title: N2_sRNA_P2_14

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Raw sequencing basecalls were demultiplexed and converted to FASTQ format using bcl2fastq v2.18.0.12 using the parameters --no-lane-splitting --mask-short-adapter-reads=10 without  specifying adapter sequences in the sample sheet CSV file.
Reads 2 were annotated with their corresponding (corrected) barcode and UMI sequences (read 1) using custom scripts.
Reads with identical barcode, UMI and sequence were collapsed and the unique reads were assigned to per-slice FASTQ files by barcode.
Small RNA reads were subject to two rounds of 3’ end trimming by flexbar v. 2.5 using the  --pre-trim-phred=30 option: first removing 3’ adapters (TGGAATTCTCGGGTGCCAAGG) and then using 10 A's as ‘adapter sequence’.
The 3 nucleotides 5’ overhang introduced by the template-switching polymerase were trimmed using a custom awk script also discarding reads with a remaining length < 18 nts.
RNA-seq reads were mapped to the ce11/WBcel235 genome assembly using STAR_2.5.1b and an index with splice junction information from the Ensembl 82 transcriptome annotation.
Alignments were sorted using sambamba v0.4.7.
Coverage tracks were generated using bedtools v2.23.0 via the genomecov command specifying the -split, -bg and -strand parameters.
The total number of mapped reads per sample/splice was determined using the flagstat command of samtools 0.1.19-96b5f2294a and converted to the corresponding -scale parameter for bedtools genomecov for reads-per-million-mapped (RPM) normalization.
Coverage BedGraph files were converted to BigWig format using bedGraphToBigWig v 4.
Downstream coverage peaks for 3’ extension of the WS260 transcriptome were idenified using a custom R script: For each protein coding gene, the intergenic distance to the next downstream protein coding, ncRNA, lincRNA, pseudogene, rRNA or snoRNA gene (on the same strand) was calculated. Intergenic regions longer than 10 kb were truncated and the RPM-scaled genome coverage per sample of those regions was extracted from the BigWig files generated before. The per-sample coverage vectors were averaged per genomic position and binarized into uncovered regions (< 5 RPM mean coverage) and covered regions (>= 5 RPM mean coverage). Covered regions with a length of >= 50 nucleotides were considered as coverage peaks. Per downstream intergenic region, the downstream-most coverage peak was selected for the 3’ extension of the corresponding upstream gene. Only downstream extensions with a length up to 3 kb were considered for downstream analyses. For each gene with a downstream extension, all annotated transcript isoforms extending to the 3’ most genomic position of the corresponding gene were kept and got their 3’ UTRs extended by until the 3’ position of the respective downstream peak. Those 3’ extended transcripts were exported to a GTF file and merged with the WS260 transcriptome annotation using custom awk scripts.
To enable the assignment of 3’ end RNA-seq reads to transcript isoforms, the 3’ extended WS260 transcriptome annotation was pre-processed using a series of custom R scripts: 3’ A’s were trimmed from all annotated transcripts as they would be indistinguishable from poly(A)-tails. The resulting transcripts were truncated to the 3’ most 500 nucleotides. Transcript isoforms with the same genomic coordinates and internal structure were collapsed and enumerated by decreasing corresponding (max.) 3’ UTR length.
RNA-seq reads were assigned to transcripts using kallisto 0.43.1: For 3’ reads, an index of the collapsed transcriptome annotation described above was used. For full-length coverage reads (poly(A)+ and ribodepleted total RNA-seq libraries), an index of the full 3’ extended transcriptome annotation was used. For all libraries, the --bias and --plaintext flags were passed to kallisto quant. For single end reads, additionally the --single, --fragment-length=1 and --sd=1 options were used. Poly(A)+ and ribodepleted total RNA-seq samples were analyzed in --rf-stranded mode.  3’ reads were presented to kallisto as single-end reads using  the --fr-stranded mode of kallisto quant.
Transcripts not annotated as protein coding were discarded.
For gene-level analyses, isoform-level read counts were summed across all isoforms.
Raw read counts were normalized to counts-per-million (CPM) for CEL-Seq1/2 samples and transcripts-per-million (TPM) for poly(A)+ and ribodepleted total RNA-seq samples.
Small RNA libraries were mapped to the E.coli genome (NC_000913.3, K-12, MG1655) with bowtie2 (version 2.3.3.1) using the parameters --very-fast-local --phred33 --local keeping unmapped reads (--un option).
The cleaned-up libraries were pooled.
MiRDeep2 (version 2.0.0.7) was ran on the pooled libraries with the miRBase21 reference.
The novel miRNA predictions found were added to the miRBase21 reference.
The combined reference of known and novel miRNAs was used for a second run of miRDeep2 on each library separately and on the pooled library as well to obtain CPM estimates.
Slice-data were arranged from distal to proximal by the known order of their barcodes and assigned to a relative position scale representing each slice by its center and accounting for differences in the number of slices per sample.
The replicates were aligned by adding the corresponding sample shift to the distal-to-proximal position of each slice.
Genome_build: ce11/WBcel235
Supplementary_files_format_and_content: All processed data files are tab-separated values (TSV) formatted text files with the first six columns following the BED6 format specifications defining the genomic coordinates (0-based, end-exclusive) of the quantified feature, identifying it by name and scoring it by the estimated abundance. The remaining columns contain further information about the corresponding measurement. All files start with a single header line (beginning with a #) naming the columns. The processed data file mRNA_bulk.tsv.gz contains isoform-level abundance estimates from RNAse H + Illumina stranded total RNA and Illumina stranded poly(A) selected libraries as well as CEL-Seq1/2 libraries before barcode assignment (i.e. incl. non-assignable reads). The file contains the following columns: 1. gene_contig: UCSC-style name of the chromosome/contig the gene is transcribed from; 2. transcript_start: start coordinate (0-based, inclusive) of the transcript; 3. transcript_end: end coordinated (0-based, exclusive) of the transcript; 4. transcript_id: ID of the transcript - for full length transcripts the Ensembl transcript name followed by ‘_3utr’ and the 3’ UTR length in nucleotides, ‘_’, the number of As clipped from the 3’ end and ‘_A3p_clipped’, for truncated & collapsed transcripts the Ensembl gene name followed by ‘_3p500.’ and the isoform index (1-based) sorted by (max.) 3’ UTR length in descending order; 5. abundance_0_to_1000: 60 * log2(CPM/TPM) censored at 1 and 1,000 for transcripts with reads assigned, 0 otherwise; 6. gene_strand: strand (+/-) the gene is transcribed from; 7. transcript_biotype: Ensembl biotype of the transcript; 8. gene_id: Ensembl/WormBase gene ID; 9. gene_name: Ensembl gene name; 10. gene_biotype: Ensembl biotype of the gene; 11. sample_name: name of the sample the abundance was estimated for; 12. genotype: genotype (N2/gld-2 gld-1/glp-1) of the sample; 13. gonad_arm: gonad arm (anterior/posterior) the sample was obtained from; 14. protocol: protocol (RNAse H + Illumina stranded total RNA/Illumina stranded poly(A) selected/CEL-Seq1/2) the sample was subject to; 15. read_count: number of reads assigned to the transcript; 16. cpm_tpm: library size normalized abundance estimate - for full length transcripts transcripts per million (TPM), for truncated & collapsed transcript counts per million mapped reads (CPM).  The processed data file mRNA_slices.tsv.gz contains isoform-level abundance estimates for CEL-Seq1/2 libraries per assigned barcode (i.e. excl. non-assignable reads). The file contains the f

source_name: posterior gonad arm

extract_protocol:
Gonads were dissected, embedded, flash frozen at -80 °C and cyro-sectioned at 50 µm resolution. RNA from each slice was extracted using Trizol reagent.  CEL-Seq1/2 was used for library construction mRNA transcriptome and SMARTer small RNA-Seq was used for library construction of small RNA transcriptome using all the extracted RNA as input.
mRNA lbraries were prepared for sequencing using the CEL-Seq1/2 protocol (Hashimshony et al., 2012; Hashimshony et al., 2016). sRNA libraries were prepared for sequencing using the SMARTer small RNA-Seq according to manufacturers instructions. Poly(A)+-selected RNA libraries and total RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: wild type

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: N2_sRNA_P2_13

status: Public on Nov 15 2018

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Caenorhabditis elegans

tag: genotype

tag: tissue

tag: Sex

tag: age


title: N2_sRNA_P2_12


title: Ca922

city: Houston

first: Curtis

last: Pickering

state: TX

address: 1515 Holcombe Blvd

department: Head and Neck Surgery

country: USA

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Alignment was performed using tophat2
Aligment quality was accessed by fastqc, samtools and htseq-qa
Counting reads was using htseq-count with parameters: python -m HTSeq.scripts.count -s no -t exon sortByName.sam.mod REFFILE > OUTFILE
The normalization of raw read counts was performed by edgeR package in R. The procedure was described in limma package in R. The features were first filtered out if the total counts less than 50
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.

organism: Homo sapiens

extract_protocol:
RNeasy Plus (Qiagen)
TruSeq Stranded Total RNA Sample Prep Kit (Illumina); 75-bp paired-end (Illumina HiSeq3000)

tag: cell line

tag: cell type

value: head and neck squamous cell carcinoma (HNSCC) cell line


title: gIR_vs_mock_DREMmodel_wt_rep1_1h30min_+y

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: mRNA-seq reads were mapped to TAIR10 reference genome using STAR (v2.5.0c) allowing 2 mismatches.
UCSC browser tracks (bedGraph files) were generated using the Homer suite of NGS tools and normalized to a million (1e7) reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: 6 day-old Seedlings

growth_protocol: Arabidopsis seedlings used in this study were in the Columbia-0 (Col) ecotype for the wt and in a mixed Landsberg erecta (Ler)/Col background containing a CYCB1;1promoter::GUS fusion for the sog1-1 mutant. Seedlings were grown under constqnt light at 23°C in a Percival growth cabinet.

extract_protocol:
8 seedlings were collected and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) for mRNA purification and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.

treatment_protocol: 100 Gy using a Co60 radioactive source at a dose-rate of 10 Gy/min

value: wild-type

tag: treatment

value: 100 Gy Gamma-IR

tag: time after ir


title: N2_sRNA_P2_11


title: LIN-41_IP_1

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description: 671F7-1_151210_D00404_0198_BC8154ANXX_CGATGT-NoIndex_L004

data_processing:
Basecalling was performed using RTA v. 1.13.48.
PCR duplicates were removed by collapsing reads with an identical 5’ end coordinate to a single read using the SAMtools rmdup command.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from WormBase. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (WormBase identifiers), following columns contain raw counts of reads overlapping each gene for each sample, after removing duplicate reads.

