day03

description:
PBMC_RNA_NK_d3_AFC_16_03_22_TCCTGA_S99_L007
NK-Day03/ FPKM

source_name: Natural Killer Cell

value: Natural Killer Cell

value: 3 days


title: NGO_sc48


title: CTR Sample10 treated with compound3

source_name: blood


title: genomic DNA from neuroblastoma 230

source_name: neuroblastoma 230

value: TERT non-rearranged

value: ALT positive

value: MYCN-non-amplified

value: neuroblastoma


title: NK-Day06

description:
PBMC_RNA_NK_d6_AFC_16_03_25_GCTACG_S103_L007
NK-Day06/ FPKM

value: 6 days


title: genomic DNA from neuroblastoma 28

source_name: neuroblastoma 28

value: ALT negative

value: MYCN-amplified

value: ATRX non-mutated

value: TERT expression low


title: NGO_sc49


title: MyeloidDC-Day17

description:
PBMC_RNA_myeloidDC_d17_2_AFC_16_04_04_S69_L005
MyeloidDC-Day17/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: Myeloid Dendritic Cell

value: 17 days


title: NK-Day48

description:
PBMC_RNA_NK_d48_AFC_16_05_05_GGACTC_S70_L004
NK-Day48/ FPKM

value: 48 days


title: CTR Sample9 treated with AB and compound1

value: Helathy Control

value: AB

value: Peripheral blood mononuclear cells (PBMCs)


title: MyeloidDC-Day06

description:
PBMC_RNA_myeloidDC_d6_AFC_16_03_25_S72_L005
MyeloidDC-Day06/ FPKM


title: genomic DNA from neuroblastoma 193

source_name: neuroblastoma 193

value: TERT non-rearranged

value: TERT expression high


title: CTR Sample11 treated with AB and compound2


title: NGO_sc46

value: ICR

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: MyeloidDC-Day03

description:
PBMC_RNA_myeloidDC_d3_AFC_16_03_22_S71_L005
MyeloidDC-Day03/ FPKM

value: 3 days


title: genomic DNA from neuroblastoma 180

source_name: neuroblastoma 180

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: TERT expression low

value: neuroblastoma


title: NGO_sc45


title: genomic DNA from neuroblastoma 185

source_name: neuroblastoma 185

value: MYCN-amplified


title: genomic DNA from neuroblastoma 194

source_name: neuroblastoma 194

value: TERT rearranged


title: NGO_sc52


title: NGO_sc47


title: CTR Sample8 treated with AB and compound3

value: Helathy Control


title: CTR Sample8

value: untreated

value: Peripheral blood mononuclear cells (PBMCs)


title: CD8Tcell-Day17

description:
PBMC_RNA_CD8pos_Tcell_d17_AFC_16_04_04_S80_L006
CD8Tcell-Day17/ FPKM

source_name: CD8 T cell

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: CD8 T cell

value: 17 days


title: CD8Tcell-Day48

description:
PBMC_RNA_CD8pos_Tcell_d48_AFC_16_05_05_S82_L006
CD8Tcell-Day48/ FPKM

value: 48 days


title: genomic DNA from neuroblastoma 152

source_name: neuroblastoma 152

value: TERT non-rearranged


title: genomic DNA from neuroblastoma 32

source_name: neuroblastoma 32

value: TERT expression high


title: genomic DNA from neuroblastoma 192

source_name: neuroblastoma 192

value: ALT negative


title: CTR Sample8 treated with AB

value: AB


title: CTR Sample10 treated with AB


title: NGO_sc43

value: ICR

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: CD8Tcell-Day06

description:
PBMC_RNA_CD8pos_Tcell_d6_AFC_16_03_25_S78_L006
CD8Tcell-Day06/ FPKM

value: 6 days


title: CTR Sample7

value: Helathy Control

value: untreated


title: CD8Tcell-Day03

description:
PBMC_RNA_CD8pos_Tcell_d3_AFC_16_03_22_S76_L006
CD8Tcell-Day03/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: 3 days


title: CTR Sample6 treated with compound1

value: Peripheral blood mononuclear cells (PBMCs)


title: CTR Sample6 treated with AB and compound1


title: NGO_sc42


title: NGO_sc41


title: CD4Tcell-Day17

description:
PBMC_RNA_CD4pos_Tcell_d17_AFC_16_04_04_S79_L006
CD4Tcell-Day17/ FPKM

source_name: CD4 T cell

value: PBMC

value: CD4 T cell

value: 17 days


title: CD4Tcell-Day48

description:
PBMC_RNA_CD4pos_Tcell_d48_AFC_16_05_05_S81_L006
CD4Tcell-Day48/ FPKM

value: 48 days


title: NGO_sc40


title: Spb4-HTP

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the S.cerevisiae genome by Bowtie2 (version 2.2.4).

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Wild-type BY4741 yeast cells or yeast cells expressing C-terminally His-Tev-ProtA tagged Has1, Mak5 or Spb4 from their genomic loci were grown in exponential phase in low uracil media supplemented with 4-thiouracil as previously described (Baejen et al., 2014).

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-ProtA-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Cells were crosslinked in vivo using light at 365 nm

value: cells expressing His-Tev-ProtA-tagged Spb4


title: CTR Sample6 treated with AB

value: AB


title: CTR Sample5


title: NGO_sc39

value: ICR


title: CD4Tcell-Day06

description:
PBMC_RNA_CD4pos_Tcell_d6_AFC_16_03_25_S77_L006
CD4Tcell-Day06/ FPKM


title: genomic DNA from neuroblastoma 216

source_name: neuroblastoma 216

value: TERT rearranged

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: TERT expression high

value: neuroblastoma


title: Has1-HTP

value: cells expressing His-Tev-ProtA-tagged Has1


title: Mak5-HTP

value: cells expressing His-Tev-ProtA-tagged Mak5


title: CD4Tcell-Day03

description:
PBMC_RNA_CD4pos_Tcell_d3_AFC_16_03_22_S75_L006
CD4Tcell-Day03/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: 3 days


title: genomic DNA from neuroblastoma 151

source_name: neuroblastoma 151

value: TERT non-rearranged

value: TERT expression low


title: CTR Sample5 treated with compound1

value: Helathy Control

value: Peripheral blood mononuclear cells (PBMCs)


title: NGO_sc37

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: CD14posCD16pos-Day48

description:
PBMC_RNA_CD14pos_16pos_Mono_d48_AFC_16_05_05_AGGCAG_S68_L004
CD14posCD16pos-Day48/ FPKM

