title: USSC 4/146 14d XXL miRNA

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Read alignment: Reads with > 51bp length were cut down to 51bp first. Then, BWA aligner was used to map short reads against the reference genome hg38 (specific parameters: -n 0.04). Only uniquely mapping reads were kept using samtools (specific parameters: -q 20)
Read counting: Reads were counted in an unstranded fashion on a gene-basis within annotated miRNAs downloaded from miRBase version 21 using htseq-count (special paramters: -t miRNA -i ID -s no).
Normalization: edgeR was used to normalize read counts per sample and miRNAs were filtered for counts-per-million > 1 in at least one sample. CPM were calculated with the cpm-function of edgeR on all filtered miRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: CPM table

source_name: USSC cell line

growth_protocol: USSC were expanded in Dulbecco’s modified Eagle’s medium supplemented with 30% heat-inactivated FBS, 2 mM glutamine and penicillin / streptomycin at 37 °C, 5% CO2 and 98% humidity.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using TruSeq Small RNA Sample Prep Kit (#RS-200-0012/0024, Illumina, San Diego, CA) folllowing manufacturer's guidelines.

treatment_protocol: USSC were seeded on poly-D-lysine and laminin pre-coated glass coverslips in 6-well plates with a density of 110.000-140.000 USSC per well. 24h later, USSC were incubated with differentiation medium (XXL) including DMEM GlutaMAX, 15% FBS, penicillin/streptomycin, 50 ng/ml beta-NGF, 20 ng/ml basic FGF, 1 mM dibutyryl-cAMP, 0.5 mM 3-isobutyl-methylxanthine and 10 µM all-trans-retinoic acid. Medium was changed every 2-3 days. USSC were used in passage 7-9 for all experiments.

value: USSC

tag: cell type

value: Cord blood derived unrestricted somatic stem cells

tag: treatment

value: Treatment with XXL-medium

tag: time point

value: day 14


title: CIE vapor, ethanol drinker, mouse 3, medial prefrontal cortex

status: Public on Mar 09 2020

type: RNA

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

country: USA

institute: Virginia Commonwealth Univ.

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

hyb_protocol: Hybridization was performed according to procedures optimized by Affymetrix.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 scanner.

data_processing: Affymetrix GeneChip Mouse Genome 430, type 2 array quality was assessed by RNA degradation, average background, percent present probesets, and multi-dimensional scale plots. Background correction usingRobust Multi-array Average (RMA) and quantile normalization was performed and each brain-region was normalized separately. ComBat by RNA hybridization batch was used to correct for any batch effects present in the data.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, medial prefrontal cortex

label_protocol: Labelling was performed according to procedures optimized by Affymetrix.

growth_protocol: Male C57BL/6J mice were purchased from Jackson Laboratories at 10 weeks of age. Mice were kept under a 12-hour light/dark cycle and given free access to water and standard rodent chow. All studies were conducted in an AALAC-accredited animal facility, and approved by the Institutional Animal Care and Use Committee at Medical University of South Carolina (MUSC). All experimental and animal care procedures met guidelines outlined in the NIH Guide for the Care and Use of Laboratory Animals