growth_protocol: Embryos were extracted from gravid adults with bleaching solution (30% (v/v) sodium hypochlorite (5% chlorine) reagent, 750 mM KOH) and plated on enriched peptone plates with Escherichia coli NA22 bacteria. The plates were incubated at 25 °C for approximately 30 hours to harvest the resulting semi-synchronous worm populations.

extract_protocol:
Lysis of pellets of about 1 ml with L3/L4 stage worms was performed in extraction buffer (50 mM HEPES/KOH (pH 7.4 at 4 °C), 150 mM KCl, 5 mM MgCl2, 0.1% (v/v) Triton X-100, 10% (w/v) glycerol, 1 mM PMSF, 7 mg/ml cOmplete Protease Inhibitor Tablets (EDTA-free), 200 U/ml SUPERase In RNase Inhibitor), by adding liquid nitrogen and grinding with mortar and pestle. All subsequent steps were performed at 4 °C. Lysates were centrifuged at 12,000g for 10 min and the supernatant used for Anti-FLAG IPs. 3 mg total protein were incubated with 30 µl of anti-FLAG M2 magnetic beads (Sigma–Aldrich; M8823) for 3 h on a rotating wheel. With extraction buffer without protease and RNase inhibitors, the beads were washed 5 times for 5 min. Finally, the bound RNA was extracted by directly adding Tri Reagent to the beads. 5 IPs were performed in parallel for each condition to recover a sufficient amount of RNA. Using an aliquot of remaining input lysate, input RNA was extracted with Tri Reagent.
TruSeq Stranded mRNA HT Sample Prep Kit (Illumina; RS 122 2103)

treatment_protocol: Worms were washed off the plates and subsequently washed 3 additional times with M9 buffer (42 mM Na2HPO4, 22 mM KH2PO4, 86 mM NaCl, 1 mM MgSO4) and worm pellets frozen at -80 °C.

tag: developmental stage

value: L3/L4 stage animals

tag: genotype/variation

value: whole worm

tag: rip anitbody


title: gIR_vs_mock_DREMmodel_wt_rep2_6h_+y


title: N2_sRNA_P2_10

tag: strain

tag: replicate index


title: UMSCC10A


title: t_vs_t0_wt_rep1_0

extract_protocol:
10 seedlings were collected and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) for mRNA purification and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.

value: mock


title: gIR_vs_mock_DREMmodel_wt_rep1_3h_+y


title: N2_sRNA_P2_9

tag: slice indices

tag: slice barcodes


title: gIR_vs_mock_DREMmodel_wt_rep1_6h_+y


title: N2_sRNA_P2_8

tag: replicate alignment shift [%]

tag: molecule


title: IP_wt_1h

library_source: genomic

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: ChIP sequencing data were aligned to TAIR10 reference genome using bowtie2 allowing 2 mismatches (-v 2).
UCSC browser tracks (bedGraph files) were generated using the Homer suite of NGS tools and normalized to a million (1e7) reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: genomic DNA

source_name: 10 day-old Seedlings

growth_protocol: The Arabidopsis seedlings used in this study were in the Columbia-0 (Col) ecotype and were grown under constant light at 23°C in a Percival growth cabinet.

extract_protocol:
1.3g of 10 day-old seedlings were collected and and ground to a fine powder in liquid nitrogen and crosslinked in 1.5mM EGS for 20min at room temperature then with 1% formaldehyde (Sigma, Cat# F8775) for 10min at room temperature with slow rotation. The chromatin was then fragmented to ~500bp by sonication and the lysate was incubated with the anti-Flag M2 Magnetic beads (Sigma, Cat# M8823) at 4°C for 2h. The beads were washed 5 times, for 5min at 4°C and then the crosslinking was reversed by incubation at 65°C overnight and further purified using the phenol:Chloroform:Isoamyl Alcohol (Thermo scientific, Cat# 17908).
DNA from the ChIP experiments was used for library preparation with NEBNext Ultra II DNA Library Prep Kit (NEB, Cat# 7645). The ChIP libraries were sequenced in SE50 mode on a HiSeq2500 machine.

treatment_protocol: 75 Gy using a Co60 radioactive source at a dose-rate of 3.75 Gy/min

tag: genotype

value: 75 Gy Gamma-IR

tag: antibody

value: anti-Flag M2


title: gIR_vs_mock_DREMmodel_wt_rep1_20min_+y


title: P14 MNTB Litter #5

type: RNA

city: Morgantown

first: George

last: Spirou

state: WV

address: One Medical Center Drive

department: Otolaryngology

institute: West Virginia University

description: Wild-type FVB single mouse

hyb_protocol: Samples were hybridized to mouse GeneChip 1.0 ST Exon Arrays (Affymetrix) using a GeneChip Hybridization Oven 640 (Affymetrix) according to manufacturer’s instruction.

scan_protocol: Array scanning was performed with GeneChip Scanner 3000 G7 Plus (Affymetrix) according to the manufacturer's instruction (Affymetrix).

data_processing:
The microarray data were normalized using Partek Genomics Suite software version 6.3 with GC pre-background adjustment, RMA background normalization, and quantile normalization between samples. Our analysis was limited to the gene level and only used the core probes supported by RefSeq transcripts or full-length mRNAs. After removing genes whose expression levels from all samples were within the lowest 25% and very close to background levels, we used Significance Analysis of Microarrays (SAM) to identify the genes showing differential expression at any stage(s) from P0 to P6. With a one-way analysis of variance and a false discovery rate (FDR) of 0.1%, we achieved a list of 541 differentially expressed genes (DEGs) between the ages from P0 to P6. P14 data was only used for clustering and profile analysis.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps
Normalized signal intensity values from Partek Genomics Suite software version 6.3 with GC pre-background adjustment, RMA background normalization, and quantile normalization between samples. We then removed 25% of the genes with the lowest average expression levels.

label: biotin

organism: Mus musculus

source_name: P14 MNTB brain tissue

label_protocol: 5 μg of the amplified cDNA was used as a template to create sense strand cDNA with the WT-Ovation Exon Module (NuGEN). This was followed by fragmentation and biotin-labeling using the FL-Ovation cDNA Biotin Module V2 (NuGEN).

growth_protocol: The MNTB regions within the live mouse brain slice were carefully removed using a 26-gauge needle under a dissecting scope to obtain an enriched population of MNTB cells at various developmental ages.

extract_protocol: The dissected tissue was transferred directly into lysis solution (Stratagene, La Jolla, CA) and frozen at −80°C. The RNA extraction was performed using the Absolutely RNA Nanoprep kit (Stratagene) according to manufacturer's instructions. An Agilent 2100 Bioanalyzer (Santa Clara, CA) was used to measure the concentration and assess the quality of the RNA with a minimum RNA integrity number (RIN) value of 5.0 being acceptable for further analysis. RNA obtained in the previous steps was amplified using the WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, San Carlos, CA).

tag: tissue

value: medial nucleus of the trapezoid body

value: Postnatal day 14

value: FVN


title: N2_sRNA_P2_7

value: wild type

tag: Sex

tag: age

tag: protocol


title: N2_sRNA_P2_6

value: gonad


title: IP_SOG1-3xFLAG_1h

tag: treatment


title: IP_SOG1-3xFLAG_20min

tag: time after ir


title: gIR_vs_mock_DREMmodel_wt_rep2_20min_+y


title: N2_sRNA_P2_5

value: hermaphrodite


title: input_SOG1-3xFLAG_1h


title: P6 MNTB Litter #5

description: Wild-type FVB single mouse

source_name: P6 MNTB brain tissue

value: Postnatal day 6


title: MDA1686

tag: cell line

tag: cell type


title: N2_sRNA_P2_4

value: young adults

value: small RNA


title: IP_wt_20min


title: P6 MNTB Litter #4

description: Wild-type FVB single mouse


title: input_SOG1-3xFLAG_20min


title: P14 MNTB Litter #3

description: Wild-type FVB single mouse


title: P6 MNTB Litter #3

description: Wild-type FVB single mouse


title: P6 MNTB Litter #2

description: Wild-type FVB single mouse


title: P4 MNTB Litter #1

description: Wild-type FVB single mouse

source_name: P4 MNTB brain tissue

value: Postnatal day 4


title: P4 MNTB Litter #3

description: Wild-type FVB single mouse


title: P4 MNTB Litter #2

description: Wild-type FVB single mouse


title: P3 MNTB Litter #5

description: Wild-type FVB single mouse

source_name: P3 MNTB brain tissue

value: Postnatal day 3


title: P6 MNTB Litter #1

description: Wild-type FVB single mouse


title: N2_sRNA_P2_2

value: SMARTer small RNA-Seq


title: P14 MNTB Litter #2

description: Wild-type FVB single mouse


title: P3 MNTB Litter #3

description: Wild-type FVB single mouse


title: P3 MNTB Litter #4

description: Wild-type FVB single mouse


title: P14 MNTB Litter #1

description: Wild-type FVB single mouse


title: P4 MNTB Litter #5

description: Wild-type FVB single mouse


title: P3 MNTB Litter #2

description: Wild-type FVB single mouse


title: P3 MNTB Litter #1

description: Wild-type FVB single mouse


title: N2_sRNA_P2_3


title: P2 MNTB Litter #4

description: Wild-type FVB single mouse

source_name: P2 MNTB brain tissue

value: Postnatal day 2


title: N2_sRNA_P1_12


title: N2_sRNA_P1_13


title: P2 MNTB Litter #3

description: Wild-type FVB single mouse


title: P2 MNTB Litter #2

description: Wild-type FVB single mouse


title: P2 MNTB Litter #5

description: Wild-type FVB single mouse


title: N2_sRNA_P1_11


title: P1 MNTB Litter #5

description: Wild-type FVB single mouse

source_name: P1 MNTB brain tissue

value: Postnatal day 1


title: N2_sRNA_P2_1


title: N2_sRNA_P1_9


title: N2_sRNA_P1_8


title: N2_sRNA_P1_10


title: P2 MNTB Litter #1

description: Wild-type FVB single mouse


title: N2_sRNA_P1_7


title: N2_sRNA_P1_6


title: P1 MNTB Litter #1

description: Wild-type FVB single mouse


title: P0 MNTB Litter #1

description: Wild-type FVB single mouse

source_name: P0 MNTB brain tissue

value: Postnatal day 0


title: N2_sRNA_P1_5


title: P1 MNTB Litter #4

description: Wild-type FVB single mouse


title: P0 MNTB Litter #5

description: Wild-type FVB single mouse


title: P0 MNTB Litter #2

description: Wild-type FVB single mouse


title: P1 MNTB Litter #2

description: Wild-type FVB single mouse


title: P0 MNTB Litter #4

description: Wild-type FVB single mouse


title: N2_sRNA_P1_3


title: N2_sRNA_P1_4


title: N2_sRNA_P1_1


title: N2_sRNA_A3_14

source_name: anterior gonad arm


title: N2_sRNA_P1_2


title: N2_sRNA_A3_13


title: Non-Infected, 20-TNT, Rep 6

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: Western Fence Lizard

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array: AMADID 028809) was used for transcript expression assays (Agilent Technologies). The Agilent One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 500 ng of total RNA was used as the starting material for each exposure replicate. At least 4 replicate liver samples (most treatments included 6 replicates) collected from individual lizards per experimental condition were hybridized to microarrays in a completely randomized design using a random number generator. Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