source_name: CD14posCD16pos monocyte

value: PBMC

value: CD14posCD16pos monocyte

value: 48 days


title: CTR Sample5 treated with AB and compound1

value: AB


title: NGO_sc36

source_name: Non-Growing Oocyte

value: ICR


title: NGO_sc38


title: genomic DNA from neuroblastoma 116

source_name: neuroblastoma 116

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: neuroblastoma


title: eMSCs_T1_S12

city: Clayton

first: Shanti

last: Gurung

state: Vic

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Quality filtering used Illumina CASAVA v1.8.2 software (Illumina, Hayward, CA) with >97% of reads having quality >Q30.
Illumina adaptor sequences were removed.
RNA sequenced reads were mapped against the Human Reference Genome GRCh38 and Ensembl 87 gene annotation using STAR (v2.5.2) with the RNAsik pipeline and manipulated with samtools (v1.3.1) and picard tools.
Gene-level counts were generated using HTseq-count (v0.6.1p1).
Genes were then filtered to those having >10 reads in at least one sample for subsequent analysis and differential expression was calculated across paired A83-01-treated and untreated samples using voom and limma (v3.26.9) via the degust interface
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of sequence fragments aligned to each gene.

source_name: Human endometrial mesenchymal stem cells

growth_protocol: eMSCs were cultured in in-house serum free culture medium with bFGF and EGF at 5% oxygen and passaged at 5000cell/cm2. At pasage 6, the cells were treated with DMSO vehicle control for 7 days with media change every 48 hours.

extract_protocol:
RNA was extracted using PureLink® RNA mini Kit (Ambion, Invitrogen) including treatment with RNase-free DNase (QIAGEN).
Sequencing libraries prepared from 1mg input RNA (depleted of ribosomal RNA) with Illumina TruSeq Poly-A mRNA Library Pro Kit protocol 15031047 RevD (Illumina, Hayward, CA)

treatment_protocol: eMSCs were cultured in in-house serum free culture medium with bFGF and EGF at 5% oxygen and passaged at 5000cell/cm2. At pasage 6, the cells were treated with 1mM A83-01 for 7 days with media change every 48 hours.

tag: replicate

tag: tissue source and immunoselection of cells

value: Primary cells derived from human endometrium using SUSD antibody

tag: passage


title: NGO_sc44

tag: tissue


title: WT

source_name: no tag


title: CD14posCD16pos-Day17

description:
PBMC_RNA_CD14pos_16pos_Mono_d17_2_AFC_16_04_04_S66_L005
CD14posCD16pos-Day17/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: 17 days


title: genomic DNA from neuroblastoma 106

source_name: neuroblastoma 106

tag: tert status

value: TERT non-rearranged

value: ALT positive

value: TERT expression low


title: CTR Sample5 treated with AB

source_name: blood

value: Helathy Control

value: Peripheral blood mononuclear cells (PBMCs)


title: CTR Sample9 treated with AB


title: NGO_sc35

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: CD14posCD16pos-Day06

description:
PBMC_RNA_CD14pos_16pos_Mono_d6_AFC_16_03_25_CTCTCT_S101_L007
CD14posCD16pos-Day06/ FPKM

value: PBMC

value: CD14posCD16pos monocyte

value: 6 days


title: genomic DNA from neuroblastoma 132

source_name: neuroblastoma 132

tag: alt status

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated


title: eMSCs_T1_S10

value: Primary cells derived from human endometrium using SUSD antibody


title: genomic DNA from neuroblastoma 16

source_name: neuroblastoma 16

tag: mycn status

value: ATRX mutated

value: neuroblastoma


title: NGO_sc34

value: ICR


title: CD14posCD16pos-Day03

description:
PBMC_RNA_CD14pos_16pos_Mono_d3_AFC_16_03_22_CGTACT_S97_L007
CD14posCD16pos-Day03/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: 3 days


title: CTR Sample4 treated with AB and compound2

value: Helathy Control

value: Peripheral blood mononuclear cells (PBMCs)


title: CTR Sample4 treated with compound2


title: NGO_sc33

value: wild type

value: Ovary


title: eMSCs_T1_S9


title: genomic DNA from neuroblastoma 100

source_name: neuroblastoma 100

value: TERT non-rearranged

tag: atrx status

value: TERT expression low


title: eMSCs_T1_S11


title: eMSCs_T1_S8


title: CD14posCD16neg-Day48

description:
PBMC_RNA_CD14pos_16neg_Mono_d48_AFC_16_05_05_TAAGGC_S67_L004
CD14posCD16neg-Day48/ FPKM

source_name: CD14posCD16neg monocyte

value: PBMC

value: CD14posCD16neg monocyte

value: 48 days


title: NGO_sc32

tag: genotype

value: oocyte

value: < 20 microns


title: NGO_sc31

tag: oocyte size


title: CD14posCD16neg-Day17

description:
PBMC_RNA_CD14pos_16neg_Mono_d17_2_AFC_16_04_04_S65_L005
CD14posCD16neg-Day17/ FPKM

tag: subject status

value: 17 days


title: CTR Sample3

value: untreated


title: eMSCs_T1_S7

value: Primary cells derived from human endometrium using SUSD antibody


title: genomic DNA from neuroblastoma 97

source_name: neuroblastoma 97

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: neuroblastoma


title: CTR Sample4 treated with AB

value: Helathy Control

value: AB

value: Peripheral blood mononuclear cells (PBMCs)


title: CTR Sample2


title: CD14posCD16neg-Day06

description:
PBMC_RNA_CD14pos_16neg_Mono_d6_AFC_16_03_25_GGACTC_S100_L007
CD14posCD16neg-Day06/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

tag: cell subtype

value: 6 days


title: NGO_sc30

value: ICR

value: wild type

value: Ovary

tag: cell type


title: CD14posCD16neg-Day03

description:
PBMC_RNA_CD14pos_16neg_Mono_d3_AFC_16_03_22_TAAGGC_S96_L007
CD14posCD16neg-Day03/ FPKM

value: PBMC

value: CD14posCD16neg monocyte

tag: time post onset of symptoms

value: 3 days


title: genomic DNA from neuroblastoma 61

source_name: neuroblastoma 61

value: TERT non-rearranged

value: MYCN-amplified

value: TERT expression high


title: CTR Sample1

value: untreated


title: CD14dimCD16pos-Day48

description:
PBMC_RNA_CD14dim_16pos_Mono_d48_AFC_16_05_05_TCCTGA_S69_L004
CD14dimCD16pos-Day48/ FPKM

