title: D8_E1_S3

description: cytotrophoblast (CTB)


title: Control-3

status: Public on Oct 21 2019

type: SRA

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Illumina HiSeq 2500 sequencing, 50bp reads.
Adapter removal with cutadapt v1.16
Alignment to Mus musculus genome with hisat v2.1.0
Assignment of reads to gene features with Subread featureCounts v1.6.1
Signal detection via differential expression analysis between triplicate groups with DESeq2 1.18.1
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads assigned to gene features, as computed by Subread featureCounts v1.6.1

molecule: polyA RNA

organism: Mus musculus

source_name: testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P2 or P7 aged control and knockout mice.

extract_protocol:
Testes were isolated, total RNA was isolated using RNeasy Mini Kit and mRNA was purified by Dynabeads mRNA Purification Kit.
First strand cDNA was synthesized with SuperScript III Reverse Transcriptase. For second strand cDNA synthesis, the 100 μl reaction system included: 20 μl of first strand cDNA synthesis mix, 10 μl of 10x second strand buffer (500 mM Tris-HCl, pH 7.5; 50 mM MgCl2; 10 mM DTT), 3 μl of dNTP mix (10 mM), 1 μl of RNase H (2U/μl), 5 μl of DNA Pol I (10U/μl) and 61 μl water. The mixtures were incubated for 2 h at 16°C. The libraries were constructed with Nextera DNA Sample Preparation Kit (Illumina) per the manufacturer’s protocol. Generally, double-strand cDNA was fragmented, subjected to adapter ligation and amplified.

tag: strain

value: B6D2F1 inbred

tag: tissue

value: testis

tag: age

value: post natal day 2

tag: genotype


title: Control-1


title: D8_E2_S7

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: cytotrophoblast (CTB)

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the human genome (hg38) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference.
Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. DAVID (https://david.ncifcrf.gov) and IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively. Cells with more than 8,000 detected genes and for which genes with FPKM > 0.3 were kept in downstream analysis for lineage specification. Lineage specification was performed by Spearman correlation. Principle Component Analysis (PCA) and cluster analysis were performed using R
Genome_build: hg38
Supplementary_files_format_and_content: FASTQ

molecule: total RNA

organism: Homo sapiens

source_name: trophoblast cells

extract_protocol: The RNA-seq libraries were generated from individually cells using Smart-seq2 with minor modification. Briefly, individually cells were lysed and mRNA was captured and amplified by using Smart-seq2 v4 kit (Clontech). After pre-amplification and AMPure XP beads purification, amplified RNAs were quality checked using Agilent High Sensitivity D5000 kit (Agilent Technologies). High quality of amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The quality and quantity of sequencing libraries were determined using Qubit 3.0 assay (Life Technologies) and Agilent High Sensitivity kit at Tapestation 4200 system (Agilent), respectively. Pooled indexed libraries were then sequenced on Illumina HiSeq X platform with 125 bp pair-end reads.

tag: cell type

value: trophoblast cells

tag: time

value: Day 8 (Extended culture)


title: D12_EVT5

description: migratory cells (MTB)

value: Day 12 (Extended culture)


title: KO-4

value: post natal day 7


title: Control-6


title: D12_EVT3

description: migratory cells (MTB)


title: B6ES_FAIRE_Rep2

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

library_source: genomic

data_processing:
Paired-end sequencing (101bp x2) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Paired-end reads were mapped to the mm9 reference genome using the COBWeB Algorithm implemented in Avadis NGS (Agilent).
Reads with average base quality below 30, PCR duplicate reads, non-primary multiply mapped reads were removed.
The mapping results (.bam file) were subjected to the MACS peak detection algorithm implemented in Strand NGS (Agilent) to detect FAIRE peaks.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peak calling output (peak location, p-score, q-score, and fold change)

molecule: genomic DNA

source_name: Embryonic stem cell line

growth_protocol: Mouse ES cells were cultured on feeder cells in knockout DMEM (Life Technologies) containing recombinant human leukemia inhibitory factor culture supernatant for mouse ES cell culture, GlutaMAX, 2-mercaptoethanol, non-essential amino acids, and 15% KSR (all from Life Technologies). Mouse TS cells were cultured on feeder cells in the presence FGF-4 (PeproTech, London, UK) and heparin (Sigma Chemical Company) to maintain their undifferentiated state.

extract_protocol:
Trypsinised feeder-free cells (1×10^6) were collected and fixed with 1% formaldehyde at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were resuspended in SDS lysis buffer (ChIP Reagent, Nippon Gene Co., Ltd.), and the lysate was sonicated to fragment chromatin using a Covaris S220 (Covaris, Woburn, MA, USA). DNA was purified from sonicated lysate using phenol-chloroform (Sigma #P3803 phenol, chloroform, and isoamyl alcohol 25:24:1 saturated with 10 mM Tris at pH 8.0, 1 mM EDTA), and ethanol-precipitated.
Sequencing libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set and Multiplex Oligos from Illumina (New England BioLabs Inc., Ipswich, MA, USA) according to the manufacturer's instructions. FAIRE DNA (1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 9 cycles of PCR.
The formaldehyde-assisted isolation of regulatory elements combined with the high-throughput sequencing (FAIRE-seq)

value: Embryonic stem cell line


title: B6TS_FAIRE_Rep2

source_name: trophoblast stem cell line

value: trophoblast stem cell line


title: D12_EVT2

description: migratory cells (MTB)


title: D12_EVT4

description: migratory cells (MTB)


title: D12_E6_S3

description: cytotrophoblast (CTB)


title: D12_E6_S4

description: cytotrophoblast (CTB)


title: D12_E6_S2

description: cytotrophoblast (CTB)


title: B6TS_ChIP_input_Rep1

data_processing:
Single end sequencing (51bp or 101bp) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
For ChIP-seq data for TEAD4 and KLF5, single-end reads (51 bp) were mapped to the mm9 reference genome using the COBWeB Algorithm implemented in Avadis NGS (Agilent). Reads with average base quality below 30, PCR duplicate reads, non-primary multiply mapped reads were removed. The resultant mapped reads (.bam file) were subjected to the MACS peak detection algorithm implemented in Strand NGS (Agilent) to detect ChIP-seq peaks with the mapped reads from the matching IgG library as a control.
For ChIP-seq data for histone modifications, single-end reads (51 or 101 bp) from each sample were first trimmed by removing adapters and low quality bases at ends using Trimmomatic 0.22, and were aligned to the mouse reference genome (mm9) using the Burrows-Wheeler Aligner 0.6.2. Uniquely mapped reads were selected by a custom script, converted from sam to bam using SAMtools 0.1.18. Reads with mapping quality < 20 were removed using SAMtools 0.1.18. The uniquely mapped reads (.bam files) were subjected the MACS peak detection algorithm (version 1.4.2 to identify ChIP-seq peaks with the matched input DNA reads as a control.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peak calling output

extract_protocol:
Trypsinised feeder-free ES and TS cells (1×10^6) were collected and fixed with 1% formaldehyde at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were resuspended in SDS lysis buffer (ChIP Reagent, Nippon Gene Co., Ltd.), and the lysate was sonicated to fragment chromatin using a Covaris S220 (Covaris, Woburn, MA, USA). The sonicated lysate was subjected to immunoprecipitation with a monoclonal antibody against TEDA4, KLF5, H3K4me1, or H3K27ac.
The immunoprecipitated and reverse-crosslinked DNA was purified using AMPure XP beads (Beckman Coulter, Inc., Pasadena, CA, USA) according to the manufacturer’s instructions. ChIP or input DNA (0.1 ~ 1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 6-13 cycles of PCR.

tag: chip antibody


title: B6TS_ChIP_H3K4me1_Rep1

value: anti-H3K4me1 antibody (CMA302 provided by Dr. H. Kimura)


title: D8_E1_S2

description: cytotrophoblast (CTB)


title: B6TS_ChIP_TEAD4_Rep1

value: anti-TEAD4 antibody (Abcam:ab58310)


title: D12_E6_S1

description: cytotrophoblast (CTB)


title: B6ES_FAIRE_Rep1


title: B6TS_FAIRE_Rep1


title: D12_E6_L6

description: multinucleated primitive syncytium (STB)


title: B6TS_ChIP_rIgG

value: rabbit IgG (CST:2729P)


title: Control-2


title: D8_E1_S1

description: cytotrophoblast (CTB)


title: B6TS_ChIP_H3K27ac_Rep1

value: anti-H3K27ac antibody (CMA309 provided by Dr. H. Kimura)


title: B6TS_ChIP_mIgG

value: mouse IgG (Millipore:12-371)


title: D12_E6_L5


title: B6TS_ChIP_KLF5

value: anti-KLF5 antibody (Millipore:07-1580)


title: B6ES_ChIP_TEAD4


title: D12_E6_L2


title: D12_E6_L1


title: B6ES_ChIP_rIgG


title: D12_E6_L4


title: B6ES_ChIP_KLF5


title: D12_E4_S3

description: cytotrophoblast (CTB)


title: D12_E4_S2

description: cytotrophoblast (CTB)


title: B6TS_4C_Tead4-promoter_Rep1

data_processing:
Library strategy: 4C-seq
Paired-end sequencing (101bp x2) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Sequencing reads for each sample were demultiplexed and subjected to the trimming of the sequences within the bait region, a MspI-HindIII fragment corresponding to chr6:128,251,076-  128,251,379 (mm9). The exact nucleotide coordinates of the trimmed sequences are chr6:128,251,076-128,251,117 and chr6:128,251,328-128,251,379. The former region ranges from the base immediately after the MspI site to the 5' end of the target-specific sequence in the Tead4_4C-Msp1R(-) primer, and the latter region ranges from the 5' end of the target-specific sequence in the Tead4_4C-Hind3F(+) primer to the fifth base of the HindIII site.
Trimmed reads were mapped with the Burrows-Wheeler Aligner (BWA) and assgined to a specific HindIII fragment in the HindIII fragment database prepared from the mouse reference genome sequence(mm9)
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read numbers counted for each of HindIII fragments are listed in bed format.