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: Mice were divided into 4 treatment groups: the CIE-Drinking group received inhaled ethanol in the vapor chambers followed by 2-bottle choice ethanol drinking in between vapor exposure cycles;the Air-Drinking group received only air in the vapor chambers, but had2-bottle choice ethanol drinking between CIE cycles;the CIE-NonDrinking group received inhaled ethanol in the vapor chambers but only water accessin between CIE cycles;and the Air-NonDrinking group remained ethanol naïve with air exposure in vapor chambers and only water consumption between CIE cycles. Following a 2-week acclimation period, mice in the CIE-Drinking and Air-Drinking groups underwent 6-weeks of 2-bottle choice drinking to establish baseline drinking levels.The 2-hr limited access session to ethanol (15 v/v)vs. water started 30 min before lights off. Ethanol and water intake for each individual mouse was measured daily. Following 6-weeks of baseline drinking, mice were placed in Plexiglass inhalation chambers (60x36x60 cm) 16 hours/day for 4 days. Ethanol was volatilized with an air stone submerged in 95% ethanol. Vapor chamber ethanol concentrations were monitored daily and air flow was adjusted to ethanol concentrations within 10-13 mg/l air. Before each vapor chamber session, intoxication was initiated in the CIE group by administration of 1.6 138g/kg ethanol and 1 mmol/kg pyrazole intraperitoneally (i.p.) at a volume of 0.02 ml/g body 139weight. All mice received the same number and timing of pyrazole injections prior to final removal from the inhalation chambers with control mice receiving saline and pyrazole (i.p.), also at a volume of 0.02 ml/g body weight, prior to being placed into control vapor chambers. Control vapor chambers delivered only airwithoutethanol vapor. After 4 days in the inhalation chambers, mice underwent a 72-hour period of total abstinence from ethanol. Following the abstinence period, mice in the CIE-Drinking and Air-Drinking groups were given 2-bottle choice drinking for 2 hours per day for 5 days. A total of 4 cycles of CIE-abstinence-drinking were performed. After the end of the 4th cycle mice were sacrificed on the 5th drinking day before receiving ethanol/water access on that day at the time they received 2-bottle choice drinking all previous drinking days.

tag: strain

tag: vapor treatment

value: CIE

tag: drinking treatment

value: Drinker

tag: brain region

value: prefrontal cortex

tag: Sex

value: male


title: CIE vapor, ethanol drinker, mouse 9, medial prefrontal cortex


title: CIE vapor, ethanol drinker, mouse 5, medial prefrontal cortex


title: TAIL-seq exp #1 siTENT4 Set1

type: SRA

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

description: TAIL-seq for TENT4A/B knockdown HepG2.2.15 cells, Set1

library_source: transcriptomic

data_processing:
Library strategy: Tail-seq
TAIL-seq analysis was carried out using Tailseeker 3.1.5. Briefly, Read 1 was used for gene identification, and read 2 was used to detect 3′ end modifications and measure the length of the poly(A) tail. For each TAIL-seq library, read 1 was mapped to human genome GRCh38 with STAR 2.5.2b and HBV genome NCBI:U95551.1 with bowtie2.2.6.
Genome_build: hg38
Supplementary_files_format_and_content: The .all.txt, .mapped.txt and .txt file are output files of tailseeker3 with the untemplated tail informtion of the RNA fragment. The first two columns represent the tile and cluster id of the RNA fragment. The third column of the .txt file is the ensembl gene id. The sixth column of the .all.txt and .mapped.txt file is the estimated poly(A) tail length and the last column is the untemplated tail sequence. The .mapped.txt file only contains RNA fragments from .all.txt that are mapped to the genome.

organism: Homo sapiens

source_name: HepG2.2.15 cells

growth_protocol: HepG2.2.15 cells were grown in DMEM (Welgene, LM 001-05) containing 10% FBS (Welgene, S001-01). Primary human foreskin fibroblast (HFF, ATCC SCRC-1041) cells were grown in DMEM (HyClone) containing 10% FBS (HyClone), GlutaMAX-I (Gibco) and penicillin-streptomycin (Gibco). Before transfection, primary HFF were grown in antibiotics-free media.

extract_protocol:
Total RNAs were extracted from HepG2.2.15 cells and HFF cells by TRIzol reagent (Invitrogen, 15596018) and purified with RNeasy MinElute Cleanup Kit (Qiagen) according to manufacturer’s instruction.
TAIL-seq was conducted as previously described. In brief, ~50 μg of DNaseI (Takara, 2270A) treated total RNA (>200 nt) was used to deplete rRNA twice by Ribo-Zero kit (Epicentre, MRZH11124 [discontinued] for primary HFF library or Illumina, TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 20020596 for HepG2.2.15 library). The rRNA-depleted RNAs were ligated to the 3′ adaptor and partially fragmented by RNase T1 (Ambion). The fragmented RNAs were pulled-down with streptavidin beads (Invitrogen), 5′ phosphorylated and purified by 6% urea-PAGE gel (500–1,000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed and amplified by PCR. The libraries were sequenced by paired-end run (51×251 cycles) on Illumina platform (MiSeq) with PhiX control library v3 (Illumina) and spike-in mixture.