source_name: CD14dimCD16pos monocyte

value: CD14dimCD16pos monocyte

value: 48 days


title: genomic DNA from neuroblastoma 49

source_name: neuroblastoma 49

value: TERT rearranged

value: ALT negative

value: MYCN-non-amplified

value: ATRX non-mutated

value: neuroblastoma


title: eMSCs_U_S5

value: Primary cells derived from human endometrium using SUSD antibody

value: U-Untreated/DMSO vehicle Control


title: NGO_sc29

tag: strain

value: ICR

value: wild type

value: Ovary

value: oocyte

value: < 20 microns


title: genomic DNA from neuroblastoma 123

source_name: neuroblastoma 123

value: TERT non-rearranged

value: ALT positive

value: ATRX mutated


title: eMSCs_U_S4


title: NGO_sc28


title: eMSCs_U_S6


title: CD14dimCD16pos-Day17

description:
PBMC_RNA_CD14dim_16pos_Mono_d17_2_AFC_16_04_04_S67_L005
CD14dimCD16pos-Day17/ FPKM

value: individual with NAAT confirmed acute Zika virus infection

value: PBMC

value: CD14dimCD16pos monocyte

value: 17 days


title: AD Sample10

tag: diagnosis

value: Alzheimer’s Disease

value: untreated

value: Peripheral blood mononuclear cells (PBMCs)


title: NGO_sc27


title: eMSCs_U_S3

value: Primary cells derived from human endometrium using SUSD antibody

tag: treatment


title: AD Sample10 treated with AB and compound3


title: CD14dimCD16pos-Day06

description:
PBMC_RNA_CD14dim_16pos_Mono_d6_AFC_16_03_25_CAGAGA_S102_L007
CD14dimCD16pos-Day06/ FPKM

value: 6 days


title: eMSCs_U_S2

tag: replicate

value: U-Untreated/DMSO vehicle Control


title: CD14dimCD16pos-Day03

description:
PBMC_RNA_CD14dim_16pos_Mono_d3_AFC_16_03_22_AGGCAG_S98_L007
CD14dimCD16pos-Day03/ FPKM

value: 3 days


title: AD Sample10 treated with compound3


title: NGO_sc26

value: ICR

value: wild type

value: Ovary


title: NGO_sc24

value: oocyte

value: < 20 microns


title: eMSCs_U_S1

tag: tissue source and immunoselection of cells


title: AD Sample10 treated with AB and compound2


title: EL08 with AZA replicate 16

city: Planegg-Martinsried

first: Sonja

last: Grath

state: Bavaria

address: Grosshaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

data_processing:
Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015).
Reads were aligned to the mouse genome mm10 using STAR 2.4.0 (Dobin et al., 2013).
Unique gene-wise counts were generated using the Drop-seq pipeline.
For data deposition, samples were demultiplexed using UMItools and individual fastq files were created with bedtools v2.17.0.
Genome_build: mm10
Supplementary_files_format_and_content: text file with sample- and gene-wise expression table

source_name: stromal cell line

extract_protocol:
Total RNA was isolated from murine EL08 cells using the Rneasy Mini Kit (Quiagen).
CDNA was synthesized, barcoded, pooled and pre-amplified according to the UMI-seq protocol in Parekh et al. 2016. 800 pg of the cDNA pool was used for library preparation using the Nextera XT Kit (Illumina).

value: with Azacitidine


title: AD Sample11 treated with AB

value: AB


title: genomic DNA from neuroblastoma 99

source_name: neuroblastoma 99

value: TERT non-rearranged

value: ALT positive

value: MYCN-non-amplified

value: ATRX non-mutated

value: TERT expression low

value: neuroblastoma


title: EL08 with AZA replicate 15


title: AD Sample10 treated with AB

value: Alzheimer’s Disease

value: Peripheral blood mononuclear cells (PBMCs)


title: NGO_sc22

source_name: Non-Growing Oocyte


title: EL08 with AZA replicate 14


title: AD Sample10 treated with compound2


title: NGO_sc21


title: AD Sample9 treated with compound2

value: untreated


title: EL08 with AZA replicate 12


title: EL08 with AZA replicate 13


title: NGO_sc23


title: NGO_sc19


title: NGO_sc20


title: NGO_sc25


title: EL08 with AZA replicate 11


title: AD Sample8


title: PHH-PA_OA+TNFa_72h-2

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

institute: Hannover Medical School

hyb_protocol: The labelled cRNA was  hybridized overnight onto the Affymetrix HG-U133+PM-strip (16h at 45°C) in a hybridization chamber.

scan_protocol: The Affymetrix HG-U133+PM-strip was first washed on fluidic station  and the arrays were scanned using the Gene Atlas System

data_processing: The data were normalized using Robust Multi-array Average (RMA) algorithm using GeneExpression Console software and TAC software was used for differentielly expressed genes.

label: biotin

source_name: PHH

label_protocol: The extracted total RNA were processed for GeneAtlas microarray analysis with the 3'IVT Express Kit (Affymetrix)

growth_protocol: Hepatoma cells were grown in complete media, after trypsination, cells were seeded out at a concentraion of 6*10E6. Cells were treated with FA, FA+TNFa or control vehicle (DMSO) PHH were isolated by established protcols and seeded at a concentraion of 2*10E6/well.

extract_protocol: Total RNA was isolated from tissue culture samples pellets using Qiagen RNeasy mini spin kit and quantified.

treatment_protocol: Cells were treated with 0,5 mM PA/OA +/- TNFa 5 ng/ml or vehicle control +/- TNFa (5ng/ml) in complete media for 48 and 72h; the media was changed every day