extract_protocol:
Cells (3x10^6) were cross-linked with 2% formaldehyde, lysed in the lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40), digested with HindIII, treated with Klenow fragment and dNTPs to fill in the HindIII digested overhangs, and ligated under a dilute condition. After reversing crosslinks, DNA was purified as a 3C library. The 3C library was digested wth MspI, ligated, and amplified by PCR tp generate a 4C library.
4C library was amplified by PCR using two sets of PCR primers. The fist set of primers, Tead4_4C-Hind3F(+)   "5'-TCTTTCCCTACACGACGCTCTTCCGATCTGCCTTCACTATTCCCCAAAA-3'" and Tead4_4C-Msp1R(-)   "5'-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAACCACTGCTGGGACCTAA-3'", contain a sequence specific to the mouse Tead4 promoter region at the 3' end and a partial sequence of illumina TruSeq adaptor at the 5' end.   The second primers are   "5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'" (TruSeq Universal Adapter sequence) and "CAAGCAGAAGACGGCATACGAGAT[6bp_index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'" (TruSeq Index Adapter sequence).

tag: restriction enzymes

value: HindIII, MspI


title: INPUT DNA

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

country: Germany

institute: HelmholtzZentrum München - IDC

data_processing:
Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: narrowpeak files were produced using macs2 representing GR peaks

source_name: INPUT DNA

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 200 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

value: Liver


title: PPARA_ZT12 HFD REP1

source_name: PPARA_ZT12 HFD_liver

tag: treatment

value: 12 wk High Fat Diet (Research Diet, D12331)

value: PPARalpha (Santa Cruz, sc-9000X)


title: D12_E4_L6


title: GR_ZT8 HFD REP2

source_name: GR_ZT8 HFD_liver

value: GR (Santa Cruz, sc-1004X)


title: PPARA_ZT12 control REP1

source_name: PPARA_ZT12 control_liver

value: 12 wk control Diet (Research Diet, D12329)


title: D12_E4_L4

value: trophoblast cells


title: D12_E4_S1

description: cytotrophoblast (CTB)

value: Day 12 (Extended culture)


title: D12_E4_L2


title: B6ES_ChIP_mIgG


title: D12_E4_L5


title: D12_E6_L3


title: GR_ZT4 HFD REP1

source_name: GR_ZT4 HFD_liver


title: GR_ZT8 HFD REP1


title: D12_E4_L3


title: D12_E4_L1


title: D12_E4_EVT7

description: migratory cells (MTB)


title: GR_ZT0 HFD REP1

source_name: GR_ZT0 HFD_liver


title: GR_ZT0 HFD REP2


title: D12_E4_EVT6

description: migratory cells (MTB)


title: GR_ZT20 control REP2

source_name: GR_ZT20 control_liver


title: B6ES_4C_Tead4-promoter_Rep1


title: D12_E4_S4

description: cytotrophoblast (CTB)


title: GR_ZT12 HFD REP2

source_name: GR_ZT12 HFD_liver


title: D12_E4_EVT5

description: migratory cells (MTB)


title: GR_ZT16 control REP2

source_name: GR_ZT16 control_liver


title: D12_E4_EVT4

description: migratory cells (MTB)


title: D12_E4_EVT3

description: migratory cells (MTB)


title: GR_ZT16 control REP1


title: D12_E4_EVT2

description: migratory cells (MTB)


title: GR_ZT8 control REP1

source_name: GR_ZT8 control_liver


title: D12_E4_EVT8

description: migratory cells (MTB)


title: D12_E4_EVT1

description: migratory cells (MTB)


title: D12_E4_EVT13

description: migratory cells (MTB)


title: GR_ZT4 HFD REP2


title: D12_E4_EVT11

description: migratory cells (MTB)


title: GR_ZT4 control REP2

source_name: GR_ZT4 control_liver


title: D12_E3_S9

description: cytotrophoblast (CTB)


title: GR_ZT0 control REP1

source_name: GR_ZT0 control_liver


title: D12_E4_EVT12

description: migratory cells (MTB)


title: GR_ZT0 control REP2


title: D12_E3_S8

description: cytotrophoblast (CTB)


title: D12_E3_S7

description: cytotrophoblast (CTB)


title: GR_ZT20 control REP1


title: D12_E3_S6

description: cytotrophoblast (CTB)


title: D12_E3_S5

description: cytotrophoblast (CTB)


title: D12_E3_S4

description: cytotrophoblast (CTB)


title: D12_E3_S3

description: cytotrophoblast (CTB)


title: GR_ZT4 control REP1


title: D12_E3_S2

description: cytotrophoblast (CTB)


title: D12_E3_S23

description: cytotrophoblast (CTB)


title: D12_E4_EVT10

description: migratory cells (MTB)


title: D12_E3_S22

description: cytotrophoblast (CTB)


title: D12_E3_S24

description: cytotrophoblast (CTB)


title: RNA-seq_ZT20 HFD REP3

description:
sample code: BH63
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

data_processing:
Reads were aligned to the mm9 genome with STAR v2.4.2a and the output SAM files were converted to BAM using samtools v1.3.1
Feature counting: counting all reads which were located within an exon, do not overlap multiple features, are not chimeric, and have a minimum mapping quality of 4. Using featureCounts v1.4.6: featureCounts -p -C -F GTF -t exon -Q 4 -a gencode.vM1.annotation.gtf -g gene_id -o $output $input -T 16  However for further processing steps, the count matrix was filtered (0 count rows and those where the average was less then 50 were left out). These filtered tables were than the input tables for DESeq2 and for the normalization step.
Finding differentially expressed genes using DESeq2 v1.15.51
Finding oscillating genes with JTK_Cycle v3.1
Genome_build: mm9
Supplementary_files_format_and_content: .txt tables. Those with the name table_featureCounts*.txt are the count matrices, where the rows are the genes and the columns the samples. A cell in the matrix contains the count number for gene i in sample j. The table table_filtered_featureCounts_DL-DH-BL-BH.txt is a combined count table, which is formed from the table table_featureCounts_DL-DH.txt and some columns of the table_featureCounts.txt matrix. Tables named table_filtered_VST*.txt are the prefiltered, VST normalized tables. The file table_filtered_VST_DL-DH-BL-BH.txt is the filtered, VST normalized  table_filtered_featureCounts_DL-DH-BL-BH.txt table.

source_name: ZT20 HFD_liver

extract_protocol:
Total RNA was isolated from 50 mg of liver using QIAZOL reagent. Quality of the RNA was assayed by using  Agilent RNA 6000 Nano Kit (Agilent) in a 2100 Bioanalyzer (Agilent).
Libraries were prepped from 1 µg RNA by Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilents Bravo liquid handling platform). Libraries run in a HighSeq2500 sequencer (Illumina).

value: liver


title: RNA-seq_ZT20 HFD REP1

description:
sample code: BH61
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: RNA-seq_ZT20 HFD REP2

description:
sample code: BH62
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: ScRNA-seq KO

description: KO scRNA-seq libraries processed with CellRanger. Paired libraries split across two lanes. Processed data are filtered feature matrices from CellRanger.

data_processing:
Raw base call (BCL) files were demultiplexed with bcl2fastq; Cell Ranger (version 3.0.0) from 10x genomics was used to align reads, generate feature-barcode matrices for both Control and KO samples
cellranger mkfastq was used to generate FASTQ files;
cellranger count performs alignment, filtering, barcode counting, and UMI counting
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger filtered feature matrix files for each condition.

source_name: testicular cells

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testicular cells were isolated from P7 control and knockout mice by FACS.

extract_protocol:
Single testicular cells were isolated from P7 control and knockout mice. Testes were digested into single cell suspensions with 0.25% trypsin/EDTA, stained with DAPI and DRAQ5 dye. Single and live cells were sorted by FACS.
Single-cell RNA-seq libraries were prepared using single cell 3’ reagent kits v2 (10X Genomics) according to the manufacturer’s instructions at NHLBI Core Facility. Briefly, cells obtained from FACS were mixed with a suspension containing barcoded beads and UMI (unique molecular identifier) elements that allow specific tagging of messenger RNA. After partitioning thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and barcoding, full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction. Libraries were constructed by fragmentation, end repair, A-tailing, adaptor ligation and index PCR. After ensuring adequate quality of the cDNA libraries, the samples were sequenced at the NHLBI Genomic Core Facility.
Single-cell RNA-seq

value: B6D2F1 inbred

value: testis

value: post natal day 7


title: D12_E3_S20

description: cytotrophoblast (CTB)

source_name: trophoblast cells


title: ScRNA-seq Control

description: Control scRNA-seq libraries processed with CellRanger. Paired libraries split across two lanes. Processed data are filtered feature matrices from CellRanger.


title: RNA-seq_ZT8 HFD REP1

description:
sample code: BH31
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT8 HFD_liver


title: RNA-seq_ZT16 HFD REP2

description:
sample code: BH52
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT16 HFD_liver


title: RNA-seq_ZT12 HFD REP2

description:
sample code: BH42
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT12 HFD_liver


title: RNA-seq_ZT16 HFD REP1

description:
sample code: BH51
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from ME Replicate 2 [smRNA-Seq]

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

description: Calli tissue obtained from Mature Embryos at one month of subculture (Variety VS-535)

data_processing:
bcl2fastq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.36, and filtered for quality above PHRED score 20 , then mapped to AGPv4.37 whole genome using bowtie v2 with standard parameters ( -n assigned as "1" to allow one mismatch for sRNAs reads), using the single-end format .
Sequences mapping to tRNA, rRNA, snRNA, and snoRNA loci were excluded. Alignment BAM final files were converted to Fastq files using bamtofastq from Bedtools v2.26.0 toolset . To control the length of the reads (to the size of 18 to 27 nt) and for the generation of tag-count files (i.e. sequence plus abundance), we used a published preprocessing script (Mathioni et al., 2017) . Normalization was performed to adjust the reads in each library to Reads Per Ten Million (RPTM).
Genome_build: AGPv4.37
Supplementary_files_format_and_content: tab-delimited text files include total count values for each Sample ...