treatment_protocol: For TENT4A and TENT4B knockdown, HepG2.2.15 cells were transfected with 100 nM siRNAs by Lipofectamine RNAiMAX (Invitrogen) at Day 0, 2 and 4 and harvested at Day 6. For ZCCHC14 knockdown, HepG2.2.15 cells were transfected with 100 nM siRNAs by Lipofectamine RNAiMAX (Invitrogen) at Day 0 and 2, and harvested at Day 4. Primary HFF cells were transfected with 20 nM siRNAs by DharmaFECT 1 (Dharmacon) at Day 0 and 2 and harvested at Day 5.

tag: cell line

tag: condition


title: CIE vapor, ethanol drinker, mouse 10, medial prefrontal cortex


title: subject ID 20129-3 at diease time point 2_Female, a T1D control and 1.3004791yrs old_450K array [3998909086_R01C02]

type: genomic

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe (v1.0.0) pipeline was used to normalize data (via Noob), perform dye bias correction and perform probe specific QC (via pOOBAH).
ComBat was used to adjust for batch effects were batch was considered to be plate and row position combination
Filtered probes with a small Beta range (range < 0.05), those with known SNPs in the CpG site, and those located on the sex chromosomes
Mvalues.normalized.*.txt contains methylation M-value

label: cy3, cy5

molecule: genomic DNA

source_name: T1D control_Female_time point 2

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human450K or EPIC Beadchip using standard Illumina protocol

extract_protocol: Standard Illumina Protocol

tag: subject id

tag: disease time point

tag: age

value: Female

tag: t1d status

value: T1D control

tag: tissue

value: peripheral blood sample


title: USSC 4/146 3d XXL miRNA

value: day 3


title: TAIL-seq exp #1 siCont Set2

description: TAIL-seq for control knockdown HepG2.2.15 cells, Set2

value: siCont


title: subject ID 70066-0 at diease time point 5_Male, a T1D case and 1.3223819yrs old_450K array [3998909086_R06C01]

source_name: T1D case_Male_time point 5

value: Male

value: T1D case


title: EV_Input

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

library_source: genomic

data_processing:
Reads were trimmed for adapter sequences using Cutadapt v1.11 and aligned using bwa v0.7.15. Duplicated reads were marked using Picard v2.19
Duplicated reads or reads without maped mate were removed using samtools v1.9.
Peaks were called for the Flag with input as contron using MACS2 v2.1 with  parameters -q 0.01  --nomodel --shift -100 --extsize 200.
Bedgraphs were generated and normalised using bedtools2 v2.27.1 genomecov.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwigs were generated from normalised bedgraphs using homer v4.9 bedGraphToBigWig.

source_name: Lineage depleted bone marrow

growth_protocol: Bone marrow was isolated from wild-type mice, RBC lysed and lineage depleted using a cocktail of antibodies consisting of anti-B220, anti-Ter119, anti-Gr1, anti-CD11b, anti-CD3 and anti-CD5. Cells were cultured in RPM1/10%FBS with 10ng/mL GCSF, 50ng/mL mSCF, 10ng/mL mTPO and 30mM HEPES at a concentration of 1x10^6 cells per mL.

extract_protocol:
The heterogeneous population of infected cells were harvested and fixed for ChIP at 48hrs post infection
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).  Libraries were quantified using  the  Qubit DNA HS Assay Kit and analysed for size distribution using the TapeStation (Agilent)  prior to pooling and sequencing using 2x 75 bp paired -end on the NextSeq 550 (Illumina) platform

treatment_protocol: Cells were infected with retrovirus with Cdx2 3 tag flag or an empty vector (EV) at a MOI of 10 in the presence on 8ug/mL polybrene and spun at 2500rpm at 30C for 90mins and subsequently incubated at 37C. Media was changed 16hrs post infection.