tag: hrs of treatment


title: NGO_sc18

tag: tissue


title: PHH-PA_OA+TNFa_72h-3


title: AD Sample8 treated with compound3


title: EL08 with AZA replicate 10


title: PHH-PA_OA+TNFa_72h-1


title: PHH-PA_OA_72h-2


title: NGO_sc17


title: AD Sample9


title: EL08 with AZA replicate 9


title: PHH-PA_OA_72h-3


title: PHH-DMSO_72h-3

value: DMSO


title: EL08 with AZA replicate 8


title: AD Sample7


title: AD Sample8 treated with AB


title: PHH-PA_OA_72h-1


title: EL08 with AZA replicate 7


title: NGO_sc16

value: ICR


title: EL08 with AZA replicate 6


title: NGO_sc15

value: wild type


title: PHH-DMSO_72h-2


title: AD Sample7 treated with compound3


title: AD Sample7 treated with AB and compound3


title: NGO_sc14

value: Ovary


title: NGO_sc13

value: oocyte


title: PHH-PA_OA_48h-3


title: AD Sample7 treated with AB


title: NGO_sc12

value: < 20 microns


title: EL08 with AZA replicate 4

value: with Azacitidine


title: EL08 with AZA replicate 5


title: AD Sample9 treated with AB


title: AD Sample6


title: NGO_sc11


title: EL08 with AZA replicate 3


title: AD Sample6 treated with AB and compound3


title: EL08 with AZA replicate 2


title: EL08 with AZA replicate 1


title: PHH-DMSO_72h-1


title: AD Sample6 treated with compound3


title: PHH-PA_OA_48h-1


title: AD Sample6 treated with AB

value: AB


title: EL08 without AZA replicate 16

value: without Azacitidine


title: PHH-DMSO_48h-3


title: AD Sample5


title: PHH-DMSO_48h-2


title: NGO_sc8


title: EL08 without AZA replicate 15


title: NGO_sc9


title: NGO_sc7


title: EL08 without AZA replicate 14


title: AD Sample5 treated with AB and compound2


title: NGO_sc10


title: NGO_sc6


title: EL08 without AZA replicate 13


title: HuH7-PA_OA+TNFA-3


title: NGO_sc5


title: NGO_sc4


title: HuH7-PA_OA+TNFA-1


title: EL08 without AZA replicate 12


title: HuH7-PA_OA-2


title: PHH-DMSO_48h-1


title: HuH7-PA_OA+TNFA-2


title: NGO_sc3


title: AD Sample4


title: EL08 without AZA replicate 10


title: AD Sample4 treated with AB and compound2


title: HuH7-PA_OA-1


title: AD Sample4 treated with compound2


title: AD Sample5 treated with compound2


title: PHH-PA_OA_48h-2


title: EL08 without AZA replicate 9


title: AD Sample5 treated with AB


title: AD Sample4 treated with AB


title: EL08 without AZA replicate 8


title: NGO_sc1


title: mOocy_rna_batch4

description:
mOocy_rna_rawCounts.txt
mOocy_rna_barcodes.txt

source_name: Growing Oocyte

value: not provided


title: HuH7-DMSO-2


title: HuH7-DMSO-3


title: mOocy_rna_batch3


title: HuH7-PA_OA-3


title: AD Sample3


title: EL08 without AZA replicate 11


title: NGO_sc2


title: EL08 without AZA replicate 7


title: AD Sample3 treated with AB and compound1


title: EL08 without AZA replicate 6


title: mOocy_rna_batch1


title: AD Sample3 treated with compound1


title: mOocy_rna_batch2


title: AD Sample3 treated with AB


title: EL08 without AZA replicate 5


title: EL08 without AZA replicate 4


title: HepG2-PA_OA+TNFa-3


title: NS2_19.nostress_F2

city: Philadelphia

first: Melissa

middle: T

last: Manners

state: PA

address: 125 S 31st Street

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq reads were aligned to the GRCm38 build of the mouse genome using STAR v2.5.3a. STAR was provided with gene models from the Ensembl v90 genome annotation.
The Pipeline of RNA-Seq Transformations (PORT) v0.8.4-beta was used to perform gene-level normalization and quantification of the aligned data. PORT is an implementation of the re-sampling approach for normalization proposed by Li and Tibshirani. Briefly, PORT accounts for potential confounding factors like reads mapping to rRNA and mitochondrial DNA. Next, PORT determines the input samples with the fewest number of gene-mapping reads and re-samples all datasets to the same number of reads. Lastly, PORT quantifies the normalized gene-level reads counts for each sample.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

source_name: Brain

growth_protocol: PND 84 male C57B6 mice bread in house, original strain from Taconic

extract_protocol:
Brains were rapidly removed from a subset of behaviorally naive F1 and F2 male mice, from both stressed and non-stressed lineages (n=5 mice per group), at PND84 and sectioned in a brain block. 200 mm coronal brain sections were used to collect 1.2 mm punches of the amygdala bilaterally.
TruSeq® Stranded mRNA kit poly-A enrichment (Illumina, RS 122-2101)

treatment_protocol: Mice were the F1 or F2 generation following the initial chronic unpredictable stress procedure

value: Amygdala

tag: generation

value: no stress


title: NS2_20.nostress_F2


title: HuH7-DMSO-1


title: NS2_18.nostress_F2


title: AD Sample2 treated with AB and compound1


title: EL08 without AZA replicate 2


title: NS2_17.nostress_F2


title: AD Sample2 treated with AB


title: AD Sample1


title: SC_04_S24

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: 1156 High Street

department: Molecular Cell and Developmental Biology

institute: University of California Santa Cruz

data_processing:
Step1: Download fastq files and unzip
Step 2:grep allele specfic sequence sequences and do line count using "wc -l" (see below)
Step 2:C57/BL6 allele: grep 'GGAGAGAAGGAAATGGCTGCAGAATTGAAA' SC01_S21.fastq | wc -l
Step 2:MOLF allele: grep 'GGAGAGAAGGAAATGGCTGCAGAGTTGAAA' SC01_S21.fastq | wc -l
Step 3:Obtain raw counts for C57/BL6 and MOLF alleles
Step 4: Normalize to total counts for each fastq file.
Step 5: Normalize C57/BL6 vs MOLF, MOLF=1
Step 6: Normalize KO vs WT, WT=1
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet containing read counts for each allele

extract_protocol:
Bone marrow was removed from C57WT/MOLF and C57KO/MOLF and differentiated for 8 days with MCSF to generate bone marrow derived macrophages. Cells were placed in Trizol and RNA was extracted.
Primers were designed to the last exon of Ptgs2. The area was amplified, isolated and illumina primers were added for custom sequencing on MiSeq

tag: genotype/variation

tag: cells

value: macrophages


title: AD Sample1 treated with AB and compound1


title: SC_03_S23


title: AD Sample1 treated with compound1


title: AD Sample2


title: NS2_16.nostress_F2


title: S2_14.stress_F2

value: stress


title: S2_15.stress_F2


title: SC_02_S22


title: S2_13.stress_F2


title: SC_01_S21


title: EL08 without AZA replicate 1


title: S2_12.stress_F2


title: NS_10.nostress_F1


title: HepG2-PA_OA+TNFa-2


title: S2_11.stress_F2


title: AD Sample1 treated with AB

value: Alzheimer’s Disease


title: NS_9.nostress_F1


title: 10

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Raw reads were analysed with the sRNAbench module. This program performed the preprocessing, mapping, expression profiling and novel miRNA prediction. Parameters were set to minimum read count of four, allowing one mismatch, with full read alignment.
For anotation of miRNAs not present in miRBase, newly predicted miRNAs were locally blasted against the whole RNAcentral database
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: xls file with total counts of miRNAs present in mirbase 21 and predicted miRNAs

organism: Ovis aries

source_name: Lung

growth_protocol: Naturally ocurring in vivo infection

extract_protocol:
Total RNA was isolated from lung tissue using Trizol (Invitrogen, Carlsbad, CA, USA) extraction
The small RNA libraries were generated with Illumina’s TruSeq small RNA library preparation kit following manufacturer’s instructions.