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

data_processing: Data were extracted using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies). Internal control spots were analyzed to confirm that signal data was within the linear range of detection. GeneSpring version GX 11.0.2 (Agilent Technologies) was used to normalize data using quantile normalization followed by baseline transformation to the median of all samples. Statistical analysis was performed using GeneSpring where two-way ANOVA (p ≤ 0.05) with Benjamini-Hochberg multiple-testing correction and 1.5 fold-change cutoff was used to identify differentially expressed transcripts.

organism: Sceloporus occidentalis

source_name: liver tissue

label_protocol: The Agilent One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations and 500 ng of total RNA extracted from liver tissues in each individual lizard replicate.

growth_protocol: The original laboratory colony of WFLs was established from lizards collected from the San Joaquin Valley in Fresno and Tulare Counties, California. Lizards for this study were males obtained from generations F4 and F5. Within 24 h after hatching, lizards were housed 10–15 per cage on corncob substrate in 74.2 l glass aquaria that were covered with a 3-mm steel mesh lid. Heat and light were provided by a 40-W incandescent light bulb positioned over one end of each cage to permit thermoregulation across an approximate temperature gradient of 26–40 C. Ambient room temperature was maintained at approximately 22 C along with a 14:10 h light:dark light cycle. Lizards were provided with a water source and fed daily with house crickets (Acheta domesticus) that were fed a mixture consisting of ground poultry laying pellets, Herptivite, and Rep-Cal (Rep-Cal Research Labs, Los Gatos, CA, USA). At 6 months of age, male lizards were randomly separated into groups for the different phases of the study.

extract_protocol: At the completion of the exposures, animals were euthanized by CO2 asphyxia, and dissected. Liver tissues were fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations and stored at -80°C until RNA extraction. RNA extraction was conducted using RNeasy Mini RNA extraction kits (Qiagen Inc., Valencia, CA). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® RNA. Only samples with a 28s/18s ratio ≥2.0 and RNA integrity number (RIN) ≥7.0 were used for downstream applications.

treatment_protocol: Exposure 3 - TNT x malaria infection: The study incorporated a factorial treatment arrangement within a completely randomized experimental design. The Western fence lizards were inoculated with lizard malaria or vehicle control (see McFarland et al. 2012 for methods) and then dosed by daily gavage to TNT at 0 (control), 5, 10 and 20 mg/kg/d. The lizards were fed ad libitum feeding (10 crickets/day) through the course of the experiment. All treatments included 10 biological replicates (10 individually caged lizards) per condition.

value: Liver

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection

value: Non-Infected

value: 20 mg/kg/d TNT


title: P0 MNTB Litter #3

description: Wild-type FVB single mouse

value: medial nucleus of the trapezoid body

tag: strain

value: FVN


title: Non-Infected, 20-TNT, Rep 4

description: Western Fence Lizard


title: N2_sRNA_A3_11

value: wild type

value: gonad

value: hermaphrodite

tag: replicate index

tag: slice indices

tag: slice barcodes


title: N2_sRNA_A3_10

tag: genotype

value: young adults

tag: replicate alignment shift [%]

tag: molecule

value: small RNA


title: Non-Infected, 20-TNT, Rep 5

description: Western Fence Lizard

tag: tissue


title: Non-Infected, 20-TNT, Rep 2

description: Western Fence Lizard

tag: age


title: Non-Infected, 20-TNT, Rep 3

description: Western Fence Lizard


title: Non-Infected, 10-TNT, Rep 4

description: Western Fence Lizard

value: 10 mg/kg/d TNT


title: Non-Infected, 10-TNT, Rep 5

description: Western Fence Lizard


title: N2_sRNA_A3_12

tag: Sex

tag: protocol

value: SMARTer small RNA-Seq


title: Non-Infected, 20-TNT, Rep 1

description: Western Fence Lizard

tag: treatment


title: Non-Infected, 10-TNT, Rep 3

description: Western Fence Lizard


title: N2_sRNA_A3_9


title: N2_sRNA_A3_7


title: Non-Infected, 10-TNT, Rep 1

description: Western Fence Lizard


title: N2_sRNA_A3_6


title: Non-Infected, 10-TNT, Rep 2

description: Western Fence Lizard


title: N2_sRNA_A3_5


title: Non-Infected, 5-TNT, Rep 4

description: Western Fence Lizard

value: 5 mg/kg/d TNT


title: Non-Infected, 5-TNT, Rep 5

description: Western Fence Lizard


title: N2_sRNA_A3_8


title: TNBC-51

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: Resected Triple negative breast cancer

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes while the smaller fragmented FFPE-derived DNA samples were digested for only 1 minute. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [22]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Tumor samples from patients with triple negative breast cancer were flash-frozen and maintained at -80 degrees C

extract_protocol: Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

tag: Stage

value: IIIb

tag: grade

tag: t n

value: T4d N1

source_name: Reference pooled 46XX

tag: reference

value: Normal female genome


title: Non-Infected, 5-TNT, Rep 2

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection


title: Non-Infected, 5-TNT, Rep 6

description: Western Fence Lizard

value: Non-Infected


title: TNBC-55

value: PD-1 2/PD-L1 4 Non tumor

value: IIIA

value: T3 N1


title: N2_sRNA_A3_3

tag: strain

value: wild type

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes


title: Non-Infected, 5-TNT, Rep 3

description: Western Fence Lizard

tag: tissue

value: 5 mg/kg/d TNT


title: TNBC-52

value: Triple negative breast cancer

value: PD-1 2/PD-L1 3 Tumor+Non tumor

value: T1c N0


title: TNBC-47

value: PD-1 2/PD-L1 2 Non tumor

value: T2 NX

value: Normal female genome


title: TNBC-53

value: PD-1 3/PD-L1 3 Non tumor

value: T4d N2


title: TNBC-54

value: PD-1 2/PD-L1 2 Tumor+Non tumor

value: T2 N1


title: N2_sRNA_A3_4

tag: genotype

tag: age

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

value: SMARTer small RNA-Seq


title: Non-Infected, 5-TNT, Rep 1

description: Western Fence Lizard

value: Liver

value: Male

value: Adult

value: ad libitum

value: Non-Infected

tag: treatment


title: N2_sRNA_A3_2

value: wild type

value: gonad

tag: Sex

value: hermaphrodite

value: young adults

tag: protocol


title: Non-Infected, 0-TNT, Rep 3

description: Western Fence Lizard

value: 0 mg/kg/d TNT


title: TNBC-42

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 2/PD-L1 2 Non tumor

tag: grade

tag: t n

value: T1c N0

value: Normal female genome


title: TNBC-50

value: PD-1 1/PD-L1 4 Tumor+Non tumor

tag: Stage

value: Ia

value: T1b N0

tag: reference


title: TNBC-44

value: PD-1 3/PD-L1 4 Tumor

value: T1c N2


title: TNBC-49

value: PD-1 3/PD-L1 2 Non tumor

value: T1b NX


title: TNBC-41

value: PD-1 2/PD-L1 2 Tumor+Non tumor

value: T2 N0


title: N2_sRNA_A2_14

tag: strain

value: wild type

value: gonad

value: small RNA

value: SMARTer small RNA-Seq


title: Non-Infected, 0-TNT, Rep 5

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection

value: Non-Infected

value: 0 mg/kg/d TNT


title: Non-Infected, 0-TNT, Rep 2

description: Western Fence Lizard

tag: tissue


title: TNBC-43

value: Triple negative breast cancer

value: PD-1 2/PD-L1 3 Tumor+Non tumor

value: T1c N0

value: Normal female genome


title: TNBC-39

value: PD-1 2/PD-L1 2Tumor+Non tumor


title: TNBC-38

value: PD-1 2/PD-L1 2 Tumor+Non tumor


title: TNBC-40

value: PD-1 3/PD-L1 4 Non tumor

value: Ia


title: TNBC-45


title: N2_sRNA_A2_11

tag: genotype

value: wild type

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes


title: Non-Infected, 0-TNT, Rep 1

description: Western Fence Lizard

value: Liver

value: Male

tag: age

tag: treatment


title: N2_sRNA_A3_1

tag: Sex

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: TNBC-36

tag: pd-1/pd-l1 expression

value: PD-1 3/PD-L1 3 Tumor+Non tumor

tag: grade

tag: t n

value: T3 N0


title: Non-Infected, 0-TNT, Rep 4

description: Western Fence Lizard

tag: gender

value: Adult

value: ad libitum

value: Non-Infected

value: 0 mg/kg/d TNT


title: P1 MNTB Litter #3

description: Wild-type FVB single mouse

value: medial nucleus of the trapezoid body

value: Postnatal day 1

tag: strain

value: FVN


title: N2_sRNA_A2_13

value: wild type


title: N2_sRNA_A2_9

value: gonad


title: N2_sRNA_A2_12

value: hermaphrodite


title: OF14_ContNegM

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

description: Gene expression data from human primary osteoblast transfected with control mimic