value: Lineage depleted bone marrow

value: bone marrow

value: 48hrs post infection

tag: genotype

value: WT

tag: infection

value: empty vector

tag: antibody


title: USSC 4/146 native  miRNA

value: USSC

tag: cell type

value: Cord blood derived unrestricted somatic stem cells

tag: treatment

value: day 0


title: EV_Flag

tag: strain

tag: time point

value: anti-Flag (Cell Signalling, 147935)


title: CIE vapor, ethanol drinker, mouse 2, medial prefrontal cortex

tag: vapor treatment

value: CIE

tag: drinking treatment

value: Drinker

value: prefrontal cortex

value: male


title: TAIL-seq exp #1 siCont Set1

description: TAIL-seq for control knockdown HepG2.2.15 cells, Set1


title: USSC 4/146 7d XXL miRNA

value: Treatment with XXL-medium

value: day 7


title: USSC 5/03 14d XXL miRNA

value: day 14


title: Cdx2_Input

value: Cdx2 3 tag Flag vector


title: subject ID 70066-0 at diease time point 4_Male, a T1D case and 0.7693361yrs old_450K array [3998909086_R05C01]

source_name: T1D case_Male_time point 4

tag: Sex

value: Male

value: T1D case

value: peripheral blood sample


title: Cdx2_Flag

value: Lineage depleted bone marrow

value: bone marrow

value: 48hrs post infection

value: WT


title: TENT4B_Replicate2

description: TENT4B fCLIP-seq from HepG2.2.15

data_processing:
For each fCLIP-seq library, pair-end reads were assembled with pear v0.9.10 and aligned to human genome GRCh38 with STAR 2.5.2b and HBV genome NCBI:U95551.1 with bowtie2.2.6.
Raw read coverage of fCLIP-seq libraries were computed with bedtools v2.26.0.
Genome_build: hg38
Supplementary_files_format_and_content: .depth files are in BED format and the last column represents the number of fCLIP reads mapped at the single nucleotide location.

growth_protocol: HepG2.2.15 cells were grown in DMEM (Welgene, LM 001-05) containing 10% FBS (Welgene, S001-01).

extract_protocol:
HepG2.2.15 cells on two 150 mm dishes were cross-linked with 0.1% paraformaldehyde (Pierce, 28906), harvested and lysed. Each 15 μg antibody (Normal mouse IgG, Santa Cruz, sc-2025; TENT4A, labmade; TENT4B, labmade) was conjugated to protein A and G sepharose beads (1:1 mix, total 20 μl, GE Healthcare, 17-5138-01 and 17-0618-01, respectively). Lysates were incubated with antibody-conjugated beads, and RNAs were purified from the eluates followed by DNaseI treatment and washing.
1 μg of input RNAs or RNAs from each sample were prepared for the libraries. rRNAs were depleted twice by Ribo-Zero kit (Illumina, TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 20020596). The rRNA-depleted RNAs were ligated to the 3′ adaptor and purified by 6% urea-PAGE gel (80–500 nt, corresponding to 50–470 nt RNAs which were fragmented by sonication) followed by 5′ phosphorylation, 5′ adaptor ligation, reverse-transcription and PCR amplification. The fCLIP-seq libraries were sequenced by paired-end run (151×151 cycles) on Illumina platform (MiSeq) with PhiX control library v3 (Illumina).

tag: cell line

tag: fraction

value: Co-immunoprecipitated RNAs


title: CIE vapor, ethanol drinker, mouse 1, medial prefrontal cortex

tag: brain region


title: subject ID 25505-0 at diease time point 5_Female, a T1D control and 3.0088980yrs old_450K array [3998909086_R03C01]