treatment_protocol: Lung samples were aseptically taken and tissue sections were preserved in RNAlater solution (Ambion, Austin, TX, USA) at −80 ⁰C.

value: Lung

tag: infection state

value: Seronegative

tag: breed

value: Rasa Aragonesa


title: 14


title: 13


title: 11


title: HepG2-PA_OA-2


title: HepG2-PA_OA-3


title: HepG2-PA_OA+TNFa-1


title: HepG2-PA_OA-1


title: HepG2-DMSO-2

value: DMSO


title: HepG2-DMSO-1


title: 5: Eutopic endometrium of the normal group

city: Guangzhou

first: min juan

last: liu

address: gong ye da dao No.253

institute: ZhuJiang Hospital of Southern Medical University

description: MicroRNA expression of the normal group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarrays (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using oneAgilentG3_miRNA setting for  8x60K  array slides.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software V.11.5 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Eutopic endometrium

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

extract_protocol: RNA was extracted by Absolutely RNA miRNA Kit (Agilent p/n 400814)  following the manufacturer’s instructions.

treatment_protocol: The isolated tissues were stored in cryobiolgical inventory system in 10 minutes to avoid the total RNA extraction

value: Eutopic endometrium

tag: gender

value: female

tag: age

value: normal


title: FXS_1

city: Helsinki

first: Maija

middle: L

last: Castrén

state: Helsinki

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL69.5

hyb_protocol: Following fragmentation, 5.2 ug of cRNA was hybridized for 16 hr at 45oC on Affymetrix Human Clariom D arrays. The Clariom D arrays were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, P/N 702731 Rev. 4,  Affymetrix).

scan_protocol: Clariom D arrays were scanned using the Hewlett-Packard GeneChip Scanner 3000 (GCS3000).

data_processing: The CEL files were processed and normalized using Expression Console Software using Affymetrix default analysis settings to perform Gene Level Analysis (Gene Level-SST-RMA). Gene level data files (sst-rma-gene-full.chp) were then loaded into Affymetrix’s Transcriptome Analysis Console software to perform gene level analysis.

label: Biotin

source_name: FXS patient

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus reagent Kit, Manual Target Preparation for GeneChip Whole Transcript Expression Arrays, P/N 703174 Rev.5, Affymetrix).

growth_protocol: Human iPS cell clusters were grown as neurospheres in neuronal differentiation medium. After 6 weeks, neurospheres were plated on poly-D-lysin/laminin coated plates and allowed to differentiate for 1 day. Following day cells were scraped in PBS and the cell pellet was collected.

extract_protocol: Total RNA was extracted using RNA Purification Kit (Norgen Biotek Corp.) according to the manufacturer’s instructions.

value: iPS cell-derived neural progenitors

tag: disease state

value: fragile X syndrome


title: 6: Eutopic endometrium of the endometriosis group

description: MicroRNA expression of the endometriosis group

value: endometriosis


title: HepG2-DMSO-3


title: Control_2

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL23.3

source_name: Healthy subject

tag: cell type

value: healthy


title: Control_3

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL46.11


title: FXS_2

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL70.3


title: 7


title: 4

value: Seropositive asymptomatic


title: NS_7.nostress_F1

value: Amygdala


title: NS_6.nostress_F1

value: no stress


title: 19_P


title: Control_1

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL11.4


title: NS_8.nostress_F1


title: FXS_3

description:
SST-RMA expression value derived from Affymetrix Expression Console Software
HEL100.2


title: S_5.stress_F1


title: 12_P


title: 3: Eutopic endometrium of the normal group

description: MicroRNA expression of the normal group


title: S_4.stress_F1


title: 4-2: Eutopic endometrium of the endometriosis group


title: Kwon201408_XenopusHybrid_TETS3

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

description:
Xenopus tropicalis
TETS3

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Genome_build: Xenopus transcripts UTA2014 version (uploaded to GEO)
Supplementary_files_format_and_content: indiv_tpm.txt.gz - TPM for each samples
Supplementary_files_format_and_content: fa.gz - transcripts FASTA file

organism: Xenopus tropicalis

source_name: 9 hpf whole embryo

growth_protocol: Embryos at 9 hpf were collected

extract_protocol:
To isolate RNA, embryos at stage 9 were homogenized mechanically in TRIzol® (Thermo Fisher Scientific, Waltham, MA) using up to a 30-gauge needle and processed according to manufacturer instructions. After resuspension in nuclease-free H2O, RNAs were cleaned using a RNeasy kit (Qiagen Inc.) according to manufacturer instructions.
Libraries were prepared using manufacturer’s non-standard specific RNA-seq library protocol with poly-A capturing mRNA enrichment method (Illumina, CA, USA)

tag: developmental stage

value: 9 hpf


title: 2: Eutopic endometrium of the endometriosis group


title: 1: Eutopic endometrium of the normal group

description: MicroRNA expression of the normal group


title: 11_P


title: S_3.stress_F1

tag: strain

value: stress


title: S_2.stress_F1


title: Kwon201408_XenopusHybrid_TETS1

description:
Xenopus tropicalis
TETS1


title: lM12

first: Bing

last: Zhang

address: Rm 437, School of Environment, Tsinghua University

department: School of Environment

institute: Tsinghua University

description:
GeoChip data for activated sludge sample collected at System MBR, Week 12
raw data file: Activated sludge raw data2.txt

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Data pretreatment was performed online (ieg.ou.edu). The percentages of thermophile probes (negative controls) in each sample were made less than 5% by the removal of low quality spots. The genes detected in only one out of three samples from the same system were removed.  The genes detected only in 3 or fewer samples out of 12 samples from the same system were removed to avoid potential noises. For each sample, intensities of the genes were then transformed to the natural logarithmic form and divided by the mean signal intensity.

organism: activated sludge metagenome

source_name: antibiotic resistance genes and virulence genes in activated sludge of full-scale wastewater treatment systems

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 12.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: wastewater treatment system

value: Wastewater treatment system of MBR in the long term


title: 10_P

value: Lung

value: Seropositive with lessions


title: 8_P

value: Rasa Aragonesa


title: lM11

description:
GeoChip data for activated sludge sample collected at System MBR, Week 11
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 11.

value: activated sludge of full-scale wastewater treatment system


title: S_1.stress_F1

tag: treatment


title: 9_P


title: lM10

description:
GeoChip data for activated sludge sample collected at System MBR, Week 10
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 10.


title: 7_P


title: lM9

description:
GeoChip data for activated sludge sample collected at System MBR, Week 9
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 9.