organism: Zea mays

source_name: Calli

extract_protocol:
RNA was isolated and fractionated by size using the Quick-RNA TM MiniPrep system (Zymo Research). This method allowed simultaneous separation of large (>200 nt) and small (17 to 200 nt) from each sample (López-Ruiz et al., 2018) small RNA fractions were used to sRNAs libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Calli

tag: cultivar


title: RNA-seq_ZT12 HFD REP3

description:
sample code: BH43
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: RNA-seq_ZT8 HFD REP3

description:
sample code: BH33
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D12_E3_S21

description: cytotrophoblast (CTB)


title: RNA-seq_ZT4 HFD REP3

description:
sample code: BH23
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT4 HFD_liver


title: Calli obtained from ME Replicate 1 [smRNA-Seq]

value: Mature Embryos at one month of subculture


title: RNA-seq_ZT4 HFD REP2

description:
sample code: BH22
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from IE23 Replicate 2 [smRNA-Seq]

description: Calli tissue obtained from Immature Embryos 23 days after pollination at one month of subculture (Variety VS-535)


title: RNA-seq_ZT8 HFD REP2

description:
sample code: BH32
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from IE15 Replicate 2 [smRNA-Seq]

description: Calli tissue obtained from Immature Embryos 15 days after pollination at one month of subculture (Variety VS-535)


title: D12_E3_S1

description: cytotrophoblast (CTB)


title: Calli obtained from IE23 Replicate 1 [smRNA-Seq]

value: Immature Embryos 23 days after pollination at one month of subculture


title: RNA-seq_ZT12 HFD REP1

description:
sample code: BH41
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from IE15 Replicate 1 [smRNA-Seq]

value: Immature Embryos 15 days after pollination at one month of subculture


title: RNA-seq_ZT0 HFD REP3

description:
sample code: BH13
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT0 HFD_liver


title: RNA-seq_ZT0 HFD REP2

description:
sample code: BH12
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Immature Embryo 23 DAP Replicate 2 [smRNA-Seq]

description: Embryos obtained at 23 days after pollination (Variety VS-535)

source_name: Immature Embryo

value: Immature Embryo 23 DAP

value: Embryo


title: Mature Embryo Replicate 2 [smRNA-Seq]

description: Mature Embryo obtained at 45 days after pollination (Variety VS-535)

source_name: Mature Embryo

value: Mature Embryo 45 DAP


title: Mature Embryo Replicate 1 [smRNA-Seq]


title: D12_E3_S18

description: cytotrophoblast (CTB)


title: Immature Embryo 23 DAP Replicate 1 [smRNA-Seq]


title: D12_E3_S17

description: cytotrophoblast (CTB)


title: D12_E3_S16

description: cytotrophoblast (CTB)


title: Immature Embryo 15 DAP Replicate 2 [smRNA-Seq]

description: Embryos obtained at 15 days after pollination (Variety VS-535)

value: Immature Embryo 15 DAP


title: Calli obtained from ME Replicate 1

description:
TDD_CM_1
Calli tissue obtained from Mature Embryos at one month of subculture (Variety VS-535)

data_processing:
bcl2fastq v1.8.4
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.36, and filtered for quality above PHRED score 20 , then mapped to AGPv4.37 whole genome using bowtie v2 with standard parameters in paired end format
Transcript abundance quantification was performed using RSEM v1.2.31. Normalization was performed to adjust the reads in each library to Reads Per Ten  Million (RPTM).
Genome_build: AGPv4.37
Supplementary_files_format_and_content: tab-delimited text files include total count values for each Sample ...

extract_protocol:
RNA was isolated and fractionated by size using the Quick-RNA TM MiniPrep system (Zymo Research). This method allowed simultaneous separation of large (>200 nt) and small (17 to 200 nt) from each sample (López-Ruiz et al., 2018) .
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA-seq_ZT20 control REP3

description:
sample code: BL63
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT20 control_liver


title: Calli obtained from ME Replicate 2

description:
TDD_CM_2
Calli tissue obtained from Mature Embryos at one month of subculture (Variety VS-535)


title: RNA-seq_ZT16 HFD REP3

description:
sample code: BH53
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

value: 12 wk High Fat Diet (Research Diet, D12331)


title: Immature Embryo 15 DAP Replicate 1 [smRNA-Seq]


title: D12_E3_S15

description: cytotrophoblast (CTB)


title: RNA-seq_ZT0 HFD REP1

description:
sample code: BH11
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from IE23 Replicate 2

description:
TDD_C23_2
Calli tissue obtained from Immature Embryos 23 days after pollination at one month of subculture (Variety VS-535)


title: RNA-seq_ZT20 control REP2

description:
sample code: BL62
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: RNA-seq_ZT20 control REP1

description:
sample code: BL61
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: RNA-seq_ZT4 HFD REP1

description:
sample code: BH21
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Calli obtained from IE15 Replicate 1

description:
TDD_C15_1
Calli tissue obtained from Immature Embryos 15 days after pollination at one month of subculture (Variety VS-535)


title: Calli obtained from IE23 Replicate 1

description:
TDD_C23_1
Calli tissue obtained from Immature Embryos 23 days after pollination at one month of subculture (Variety VS-535)


title: D12_E3_S14

description: cytotrophoblast (CTB)


title: D12_E3_S13

description: cytotrophoblast (CTB)


title: Calli obtained from IE15 Replicate 2

description:
TDD_C15_2
Calli tissue obtained from Immature Embryos 15 days after pollination at one month of subculture (Variety VS-535)


title: D12_E3_S12

description: cytotrophoblast (CTB)


title: Mature Embryo Replicate 2

description:
TDD_ME_2
Mature Embryo obtained at 45 days after pollination (Variety VS-535)

value: Embryo 45 DAP


title: RNA-seq_ZT16 control REP3

description:
sample code: BL53
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT16 control_liver

value: 12 wk control Diet (Research Diet, D12329)


title: D12_E3_S19

description: cytotrophoblast (CTB)

value: trophoblast cells


title: Mature Embryo Replicate 1

description:
TDD_ME_1
Mature Embryo obtained at 45 days after pollination (Variety VS-535)


title: Immature Embryo 23 DAP Replicate 2

description:
TDD_IE23_2
Embryos obtained at 23 days after pollination (Variety VS-535)

value: Embryo 23 DAP


title: D12_E3_S11

description: cytotrophoblast (CTB)

value: Day 12 (Extended culture)


title: Immature Embryo 23 DAP Replicate 1

description:
TDD_IE23_1
Embryos obtained at 23 days after pollination (Variety VS-535)


title: RNA-seq_ZT16 control REP2

description:
sample code: BL52
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

value: liver


title: Immature Embryo 15 DAP Replicate 2

description:
TDD_IE15_2
Embryos obtained at 15 days after pollination (Variety VS-535)

value: Embryo 15 DAP


title: D12_E3_S10

description: cytotrophoblast (CTB)


title: Immature Embryo 15 DAP Replicate 1

description:
TDD_IE15_1
Embryos obtained at 15 days after pollination (Variety VS-535)


title: RNA-seq_ZT12 control REP3

description:
sample code: BL43
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT12 control_liver


title: RNA-seq_ZT12 control REP2

description:
sample code: BL42
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D10_E4_S3

description: cytotrophoblast (CTB)

value: Day 10 (Extended culture)


title: D10_E4_S4

description: cytotrophoblast (CTB)


title: RNA-seq_ZT12 control REP1

description:
sample code: BL41
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D10_E4_S2

description: cytotrophoblast (CTB)


title: RNA-seq_ZT8 control REP3

description:
sample code: BL33
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT8 control_liver


title: RNA-seq_ZT8 control REP2

description:
sample code: BL32
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Exp-2_20L:04D_ExposureRep-3_SubSample-B

type: RNA

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: An Agilent Technologies (Agilent Technologies, Santa Clara, CA, USA) single color custom 8 x 15K microarray format (Amadid #: 237101) was used for all investigations.  The experimental design for the microarray experiments utilized animals collected directly from the photo-period exposures.  The present GEO dataset was collected from Experiment 2.  Within each exposure replicate, two population sub-samples consisting of single, unique D. magna were used for hybridization to microarrays.  These population sub-samples were selected at random (using a random number generator) from 2-6 D. magna sampled for the genomics investigation that met the RNA quality criteria described in the following paragraph.  In summary, the hybridization included 5 photoperiods x 3 exposure replicates x 2 population subsamples for a total of 30 total microarray hybridizations per experiment

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: An Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C, Agilent Technologies, Santa Clara, CA, USA) was used to scan microarray images at 2 μm resolution. Data were extracted from microarray images using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies).  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX12.5 (Agilent Technologies).  Two-way ANOVAs (p = 0.01) were conducted in GeneSpring to investigate variance within and among the photoperiod treatments.  Specifically, the primary variable of interest, photoperiod, was investigated in addition to the contribution of variance from population sub-sampling within each photo-period treatment.  Post-hoc pair-wise tests consisting of moderated t-tests (p = 0.05) including ≥ 1.5 fold change cutoff were conducted to identify transcripts differentially expressed in each experimental photo-period (4L:20D, 8L:16D, 12L:12D, and 20L:4D) relative to the control (16L:8D).

organism: Daphnia magna

source_name: whole animal

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (one color) and hybridization protocol (Agilent Technologies) were utilized for microarray hybridizations following manufacturer’s recommendations using 80 ng of total RNA as starting material from each biological sample.

growth_protocol: Daphnia magna neonates (<24-h old), obtained from 16L:8D in-house cultures, were immediately used in the photoperiod experiments.  Organisms were originally purchased from a commercial source in May 2009 (Aquatic Biosystems, Fort Collins, CO, USA; EPA Ohio, AROF2, Lot No. 070092DM) and in-house cultures were started using one individual to ensure testing utilized a single genotype.  All culturing and test methods used hard reconstituted water (HRW), formulated according to USEPA (2002).  Test organisms in cultures and experiments were provided a daily ration of 2X105 algae cells/mL (Raphidocelis subcapitata, formerly Selenastrum capricornutum) and 0.01 mL/mL yeast-cerophyl-trout chow (YCT) (Aquatic Biosystems) as prescribed by guidance (ASTM 2012; USEPA 2002).

extract_protocol: Frozen samples were homogenized using a pellet pestle (Kimble Kontes, Vineland, NJ) and mortar (Kimble Kontes). Total RNA isolation was conducted using the Qiagen RNeasy Mini Kit (Qiagen, Germantown, MD) following manufacturer’s recommendations.  RNA quantity was estimated using a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) and final quantity and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Only samples with a 28s/18s ratio ≥2.0 and RNA integrity number (RIN) ≥7.0 were used for downstream applications.