source_name: T1D control_Female_time point 5

tag: subject id

tag: disease time point

value: Female

value: T1D control


title: USSC 5/03 7d XXL miRNA

value: USSC

value: Cord blood derived unrestricted somatic stem cells


title: genomic DNA from distal femur trabecular bone Ptro04

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

description: medial condyle distal femur trabecular bone from chimpanzee

hyb_protocol: Infinium MethylationEPIC array

scan_protocol: standard illumina scanner

data_processing:
Raw fluorescent data were normalized using the Noob background correction    method with dye-bias normalization followed with a between-array    normalization method (functional normalization) as implemented in the R    package minfi. After normalization, methylation values (beta values) for    each site were calculated as the ratio of methylated probe signal intensity    to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than    10% of samples were removed. Cross-reactive probes, probes containing SNPs    at the CpG site, probes detecting SNP information, probes detecting    methylation at non-CpG sites, and probes targeting sites within the sex    chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to each nonhuman    primate genome were also removed. Filtering for these files was based    on Hernando-Herraez  et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate    nonhuman primate genome, and only those probes that successfully mapped to    the genome, had only 1 unique hit, and targeted CpG sites were retained.    Additionally, probes were kept for subsequent analyses only if they had 0    mismatches in 5bp closest to and including the CpG site, and had 0-2    mismatches in 45bp not including the CpG site.
- Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M,       Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and       great ape evolution. PLOS Genet 2013;9:e1003763.
Nonhuman Primate Genome: Pan troglodytes

label: Cy5 and Cy3

organism: Pan troglodytes

label_protocol: 400ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)

extract_protocol: genomic DNA was extracted from pulverized trabecular bone using a phenol-cholorform protocol

value: male

tag: age (years)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: NMG_Replicate2

description: Negative control for fCLIP-seq from HepG2.2.15

tag: cell line

tag: fraction

tag: antibody

value: NMG


title: FGIN-1-27 replicate 3

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
Reads were aligned to the mm10 genome and the GRCm38 v87 transcriptome with STAR v2.5.2a using default parameters and output tracks normalized by RPM (--outWigNorm RPM).
RSEM v1.3 was used to calculate gene counts and TPMs on the transcriptome-aligned reads.
Differential expression analysis was performed in R v3.5.2, using DESeq2 v1.22.2.
Pathway enrichment analysis was performed on the differentially expressed genes using InnateDB v5.4, against the INOH, KEGG and REACTOME databases.
Heatmaps were generated with the R package, pheatmap. Integrative Genomics Viewer v2.4.19 was used for visualization of normalized bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM counts, RSEM TPM and DESeq2 results tab-delimited text files

molecule: polyA RNA

source_name: CD4 T cells from spleen & lymph nodes

growth_protocol: Purified CD4 T cells were activated with plate bound anti-CD3/anti-CD28 under Th17 polarization conditions

extract_protocol:
Total RNA extractions for RNA-seq were performed using the mirVana kit (Applied Biosystems). RNA concentration was measured using the Qubit RNA broad range assay in the Qubit Flurometer (Invitrogen) and RNA integrity was determined with Eukaryote Total RNA Nano Series II ChIP on a 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared using TruSeq RNA sample preparation kit (Illumina)
Oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors and PCR amplified to enrich for the fragments ligated to adaptors. The resulting cDNA libraries were verified and quantified on Agilent Bioanalyzer before they were sequenced (paired-end 2x75 bp).

treatment_protocol: Cells were treated with DMSO or FGIN-1-27 for 24 hours ( treatment started at 18 hours post cell plating)

tag: cell type

value: Th17 polarized CD4+ T Cells

tag: strain

tag: age

value: 8 weeks

tag: genotype

value: wild type


title: USSC 5/03 3d XXL miRNA

tag: treatment

value: Treatment with XXL-medium

tag: time point

value: day 3


title: FGIN-1-27 replicate 2


title: subject ID 14725-0 at diease time point 4_Female, a T1D case and 1.2292950yrs old_450K array [3998909085_R06C02]

source_name: T1D case_Female_time point 4

tag: subject id

tag: disease time point

tag: Sex

tag: t1d status

value: T1D case

tag: tissue

value: peripheral blood sample


title: USSC 5/03 native  miRNA

value: day 0


title: USSC 4/101 14d XXL miRNA

value: day 14


title: DMSO replicate 3


title: genomic DNA from distal femur trabecular bone Ptro02

source_name: distal femur trabecular bone from chimpanzee

tag: age (years)

value: medial condyle distal femur trabecular bone

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)


title: USSC 4/101 7d XXL miRNA

tag: cell line

tag: cell type

tag: treatment

tag: time point

value: day 7


title: FGIN-1-27 replicate 1

tag: strain

tag: age

tag: genotype


title: USSC 4/101 3d XXL miRNA


title: DMSO replicate 2


title: DMSO replicate 1


title: nip1_nip2_nip3_rep3_totalRNA

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Trimmed reads were aligned to ce11 reference genome using the STAR aligner with multipmapping options.
Read counts on exons was extracted using the FeatureCounts with --fraction option.
data was normalized  with DeSEQ2.
heatmaps and volcano plots were generated with a custom script on Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: bam, txt

organism: Caenorhabditis elegans

source_name: YA (young adults)

growth_protocol: C. elegans was grown at 20C, with HB101 bacteria on agar plates.