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2) (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted following RNeasy® Mini Kit (Qiagen, Hilden, Germany) protocol

tag: patient

value: patient OF14

tag: cell type

value: osteoblast

value: transfected with control mimic (CM)


title: Infected, 20-TNT, Rep 6

description: Western Fence Lizard

tag: tissue

value: Liver

value: Male

tag: diet

tag: infection

value: Malaria

value: 20 mg/kg/d TNT


title: Infected, 20-TNT, Rep 3

description: Western Fence Lizard

value: Adult


title: TNBC-34

value: Triple negative breast cancer

value: PD-1 2/PD-L1 3 Non tumor

value: T2 N1

tag: reference

value: Normal female genome


title: OF7_ContNegM

source_name: human primary osteoblast transfected with control mimic

value: patient OF7


title: Infected, 20-TNT, Rep 5

description: Western Fence Lizard

tag: age

value: ad libitum


title: TNBC-33

value: PD-1 2/PD-L1 4 Tumor

value: T2 N0


title: TNBC-35

value: PD-1 1/PD-L1 2 Non tumor

value: T1b N0


title: N2_sRNA_A2_10

tag: genotype

value: wild type

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes

value: small RNA

value: SMARTer small RNA-Seq


title: TNBC-31

value: PD-1 3/PD-L1 2 Non tumor

tag: Stage

value: Ia

value: T1c N0


title: OF14_ContNegi

description: Gene expression data from human primary osteoblast transfected with control inhibitor

value: patient OF14

value: osteoblast

tag: treatment

value: transfected with control inhibitor (CI)


title: TNBC-30

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 1/PD-L1 1 Non tumor

value: I

tag: grade

value: Normal female genome


title: OF14_320i

description: Gene expression data from human primary osteoblast transfected with miR-320a inhibitor

value: transfected with miR-320a inhibitor (I)


title: Infected, 20-TNT, Rep 4

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

value: ad libitum

value: Malaria

value: 20 mg/kg/d TNT


title: OF7_320i

source_name: human primary osteoblast transfected with miR-320a inhibitor

value: patient OF7


title: Infected, 10-TNT, Rep 4

description: Western Fence Lizard

value: 10 mg/kg/d TNT


title: OF14_320M

description: Gene expression data from human primary osteoblast transfected with miR-320a mimic

value: transfected with miR-320a mimic (M)


title: N2_sRNA_A2_8

tag: strain

value: wild type

value: gonad

tag: Sex

value: hermaphrodite

value: young adults

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: OF7_320M

source_name: human primary osteoblast transfected with miR-320a mimic

tag: patient

tag: cell type

value: osteoblast


title: Infected, 10-TNT, Rep 5

description: Western Fence Lizard

tag: tissue

tag: age

tag: diet

tag: infection


title: Infected, 20-TNT, Rep 1

description: Western Fence Lizard


title: Infected, 20-TNT, Rep 2

description: Western Fence Lizard


title: TNBC-25

value: Triple negative breast cancer

value: PD-1 2/PD-L1 2 Non tumor

tag: t n

value: T1b N0

tag: reference

value: Normal female genome


title: TNBC-37

value: PD-1 4/PD-L1 5 Tumor

tag: Stage

value: IIa

value: T2 N0


title: N2_sRNA_A2_7

tag: genotype

tag: replicate index

tag: slice indices

tag: slice barcodes


title: Infected, 10-TNT, Rep 2

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

value: ad libitum

value: Malaria

tag: treatment


title: OF7_ContNegi

source_name: human primary osteoblast transfected with control inhibitor

value: patient OF7

value: transfected with control inhibitor (CI)


title: N2_sRNA_A2_2

tag: strain

value: wild type

value: gonad

tag: Sex

value: hermaphrodite

value: young adults

tag: replicate alignment shift [%]

tag: molecule

value: small RNA


title: N2_sRNA_A2_6

tag: tissue

tag: protocol

value: SMARTer small RNA-Seq


title: N2_sRNA_A2_5

tag: age


title: N2_sRNA_A2_1


title: N2_sRNA_A2_4


title: Infected, 10-TNT, Rep 3

description: Western Fence Lizard

tag: diet

tag: infection

value: 10 mg/kg/d TNT


title: TNBC-20

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

tag: grade

tag: t n

tag: reference

value: Normal female genome


title: TNBC-28

value: PD-1 1/PD-L1 3 Tumor+Non tumor

value: T1c N0


title: TNBC-29

value: PD-1 2/PD-L1 4 Tumor

value: T1c N1


title: N2_sRNA_A1_16

tag: genotype

tag: replicate index

tag: slice indices


title: M80

tag: patient

value: patient 80

tag: cell type

value: osteoblast

tag: treatment

value: transfected with miR-320a mimic (M)


title: N2_sRNA_A2_3

tag: strain

tag: Sex

tag: slice barcodes

tag: replicate alignment shift [%]


title: N2_sRNA_A1_15

tag: tissue

tag: age

tag: molecule

tag: protocol


title: Infected, 5-TNT, Rep 4

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection

value: Malaria

value: 5 mg/kg/d TNT


title: I78

value: patient 78

value: transfected with miR-320a inhibitor (I)


title: M78


title: Infected, 5-TNT, Rep 6

description: Western Fence Lizard


title: I80


title: TNBC-27

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 2/PD-L1 2 Non tumor

tag: grade

tag: t n

value: T4c N2

tag: reference


title: Infected, 10-TNT, Rep 1

description: Western Fence Lizard

value: 10 mg/kg/d TNT


title: CM78

tag: patient

tag: cell type

value: transfected with control mimic (CM)


title: Infected, 5-TNT, Rep 1

description: Western Fence Lizard

tag: treatment


title: Infected, 5-TNT, Rep 3

description: Western Fence Lizard


title: CM80


title: TNBC-19

value: PD-1 2/PD-L1 3 Tumor+Non tumor

tag: Stage

value: I

value: T1 N0

value: Normal female genome


title: Infected, 5-TNT, Rep 5

description: Western Fence Lizard

value: Liver


title: TNBC-23

value: PD-1 3/PD-L1 4 Tumor+Non tumor

value: IIa

value: T2 N0


title: M75

value: patient 75

value: osteoblast

value: transfected with miR-320a mimic (M)


title: N2_sRNA_A1_14

tag: strain

tag: genotype

value: wild type

value: gonad

tag: Sex

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes

value: small RNA

value: SMARTer small RNA-Seq


title: N2_sRNA_A1_12

tag: tissue

tag: age

tag: replicate alignment shift [%]

tag: molecule

tag: protocol


title: I75

value: transfected with miR-320a inhibitor (I)


title: N2_sRNA_A1_13


title: Infected, 5-TNT, Rep 2

description: Western Fence Lizard

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection

value: Malaria

value: 5 mg/kg/d TNT


title: N2_sRNA_A1_11


title: TNBC-21

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 3/PD-L1 4 Tumor

value: IIa

tag: grade

tag: t n

tag: reference

value: Normal female genome


title: N2_sRNA_A1_10

tag: strain

tag: genotype


title: TNBC-24

value: PD-1 4/PD-L1 4 Tumor

tag: Stage

value: T1c N1


title: N2_sRNA_A1_9

value: wild type

value: gonad

tag: Sex

tag: replicate index

tag: slice indices


title: TNBC-13

tag: tissue

value: PD-1 2/PD-L1 2 Non tumor

value: IIb

value: T2 N1


title: CI78

tag: patient

value: patient 78

tag: cell type

value: osteoblast

tag: treatment

value: transfected with control inhibitor (CI)


title: N2_sRNA_A1_8

value: hermaphrodite

tag: age

value: young adults

tag: slice barcodes

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: CM75

value: patient 75

value: transfected with control mimic (CM)


title: Infected, 0-TNT, Rep 5

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

tag: diet

value: ad libitum

tag: infection

value: Malaria

value: 0 mg/kg/d TNT


title: TNBC-11

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 1/PD-L1 2 Tumor+Non tumor

value: IIa

tag: grade

tag: t n

value: T1c N1b

tag: reference

value: Normal female genome


title: TNBC-14

value: PD-1 3/PD-L1 4 Tumor

tag: Stage

value: IIb

value: T3 N0


title: TNBC-10

tag: tissue

value: PD-1 2/PD-L1 3 Tumor+Non tumor

value: T3 N2


title: Infected, 0-TNT, Rep 3

description: Western Fence Lizard


title: CI80

tag: patient

value: patient 80

value: osteoblast

value: transfected with control inhibitor (CI)


title: Infected, 0-TNT, Rep 4

description: Western Fence Lizard

value: Liver

value: Male

value: Adult


title: CI75

value: patient 75

tag: cell type


title: TNBC-16

value: Triple negative breast cancer

value: PD-1 3/PD-L1 3 Tumor

value: Ia

value: T1a n0


title: Infected, 0-TNT, Rep 6

description: Western Fence Lizard

value: ad libitum

value: Malaria

tag: treatment

value: 0 mg/kg/d TNT


title: TNBC-18

value: PD-1 2/PD-L1 1 Non tumor

value: T1c N0

value: Normal female genome


title: N2_sRNA_A1_7

tag: strain

tag: genotype

value: wild type

value: gonad

tag: Sex

value: hermaphrodite

tag: age

value: young adults

tag: replicate index

tag: slice indices

value: small RNA

value: SMARTer small RNA-Seq


title: Infected, 0-TNT, Rep 1

description: Western Fence Lizard

value: Liver

tag: gender

value: Male

value: Adult

tag: diet


title: Infected, 0-TNT, Rep 2

description: Western Fence Lizard

tag: infection


title: N2_sRNA_A1_5

tag: slice barcodes

tag: replicate alignment shift [%]

tag: molecule

tag: protocol


title: small intestine_KO-1

city: Sendai

first: Rumiko

last: SAITO

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Dermatology

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containig 10×Blocking Agent, Nuclease-free water, and 25×Fragmentation Buffer following the manufature's instructions. On completion of the fragmentation reaction, 55 μl of 2×GE Hybridization Buffer (HI-RPM) was added to the fragmentation mixture and hybridized to 44K Agilent Whole Human Genome Oligo Microarays (G4846A) containing  44,397 features representing 39,429 biological probes for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minutes at room temparature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: After washing microarrays according to manufacture's instructions, microarray slides were scanned immediately on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 4×44K array slides (Scan Area 61×21.6 mm, Scan resolution 5 μm, Dye channel is set to green, and 20 bit scan mode (no XDR scan mode)).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20140728). The data from all microarrays were analyzed using GeneSpringGX 14.5 (Agilent Technologies). After data transformation (to convert any negative value to 0.01), Intensity value of green Processedsignal from the Feature Extraction was normalized per chip to the 75th percentile.

source_name: small intestine from Cyp3a-cluster knockout (Cyp3a-/-) mouse, KO, replicate 1

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

extract_protocol: Total RNA from small intestine of wild type or Cyp3a-/- mice was prepared using ISOGEN (Nippon Gene, Tokyo, Japan) and treated with RNase-free DNase I (Wako Pure Chemicals, Osaka, Japan), and were then purified using RNeasy columns (Qiagen, Hilden, Germany), in accordance with the manufacturer’s instructions.The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA quality was determined using the RNA ScreenTape and Reagent Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2200 TapeStation (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC.

tag: tissue

value: small intestine


title: small intestine_control-1

source_name: small intestine from WT mouse, Control, replicate 1


title: TNBC-17

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 1/PD-L1 2 Non tumor

tag: grade

tag: t n

tag: reference


title: Non-Infected, ad libitum, Rep 5

description: Western Fence Lizard

treatment_protocol: Exposure 2 - food limitation x malaria infection: The study incorporated a factorial treatment arrangement within a completely randomized experimental design. The Western fence lizards were inoculated with lizard malaria or vehicle control (see McFarland et al., 2012 for methods) paired with either ad libitum feeding (10 crickets/day) or restricted feeding treatments of 5 or 2 crickets per day. All treatments included 10 biological replicates (10 individually caged lizards) per condition.