treatment_protocol: Specialized exposure chambers resembling ant farms were constructed from clear acrylic (JR's Custom Acrylics, Vandalia, OH).  The chamber dimensions were 35 X 17 X 2 cm  and contained approximately 1190 mL HRW (34.5 cm water height); each was initially loaded with 20 D. magna.  To isolate the exposures from ambient laboratory lighting, sets of 3 replicate exposure chambers were placed within five separate wooden boxes (36 X 70 X 70 cm) where each photoperiod treatment was administered.  Each photoperiod box had a black interior and was equipped with a wide-spectrum fluorescent lamp (Exo Terra PT2151, Rolf C. Hagen Corp., Mansfield, MA) providing overhead lighting that was uniform across all three exposure chambers.  The photoperiods within each photoperiod box were separately regulated by digital light timers (Woods Digital Indoor Timer #50008, Coleman Cable, Inc., Waukegan, IL).  The light penetration within the test chambers ranged from 730 to 6750 lux, depending on depth.  The photoperiod exposures were run twice providing two sets of three replicates for each photoperiod.  Both experiments were conducted for 21 days, adapted from the standard ASTM method E1193-97 (ASTM 2012) duration, at 25 ± 1ºC within Darwin Environmental Chambers (Darwin, St. Louis, Missouri, USA).  Complete (100%) water renewals using HRW were performed three times a week (Monday, Wednesday, Friday); viable neonates per adult were enumerated and removed from the experimental chambers at each water exchange.  Thus, only the original individuals loaded into the chambers remained for the duration of the experiment.  Water quality monitoring included temperature, pH, dissolved oxygen, specific conductivity and ammonia.

value: whole animal

value: Adult - 21d old

tag: Sex

value: Female


title: D10_E4_L6

description: multinucleated primitive syncytium (STB)


title: RNA-seq_ZT8 control REP1

description:
sample code: BL31
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D10_E4_L5


title: RNA-seq_ZT16 control REP1

description:
sample code: BL51
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D10_E4_L4


title: RNA-seq_ZT4 control REP3

description:
sample code: BL23
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT4 control_liver


title: RNA-seq_ZT4 control REP2

description:
sample code: BL22
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: D10_E4_L3


title: RNA-seq_ZT0 control REP3

description:
sample code: BL13
processed data file:
table_featureCounts.txt
table_filtered_VST.txt

source_name: ZT0 control_liver


title: Exp-2_20L:04D_ExposureRep-3_SubSample-A


title: Exp-2_20L:04D_ExposureRep-2_SubSample-B


title: D10_E4_S1

description: cytotrophoblast (CTB)


title: D10_E4_L2


title: Exp-2_16L:08D_ExposureRep-1_SubSample-B


title: Exp-2_20L:04D_ExposureRep-2_SubSample-A


title: Exp-2_16L:08D_ExposureRep-2_SubSample-B


title: Exp-2_16L:08D_ExposureRep-2_SubSample-A


title: Exp-2_16L:08D_ExposureRep-3_SubSample-A


title: Exp-2_16L:08D_ExposureRep-1_SubSample-A


title: Exp-2_12L:12D_ExposureRep-3_SubSample-A


title: Exp-2_12L:12D_ExposureRep-3_SubSample-B


title: Exp-2_20L:04D_ExposureRep-1_SubSample-B


title: RNA-seq_ZT0 control REP2

description:
sample code: BL12
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Exp-2_12L:12D_ExposureRep-2_SubSample-B


title: D10_E4_L1


title: Exp-2_12L:12D_ExposureRep-1_SubSample-B


title: D10_E3_S8

description: cytotrophoblast (CTB)


title: RNA-seq_ZT0 control REP1

description:
sample code: BL11
processed data file:
table_featureCounts.txt
table_filtered_VST.txt


title: Exp-2_20L:04D_ExposureRep-1_SubSample-A


title: Exp-2_8L:16D_ExposureRep-3_SubSample-B


title: MTX3_5

city: Seattle

first: Douglas

middle: M

last: Fowler

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Library strategy: DNA-seq
We performed paired-end seq, but provide the paired reads here.
Enrich2 was used to calculate solubility scores for each Aβ variant from sequencing fastq files (Rubin et al. 2017). The Enrich2 pipeline calculates a variant’s score in three steps. First, a variant’s normalized frequency ratios are tabulated for each timepoint by dividing the frequency of a variant’s sequencing reads by all mapped reads and normalizing by the wild-type frequency ratio. Sequencing reads were stringently filtered for quality; we require each base have a Phred score greater than 20 and no uncalled bases. Second, a weighted linear least squares regression line is fit to the normalized frequency ratios across time points. Third, the slope of the regression line is calculated, averaged across the three replicates and log2 transformed. This averaged log2 slope reflects a variant’s aggregation propensity. Solubility scores below 0 denote variants that are more aggregation-prone than wild-type, whereas scores above 0 indicate that a variant has increased solubility compared to wild-type.
Supplementary_files_format_and_content: Enrich2 mutational effect scores via weighted linear regression

molecule: other

source_name: Amyloid Beta (1-42) Mutant Library

growth_protocol: Transformed yeast were inoculated into  300 mL  of C-Ura, 2% glucose media, grown in a rotating/shaking, 30C incubator overnight and then transferred to  300 mL 2% raffinose media to remove the glucose repression acting on the gal1 promoter. After two hours in 2% raffinose, yeast were back-diluted to an OD of 0.01 into 300 mL 2% galactose to induce Aβ42-DHFR expression in the presence or absence of 80 μΜ methotrexate (TCI America, M-1664) and 1 mM sulfanilamide (Sigma, S-9251).

extract_protocol:
Plasmids were extracted from yeast with Yeast Plasmid Miniprep 1 kit (Zymo Research, D-2001).
Library fragments were amplified in 17 PCR cycles using primers specific to DNA sequences that flank Aβ-DHFR in p416, and sequenced by an Illumina NextSeq sequencer using paired-end reads

treatment_protocol: 10OD units of 300 mL cultures were sampled at the following timepoints: input, 28h (OD ≈ 1.0),  31.5h (OD ≈ 2.0), 35h (OD ≈ 3.0), 38h (OD ≈ 4.5), and 40h (OD ≈ 6.0). Cultures were spun down, concentrated and stored in -80C.

tag: timepoint

tag: od point


title: D10_E3_S7

description: cytotrophoblast (CTB)

source_name: trophoblast cells


title: Exp-2_12L:12D_ExposureRep-1_SubSample-A


title: Exp-2_12L:12D_ExposureRep-2_SubSample-A


title: Exp-2_8L:16D_ExposureRep-2_SubSample-A


title: Exp-2_8L:16D_ExposureRep-2_SubSample-B


title: Exp-2_8L:16D_ExposureRep-3_SubSample-A


title: Exp-2_16L:08D_ExposureRep-3_SubSample-B


title: MTX3_3


title: Exp-2_8L:16D_ExposureRep-1_SubSample-B


title: MTX3_2


title: D10_E3_S5

description: cytotrophoblast (CTB)


title: D10_E3_S4

description: cytotrophoblast (CTB)


title: D10_E3_S6

description: cytotrophoblast (CTB)


title: D10_E3_S2

description: cytotrophoblast (CTB)


title: MTX3_input


title: D10_E3_S3

description: cytotrophoblast (CTB)


title: MTX3_1


title: MTX2_5


title: Exp-2_8L:16D_ExposureRep-1_SubSample-A


title: MTX3_4


title: D10_E3_S1

description: cytotrophoblast (CTB)


title: MTX2_4


title: D10_E2_S8

description: cytotrophoblast (CTB)


title: Exp-1_20L:04D_ExposureRep-3_SubSample-B

hyb_protocol: An Agilent Technologies (Agilent Technologies, Santa Clara, CA, USA) single color custom 8 x 15K microarray format (Amadid #: 237101) was used for all investigations.  The experimental design for the microarray experiments utilized animals collected directly from the photo-period exposures.  The present GEO dataset was collected from Experiment 1.  Within each exposure replicate, two population sub-samples consisting of single, unique D. magna were used for hybridization to microarrays.  These population sub-samples were selected at random (using a random number generator) from 2-6 D. magna sampled for the genomics investigation that met the RNA quality criteria described in the following paragraph.  In summary, the hybridization included 5 photoperiods x 3 exposure replicates x 2 population subsamples for a total of 30 total microarray hybridizations per experiment


title: Exp-2_4L:20D_ExposureRep-3_SubSample-B


title: Exp-2_4L:20D_ExposureRep-1_SubSample-B


title: Exp-2_4L:20D_ExposureRep-3_SubSample-A


title: Exp-2_4L:20D_ExposureRep-1_SubSample-A


title: Exp-2_4L:20D_ExposureRep-2_SubSample-A


title: MTX2_3


title: Exp-1_20L:04D_ExposureRep-2_SubSample-B


title: Exp-2_4L:20D_ExposureRep-2_SubSample-B


title: Exp-1_20L:04D_ExposureRep-3_SubSample-A


title: D10_E2_S7

description: cytotrophoblast (CTB)


title: MTX2_2


title: Exp-1_20L:04D_ExposureRep-2_SubSample-A


title: Exp-1_20L:04D_ExposureRep-1_SubSample-A


title: Exp-1_16L:08D_ExposureRep-2_SubSample-B


title: Exp-1_16L:08D_ExposureRep-2_SubSample-A


title: Exp-1_16L:08D_ExposureRep-3_SubSample-B


title: D10_E2_S6

description: cytotrophoblast (CTB)


title: MTX2_1


title: Exp-1_16L:08D_ExposureRep-3_SubSample-A


title: Exp-1_16L:08D_ExposureRep-1_SubSample-B


title: MTX2_input


title: D10_E2_S4

description: cytotrophoblast (CTB)


title: D10_E2_S5

description: cytotrophoblast (CTB)


title: Exp-1_20L:04D_ExposureRep-1_SubSample-B


title: MTX1_4


title: D10_E2_S3

description: cytotrophoblast (CTB)


title: Exp-1_16L:08D_ExposureRep-1_SubSample-A


title: D10_E2_S2

description: cytotrophoblast (CTB)


title: Exp-1_12L:12D_ExposureRep-3_SubSample-B


title: Exp-1_12L:12D_ExposureRep-3_SubSample-A


title: MTX1_5


title: Exp-1_12L:12D_ExposureRep-2_SubSample-B


title: D10_E2_S1

description: cytotrophoblast (CTB)


title: MTX1_2


title: MTX1_1


title: D10_E2_L9


title: Exp-1_8L:16D_ExposureRep-3_SubSample-B


title: Exp-1_8L:16D_ExposureRep-3_SubSample-A


title: Exp-1_12L:12D_ExposureRep-2_SubSample-A


title: D10_E2_L8


title: Exp-1_8L:16D_ExposureRep-2_SubSample-B


title: MTX1_input


title: Exp-1_12L:12D_ExposureRep-1_SubSample-A


title: Exp-1_12L:12D_ExposureRep-1_SubSample-B


title: Exp-1_8L:16D_ExposureRep-1_SubSample-A


title: Exp-1_8L:16D_ExposureRep-1_SubSample-B


title: MTX1_3


title: D10_E2_L7


title: Exp-1_4L:20D_ExposureRep-3_SubSample-B


title: D10_E2_L5


title: D10_E2_L6


title: Exp-1_4L:20D_ExposureRep-3_SubSample-A


title: D4 hPGCLC

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg

department: Chemical Engineering

institute: University of California Santa Barbara

description: scMspJI-seq on D4 hPGCLCs

data_processing:
Illumina bcl2fastq2 v 2.20 software used for basecalling
Sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 12 -B 11
A custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. This code is available on request.
Genome_build: hg19 version
Supplementary_files_format_and_content: Raw Data in FASTQ Format.  Process files give called 5mCpG sites in space delimited format, Cell #, Chromosome #, Location, unique molecule identifier (UMI), Strand.