extract_protocol:
Trizol-Dnase
NEB NEXT Ultra

value: YA (young adults)


title: USSC 4/101 native miRNA


title: nip1_nip2_nip3_rep2_totalRNA


title: nip1_nip2_nip3_rep1_totalRNA


title: Chx10-Cre Rb1/p107-3 [ATAC-seq]

city: Irvine

first: Claudia

last: Benavente

state: CA

address: 839 Medical Sciences Ct, Sprague Hall 108

institute: University of California, Irvine

data_processing:
Reads were trimmed by Illumina adapters and base quality scores >20 and mapped to the mm10 genome with Bowtie2 (--dovetail -X 2000).
Duplicated reads were removed. Blacklist regions on the genome were excluded.
Peaks were called using MACS2 (-p 0.0001 -g mm -f BAMPE --nomodel --nolambd).
BigWig files were created using bedGraphToBigWig.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: bigWig files

source_name: Retina

extract_protocol:
Approximately 50,000 cells were harvested for ATAC-seq for each replicate. Briefly, retinae were dissociated, flow sorted into EGFP- or EGFP+, assessed for cell viability, counted, and washed with PBS.
ATAC-seq was performed as previously described (Buenrostro et al. 2015, Nature 523:486-490).

tag: genotype/variation

value: Chx10-Cre Rb1/p107

tag: tissue

value: Retina EGFP+ cells


title: Chx10-Cre Rb1/p107-2 [ATAC-seq]


title: nip2_tb1609_rep3_totalRNA


title: Chx10-Cre Rb1/p107-1 [ATAC-seq]


title: Chx10-Cre Rb1/p107/Hells-3 [ATAC-seq]

value: Chx10-Cre Rb1/p107/Hells


title: subject ID 25505-0 at diease time point 4_Female, a T1D control and 1.2758385yrs old_450K array [3998909086_R02C01]

source_name: T1D control_Female_time point 4

tag: subject id

tag: disease time point

tag: Sex

value: Female

tag: t1d status

value: T1D control


title: nip2_tb1609_rep1_totalRNA


title: Chx10-Cre Rb1/p107/Hells-2 [ATAC-seq]


title: subject ID 00707-0 at diease time point 3_Male, a T1D case and 8.4709103yrs old_450K array [3998909085_R06C01]

source_name: T1D case_Male_time point 3

value: Male


title: subject ID 31320-0 at diease time point 3_Male, a T1D control and 7.6468172yrs old_450K array [3998909085_R02C01]

source_name: T1D control_Male_time point 3


title: subject ID 00707-0 at diease time point 2_Male, a T1D case and 1.1526352yrs old_450K array [3998909085_R05C01]

source_name: T1D case_Male_time point 2


title: subject ID 31320-0 at diease time point 5_Male, a T1D control and 11.6167009yrs old_450K array [3998909085_R04C01]

source_name: T1D control_Male_time point 5


title: subject ID 00707-0 at diease time point 4_Male, a T1D case and 9.4839151yrs old_450K array [3998909085_R01C02]


title: subject ID 00707-0 at diease time point 5_Male, a T1D case and 12.6050650yrs old_450K array [3998909085_R02C02]


title: subject ID 11309-0 at diease time point 4_Male, a T1D control and 0.7967146yrs old_450K array [3998909085_R04C02]

source_name: T1D control_Male_time point 4


title: subject ID 31320-0 at diease time point 4_Male, a T1D control and 8.5886379yrs old_450K array [3998909085_R03C01]