value: ad libitum

value: Non-Infected


title: small intestine_control-2

source_name: small intestine from WT mouse, Control, replicate 2

tag: genotype


title: small intestine_KO-2

source_name: small intestine from Cyp3a-cluster knockout (Cyp3a-/-) mouse, KO, replicate 2


title: N2_sRNA_A1_3

tag: strain

tag: Sex


title: glp-1_gf_mRNA_P2

source_name: posterior gonad arm

value: glp-1(ar202) III

tag: age

tag: replicate index

value: mRNA


title: N2_sRNA_A1_4

tag: slice indices


title: N2_sRNA_A1_2


title: glp-1_gf_mRNA_P1


title: N2_sRNA_A1_1


title: liver_KO-2

source_name: liver from Cyp3a-cluster knockout (Cyp3a-/-) mouse, KO, replicate 2

extract_protocol: Total RNA from liver of wild type or Cyp3a-/- mice was prepared using ISOGEN (Nippon Gene, Tokyo, Japan) and treated with RNase-free DNase I (Wako Pure Chemicals, Osaka, Japan), and were then purified using RNeasy columns (Qiagen, Hilden, Germany), in accordance with the manufacturer’s instructions. The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA quality was determined using the RNA ScreenTape and Reagent Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2200 TapeStation (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC.

value: liver


title: TNBC-8

value: PD-1 2/PD-L1 3 Non tumor

value: T2 N0

value: Normal female genome


title: Non-Infected, ad libitum, Rep 3

description: Western Fence Lizard

tag: gender

tag: diet


title: liver_KO-1

source_name: liver from Cyp3a-cluster knockout (Cyp3a-/-) mouse, KO, replicate 1


title: Non-Infected, ad libitum, Rep 4

description: Western Fence Lizard

tag: infection


title: Non-Infected, ad libitum, Rep 2

description: Western Fence Lizard


title: glp-1_gf_mRNA_A2

value: gonad

value: hermaphrodite

value: young adults

tag: slice barcodes

tag: replicate alignment shift [%]


title: TNBC-5

value: PD-1 4/PD-L1 4 Tumor

value: T2 N1


title: TNBC-6

value: PD-1 3/PD-L1 5 Tumor

tag: Stage

value: IIa

value: T1 N1


title: N2_sRNA_uncut_A5

value: wild type

tag: tissue

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: glp-1_gf_mRNA_A1

value: glp-1(ar202) III


title: N2_sRNA_uncut_A4


title: TNBC-4

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 1/PD-L1 1 Non tumor

tag: grade

tag: t n

value: T1c N0


title: TNBC-9

value: PD-1 4/PD-L1 5 Tumor

value: T2 N0

tag: reference


title: liver_control-2

source_name: liver from WT mouse, Control, replicate 2

value: liver

tag: genotype


title: TNBC-7

value: IIIc

value: T4 N2

value: Normal female genome


title: liver_control-1

source_name: liver from WT mouse, Control, replicate 1


title: N2_sRNA_uncut_A3

source_name: anterior gonad arm

tag: strain

value: gonad

tag: Sex

value: hermaphrodite

tag: age

value: young adults


title: Non-Infected, 1/5 ration, Rep 5

description: Western Fence Lizard

source_name: liver tissue

value: Liver

tag: gender

value: Male

value: Adult

value: 1/5 ration

value: Non-Infected


title: Non-Infected, ad libitum, Rep 1

description: Western Fence Lizard

tag: diet

value: ad libitum


title: gld-2_gld-1_mRNA_P2

tag: replicate index

tag: slice indices

value: mRNA


title: N2_sRNA_uncut_A2

value: wild type

tag: slice barcodes

tag: replicate alignment shift [%]

value: small RNA

value: SMARTer small RNA-Seq


title: gld-2_gld-1_mRNA_A2

tag: tissue


title: gld-2_gld-1_mRNA_P1

tag: molecule


title: gld-2_gld-1_mRNA_A1

tag: protocol


title: N2_mRNA_P3


title: N2_mRNA_P2


title: Male_1xEMB (10173.2_Block2.txt)

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX13 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. Only entities on the array passing quality control filter criteria for each sex and treatmet combination were retained: at least 66% of the samples in any one condition had raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis

source_name: Pools of 6 pre-adult I males

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol: Atlantic L. salmonis egg strings were obtained from adult female lice infecting Atlantic salmon in a salmon farm located in BMA-2b in the Bay of Fundy, New Brunswick. Eggs were hatched in a static sea water hatch system and grown to copepodids at Huntsman Marine Science Centre, St Andrew's, NB, Canada.

extract_protocol: Lice were flash frozen individually and and kept at -80 degrees Celcius until RNA extraction. Pools of 6 preadult I lice  (n = 48 pools) were included in the study (n = 6 for each treatment and sex combination, except n = 5 for control males and n = 7 for male 3xEMB).  Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol: The base ration for all trials was an Atlantic salmon extruded diet (Corey Feed Mills Ltd, 136 Hodgson Road, Fredericton, NB, Canada E3C 2G4). Emamectin benzoate (SLICE TM) premix and its quality control were provided by the manufacturer (Intervet Schering-Plough Animal Health Corporation, Summit, New Jersey, USA) to Northeast Nutrition Inc. (Truro, Nova Scotia) and Corey Feed Mills Ltd. Ivermectin (Ivomec 0.6% w/w/ DIN 01913085) premix and its quality control were also provided by the manufacturer (Merial Canada Inc., Baie-D'Urfe, Quebec, Canada) to Northeast Nutrition Inc. Medicated diet was prepared according to industry standards by the source feed mill. Prior to the initiation of the trial, the Toxicology and Analytical Services Laboratory (TASL), University of Prince Edward Island, and Maxxam Analytics, Ontario, Canada tested nominal concentrations of EMB and IVM, respectively. The nominal concentration was used to calculate the daily ration required to attain a dose of 50 µg kg-1 (1x), 100 µg kg-1 (2x), 150 µg kg-1 (3x) EMB or 50 µg kg-1 (1x IVM) body weight. Emamectin benzoate was fed for 7 consecutive days whereas ivermectin was offered twice over a seven day period for four consecutive weeks.  Fish in the treatment groups were fed the medicated diet at a rate of 1.1% kg-1 body weight for the 1x EMB, 1.2% kg-1 body weight for the 3x EMB (per day for seven consecutive days) and 1.0% body weight for IVM at all applicable feeding days.

tag: treatment

source_name: all condition pool

tag: sample type

value: reference


title: Male_Ivermectin (10173.3_Block3.txt)

description: Ivermectin

value: Ivermectin


title: N2_mRNA_P1

value: CEL-Seq:1 – 15


title: Male_Control (10173.1_Block1.txt)

description: Control

value: Control


title: Male_Ivermectin (10173.4_Block4.txt)

description: Ivermectin


title: Female_3xEMB (10172.4_Block4.txt)

source_name: Pools of 6 pre-adult I females

value: Female


title: TNBC-3

source_name: Resected Triple negative breast cancer

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: PD-1 3/PD-L1 2 Tumor+Non tumor

tag: Stage

value: IIIa

tag: grade

tag: t n

value: T2 N1

source_name: Reference pooled 46XX

value: Normal female genome


title: Non-Infected, 1/5 ration, Rep 2

description: Western Fence Lizard

value: Liver

value: Male

value: Adult

value: 1/5 ration

tag: infection


title: Non-Infected, 1/5 ration, Rep 3

description: Western Fence Lizard

tag: age

value: Non-Infected


title: Male_3xEMB (10172.3_Block3.txt)

tag: Sex


title: Female_1xEMB (10172.2_Block2.txt)


title: Non-Infected, 1/2 ration, Rep 4

description: Western Fence Lizard

tag: gender

tag: diet

value: 1/2 ration


title: Non-Infected, 1/5 ration, Rep 1

description: Western Fence Lizard


title: Non-Infected, 1/5 ration, Rep 4

description: Western Fence Lizard


title: N2_mRNA_A3

tag: strain

tag: genotype

value: wild type

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

value: mRNA


title: TNBC-1

tag: tissue

value: PD-1 1/PD-L1 1 Tumor+Non tumor

value: Ia

value: T1c N0

tag: reference


title: Non-Infected, 1/2 ration, Rep 5

description: Western Fence Lizard


title: N2_sRNA_uncut_A1

tag: slice barcodes

tag: replicate alignment shift [%]

tag: molecule

value: small RNA

tag: protocol

value: SMARTer small RNA-Seq


title: Non-Infected, 1/2 ration, Rep 6

description: Western Fence Lizard


title: Non-Infected, 1/2 ration, Rep 3

description: Western Fence Lizard


title: TNBC-2

value: Triple negative breast cancer

tag: pd-1/pd-l1 expression

value: ND/ND

tag: grade

value: Normal female genome


title: N2_mRNA_A2


title: N2_mRNA_uncut_P


title: N2_mRNA_uncut_A


title: N2_pAp_A1

molecule: polyA RNA

value: polyA RNA

value: Illumina stranded poly(A) selected


title: N2_mRNA_A1

value: CEL-Seq:1 – 15


title: N2_total_200ng_A

value: total RNA

value: RNAse H + Illumina stranded total RNA


title: Male_Control (10150.3_Block3.txt)

description: Control

tag: treatment

value: Control

value: Male

tag: sample type

value: reference


title: Female_Ivermectin (10150.4_Block4.txt)

description: Ivermectin

value: Ivermectin

tag: Sex

value: Female


title: N2_sRNA_A1_6

value: wild type

value: gonad

value: hermaphrodite

tag: age

value: young adults


title: N2_total_100ng_A


title: Female_Ivermectin (10172.1_Block1.txt)

description: Ivermectin


title: Female_1xEMB (10150.2_Block2.txt)


title: Male_3xEMB (10150.1_Block1.txt)


title: Male_3xEMB (10139.3_Block3.txt)


title: Male_Ivermectin (10139.1_Block1.txt)

description: Ivermectin


title: Female_Control (10139.2_Block2.txt)

description: Control


title: Non-Infected, 1/2 ration, Rep 1

description: Western Fence Lizard

value: Liver

tag: gender

value: Adult

tag: diet

value: 1/2 ration

tag: infection

value: Non-Infected


title: Non-Infected, 1/2 ration, Rep 2

description: Western Fence Lizard


title: Female_Ivermectin (10139.4_Block4.txt)

description: Ivermectin


title: Infected, ad libitum, Rep 6

description: Western Fence Lizard

value: ad libitum

value: Malaria


title: Infected, ad libitum, Rep 4

description: Western Fence Lizard


title: Female_1xEMB (10137.4_Block4.txt)


title: Infected, ad libitum, Rep 1

description: Western Fence Lizard


title: Infected, ad libitum, Rep 5

description: Western Fence Lizard


title: Infected, ad libitum, Rep 3

description: Western Fence Lizard


title: 78N

city: Fuzhou

first: Yuan

last: Dang

address: Xi‘erhuanbei Road NO156

country: China

institute: Fuzhou General  Hospital

description: Gene expression in paired non-tumor tissue

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: paired non-tumor tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Fresh tissue from patients