title: EL08 without AZA replicate 3

value: without Azacitidine


title: 1_P


title: lM6

description:
GeoChip data for activated sludge sample collected at System MBR, Week 6
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 6.


title: lM5

description:
GeoChip data for activated sludge sample collected at System MBR, Week 5
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 5.


title: lM8

description:
GeoChip data for activated sludge sample collected at System MBR, Week 8
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 8.


title: lM7

description:
GeoChip data for activated sludge sample collected at System MBR, Week 7
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 7.


title: IPed by RelB antibody in human term CTB-Rep2

city: New Brunswick

first: Bingbing

last: Wang

address: 125 Paterson St Room 2143

institute: Rutgers RWJMS

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Raw data were trimmed to remove possible adapter sequences and nucleotide with poor quality using CLC Genomics Server 9.0
Trimmed reads were aligned to human genome hg20 and peaks were called using CLC Genomics Server 9.0
Genome_build: Human genome hg20
Supplementary_files_format_and_content: peaks called using CLC Genomics Server 9.0

source_name: Placenta

growth_protocol: Placental cytotrophoblast (CTB) were purified and maintained at 37C and 5% CO2 at least for 48 hr for spontaneous syncytialization prior to further analysis.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and for 5 min at room and were lysed in ChIP lysis buffer.  Chromatins were IPed by ChIP grade antibodies to RelB (Santa Cruz Biotech, sc-226), CBP (Abcam, ab2832), HDAC1 (Santa Cruz Biotech, sc-7872), or H3K9ac (Cell Signaling, 9649).
NEBNext Ultra DNA Library Prep with Beads Size Selection

treatment_protocol: Not applicable.

value: Term placenta

value: Cytotrophoblast

tag: chip antibody

value: RelB (Santa Cruz Biotech, sc-226)


title: IPed by RelB antibody in human term CTB-Rep1


title: 2_P


title: IPed by RelB antibody in human term CTB-Rep3


title: Kwon201408_XenopusHybrid_TELS3

description:
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELS3

organism: Xenopus tropicalis x Xenopus laevis


title: lM4

description:
GeoChip data for activated sludge sample collected at System MBR, Week 4
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 4.


title: A243V+piracetam

city: Shimotsuke shi

first: Takeshi

last: Kouga

state: Tochigi prefecture

address: Yakushiji 3311-1

country: Japan

institute: Jichi Medical University

hyb_protocol: 0.6 µg of Cy3-labelled cRNA was fragmented at 60 °C for 30 min in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at RT with GE Wash Buffer 1 (Agilent) and 1 min with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: The slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. Trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Then normalized signal intensities were calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 0.1 µg total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., CA, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation was checked and cRNA yield with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy® Mini kit (QIAGEN N.V., Venlo, Netherlands) following the manufacturer's recommendations, in MO3.13 cells stably expressing PLP1A243V 24 h after adding piracetam at 10 µM, PLP1A243V without piracetam, and PLP1WT.

value: oligodendrocyte


title: Kwon201408_XenopusHybrid_TELS1

description:
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELS1


title: IPed by HDAC1 antibody in human term CTB-Rep2

value: HDAC1 (Santa Cruz Biotech, sc-7872)


title: lM3

description:
GeoChip data for activated sludge sample collected at System MBR, Week 3
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 3.


title: Wild type


title: lM2

description:
GeoChip data for activated sludge sample collected at System MBR, Week 2
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 2.


title: IPed by HDAC1 antibody in human term CTB-Rep1


title: A243V


title: IPed by HDAC1 antibody in human term CTB-Rep3


title: Kwon201408_XenopusHybrid_LETS3

description:
Xenopus laevis (egg) x Xenopus tropicalis (sperm) hybrid
LETS3


title: Kwon201408_XenopusHybrid_LETS1

description:
Xenopus laevis (egg) x Xenopus tropicalis (sperm) hybrid
LETS1


title: lM1

description:
GeoChip data for activated sludge sample collected at System MBR, Week 1
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the MBR system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 1.


title: IPed by H3K9ac antibody in human term CTB-Rep3

value: H3K9ac (Cell Signaling, 9649)


title: lO12

description:
GeoChip data for activated sludge sample collected at System OD, Week 12
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 12.

value: Wastewater treatment system of OD in the long term


title: 3m7b

city: Washington

first: Scott

middle: Nathan

last: Dean

state: DC

address: 4555 Overlook Ave SW

institute: Naval Research Laboratory

description:
rpkm_0_ADTV7.txt
rpkm_1_ADTV7.txt
rpkm_2_ADTV7.txt
rpkm_3_ADTV7.txt

data_processing:
Generated MiSeq reads were then analyzed via the RNAseq pipeline described by Li et al. (Li et al., 2018).
Read quality control was performed where Phred scores of <20 were trimmed using FastQC and Cutadapt as part of Trim Galore! (Krueger, 2015)
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) (Magoc et al., 2013) for paired end reads was used with default settings on the remaining reads for alignment to the L. plantarum WCFS1 genome from NCBI (ftp://ftp.ncbi. nih.gov/genomes/Bacteria) generating RPKM files and count tables.
Each count table was read into R where DESeq2 (Love et al., 2014) was used for differential expression analysis and generating associated statistics as a function of treatment with 3OC12 and time.
Supplementary_files_format_and_content: Count tables
Supplementary_files_format_and_content: counts for all genes in files that begin with rpkm_0

organism: Lactiplantibacillus plantarum

source_name: culture

extract_protocol:
Frozen sample aliquots thawed at room temperature and pelleted to remove residual RNA Later before treating with 400 µL Lysozyme Solution (1 mg mL-1 lysozyme, 40 mM EDTA, pH 8) for 1 h at 37 °C. Lysozyme treated cells were pelleted and resuspended in RNAzol RT following the manufacturer’s protocol for large RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 7 h


title: 2m7b

value: 4 h


title: lO10

description:
GeoChip data for activated sludge sample collected at System OD, Week 10
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 10.


title: 1m7b

value: 1 h


title: IPed by CBP antibody in human term CTB-Rep3

value: CBP (Abcam, ab2832)


title: IPed by H3K9ac antibody in human term CTB-Rep2


title: lO11

description:
GeoChip data for activated sludge sample collected at System OD, Week 11
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 11.


title: lO9

description:
GeoChip data for activated sludge sample collected at System OD, Week 9
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 9.


title: 2p7b


title: lO8

description:
GeoChip data for activated sludge sample collected at System OD, Week 8
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 8.


title: IPed by CBP antibody in human term CTB-Rep2


title: lO7

description:
GeoChip data for activated sludge sample collected at System OD, Week 7
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 7.