title: nip1_tb1601_rep2_totalRNA


title: nip2_tb1609_rep2_totalRNA


title: Chx10-Cre Rb1/p107/Hells-1 [ATAC-seq]


title: subject ID 18963-0 at diease time point 5_Male, a T1D case and 11.4195756yrs old_450K array [3998909079_R06C02]


title: subject ID 31320-0 at diease time point 2_Male, a T1D control and 0.7638604yrs old_450K array [3998909085_R01C01]

source_name: T1D control_Male_time point 2


title: USSC SA 4/146 7d XXL mRNA

data_processing:
Read alignment: STAR aligner was used to map reads against the reference genome hg38. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: Reads were counted in an unstranded fashion on a gene-basis within annotated exons downloaded from Ensembl Genes V85 using htseq-count (special paramters: -t exon -i gene_id -s no).
Normalization: edgeR was used to normalize read counts per sample and genes were filtered for counts-per-million > 1 in at least one sample. CPM were calculated with the cpm-function of edgeR on all filtered genes.
Genome_build: hg38
Supplementary_files_format_and_content: CPM table

source_name: USSC cell line

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (#RS-122-2301, Illumina) folllowing manufacturer's guidelines.

value: USSC

value: Cord blood derived unrestricted somatic stem cells


title: USSC SA 4/146 3d XXL mRNA

value: Treatment with XXL-medium


title: USSC 4/146 native  mRNA


title: USSC 5/03 14d XXL mRNA


title: USSC 5/03 7d XXL mRNA


title: USSC 4/146 14d XXL mRNA


title: nip1_tb1601_rep1_totalRNA


title: Rb1/p107/Hells-1 [ATAC-seq]

value: Retina EGFP- cells


title: subject ID 18963-0 at diease time point 3_Male, a T1D case and 4.0766598yrs old_450K array [3998909079_R04C02]

value: T1D case


title: subject ID 18963-0 at diease time point 4_Male, a T1D case and 5.1690623yrs old_450K array [3998909079_R05C02]

value: peripheral blood sample


title: Chx10-Cre Rb1/p107-2 [retina RNA-seq]

description:
5-7D-265
processed data file: raw_counts.tsv

data_processing:
Reads were trimmed by base quality scores >20 and mapped to the mm10 genome with Tophat2.
Counts per gene were calculated by counting reads mapping to constitutive exons using featureCount.
Counts for each gene were then analyzed with the R package DESeq2 to identify differentially expressed genes. A 5% false discovery rate cutoff was used for significance.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw_counts.tsv: Tab-separated text file includes raw counts.

extract_protocol:
Total RNA was isolated using the RNA Micro Kit (Qiagen).
500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA fragmentation through the adenylation of end-repaired cDNA fragments and cleanup (TruSeq Stranded mRNA, Illumina). The collected sample was cleaned with AMPure XP beads (Beckman Coulter) and eluted in 20 μl of 10 mM Tris buffer, pH 8, 0.1% Tween 20. 500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA.

value: Retina


title: nip3_qe20_rep2_totalRNA


title: USSC 5/03 3d XXL mRNA

value: day 3


title: Chx10-Cre Rb1/p107-3 [retina RNA-seq]

description:
6-7D-270
processed data file: raw_counts.tsv


title: nip1_nip2_rep3_totalRNA


title: subject ID 18963-0 at diease time point 2_Male, a T1D case and 1.2484600yrs old_450K array [3998909079_R03C02]


title: USSC 5/03 native  mRNA

value: day 0


title: USSC 4/101 14d XXL mRNA

value: day 14


title: Chx10-Cre Rb1/p107-1 [retina RNA-seq]

description:
4-7D-261
processed data file: raw_counts.tsv


title: nip3_qe20_rep1_totalRNA

value: YA (young adults)


title: subject ID 13629-0 at diease time point 5_Male, a T1D control and 12.6598220yrs old_450K array [3998909079_R01C02]


title: subject ID 00581-0 at diease time point 4_Female, a T1D case and 2.9103354yrs old_450K array [3998909086_R05C02]