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresi

tag: patient diagnosis

value: gastric adenocarcinoma

tag: subject id

value: paired non-tumor tissue


title: Infected, 1/5 ration, Rep 5

description: Western Fence Lizard

tag: tissue

value: 1/5 ration


title: Infected, 1/5 ration, Rep 4

description: Western Fence Lizard

value: Male


title: Infected, 1/5 ration, Rep 3

description: Western Fence Lizard


title: 78C

description: Gene expression in tumor tissue

source_name: tumor tissue

value: tumor tissue


title: Infected, ad libitum, Rep 2

description: Western Fence Lizard


title: Experiment 2, patient 10

city: CINCINNATI

first: Grant

last: Schulert

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Amplified reads were mapped with hg19_AmpliSeq_Transcriptome_ERCC_V1 reference from Ion Community.
After reads were mapped they were converted into reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: Highly purified neutrophils

growth_protocol: Freshly isolated

extract_protocol:
Total RNA from purified neutrophils was extracted using the MagMax -96 Total RNA Isolation Kit (Life Technologies)
Using the SuperScript VILO cDNA Synthesis Kit (Life Technologies), 10 ng of RNA was reverse transcribed to make cDNA. The Ion AmpliSeq Library Kit Plus (Life Technologies) and the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel was used to amplify target genes per manufacturer’s directions. Each amplicon was then barcoded with the Ion Express Barcode Adapter (Life Technologies), and purified through Agencourt AMPure XP Beads (Beckman Coulter) and freshly prepared 70% ethanol. Finally, libraries were analyzed with High Sensitivity NGS Fragment Analysis Kit (AATI). All libraries were peaked around 200 bp
Ampliseq transcriptome using Ion Torrent S5

treatment_protocol: Cells were isolated in a two-step isolation with density-gradient sedimentation followed by magnetic-bead based negative selection with the MACSexpress Human Whole Blood Neutrophil Isolation kit (Miltenyi Biotec, Germany), followed by hypotonic lysis of remaining red blood cells. Neutrophil purity was assessed by flow cytometry (see below) and was typically >98%.

tag: cell type

value: Neutrophils

tag: disease state

value: Inactive SJIA

tag: serum il-18


title: Female_Ivermectin (10137.1_Block1.txt)

description: Ivermectin

value: Ivermectin

value: Female

value: reference


title: Female_Ivermectin (10129.3_Block3.txt)

description: Ivermectin


title: Male_1xEMB (10137.2_Block2.txt)


title: Experiment 2, patient 9


title: Male_Ivermectin (10129.1_Block1.txt)

description: Ivermectin


title: Infected, 1/5 ration, Rep 2

description: Western Fence Lizard


title: 87N


title: Infected, 1/5 ration, Rep 1

description: Western Fence Lizard


title: 84N


title: Female_3xEMB (10129.2_Block2.txt)


title: 90C

description: Gene expression in tumor tissue


title: Male_3xEMB (10137.3_Block3.txt)


title: Experiment 2, patient 8


title: 87C

description:
Gene expression in tumor tissue
The raw file for this sample is corrupted and contains binary characters. However, there are 58035 lines of raw data in this file. An intact, non-corrupted file was not available at the time these records were created.


title: Male_1xEMB (10129.4_Block4.txt)


title: Female_3xEMB (10115.4_Block4.txt)


title: 90N


title: Infected, 1/2 ration, Rep 6

description: Western Fence Lizard


title: Infected, 1/2 ration, Rep 4

description: Western Fence Lizard


title: 84C

description: Gene expression in tumor tissue


title: Infected, 1/2 ration, Rep 5

description: Western Fence Lizard


title: Experiment 2, patient 7


title: 83N


title: Male_3xEMB (10115.2_Block2.txt)


title: 83C

description: Gene expression in tumor tissue


title: Infected, 1/2 ration, Rep 3

description: Western Fence Lizard


title: Experiment 2, patient 6


title: Infected, 1/2 ration, Rep 2

description: Western Fence Lizard


title: Infected, 1/2 ration, Rep 1

description: Western Fence Lizard


title: 97N


title: Female_Control (10115.3_Block3.txt)

description: Control

value: Control


title: Experiment 2, patient 5


title: Experiment 2, patient 3


title: KM_1

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

description: microRNA

data_processing:
The FastQC program was employed to assess the quality of the reads.
The fastq files were then upload to Chimira where count-based miRNA expression data were generated.
Sequences were adapter trimmed and mapped against miRBase v21 hairpin sequences allowing up to two mismatches per sequence. Further analyses  was performed using R/Bioconductor.
The edgeR package was used to identify significantly differentially expressed miRNAs following the protocol described by Law et al. (2016).
The trimmed mean of M-values (TMM) normalisation method was used for normalisation of the miRNA expression count data.
Differential expression analysis was performed using voom and limma.
P-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg.
A miRNA was considered to be differentially expressed if the adjusted p-value was <= 0.05.
Genome_build: miRBase v21

source_name: umbilical cord plasma

growth_protocol: Umbilical cord blood samples were collected immediately after delivery of all infants in this study and processed within 3 h following strict laboratory SOPs by a dedicated research team who were available 24 h a day. Samples were stored at -80◦C in a monitored storage facility until analysis. 6 ml of umbilical cord blood was collected into vacutainer tubes from the infants and processed within 3 hours of delivery.

extract_protocol:
200 μl of non-hemolyzed cord blood plasma was used to isolate RNA, using the miRCURY RNA isolation kit (Exiqon) according to the manufacturer’s protocol. RNA was eluted in 25 μl. A standard overnight RNA ethanol precipitation step was then performed and RNA was re-suspended in 10 μl RNase free water to concentrate. RNA integrity and quantity was determined using the small RNA detection kit (DNF-470) on a Fragment Analyzer (Advanced Analytical Technologies).
RNA (5 μl) from each sample was used to construct small RNA libraries using the Illumina TruSeq Small RNA library kit. Due to the small amount of input RNA the protocol was modified slightly (all kit reagents were halved) to prevent extensive adapter dimer formation.
Libraries were size selected using a Pippin Prep with 3% agarose dye free cassettes and size selection was validated using a 2100 High sensitivity DNA Bioanalyzer chip (Agilent). The concentration of each library was determined using the HS-dsDNA kit for Qubit, libraries were pooled and pooled libraries were sequenced at the Trinseq Facility at the Institute for Molecular Medicine at St. James Hospital Dublin on an Illumina miSeq.

treatment_protocol: The plasma was prepared by centrifuging the tubes at 2400 x g, for 10 minutes, at 4◦C. The supernatant was collected into an RNAase free tube and extra care was taken not to disturb the buffy coat which contains the white blood cells. Plasma was then collected into 250 μl RNAase free eppendorfs and stored at -80◦C. The level of haemolysis in the plasma samples was assessed by spectrophotometric analysis using a Nanodrop 2000 spectrophotometer. The absorbance at 414 nm was checked and a cut-off level of 0.25 was used to distinguish haemolysis free samples

value: umbilical cord plasma

tag: center

value: Karolinska


title: Male_3xEMB (10115.1_Block1.txt)


title: KM_2

description: microRNA


title: KF_1

description: microRNA


title: Experiment 2, patient 4


title: Experiment 2, patient 1


title: KF_2

description: microRNA


title: Experiment 1, patient 14

value: Control patient

value: ND


title: Experiment 2, patient 2


title: Male_Control (10114.4_Block4.txt)

description: Control


title: Female_Ivermectin (10114.2_Block2.txt)

description: Ivermectin


title: Experiment 1, patient 13


title: CM_1

description: microRNA

value: Cork


title: Male_1xEMB (10114.1_Block1.txt)


title: Female_Control (10114.3_Block3.txt)

description: Control


title: 97C

description: Gene expression in tumor tissue


title: Restricted, 20-TNT, Rep 4

description: Western Fence Lizard

treatment_protocol: Exposure 1 - TNT x food limitation: The study incorporated a factorial treatment arrangement within a completely randomized experimental design. The food limitation treatments included an ad libitum control (fed 10 crickets daily) and a reduced food ration (2 crickets daily). The TNT exposures consisted of daily oral doses of corn oil control or a corn oil-TNT suspension at 5, 10, 20, mg/kg/day. All treatments included 10 biological replicates (10 individually caged lizards) per condition.

value: Liver

value: Adult

value: Restricted

value: 20 mg/kg/d TNT


title: Restricted, 20-TNT, Rep 3

description: Western Fence Lizard

value: Male


title: Restricted, 10-TNT, Rep 6

description: Western Fence Lizard

value: 10 mg/kg/d TNT


title: Restricted, 20-TNT, Rep 1

description: Western Fence Lizard


title: Restricted, 20-TNT, Rep 2

description: Western Fence Lizard


title: Experiment 1, patient 12

value: Neutrophils


title: CF_1

description: microRNA


title: CM_2

description: microRNA


title: Restricted, 10-TNT, Rep 5

description: Western Fence Lizard


title: Restricted, 20-TNT, Rep 5

description: Western Fence Lizard


title: Female_3xEMB (10112.2_Block2.txt)


title: CF_2

description: microRNA


title: Male_Ivermectin (10112.3_Block3.txt)

description: Ivermectin


title: Male_1xEMB (10112.4_Block4.txt)


title: Experiment 1, patient 10


title: Experiment 1, patient 11


title: Experiment 1, patient 9

value: Inactive SJIA


title: Female_3xEMB (10112.1_Block1.txt)


title: Experiment 1, patient 7


title: Female_1xEMB (10109.4_Block4.txt)


title: Restricted, 10-TNT, Rep 4

description: Western Fence Lizard


title: Experiment 1, patient 6


title: Restricted, 10-TNT, Rep 3

description: Western Fence Lizard


title: Male_Control (10109.2_Block2.txt)

description: Control


title: Experiment 1, patient 5


title: Female_Control (10109.3_Block3.txt)

description: Control


title: Restricted, 10-TNT, Rep 2

description: Western Fence Lizard


title: Restricted, 5-TNT, Rep 5

description: Western Fence Lizard

value: 5 mg/kg/d TNT


title: Experiment 1, patient 8


title: Restricted, 10-TNT, Rep 1

description: Western Fence Lizard


title: Donor 1-CK-869-45min

city: Heidelberg

first: Nikolaos

last: Tsopoulidis

address: Im Neuenheimer Feld 344

institute: Universitätsklinikum Heidelberg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: CD4+ T cells 45 min post stim