source_name: D4 hPGCLC

growth_protocol: hPGCLCs were generated from primed hESC line (UCLA2, X46) through a two step differentiation protocol. Briefly, hESCs are differentiated into incipient mesoderm-like cells (iMeLCs), after 24hr exposure to activin A and Chriron,  cultured iMeLCs are aggregated in low adhession 96 well plate, at a density of 3,000 cells per well. After 4 days in the aggregate, hPGCLCs are isolated through fluorescent activated cell sorting (FACs). D4 hPGCLCs were directly sorted at the single cell level for D4 sample. D4C10 sample was generated by culturing D4 hPGCLCs for an additional 10 days on STO feeder cells. After 10 days in culture, Tra-1-85 postive hPGCLCs were single cell sorted by FACs.

extract_protocol:
Single Cells sorted into 384 well plate (FACS)
Samples were prepared as described in scMspJI-seq with minor modifications (Sen et al. 2019).  Single cells were sorted into each reaction well of a 384-well plate containing 4 µL of Vapor-Lock (Qiagen) and 200 nL of lysis buffer (0.0875% IGEPAL CA-630) and were stored at -80 °C until use.  The cells were lysed by incubating the plate at 65 °C for 3 minutes.  Then 2.3 µL of 1.09x NEB buffer 4, and 4 µg Qiagen Protease were added to each well and the plate was incubated at 50 °C for 15 h, 75 °C for 20 min and 80 °C for 5 min.  Next, 400 nL of 1x NEB buffer 4, 1 U NEB T4-BGT, and 7.25x NEB UDP-Glucose was added to glucosylate 5hmC sites in the genome, and the sample was incubated at 37 °C for 16 h.  350 nL of 1x NEB buffer 4, and 2 µg Qiagen Protease were added to each well and the plate was incubated at 50 °C for 3 h, 75 °C for 20 min and 80 °C for 5 min.  Following this step, 350 nL of 1x NEB buffer 4 was added. 400 nL of digestion mix (0.1 U MspJI (NEB), 10x Enzyme Activator Solution (NEB), and 1x NEB buffer 4) was added and the plates were incubated at 37 °C for 4.5 h, followed by 65 °C for 20 min.  Next, 200 nL of 125 nM ds-adaptors were added, followed by 800 nL of ligation mix (140 U T4 DNA Ligase (NEB), 1x T4-ligase buffer (NEB), 5 mM ATP (NEB)) and the plate was incubated at 16 °C for 16 h.  The ds-adaptor sequences used are described in scMspJI-seq (Sen et al. 2019).  Excluding the Vapor-Lock, all reagent dispenses were performed using the Nanodrop II liquid handling robot (BioNex Solutions Inc.).  Each plate was pooled into 4 libraries containing 96 uniquely barcoded cells.  For each library, DNA clean-up was then performed with 1x Agencourt Ampure XP beads and eluted in 30 µL of nuclease-free water.  The samples were vacuum centrifuged to a volume 6.4 µL and  9.6 µL of in vitro transcription mix was added (1.6 µL of each ribonucleotide, 1.6 µL of T7 buffer, 1.6 µL T7 enzyme mix (MEGAscript T7 Transcription Kit, Ambion)) and incubated at 37 °C for 13 h.  Library preparation starting from amplified RNA was performed as described previously with the following minor modifications (Mooijman et al. 2016, and Rooijers et al. 2019).  Amplified RNA was fragmented by adding 4 µL of fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500mM KOAc, 150 mM MgOAc) at 94 °C for 2 min and immediately placed on ice. 2 µL of fragmentation stop buffer (0.5 M EDTA) was added to quench the reaction, followed by 28 µL of nuclease-free water.  Next, RNA clean-up was performed using 0.825x Agencourt RNAClean beads and finally resuspended in 20 µL of nuclease-free water.  Thereafter, all library preparation steps were performed as described previously (Mooijman et al. 2016, and Rooijers et al. 2019).
scMspJI-seq

tag: origin

value: hESC derived hPGCLC

value: hPGCLC


title: Exp-1_4L:20D_ExposureRep-2_SubSample-B


title: D4C10 hPGCLC

description: scMspJI-seq on D4C10 hPGCLCs

source_name: D4C10 hPGCLC


title: Exp-1_4L:20D_ExposureRep-1_SubSample-B


title: Exp-1_4L:20D_ExposureRep-2_SubSample-A


title: Exp-1_8L:16D_ExposureRep-2_SubSample-A


title: D10_E2_L4


title: 3_24E [miRNA]

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

country: Australia

institute: Flinders University

data_processing:
Short reads were filtered for adapters and reads of low quality using Cutadapt (v.1.8) with error rate of 0.2 and minimum length of 18 bp, aligned against GENCODE human genome reference assembly GRCh38.p3 using Burrows Wheeler Aligner, and assigned to miRBase (v.21) annotations using HTSeq (v.0.6.1p2).
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: Raw_Counts.xlsx

source_name: ARPE-19 cell

growth_protocol: The ARPE-19 human retinal pigment epithelial cell line (American Type Culture Collection [ATCC], Manassas, VA) was cultured in 1:1 Dulbecco’s modified Eagle’s medium (DMEM):F12 medium (Thermo Fisher Scientific-GIBCO, Grand Island, NY) supplemented with heat-inactivated 10% fetal bovine serum (FBS) (GE Healthcare-Hyclone, Logan, UT)  at 37 °C and 5% CO2 in air. Ebola virus (Zaire ebolavirus, EBOV variant Mayinga) was amplified in Vero C1008 cells (European Collection of Authenticated Cell Cultures [ECACC], Salisbury, United Kingdom), cultured with DMEM supplemented with 10% FBS at 37 °C and 5% CO2 in air, and titrated by end-point dilution of culture supernatant in fresh Vero C1008 cell monolayers.

extract_protocol:
Total RNA was extracted from TRIzol Reagent-lysed ARPE-19 cells, according to the manufacturer’s instructions, and stored at -80 °C ahead of use for RNA-seq. RNA concentration was determined by spectrophotometry on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific-Invitrogen) for RNA-seq. RNA integrity was confirmed on the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
Small RNA was selectively enriched from total RNA using the TruSeq Small RNA Library Preparation Kit (Illumina, San Diego, CA).
The library was sequenced on Illumina NextSeq 500, using NextSeq 75-cycle High Output Kits (Illumina), with the PhiX Control v3 library (Illumina) as sequencing control.

treatment_protocol: Confluent monolayers of ARPE-19 cells were inoculated with EBOV at a multiplicity of infection of 5, or mock-infected, in minimum volumes of DMEM:F12 medium with 10% FBS for 30-40 minutes, subsequently washed twice with fresh medium, and finally returned to standard volumes of medium, all at 37 °C and 5% CO2 in air. Infected cell monolayers were incubated for 24 hours. After 24 hours, supernatant was collected and frozen at -80 °C, and cells were lysed with TRIzol Reagent (Thermo Fisher Scientific-Invitrogen, Carlsbad, CA) and stored at -80 °C ahead of RNA extraction for RNA-seq.

tag: infection

value: EBOV


title: 2_24E [miRNA]

value: human retinal pigment epithelial cell line


title: D10_E2_L3


title: 1_24E [miRNA]


title: D10_E2_L1


title: 3_24C [miRNA]

value: Mock


title: 2_24C [miRNA]


title: AC Barrie embryo sample taken at mature stage AC-17

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In excel file format, including raw read counts of each species

organism: Triticum aestivum

source_name: mature

growth_protocol: Polyploidy wheats, AC Barrie, Strong Field and diploid wheat grass (DV92) plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 for whole life cycle. TA2780 and TA101132 were initially grown in a growth chamber at 22°C under long days (16h day/8h night), at the fifth-leaf stage, plants were moved into a cold room with 4°C and the long day photoperiod for one month (vernalization treatment), then move back to 16 h light, 22°C and 8 h dark, 20 °C; light intensity: 100 to 120 μmol m−2 s−1 again to complete its life cycle

extract_protocol:
Total RNA was extracted from embryo, endosperm and seed coat of wheat speciesat different development stages following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927), two replicates for each development stage. The quantity of RNA isolated from early stage was insufficient for preparation of libraries for the RNA-seq experiments. Therefore the mRNA of all stages was amplified and the aRNA were used for RNA-seq analysis. The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). For RNA-seq profile analysis, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), the libraries were prepared by using aRNA according to manufacturer's instruction. For HiSeq 2500 sequencing, 4 libraries were pooled per sequencing lane
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

value: AC Barrie (Hexaploid wheat, AABBDD genome)

value: embryo

tag: development stages

value: mature


title: AC Barrie endorsperm sample taken at leaf late stage endosperm  AC-19

source_name: late endorsperm

value: endorsperm

value: late endorsperm


title: AC Barrie pericarp sample taken at leaf early stage pericarp AC-20

source_name: SC (Pericarp)

value: seed coat

value: SC (Pericarp)


title: D10_E2_L11

value: trophoblast cells


title: AC Barrie embryo sample taken at leaf late stage AC-16

source_name: leaf late

value: leaf late


title: AC Barrie embryo sample taken at leaf middle stage AC-15

source_name: leaf middle

value: leaf middle


title: 1_24C [miRNA]


title: AC Barrie embryo sample taken at leaf early stage AC-14

source_name: leaf early

value: leaf early


title: D10_E2_L10

value: Day 10 (Extended culture)


title: Exp-1_4L:20D_ExposureRep-1_SubSample-A

value: whole animal

value: Adult - 21d old

value: Female


title: N14

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC hg38 genome via STAR v2.5.2b
Then assigned to Ensembl genes (GRCh38.81) by featureCounts (subread-1.4.6-p1 command line)
Genome_build: hg38
Supplementary_files_format_and_content: csv