title: 3m4b


title: Fibroblast Non_CD sample 30 from patient 15

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

hyb_protocol: bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing:
Minfi (v1.20.0) for reading the data; MethylAid (v1.8.0) for quality control
Unmethylated and methylated signal intensities in Series supplementary file

source_name: patient 15

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the fibroblasts using the QIAamp DNA mini kit (Qiagen, Valencia, CA), and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) according to manufacturer’s protocol. The bisulfite-converted DNA was subsequently analyzed on the Illumina HumanMethylation EPIC BeadChip Array at ServiceXS in Leiden, the Netherlands.

value: F

value: Non_Crohn's Disease

tag: disease stage

tag: montreal score

tag: passage

tag: sampleID

tag: thiopurine usage

value: No

tag: atnf usage

value: Ileal fibroblast


title: 2m4b


title: lO6

city: Beijing

description:
GeoChip data for activated sludge sample collected at System OD, Week 6
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 6.

tag: tissue

value: activated sludge of full-scale wastewater treatment system


title: 3p7b


title: IPed by H3K9ac antibody in human term CTB-Rep1


title: Fibroblast STEN sample 22 from patient 11

source_name: patient 11

tag: gender

value: Crohn's Disease

value: stenotic

value: Yes


title: Fibroblast STEN sample 27 from patient 14

source_name: patient 14

tag: age


title: Fibroblast STEN sample 24 from patient 12

source_name: patient 12

value: M

tag: disease state


title: lO4

description:
GeoChip data for activated sludge sample collected at System OD, Week 4
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 4.


title: 1m4b


title: lO5

description:
GeoChip data for activated sludge sample collected at System OD, Week 5
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 5.


title: Fibroblast Non_CD sample 28 from patient 15

tag: cell type


title: 15d time 0 Rep3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 15-day-old seedlings replicate 3

data_processing:
Raw RNA-seq reads were trimmed by quality using Trimmomatic and paired reads mapped to the Arabidopsis thaliana genome (TAIR10) using STAR 2.5.3.a with default settings.
The returned alignments were stringently filtered so as to remove duplicates, ambiguously mapped reads and read pairs with conflicting alignments.
RSEM v1.3.0 is used to quantitate gene abundance and the expression of individual gene is shown as the average of transcripts per million (TPM) in two biological replicates, all genes are filtered by the average of TPM in three developmental statuses < 0.5.
Differentially expressed genes were detected by EBSeq based on the combined criteria: |log2(fold change)| > 1 and false discovery rates < 0.05.
Genome_build: the Arabidopsis thaliana genome (TAIR10)
Supplementary_files_format_and_content: expression for genes(TAIR10) was provided. The format is tab delimited file format. Each row contains eight columns: gene_id, transcript_id, length, effective_length, expected_count,TPM and FPKM.

organism: Arabidopsis thaliana

source_name: leaves of 15-day-old seedlings

growth_protocol: 9-, 12- and 15-d-old A. thaliana Columbia-0 seeds were sterilized with 75% alcohol and kept at 4°C for 2d. The seeds were then germinated on 1/2 MS medium (half-strength of MS basal medium with 1% sucrose, 1% agar and 0.5 g/L MES, pH 5.7) at 22°C under 24-h constant light conditions. Detached leaf explants were cultured on B5 medium without sucrose (Gamborg B5 basal medium with 0.5 g/L MES and 0.8% agar, pH 5.7) at 22°C under 24-h light conditions.

extract_protocol:
RNA extraction using Trizol protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)

treatment_protocol: No treatment applied.

tag: protocol

value: constant light

tag: ecotype

value: Columbia

tag: agent


title: 15d 1 DAC Rep3

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 15-day-old seedlings replicate 3

treatment_protocol: cultured 1 day on B5 medium without sucrose.


title: 3p4b

tag: strain


title: Fibroblast Non_CD sample 29 from patient 15


title: 1p7b


title: lO3

description:
GeoChip data for activated sludge sample collected at System OD, Week 3
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 3.

tag: wastewater treatment system


title: 2p4b

tag: time


title: 12d 1 DAC Rep3

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 12-day-old seedlings replicate 3

source_name: leaves of 12-day-old seedlings

value: cultured 1 day on B5 medium without sucrose.


title: Fibroblast STEN sample 23 from patient 12

tag: disease stage


title: Fibroblast NINF sample 17 from patient 9

source_name: patient 9

value: non-inflamed

tag: montreal score


title: HCC38 (50)

city: Groningen

first: Francien

last: Talens

address: Hanzeplein 1

department: Medical Oncology

institute: University Medical Center Groningen

description: Corresponding sample number: 50

data_processing:
The obtained cDNA fragment libraries were sequenced on an Illumina HiSeq2500 using default parameters (single read 1x50bp or Paired End 2 x 100 bp) in pools of multiple samples
The trimmed fastQ files where aligned to build b37 human reference genome using hisat/0.1.5-beta-goolf-1.7.20 (Dobin et al., Bioinformatics, 2013) allowing for 2 mismatches
Before gene quantification SAMtools/1.2-goolf-1.7.20 (Li et al., Bioinforma, 2009) was used to sort the aligned reads
The gene level quantification was performed by HTSeq/0.6.1p1 using --mode=union --stranded=no and, Ensembl version 75 was used as gene annotation database.
QC metrics are calculated for the aligned reads using Picard-tools picard/1.130-Java-1.7.0_80 CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-Metrics and SAMtools/1.2-goolf-1.7.20 flagstat
Picard-tools picard/1.130-Java-1.7.0_80
Genome_build: b37 human reference genome
Supplementary_files_format_and_content: gene-level abundance measuremets

source_name: epithelial cells

growth_protocol: BT-549 and HCC38 were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin (100 units/mL).

extract_protocol:
RNA was isolated using the mirVANA kit (Ambion, AM1561)
Sequence libraries were generated using the TruSeq RNA sample preparation kits (Illumina) using the Sciclone NGS Liquid Handler (Perkin Elmer)

treatment_protocol: Cells were treated with 72 hours with doxycycline (1 μg/mL) or left untreated.

tag: cell line

value: breast cancer cell line HCC38

value: Breast

value: ductal carcinoma

tag: transduction with doxycycline-inducible shrna

tag: treatment

value: treatment with doxycyline 72 hours


title: HCC38 (54)

description: Corresponding sample number: 54


title: Fibroblast NINF sample 21 from patient 11

value: F

tag: passage

tag: sampleID

tag: thiopurine usage

tag: atnf usage


title: lO1

description:
GeoChip data for activated sludge sample collected at System OD, Week 1
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 1.