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Macherey und Nagel RNA extraction Kit  that includes DNase I treatment. Quality control was performed with Agilent Bioanalyser.

tag: donor id

value: Donor 1

value: CD4+ T cells

tag: time post activation

value: 45 min


title: Donor 3-CK-869-45min

value: Donor 3


title: Female_1xEMB (10108.4_Block4.txt)

value: Female

value: reference


title: Donor 3-DMSO-45min

value: DMSO


title: Restricted, 5-TNT, Rep 3

description: Western Fence Lizard


title: Female_3xEMB (10108.2_Block2.txt)


title: Female_Control (10109.1_Block1.txt)

description: Control

value: Control


title: Donor 2-CK-869-4h

source_name: CD4+ T cells 4h post stim

value: Donor 2


title: Female_Control (10108.3_Block3.txt)

description: Control


title: Experiment 1, patient 4

value: Active SJIA


title: Donor 1-DMSO-45min


title: Donor 3-CK-869-4h


title: Donor 3-DMSO-4h


title: Experiment 1, patient 3


title: Experiment 1, patient 2


title: Restricted, 0-TNT, Rep 5

description: Western Fence Lizard

value: Liver

value: Adult

value: Restricted

value: 0 mg/kg/d TNT


title: Restricted, 5-TNT, Rep 2

description: Western Fence Lizard

value: Male


title: Restricted, 5-TNT, Rep 4

description: Western Fence Lizard


title: Experiment 1, patient 1

value: Neutrophils


title: adcp1-1_RNAseq_rep1

city: Beijing

first: QIANWEN

last: SUN

address: Zhongguancun Street

department: School of life sciences

institute: Tsinghua University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trim_galore.
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie 2 version 2.3.2. BS-seq reads were aligned to TAIR10 using bismark_v0.18.1. RNA-seq reads were aligned to TAIR10 genome using HISAT2 version 2.0.5.
Peaks were called using MACS2.
Reads coverage nomalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using Computematrix,gtf files include FPKM values for each Sample.

source_name: leaves

extract_protocol:
For H3K9me2 ChIP-seq, nuclei were extracted with Honda buffer and digested with MNase, the resulting histone-DNA complexes were isolated with antibody. For GFP ChIP-seq, the nuclei were cross-linked by 1% formaldehyde and sonicated,  histone-DNA complexes were isolated with antibody. For BS-seq, DNA was extracted from 14-day-old leaves with CTAB. After complete bisulfite conversion of 2μg DNA with EZ DNA Methylation-Gold Kit (Zymo Research ,D5005), the DNA was sonicated to 250bp (Covaris) for library construction. For RNA-seq, total RNA was extracted from 14-day-old leaves using Trizol (Ambion).
ChIP-seq Libraries were constructed using ACCEL-NGS®1S PLUS DNA LIBRARY KIT ( Swift Biosciences ,Cat. No. 18096) according to the manufacturer. BS-seq library was constructed following Illumina’s manufacturer Instructions(Swift Biosciences, ACCEL-NGS® METHYL-SEQ DNA LIBRARY KIT, 30024). For RNA-seq, Libraries for two biological replicates of each genotype were constructed and sequenced according to the manufacturer’s protocol (NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®). The rRNA was depleted from total RNA using Ribo-ZeroTM rRNA removal Kit (Illumina). Illumina libraries were generated and sequenced using a 2x150 paired-end (PE) configuration on the HiSeq instrument (Illumina).

tag: developmental stage

tag: genotype

value: mutant


title: adcp1-1_RNAseq_rep2


title: Male_Control (10108.1_Block1.txt)

description: Control

tag: treatment

tag: sample type


title: gran_TNF_3

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
TNF_genes.txt
ATRATNF3

data_processing:
Read quality was confirmed with FastQC v0.11.4
Reads were aligned to hg38 and gencode annotations v27 using STAR v2.5.3a with default settings
FeatureCounts v1.5.2 was used to quantify the reads with gencode annotations v27
Differentially expressed genes were identified at FDR<0.05 using DEseq2 v1.16.1 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: FeatureCounts matrix of raw counts for each gene in each sample

source_name: Myeloid leukaemia

growth_protocol: A seed-lot store was generated of cells at 4 passages. Cells were grown in suspension in RPMI 1640 (ThermoFisher, 11875119) with 10% FBS (medi’Ray, MG-FBS0820-500ML-GEN), 1% pen/strep (ThermoFisher, 15140122), and 1% GlutaMAXTM (ThermoFisher, 35050061). Cells were differentiated into a granulocytic phenotype with 1µm all trans retinoic acid (ATRA)(Sigma Aldrich, R2625-50MG) for four days.

extract_protocol:
Cells were lysed in TRiZOL LS and phase separated with chloroform. RNA was extracted with the Qiagen RNeasy mini kit (Qiagen, 74004).
RNA lncRNA libraries were prepared by Annoroad using ribosomal RNA depletion with RiboZero Magnetic Gold Kit (Human/Mouse/Rat) (MRZG12324)

treatment_protocol: Cells were treated with 16ng/ml of TNF, or the equivalent volume of water, for two hours in calcium supplemented growth media.

tag: cell line

tag: differentiation

value: Granulocytic (4 days all-trans retinoic acid)

tag: passages

tag: tnf treatment

value: 16ng/ml TNF


title: Col-0_RNAseq_rep2

value: wild type


title: Male_Ivermectin (10107.2_Block2.txt)

description: Ivermectin

value: Ivermectin

tag: Sex


title: Col-0_RNAseq_rep1


title: gran_TNF_1

description:
TNF_genes.txt
ATRATNF1


title: Female_1xEMB (10107.3_Block3.txt)

value: Female


title: gran_3

description:
TNF_genes.txt
ATRACTRL3

value: vehicle (water)


title: gran_TNF_2

description:
TNF_genes.txt
ATRATNF2


title: Male_3xEMB (10107.1_Block1.txt)

value: reference


title: Restricted, 0-TNT, Rep 3

description: Western Fence Lizard

tag: gender

tag: age

tag: diet


title: Donor 0-DMSO-24h

source_name: CD4+ T cells 24h post stim

value: Donor 0

tag: cell type

value: CD4+ T cells

value: DMSO


title: Donor 3-CK-869-90min

source_name: CD4+ T cells 90 min post stim

value: Donor 3

value: 90 min


title: Male_1xEMB (10107.4_Block4.txt)


title: ad libitum, 20-TNT, Rep 3

description: Western Fence Lizard

tag: tissue

value: Liver

value: Adult

value: ad libitum

value: 20 mg/kg/d TNT


title: Restricted, 0-TNT, Rep 4

description: Western Fence Lizard

value: Male

value: Restricted

value: 0 mg/kg/d TNT


title: Donor 3-DMSO-90min


title: Donor 0-CK-869-24h


title: Donor 2-DMSO-90min

value: Donor 2


title: Donor 2-DMSO-4h


title: Donor 2-CK-869-90min


title: ad libitum, 20-TNT, Rep 2

description: Western Fence Lizard


title: Restricted, 0-TNT, Rep 1

description: Western Fence Lizard


title: Restricted, 0-TNT, Rep 2

description: Western Fence Lizard


title: ad libitum, 20-TNT, Rep 4

description: Western Fence Lizard


title: Donor 0-CK-869-4h


title: adcp1-1_BS-seq_rep2

value: mutant


title: gran_2

description:
TNF_genes.txt
ATRACTRL2

value: Granulocytic (4 days all-trans retinoic acid)


title: THP_BG505_viralRNA_2

city: Seattle

first: Molly

last: Ohainle

state: WA

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

description: viral RNA

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

organism: Human immunodeficiency virus

source_name: Human Immunodeficiency Virus (HIV)

growth_protocol: THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2e5 cells/mL and 1e6 cells/mL.

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen)
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

treatment_protocol: 8e6 cells (>500X coverage) were transduced with the PIKAHIV library (MOI of 0.75) and selected in 1ug/mL puromycin for 10-14 days. For each replicate, 8e6 cells were infected with or without overnight IFNα treatment with HIV. Cells and viral supernatants were harvested 3 days post-infection.

value: ZAP-KO THP-1 +CCR5

value: ZAP-KO

tag: ifn treatment

value: yes


title: THP_BG505_viralRNA_1

description: viral RNA


title: THP_BRUVSVG_viralRNA_2

description: viral RNA


title: pro_TNF_2

description:
TNF_genes.txt
HL60NTF2

value: Undifferentiated

value: 16ng/ml TNF


title: pro_TNF_3

description:
TNF_genes.txt
HL60NTF3


title: THP_BRUVSVG_viralRNA_1

description: viral RNA


title: Col-0_BS-seq_rep2

value: wild type


title: Donor 0-DMSO-4h

tag: donor id

value: Donor 0

value: CD4+ T cells

value: DMSO


title: ADCP1-GFPinput DNA_rep2

tag: chip antibody

value: trangenic


title: Col-0_BS-seq_rep1

tag: developmental stage


title: pro_TNF_1

description:
TNF_genes.txt
HL60NTF1


title: Restricted, 5-TNT, Rep 1

description: Western Fence Lizard

source_name: liver tissue

value: Liver

value: Adult

value: 5 mg/kg/d TNT


title: adcp1-1_BS-seq_rep1

tag: genotype


title: gran_1

description:
TNF_genes.txt
ATRACTRL1

value: vehicle (water)