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL. ,
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

treatment_protocol: Tissues were cut into slices by using Vibrating-blade Microtome (Leica, VT1200S) and homogenized in low temperature and then the tissues were digested using XXIV protease (Sigma, P8038-250) and Collagenase II (Worthington LS004176) to enrich myocites; tissues were  homogenized and  digested using Cardiomyocyte Isolation Enzyme 1 (with papain) for Pierce Primary Cell Isolation Kits (Thermo 88288) to enrich non-cadiomyocites.

tag: individual

tag: gender

value: M

tag: disease state

value: normal

value: heart

tag: tissue region

value: mixed sample (non-demultiplexed) of LA and LV

value: EC


title: AC Barrie embryo sample taken at transition stage AC-13

source_name: transition

tag: genotype

value: AC Barrie (Hexaploid wheat, AABBDD genome)

tag: tissue

value: embryo

value: transition


title: N13

tag: age

value: F

tag: cell type


title: Control replicate 3

city: Ioannina

first: Thomais

last: Papamarkaki

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

hyb_protocol: Affymetrix protocols and procedures were followed

data_processing: Data were processed using GeneSpring software (Agilent). RMA normalization was performed and only probes above the background threshold were considered for further evaluation.

label: biotin

organism: Danio rerio

source_name: control group

growth_protocol: Embryos were bred under standard conditions

extract_protocol: not provided

treatment_protocol: Zebrafish from the stage of 5 dpf to 42 dpf were fed with fish food supplemented with 2% mastic essential oil. 42 dpf zebrafish were sacrificed and RNA was used for subsequent DNA microarray analysis.


title: D10_E2_L2

value: trophoblast cells

tag: time


title: Mastic replicate 1

scan_protocol: Affymetrix protocols and procedures were followed

source_name: treated group


title: D10_E1_S8

description: cytotrophoblast (CTB)


title: AC Barrie embryo sample taken at two cell stage AC-11

source_name: two cell

value: two cell


title: Control replicate 2

label_protocol: Affymetrix protocols and procedures were followed


title: Control replicate 1


title: Mastic replicate 3


title: AC Barrie embryo sample taken at preembryo stage AC-12

source_name: preembryo

value: preembryo


title: AC Barrie endorsperm sample taken at transition stage endosperm  AC-18

source_name: early endorsperm

value: endorsperm

value: early endorsperm


title: Mastic replicate 2


title: D10_E1_S7

description: cytotrophoblast (CTB)

value: Day 10 (Extended culture)


title: D10_E1_S6

description: cytotrophoblast (CTB)


title: AC Barrie endorsperm sample taken at leaf late stage endosperm  AC-9

value: late endorsperm


title: AC Barrie embryo sample taken at leaf late stage AC-6_3

value: leaf late


title: D10_E1_S4

description: cytotrophoblast (CTB)


title: AC Barrie embryo sample taken at mature stage AC-7

value: mature


title: D5

value: M

value: dilated cardiomyopathy

value: LV

value: FB


title: D4

value: heart

value: mixed sample (non-demultiplexed) of LA and LV

value: mixed sample (non-demultiplexed) of EC, FB, and MP


title: AC Barrie seed coat sample taken at leaf early stage pericarp AC-10

value: AC Barrie (Hexaploid wheat, AABBDD genome)

value: seed coat

value: SC (Pericarp)


title: D10_E1_S3

description: cytotrophoblast (CTB)

value: trophoblast cells


title: AC Barrie embryo sample taken at leaf late stage AC-6

value: embryo


title: D1

value: mixed sample (non-demultiplexed) of EC and SMC


title: AC Barrie endorsperm sample taken at transition stage endosperm  AC-8

value: endorsperm

value: early endorsperm


title: AC Barrie embryo sample taken at leaf middle stage AC-5_3

value: leaf middle


title: D10_E1_S2

description: cytotrophoblast (CTB)

value: Day 10 (Extended culture)


title: AC Barrie embryo sample taken at leaf middle stage AC-5


title: AC Barrie embryo sample taken at leaf late stage AC-6_2

value: leaf late


title: AC Barrie embryo sample taken at leaf early stage AC-4

value: leaf early


title: AC Barrie embryo sample taken at leaf early stage AC-4_2


title: D10_E1_S1

description: cytotrophoblast (CTB)


title: AC Barrie embryo sample taken at leaf middle stage AC-5_2


title: C2

value: M

value: coronary atherosclerotic heart disease

value: EC


title: AC Barrie embryo sample taken at transition stage AC-3_2

value: transition


title: C1

value: heart

value: mixed sample (non-demultiplexed) of LA and LV


title: AC Barrie embryo sample taken at preembryo stage AC-2_2

value: AC Barrie (Hexaploid wheat, AABBDD genome)

value: preembryo


title: D10_E1

description: cytotrophoblast (CTB)

value: trophoblast cells


title: AC Barrie embryo sample taken at preembryo stage AC-2_3

value: embryo


title: AC Barrie embryo sample taken at transition stage AC-3


title: N7_LA

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC hg38 genome via STAR v2.5.2b
Then assigned to Ensembl genes (GRCh38.81) by featureCounts (subread-1.4.6-p1 command line)
Genome_build: hg38
Supplementary_files_format_and_content: csv file reports counts


title: AC Barrie embryo sample taken at preembryo stage AC-2


title: D2

value: dilated cardiomyopathy

value: mixed sample (non-demultiplexed) of EC, FB, and SMC


title: N8_LA

value: F


title: N12_LA


title: AC Barrie embryo sample taken at two cell  stage AC-1_2

value: two cell


title: AC Barrie embryo sample taken at two cell stage AC-1_3


title: D10_E1_L3

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the human genome (hg38) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference.
Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. DAVID (https://david.ncifcrf.gov) and IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively. Cells with more than 8,000 detected genes and for which genes with FPKM > 0.3 were kept in downstream analysis for lineage specification. Lineage specification was performed by Spearman correlation. Principle Component Analysis (PCA) and cluster analysis were performed using R
Genome_build: hg38
Supplementary_files_format_and_content: FASTQ

value: Day 10 (Extended culture)


title: NCCIT-2

city: Cambridge

first: Charles

last: Fulco

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
ATAC-seq reads were aligned to the hg19 genome with BWA
Genome_build: hg19
Supplementary_files_format_and_content: TDF: Coverage across the genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)

source_name: NCCIT cells

extract_protocol:
We lysed 10K cells in Sigma Nuclei EZ lysis buffer
ATAC-seq: We performed ATAC-seq as described in Buenrostro et al. Curr Protoc Mol Biol. (2015)

tag: cell line

value: NCCIT

tag: protocol

value: ATAC-seq


title: N10_LA

value: M


title: N11_LA


title: N9_LA


title: N3_LV


title: N1_LV


title: D10_E1_L2

source_name: trophoblast cells

extract_protocol: The RNA-seq libraries were generated from individually cells using Smart-seq2 with minor modification. Briefly, individually cells were lysed and mRNA was captured and amplified by using Smart-seq2 v4 kit (Clontech). After pre-amplification and AMPure XP beads purification, amplified RNAs were quality checked using Agilent High Sensitivity D5000 kit (Agilent Technologies). High quality of amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The quality and quantity of sequencing libraries were determined using Qubit 3.0 assay (Life Technologies) and Agilent High Sensitivity kit at Tapestation 4200 system (Agilent), respectively. Pooled indexed libraries were then sequenced on Illumina HiSeq X platform with 125 bp pair-end reads.


title: N5_LV


title: AC Barrie embryo sample taken at two cell stage AC-1


title: N4_LV


title: N6_LA


title: strong field embryo sample taken at leaf late stage ST-16

organism: Triticum turgidum

value: Strong Field (Tetraploid wheat, AABB genome)

value: leaf late


title: strong field embryo sample taken at mature stage ST-17

value: mature


title: strong field endorsperm sample taken at leaf late stage endorsperm ST-19

value: endorsperm

value: late endorsperm


title: strong field seed coat sample taken at leaf early stage pericarp ST-20

value: SC (Pericarp)


title: N2_LV


title: NCCIT-1


title: strong field endorsperm sample taken at transition stage endorsperm ST-18

value: early endorsperm


title: D10_E1_L1

value: trophoblast cells


title: strong field embryo sample taken at preembryo stage ST-12

value: embryo

value: preembryo


title: GR_ZT12 control REP1

source_name: GR_ZT12 control_liver

tag: strain

tag: treatment

value: 12 wk control Diet (Research Diet, D12329)

value: Liver

tag: chip antibody

value: GR (Santa Cruz, sc-1004X)


title: GR_ZT8 control REP2

source_name: GR_ZT8 control_liver


title: strong field embryo sample taken at leaf middle stage ST-15

value: leaf middle


title: strong field embryo sample taken at leaf early stage ST-14

value: leaf early


title: strong field embryo sample taken at transition stage ST-13

value: transition


title: Oleuropein  10 min replicate 1

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

description:
Biological replicate 1 of 3
slide:  Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned.