tag: tissue

value: Wastewater treatment system of OD in the long term


title: 1p4b

value: 1 h


title: lO2

description:
GeoChip data for activated sludge sample collected at System OD, Week 2
raw data file: Activated sludge raw data2.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during October and December, 2011. On each week, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Week 2.


title: HCC38 (53)

description: Corresponding sample number: 53

tag: disease state

value: no treatment


title: 9d 1 DAC Rep3

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 9-day-old seedlings replicate 3

source_name: leaves of 9-day-old seedlings

tag: age

tag: protocol


title: Fibroblast NINF sample 11 from patient 7

source_name: patient 7

tag: gender

tag: cell type

value: Ileal fibroblast


title: Fibroblast NINF sample 16 from patient 9

value: Crohn's Disease

value: No


title: 3m1b

tag: strain

value: 7 h


title: IPed by CBP antibody in human term CTB-Rep1

growth_protocol: Placental cytotrophoblast (CTB) were purified and maintained at 37C and 5% CO2 at least for 48 hr for spontaneous syncytialization prior to further analysis.

value: Term placenta

value: Cytotrophoblast

tag: chip antibody

value: CBP (Abcam, ab2832)


title: 9d time 0 Rep3

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 9-day-old seedlings replicate 3

value: constant light

tag: ecotype

value: Columbia

tag: agent


title: HCC38 (51)

description: Corresponding sample number: 51

tag: cell line

value: breast cancer cell line HCC38


title: sM11

description:
GeoChip data for activated sludge sample collected at System MBR, Day 11
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 11.

value: activated sludge of full-scale wastewater treatment system

tag: wastewater treatment system

value: Wastewater treatment system of MBR in the short term


title: HCC38 (6)

description: Corresponding sample number: 6

value: Breast

value: ductal carcinoma

tag: transduction with doxycycline-inducible shrna

value: Luciferase

tag: treatment

value: treatment with doxycyline 72 hours


title: Fibroblast INF sample 5 from patient 4

source_name: patient 4

value: M

tag: disease stage

value: inflamed

tag: montreal score

tag: passage

tag: sampleID


title: Fibroblast NINF sample 9 from patient 7

tag: disease state

value: Crohn's Disease

value: non-inflamed

tag: thiopurine usage

value: Yes

tag: atnf usage

value: Ileal fibroblast


title: 1m1b

description:
rpkm_0_ADTV7.txt
rpkm_1_ADTV7.txt
rpkm_2_ADTV7.txt
rpkm_3_ADTV7.txt

tag: time

value: 1 h


title: 15d 1 DAC Rep2

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 15-day-old seedlings replicate 2

tag: developmental stage

tag: growth conditions

value: Columbia (Col-0)

value: cultured 1 day on B5 medium without sucrose.


title: HCC38 (30)

description: Corresponding sample number: 30

tag: tissue


title: sM12

description:
GeoChip data for activated sludge sample collected at System MBR, Day 12
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 12.


title: 12d time 0 Rep3

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 12-day-old seedlings replicate 3

tag: age

tag: protocol

value: constant light

tag: ecotype

value: Columbia


title: 3p1b

tag: strain

value: 7 h


title: 15d 1 DAC Rep1

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 15-day-old seedlings replicate 1


title: HCC38 (18)

description: Corresponding sample number: 18

tag: cell line

value: breast cancer cell line HCC38

tag: transduction with doxycycline-inducible shrna


title: Fibroblast INF sample 10 from patient 7

tag: gender

tag: disease stage

tag: cell type


title: Fibroblast Non_CD sample 6 from patient 5

source_name: patient 5

value: Non_Crohn's Disease

tag: montreal score

tag: passage

tag: sampleID

value: No


title: sM10

description:
GeoChip data for activated sludge sample collected at System MBR, Day 10
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 10.

value: activated sludge of full-scale wastewater treatment system

tag: wastewater treatment system

value: Wastewater treatment system of MBR in the short term


title: sM9

description:
GeoChip data for activated sludge sample collected at System MBR, Day 9
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 9.


title: sM8

description:
GeoChip data for activated sludge sample collected at System MBR, Day 8
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 8.


title: 2p1b

tag: time

value: 4 h


title: 15d time 0 Rep2

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 15-day-old seedlings replicate 2

tag: developmental stage

tag: treatment

value: No treatment applied.


title: HCC38 (5)

description: Corresponding sample number: 5

tag: tissue

value: Breast

tag: disease state

value: ductal carcinoma

value: Luciferase

value: no treatment


title: sM7

description:
GeoChip data for activated sludge sample collected at System MBR, Day 7
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.


title: sM6

description:
GeoChip data for activated sludge sample collected at System MBR, Day 6
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 6.


title: 12d 1 DAC Rep2

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 12-day-old seedlings replicate 2

tag: growth conditions


title: 1p1b

value: 1 h


title: sM5

description:
GeoChip data for activated sludge sample collected at System MBR, Day 5
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 5.


title: BT-549 (4)

description: Corresponding sample number: 4

value: breast cancer cell line BT-549

value: treatment with doxycyline 72 hours


title: 2m7

description:
rpkm_0_AYR0M.txt
rpkm_1_AYR0M.txt
rpkm_2_AYR0M.txt
rpkm_3_AYR0M.txt


title: Fibroblast NINF sample 13 from patient 7

value: M

value: Crohn's Disease

value: non-inflamed

tag: age

tag: thiopurine usage

value: Yes

tag: atnf usage

value: Ileal fibroblast


title: 12d 1 DAC Rep1

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 12-day-old seedlings replicate 1

value: constant light

tag: ecotype

value: Columbia (Col-0)

value: cultured 1 day on B5 medium without sucrose.


title: 12d time 0 Rep2

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 12-day-old seedlings replicate 2


title: BT-549 (28)

description: Corresponding sample number: 28

tag: cell line

tag: transduction with doxycycline-inducible shrna


title: HCC38 (29)

description: Corresponding sample number: 29

value: breast cancer cell line HCC38


title: 1m7

tag: strain


title: sM4

description:
GeoChip data for activated sludge sample collected at System MBR, Day 4
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 4.

value: activated sludge of full-scale wastewater treatment system

value: Wastewater treatment system of MBR in the short term


title: 12d time 0 Rep1

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 12-day-old seedlings replicate 1

value: No treatment applied.


title: 3p7

value: 7 h


title: BT-549 (3)

description: Corresponding sample number: 3

value: Breast

value: ductal carcinoma

value: no treatment


title: sM3

description:
GeoChip data for activated sludge sample collected at System MBR, Day 3
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 3.


title: 9d 1 DAC Rep2

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 9-day-old seedlings replicate 2


title: sM2

description:
GeoChip data for activated sludge sample collected at System MBR, Day 2
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 2.


title: 2p7

value: 4 h