title: N2_pAp_A3

city: Berlin

first: Nikolaus

last: Rajewsky

address: Robert-Rössle-Straße 10

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Raw sequencing basecalls were demultiplexed and converted to FASTQ format using bcl2fastq v2.18.0.12 using the parameters --no-lane-splitting --mask-short-adapter-reads=10 without  specifying adapter sequences in the sample sheet CSV file.
Reads 2 were annotated with their corresponding (corrected) barcode and UMI sequences (read 1) using custom scripts.
Reads with identical barcode, UMI and sequence were collapsed and the unique reads were assigned to per-slice FASTQ files by barcode.
Small RNA reads were subject to two rounds of 3’ end trimming by flexbar v. 2.5 using the  --pre-trim-phred=30 option: first removing 3’ adapters (TGGAATTCTCGGGTGCCAAGG) and then using 10 A's as ‘adapter sequence’.
The 3 nucleotides 5’ overhang introduced by the template-switching polymerase were trimmed using a custom awk script also discarding reads with a remaining length < 18 nts.
RNA-seq reads were mapped to the ce11/WBcel235 genome assembly using STAR_2.5.1b and an index with splice junction information from the Ensembl 82 transcriptome annotation.
Alignments were sorted using sambamba v0.4.7.
Coverage tracks were generated using bedtools v2.23.0 via the genomecov command specifying the -split, -bg and -strand parameters.
The total number of mapped reads per sample/splice was determined using the flagstat command of samtools 0.1.19-96b5f2294a and converted to the corresponding -scale parameter for bedtools genomecov for reads-per-million-mapped (RPM) normalization.
Coverage BedGraph files were converted to BigWig format using bedGraphToBigWig v 4.
Downstream coverage peaks for 3’ extension of the WS260 transcriptome were idenified using a custom R script: For each protein coding gene, the intergenic distance to the next downstream protein coding, ncRNA, lincRNA, pseudogene, rRNA or snoRNA gene (on the same strand) was calculated. Intergenic regions longer than 10 kb were truncated and the RPM-scaled genome coverage per sample of those regions was extracted from the BigWig files generated before. The per-sample coverage vectors were averaged per genomic position and binarized into uncovered regions (< 5 RPM mean coverage) and covered regions (>= 5 RPM mean coverage). Covered regions with a length of >= 50 nucleotides were considered as coverage peaks. Per downstream intergenic region, the downstream-most coverage peak was selected for the 3’ extension of the corresponding upstream gene. Only downstream extensions with a length up to 3 kb were considered for downstream analyses. For each gene with a downstream extension, all annotated transcript isoforms extending to the 3’ most genomic position of the corresponding gene were kept and got their 3’ UTRs extended by until the 3’ position of the respective downstream peak. Those 3’ extended transcripts were exported to a GTF file and merged with the WS260 transcriptome annotation using custom awk scripts.
To enable the assignment of 3’ end RNA-seq reads to transcript isoforms, the 3’ extended WS260 transcriptome annotation was pre-processed using a series of custom R scripts: 3’ A’s were trimmed from all annotated transcripts as they would be indistinguishable from poly(A)-tails. The resulting transcripts were truncated to the 3’ most 500 nucleotides. Transcript isoforms with the same genomic coordinates and internal structure were collapsed and enumerated by decreasing corresponding (max.) 3’ UTR length.
RNA-seq reads were assigned to transcripts using kallisto 0.43.1: For 3’ reads, an index of the collapsed transcriptome annotation described above was used. For full-length coverage reads (poly(A)+ and ribodepleted total RNA-seq libraries), an index of the full 3’ extended transcriptome annotation was used. For all libraries, the --bias and --plaintext flags were passed to kallisto quant. For single end reads, additionally the --single, --fragment-length=1 and --sd=1 options were used. Poly(A)+ and ribodepleted total RNA-seq samples were analyzed in --rf-stranded mode.  3’ reads were presented to kallisto as single-end reads using  the --fr-stranded mode of kallisto quant.
Transcripts not annotated as protein coding were discarded.
For gene-level analyses, isoform-level read counts were summed across all isoforms.
Raw read counts were normalized to counts-per-million (CPM) for CEL-Seq1/2 samples and transcripts-per-million (TPM) for poly(A)+ and ribodepleted total RNA-seq samples.
Small RNA libraries were mapped to the E.coli genome (NC_000913.3, K-12, MG1655) with bowtie2 (version 2.3.3.1) using the parameters --very-fast-local --phred33 --local keeping unmapped reads (--un option).
The cleaned-up libraries were pooled.
MiRDeep2 (version 2.0.0.7) was ran on the pooled libraries with the miRBase21 reference.
The novel miRNA predictions found were added to the miRBase21 reference.
The combined reference of known and novel miRNAs was used for a second run of miRDeep2 on each library separately and on the pooled library as well to obtain CPM estimates.
Slice-data were arranged from distal to proximal by the known order of their barcodes and assigned to a relative position scale representing each slice by its center and accounting for differences in the number of slices per sample.
The replicates were aligned by adding the corresponding sample shift to the distal-to-proximal position of each slice.
Genome_build: ce11/WBcel235
Supplementary_files_format_and_content: All processed data files are tab-separated values (TSV) formatted text files with the first six columns following the BED6 format specifications defining the genomic coordinates (0-based, end-exclusive) of the quantified feature, identifying it by name and scoring it by the estimated abundance. The remaining columns contain further information about the corresponding measurement. All files start with a single header line (beginning with a #) naming the columns. The processed data file mRNA_bulk.tsv.gz contains isoform-level abundance estimates from RNAse H + Illumina stranded total RNA and Illumina stranded poly(A) selected libraries as well as CEL-Seq1/2 libraries before barcode assignment (i.e. incl. non-assignable reads). The file contains the following columns: 1. gene_contig: UCSC-style name of the chromosome/contig the gene is transcribed from; 2. transcript_start: start coordinate (0-based, inclusive) of the transcript; 3. transcript_end: end coordinated (0-based, exclusive) of the transcript; 4. transcript_id: ID of the transcript - for full length transcripts the Ensembl transcript name followed by ‘_3utr’ and the 3’ UTR length in nucleotides, ‘_’, the number of As clipped from the 3’ end and ‘_A3p_clipped’, for truncated & collapsed transcripts the Ensembl gene name followed by ‘_3p500.’ and the isoform index (1-based) sorted by (max.) 3’ UTR length in descending order; 5. abundance_0_to_1000: 60 * log2(CPM/TPM) censored at 1 and 1,000 for transcripts with reads assigned, 0 otherwise; 6. gene_strand: strand (+/-) the gene is transcribed from; 7. transcript_biotype: Ensembl biotype of the transcript; 8. gene_id: Ensembl/WormBase gene ID; 9. gene_name: Ensembl gene name; 10. gene_biotype: Ensembl biotype of the gene; 11. sample_name: name of the sample the abundance was estimated for; 12. genotype: genotype (N2/gld-2 gld-1/glp-1) of the sample; 13. gonad_arm: gonad arm (anterior/posterior) the sample was obtained from; 14. protocol: protocol (RNAse H + Illumina stranded total RNA/Illumina stranded poly(A) selected/CEL-Seq1/2) the sample was subject to; 15. read_count: number of reads assigned to the transcript; 16. cpm_tpm: library size normalized abundance estimate - for full length transcripts transcripts per million (TPM), for truncated & collapsed transcript counts per million mapped reads (CPM).  The processed data file mRNA_slices.tsv.gz contains isoform-level abundance estimates for CEL-Seq1/2 libraries per assigned barcode (i.e. excl. non-assignable reads). The file contains the f

source_name: anterior gonad arm

extract_protocol:
Gonads were dissected, embedded, flash frozen at -80 °C and cyro-sectioned at 50 µm resolution. RNA from each slice was extracted using Trizol reagent.  CEL-Seq1/2 was used for library construction mRNA transcriptome and SMARTer small RNA-Seq was used for library construction of small RNA transcriptome using all the extracted RNA as input.
mRNA lbraries were prepared for sequencing using the CEL-Seq1/2 protocol (Hashimshony et al., 2012; Hashimshony et al., 2016). sRNA libraries were prepared for sequencing using the SMARTer small RNA-Seq according to manufacturers instructions. Poly(A)+-selected RNA libraries and total RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: gonad

value: hermaphrodite

value: young adults

tag: replicate index

tag: slice indices

tag: slice barcodes

tag: replicate alignment shift [%]

tag: molecule

value: polyA RNA

tag: protocol

value: Illumina stranded poly(A) selected


title: ad libitum, 20-TNT, Rep 1

description: Western Fence Lizard

tag: gender

value: Male

value: ad libitum

tag: treatment

value: 20 mg/kg/d TNT


title: pro_3

description:
TNF_genes.txt
HL60CTRL3

tag: cell line

tag: differentiation

value: Undifferentiated

tag: passages

tag: tnf treatment


title: ad libitum, 10-TNT, Rep 6

description: Western Fence Lizard

tag: tissue

tag: age

tag: diet

value: 10 mg/kg/d TNT


title: ad libitum, 10-TNT, Rep 5

description: Western Fence Lizard


title: pro_2

description:
TNF_genes.txt
HL60CTRL2


title: ADCP1-GFP_input DNA_rep1

tag: developmental stage

tag: chip antibody

tag: genotype


title: N2_pAp_A2

tag: strain

value: wild type

tag: Sex

tag: replicate index

tag: slice indices


title: ADCP1-GFP_ChIPseq_rep1

value: GFP(Abcam, ab290)


title: ad libitum, 10-TNT, Rep 4

description: Western Fence Lizard


title: ad libitum, 10-TNT, Rep 2

description: Western Fence Lizard


title: Col-0_GFP_ChIPseq


title: Col-0_input DNA


title: luteal phases ovary 4

city: Fuyang

first: Yong

last: Liu

address: Qinghe West Road

institute: Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province

data_processing:
TruSeq PE Cluster Kit v3-cBot-HS (Illumina) was used to cluster the cBot clusters
(1) Transcripts with low expression levels, low credible single exon transcripts, and exon numbers <2 were filtered out; (2) transcripts <200 bp in length were filtered out; (3) through Cuffcompare software, the duplicated transcripts of the exon region of the database annotation were removed, and the lncRNA overlapped with the exon region of the splicing transcript; (4) the expression of each transcript was calculated by Cuffquant, and the transcript of FPKM<0.5 was filtered out; and (5) finally, we determined whether the encoding potential was the key condition to determine lncRNAs. We used three coding potential analysis programs (CNCI, CPC, and Pfam-sca) to screen the transcripts
The FPKM (the number of fragments per million fragments from a single gene) was used to estimate the expression levels of lncRNA and transcripts of uncertain coding potential (TUCP).
Filtering out the adaptor sequences, empty sequence, and low-quality sequences,
Genome_build: NC_030808.1
Supplementary_files_format_and_content: text files with FPKM

organism: Capra hircus

source_name: goat ovary

growth_protocol: The ovaries were washed with physiological saline containing double antibodies and then were placed into an RNase-free centrifuge tube, labeled, frozen in liquid nitrogen, and stored at -80°C within 20 days

extract_protocol:
Firsly,total RNA was extracted from the goat ovaries at the follicular and luteal phases.Finally, the RNA integrity was assessed by the RNA Nano 6000 assay kit (Agilent Technologies, CA, USA) with the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: anhui white

value: ovary

tag: estrus phase

value: luteal phase


title: luteal phases ovary 1


title: pro_1

description:
TNF_genes.txt
HL60CTRL1


title: ADCP1-GFP_ChIPseq_rep2

value: trangenic


title: luteal phases ovary 3


title: luteal phases ovary 5


title: adcp1-1_H3K9me2_ChIPSeq_rep2

value: H3K9me2(Abcam, ab1220)

value: mutant