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C / GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes.

organism: Lactiplantibacillus plantarum

source_name: Treated cells: Experimental

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking oleuropein to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to oleuropein to bring their final concentration to 15 mM. Cell cultures were centrifuged after 10 minutes of exposure to oleuropein and RNA was extracted and purified.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in the Mini-BeadBeather (BIOSPEC Products, INC.) using three treatments of 4600 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

tag: compound

value: Oleuropein

source_name: Untreated cells: Control

value: without oleuropein


title: strong field endorsperm sample taken at leaf stage late endorsperm ST-9

source_name: late endorsperm

value: Strong Field (Tetraploid wheat, AABB genome)


title: Oleuropein  10 min replicate 2

description:
Biological replicate 2 of 3
slide:  Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

treatment_protocol: Cell cultures were centrifuged after 10 minutes of exposure to oleuropein and RNA was extracted and purified.


title: Oleuropein  10 min replicate 3

description:
Biological replicate 3 of 3
slide:  Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).


title: strong field endorsperm sample taken at transition stage endorsperm ST-8


title: strong field embryo sample taken at mature stage ST-7

source_name: mature

value: mature


title: CRCNL2 NFKBIZ-KO Noggin- media condition IL17A stimulated

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

hyb_protocol: Affymetrix GeneChip® 3 ' IVT PLUS Reagent Kit.

scan_protocol: GeneChip Scanner 3000 7G procedure.

data_processing: The data was normalized by RMA (R package affy).

source_name: CRC patient 2

label_protocol: Standard protocol.

extract_protocol: QIAGEN RNeasy Plus Mini Kit procedure.

value: Colon organoid

tag: genotype/variation

value: NFKBIZ-KO

tag: medium

value: Noggin-


title: CRCNL2 NFKBIZ-KO full media condition control

value: Full

value: Control


title: strong field embryo sample taken at two cell stage ST-11

value: 2cell and quadrant

tag: development stages

value: two cell


title: CRCNL2 NFKBIZ-KO Noggin- media condition control


title: strong field embryo sample taken at leaf late stage ST-6

source_name: leaf late

value: embryo

value: leaf late


title: CRCNL2 Wildtype Noggin- media condition IL17A stimulated

value: WT


title: CRCNL2 NFKBIZ-KO full media condition IL17A stimulated


title: strong field seed coat sample taken at leaf early stage pericarp ST-10

source_name: SC (Pericarp)

value: SC (Pericarp)


title: CRCNL2 Wildtype full media condition IL17A stimulated


title: CRCNL2 Wildtype Noggin- media condition control


title: strong field embryo sample taken at leaf middle stage ST-5

source_name: leaf middle

value: leaf middle


title: CRCNL1 NFKBIZ-KO Noggin- media condition IL17A stimulated

source_name: CRC patient 1


title: Adrenal_KO4_52weeks: 52 weeks old mice, Rar-alpha KO, biological rep4

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using TAC4.0 version1 software (Thermofisher).

label: Biotin

source_name: adrenal gland from 52 weeks old Rar-alpha KO mice

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

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

value: Adrenal

tag: Sex

value: male

value: 52 weeks

value: Rar-alpha KO mice


title: CRCNL1 NFKBIZ-KO Noggin- media condition control


title: CRCNL2 Wildtype full media condition control


title: CRCNL1 NFKBIZ-KO full media condition IL17A stimulated


title: strong field embryo sample taken at transition stage ST-3

source_name: transition

value: Strong Field (Tetraploid wheat, AABB genome)

value: transition


title: strong field embryo sample taken at leaf early stage ST-4

source_name: leaf early

value: leaf early


title: strong field embryo sample taken at preembryo stage ST-2

source_name: preembryo

value: preembryo


title: Adrenal_KO1_52weeks: 52 weeks old mice, Rar-alpha KO, biological rep1


title: RNAseq_B6TS

data_processing:
Paired-end sequencing (101 bp x 2) was performed on the HiSeq1500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using  hisat2 (v2.1.0).
The read counts and Fragments Per Kilobase of exon per Megabase (FPKM) values for each gene were calculated using Cufflinks (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Mouse trophoblast stem (TS) cells

extract_protocol:
Total RNA was extracted using Allprep DNA/RNA Mini kit (QIAGEN).
RNA-seq libraries were prepared using SureSelect strand-specific RNA library preparation kit (G9691A, Agilent). One microgram of total RNA was used as a starting material.

value: B6 mouse-derived trophoblast stem (TS) cells

value: cultured cells

value: wild type


title: Adrenal_KO2_52weeks: 52 weeks old mice, Rar-alpha KO, biological rep2


title: RNAseq_B6ES

source_name: Mouse embryonic stem (ES) cells

value: B6 mouse-derived embryonic stem (ES) cells


title: Adrenal_WT4_52weeks: 52 weeks old mice, Rar-alpha WT, biological rep4

source_name: adrenal gland from 52 weeks old Rar-alpha WT mice

value: Rar-alpha WT mice


title: CRCNL1 NFKBIZ-KO full media condition control

value: Colon organoid

value: NFKBIZ-KO

value: Full

value: Control


title: RA86

type: protein

city: Madison

first: Ken

last: Lo

state: WI

address: 6014 Sandstone Drive

institute: NimbleTherapeutics

hyb_protocol: Serum was diluted 1:100 with array binding buffer (0.01M Tris-Cl, pH7.4, 1% alkali-soluble casein, 0.05% Tween-20) and bound to peptide arrays O/N at 4C.

scan_protocol: Arrays were scanned using Innopsys InnoScan 910AL at 2um resolution.

data_processing:
Signal extraction was done via Slideviewer.  Spatial Correction and background correction was performed using in-house library RNGdat.
GEO.tsv includes preprocessed signal intensity for each sample

molecule: protein

source_name: RA patient 18

tag: disease state

value: Rheumatoid Arthritis

value: F

tag: ccp2 status

value: Positive


title: RA80

source_name: RA patient 17


title: diploid grass (DV92) seed coat sample taken at leaf early  stage pericarp DV-20

organism: Triticum monococcum

tag: genotype

value: diploid grass (DV92, A genome)

value: SC (Pericarp)


title: CRCNL1 Wildtype Noggin- media condition control

tag: tissue

value: WT

value: Noggin-


title: Adrenal_WT3_52weeks: 52 weeks old mice, Rar-alpha WT, biological rep3

value: Adrenal

value: male

tag: age

value: 52 weeks


title: CRCNL1 Wildtype Noggin- media condition IL17A stimulated


title: RA75

source_name: RA patient 15


title: Adrenal_KO4_12weeks: 12 weeks old mice, Rar-alpha KO, biological rep4

source_name: adrenal gland from 12 weeks old Rar-alpha KO mice

value: 12 weeks

value: Rar-alpha KO mice


title: Adrenal_WT2_52weeks: 52 weeks old mice, Rar-alpha WT, biological rep2

value: Rar-alpha WT mice


title: RA76

source_name: RA patient 16


title: Adrenal_KO3_12weeks: 12 weeks old mice, Rar-alpha KO, biological rep3


title: Adrenal_WT1_52weeks: 52 weeks old mice, Rar-alpha WT, biological rep1


title: diploid grass (DV92) embryo sample taken at mature stage DV-17

source_name: mature

value: embryo

value: mature


title: Adrenal_KO3_52weeks: 52 weeks old mice, Rar-alpha KO, biological rep3


title: CRCNL1 Wildtype full media condition control

value: Colon organoid

value: Full


title: Adrenal_KO2_12weeks: 12 weeks old mice, Rar-alpha KO, biological rep2


title: CRCNL1 Wildtype full media condition IL17A stimulated


title: diploid grass (DV92) endorsperm sample taken at transition stage endorsperm DV-18

source_name: early endorsperm

value: endorsperm

value: early endorsperm


title: diploid grass (DV92) endorsperm sample taken at leaf late stage endorsperm DV-19

source_name: late endorsperm

value: late endorsperm


title: strong field embryo sample taken at two cell stage ST-1

source_name: two cell

value: Strong Field (Tetraploid wheat, AABB genome)

value: two cell


title: RA73

source_name: RA patient 14

value: Rheumatoid Arthritis

value: F

value: Positive


title: diploid grass (DV92) embryo sample taken at leaf late stage DV-16

source_name: leaf late

value: diploid grass (DV92, A genome)

value: leaf late


title: Adrenal_WT3_12weeks: 12 weeks old mice, Rar-alpha WT, biological rep3

source_name: adrenal gland from 12 weeks old Rar-alpha WT mice

value: Adrenal

value: male

value: 12 weeks


title: Adrenal_WT4_12weeks: 12 weeks old mice, Rar-alpha WT, biological rep4

value: Rar-alpha WT mice


title: RA71

source_name: RA patient 12


title: diploid grass (DV92) embryo sample taken at leaf early stage DV-14

source_name: leaf early

value: embryo

value: leaf early


title: RA72

source_name: RA patient 13


title: diploid grass (SP) seed coat sample taken at leaf early stage pericarp SP20

organism: Aegilops speltoides

source_name: SC (Pericarp)

value: diploid grass (TA2780, B genome)

value: SC (Pericarp)


title: diploid grass (TA) seed coat sample taken at leaf early stage pericarp TA20

organism: Aegilops tauschii

value: diploid grass (TA101132, D genome)


title: diploid grass (DV92) embryo sample taken at leaf middle stage DV-15

source_name: leaf middle

value: leaf middle


title: Adrenal_KO1_12weeks: 12 weeks old mice, Rar-alpha KO, biological rep1

value: Rar-alpha KO mice


title: diploid grass (SP) endorsperm sample taken at leaf late stage endorsperm SP19

value: endorsperm

value: late endorsperm


title: RA70

source_name: RA patient 11

value: Rheumatoid Arthritis

value: F


title: RA69

source_name: RA patient 10

value: Negative


title: diploid grass (SP) endorsperm sample taken at transition stage endorsperm  SP18

value: early endorsperm


title: diploid grass (TA) endorsperm sample taken at late leaf stage endorsperm TA19


title: RA54

source_name: RA patient 9

value: Positive


title: diploid grass (TA) endorsperm sample taken at transition stage endorsperm TA18


title: diploid grass (SP) embryo sample taken at mature stage SP17

value: mature


title: diploid grass (DV92) embryo sample taken at transition stage DV-13

source_name: transition

value: diploid grass (DV92, A genome)

value: transition


title: diploid grass (SP) embryo sample taken at leaf late stage SP16

value: embryo

value: leaf late


title: diploid grass (DV92) embryo sample taken at two cell  stage DV-11

value: two cell


title: diploid grass (TA) embryo sample taken at mature stage TA17


title: diploid grass (DV92) embryo sample taken at preembryo stage DV-12

source_name: preembryo

value: preembryo


title: RA53

source_name: RA patient 8


title: diploid grass (TA) embryo sample taken at leaf late stage TA16

value: diploid grass (TA101132, D genome)


title: diploid grass (DV92) seed coat sample taken at leaf early stage pericarp DV-10

value: SC (Pericarp)


title: RA52

source_name: RA patient 7


title: diploid grass (SP) embryo sample taken at leaf middle stage SP15

value: diploid grass (TA2780, B genome)

value: leaf middle


title: diploid grass (TA) embryo sample taken at leaf middle stage TA15


title: Adrenal_WT2_12weeks: 12 weeks old mice, Rar-alpha WT, biological rep2

value: Adrenal

value: male

value: 12 weeks

value: Rar-alpha WT mice


title: diploid grass (TA) embryo sample taken at leaf early stage TA14

value: leaf early


title: diploid grass (TA) embryo sample taken at transition stage TA13


title: Adrenal_WT1_12weeks: 12 weeks old mice, Rar-alpha WT, biological rep1


title: diploid grass (DV92) endorsperm sample taken at transition stage endorsperm  DV-8

source_name: early endorsperm

value: endorsperm

value: early endorsperm


title: RA42

source_name: RA patient 5

value: Rheumatoid Arthritis

value: F

value: Negative


title: diploid grass (DV92) embryo sample taken at mature stage DV-7

source_name: mature

value: diploid grass (DV92, A genome)

value: embryo

value: mature


title: diploid grass (SP) embryo sample taken at transition stage SP13

value: transition


title: RA41

source_name: RA patient 4


title: diploid grass (SP) embryo sample taken at preembryo stage SP12

value: preembryo


title: diploid grass (SP) embryo sample taken at two cell stage SP11

source_name: two cell

value: diploid grass (TA2780, B genome)

value: two cell


title: diploid grass (DV92) embryo sample taken at leaf late stage DV-6

source_name: leaf late

value: leaf late


title: diploid grass (TA) embryo sample taken at two cell stage TA11_2

value: diploid grass (TA101132, D genome)


title: RA39

source_name: RA patient 2

value: Positive


title: diploid grass (DV92) embryo sample taken at leaf middle stage DV-5

value: leaf middle


title: diploid grass (TA) seed coat sample taken at leaf early stage pericarp TA10_2

value: SC (Pericarp)


title: RA40

source_name: RA patient 3


title: diploid grass (TA) embryo sample taken at two cell stage TA11


title: diploid grass (DV92) embryo sample taken at leaf early stage DV-4

source_name: leaf early

value: leaf early


title: RA36

source_name: RA patient 1


title: diploid grass (SP) seed coat sample taken at leaf early stage pericarp SP10

source_name: SC (Pericarp)


title: diploid grass (TA) seed coat sample taken at leaf early stage pericarp TA10


title: RA28

source_name: control sample 8

value: control


title: diploid grass (DV92) embryo sample taken at transition stage DV-3


title: diploid grass (SP) endorsperm sample taken at transition stage endorsperm SP8

value: endorsperm

value: early endorsperm


title: diploid grass (TA) endorsperm sample taken at leaf  late stage endorsperm  TA9

source_name: late endorsperm

value: late endorsperm


title: diploid grass (DV92) embryo sample taken at preembryo stage DV-2

value: diploid grass (DV92, A genome)


title: RA43

source_name: RA patient 6

value: Rheumatoid Arthritis

value: M

value: Negative


title: diploid grass (DV92) endorsperm sample taken at leaf late stage endorsperm DV-9


title: diploid grass (SP) embryo sample taken at leaf early stage SP14

value: embryo


title: diploid grass (TA) endorsperm sample taken at transition stage endorsperm TA8


title: diploid grass (SP) embryo sample taken at mature stage SP7

value: diploid grass (TA2780, B genome)

value: mature


title: RA27

source_name: control sample 7

value: F


title: diploid grass (SP) embryo sample taken at leaf late stage SP6

value: leaf late


title: RA13

source_name: control sample 4


title: RA11

source_name: control sample 2


title: RA14

source_name: control sample 5


title: diploid grass (SP) embryo sample taken at preembryo stage SP2

source_name: preembryo

value: preembryo


title: control rep3

city: beirut

first: Ilham

middle: Hassan

last: Salman

address: Hadath

country: Lebanon

institute: Lebanese university

data_processing:
Illumina-NovaSeq 6000 System User Guide Document # 1000000019358 v02
reads were trimmed and clipped for quality control in Trimmomatic 0.38 .Trimmed reads are mapped to reference genome with Bowtie 1.2.2
After the read mapping, HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.
Read quality was checked for each sample using FastQC v0.10.1.
Genome_build: ASM284822v1 (GCF_002848225.1)
Supplementary_files_format_and_content: counts generated by Htseq analysis

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: mid-log growth OD=0.6

extract_protocol:
Methods:total RNA was extracted by bacteria protect-Rneasy Kit (qiagen) and treated by DNAase.
Library was constracted using Ribo-Zero rRNA Removal Kit (Bacteria) and  TruSeq RNA Sample Prep.
Esherchia coli DH5α Transcriptomes were generated by sequencing using  NovaSeq 6000, Illumina.

treatment_protocol: Exposure to Wi-Fi radiofrequency 2.4 GHz using a router connected to a monopole antena

tag: conditon

value: mid-log growth


title: diploid grass (TA) embryo sample taken at leaf middle stage TA5

source_name: leaf middle

value: diploid grass (TA101132, D genome)

value: leaf middle


title: exposed rep2

value: 5 hours Wi-Fi exposure


title: RA26

source_name: control sample 6

value: control

value: Borderline


title: diploid grass (SP) embryo sample taken at transition stage SP3

source_name: transition

value: transition


title: diploid grass (SP) embryo sample taken at leaf early stage SP4

value: leaf early


title: diploid grass (SP) embryo sample taken at two cell stage SP1

source_name: two cell

value: two cell


title: RA10

source_name: control sample 1


title: diploid grass (TA) embryo sample taken at leaf late stage TA6

source_name: leaf late


title: diploid grass (SP) endorsperm sample taken at leaf late stage endorsperm SP9

value: endorsperm

value: late endorsperm


title: exposed rep3


title: diploid grass (TA) embryo sample taken at leaf early stage TA4

source_name: leaf early

value: embryo


title: diploid grass (TA) embryo sample taken at mature stage TA7

source_name: mature


title: diploid grass (SP) embryo sample taken at leaf middle stage SP5

value: diploid grass (TA2780, B genome)


title: exposed rep1


title: control rep1


title: diploid grass (TA) embryo sample taken at two cell stage TA1


title: diploid grass (TA) embryo sample taken at transition stage TA3


title: unmatched reads from human donors AF and SR

status: Public on Oct 20 2019

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

description: Unmatched reads from multiple samples either mock transfected or transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

data_processing:
Samples sequenced on SN387 with HiSeq Rapid SBS Kit v2. Image analysis and base-calling was performed with RTA version 1.18.64.0.
Barcode splitting performed in Galaxy with 1 mismatch allowed unless otherwise stated in the Samples, column Special notes. Short reads were aligned to the human or the originating species’ genomes using RNA STAR  (Galaxy version 2.6.0b-1) with default parameters. Counts were generated using featureCounts with default settings (Galaxy version 1.6.3+galaxy2), downloaded, and read into R version 3.5.2 (2018-12-20) using scripts run in RStudio version 1.1.463.
htseq-count Gene counts analyzed further with DESeq2 (version 1.22.2) (Love MI, Huber W and Anders S (2014) “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi: 10.1186/s13059-014-0550-8) in RStudio (R version 3.3.3.), using two factors (donor + treatment)  as the experimental design.
genome build
Each species was aligned to human and its specific reference genome except for human (which was only aligned to the human genome) and mouse (which was only aligned to the mouse genome).
Species
Orangutan: ppyg2 (Ensembl 93)
Gorilla:  gorGor4 (Ensembl 95)
Pigtailed macaque : Mnem_1.0 (Ensembl 95)
Rhesus macaque: Mmul_8_0_1 (Ensembl 95)
Bonobo: panpan1.1 (Ensembl 95)
Chimpanzee: Pan_tro_3.0 (Ensembl 95)
Olive baboon: papAnu2 (Ensembl 95)
Squirrel monkey: SaiBol1.0 (Ensembl 95)
Human: GRCh38 (Ensembl 96)
Mouse: GRCm38 (Ensembl 85)
processed data files format and content: all tab-delimited text files of htseq-count "Gene counts" :

source_name: Dermal fibroblasts

growth_protocol: All cells were grown under standard conditions in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum (FBS) and 1% v/v penicillin/streptomycin.

extract_protocol:
Total RNA extracted using Qiagen Rneasy Mini Kit per manufacturer's directions.
The integrity of total RNA from the primate samples were assessed on Bioanalyzer 2100 using RNA 6000 Nano chip (Agilent Technologies, CA), only samples with RNA Integrity Number (RIN) greater than 9.0 were used for RNA-seq.  One microgram of total RNA from each sample was subject to poly-A containing RNA enrichment by oligo-dT bead and converted to cDNA then sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Wafergen Biosystems, CA) according to the manufacturer's protocol.  Different DNA barcodes were added to each library.  The libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA).  The RNA-seq libraries were pooled at equal molar amount and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75nt reads following the standard protocol.  Raw sequencing reads were filtered by Illumina HiSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: Cells were seeded the night before transfection with 200,000 cells/well in a 6 well format so that at the time of transfection they were at least 80% confluent. Each well received 0.5 ug high molecular weight poly(I:C) using using X-tremegene HP DNA transfection reagent in Opti-MEM.

tag: cell type

value: primary dermal fibroblasts

value: 24 h transfection 0.05 ug/cm2 poly(I:C) and 24 h mock transfected

tag: passage


title: RA12

source_name: control sample 3

value: F

value: Negative


title: human donor NHDF mock C

description: Cells mock transfected in triplicate in a 6 well format for 24 h

value: 24 h mock transfected


title: control rep2

value: mid-log growth


title: human donor NHDF mock A


title: human donor NHDF treated C

description: Cells transfected in triplicate in a 6 well format for 24 h with 0.5 ug poly(I:C) (~0.05 ug/cm2) per well

value: 24 h transfection 0.05 ug/cm2 poly(I:C)


title: human donor NHDF treated B


title: human donor SR mock 1


title: human donor SR mock 3


title: human donor SR mock 2


title: human donor SR treated 3


title: human donor NHDF treated A


title: human donor SR treated 2