title: nip3_qe17_rep3_totalRNA


title: USSC 4/101 3d XXL mRNA


title: nip3_qe17_rep2_totalRNA


title: subject ID 13629-0 at diease time point 4_Male, a T1D control and 5.1170431yrs old_450K array [3998909079_R06C01]


title: subject ID 13629-0 at diease time point 3_Male, a T1D control and 4.0985626yrs old_450K array [3998909079_R05C01]


title: Chx10-Cre Rb1/p107/Hells-3 [retina RNA-seq]

description:
3-HTKO-776
processed data file: raw_counts.tsv


title: Chx10-Cre Rb1/p107/Hells-2 [retina RNA-seq]

description:
2-HTKO-774
processed data file: raw_counts.tsv


title: Input_Replicate1

description: Input control for fCLIP-seq from HepG2.2.15

source_name: HepG2.2.15 cells

tag: fraction

value: Input RNAs


title: TENT4A_Replicate1

description: TENT4A fCLIP-seq from HepG2.2.15

value: Co-immunoprecipitated RNAs

tag: antibody


title: Chx10-Cre Rb1/p107/Hells-1 [retina RNA-seq]

description:
1-HTKO-709
processed data file: raw_counts.tsv

value: Chx10-Cre Rb1/p107/Hells


title: NMG_Replicate1

value: NMG


title: TENT4B_Replicate1

description: TENT4B fCLIP-seq from HepG2.2.15


title: nip2_nip3_rep3_totalRNA


title: subject ID 00060-0 at diease time point 5_Male, a T1D case and 9.3908282yrs old_450K array [3998909079_R02C01]

source_name: T1D case_Male_time point 5


title: USSC 4/101 7d XXL mRNA

value: day 7


title: nip2_nip3_rep2_totalRNA


title: USSC 4/101 native mRNA


title: nip2_nip3_rep1_totalRNA


title: subject ID 00553-0 at diease time point 4_Male, a T1D control and 8.2847365yrs old_450K array [3998909068_R05C02]

value: Male

value: T1D control


title: subject ID 00863-0 at diease time point 5_Female, a T1D control and 8.9144422yrs old_450K array [3998909079_R01C01]

value: Female


title: nip3_qe17_rep1_totalRNA


title: wt_rep3_totalRNA

value: wt


title: subject ID 20770-0 at diease time point 5_Male, a T1D case and 9.4346338yrs old_450K array [3998909068_R03C02]


title: wt_rep1_totalRNA


title: subject ID 00553-0 at diease time point 3_Male, a T1D control and 6.3545517yrs old_450K array [3998909068_R04C02]


title: wt_rep2_totalRNA


title: subject ID 20770-0 at diease time point 3_Male, a T1D case and 5.0266940yrs old_450K array [3998909068_R02C02]


title: EE_nipnip2_3_IP

description:
5` independent small RNA-seq
NRDE3:FLAG_IP
IP_embryo_rawcounts.csv
IP_embryo_rawcounts_TE.csv

data_processing:
Reads were trimmed with CutAdapt.
Trimmed reads were aligned to ce11 reference genome using the STAR aligner with multipmapping options.
Read counts on exons was extracted using the FeatureCounts with --fraction option.
data was normalized with unique reads per million or with DeSEQ2.
heatmaps and volcano plots were generated with a custom script on Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: csv

source_name: early embyo mixed stage

extract_protocol:
Trizol-Dnase
Illumina TruSeq small RNA

value: embryo

tag: ip tag

value: FLAG

value: anti-FLAG M2


title: Nano OF5 mouse

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

data_processing:
The paired reads were merged using the PEAR (v 0.9.10)
Low quality reads were filtered out using fastq_quality_filter with following options: -q 30, -p 90 -Q33
Reads were again filtered by requiring perfect matches to the primer sequences (plus 5bp) which were used for amplification. In house scripts were used
Genome_build: They were not aligned to the genomic sequence
Supplementary_files_format_and_content: fasta (target site selected)

source_name: Mouse brain

extract_protocol:
Total genomic DNAs were isolated. On-target and designed off-target was PCR amplified between 150 and 200 bp size (targeted PCR).
Sequencing libraries were prepared using TruSeq DNA samples prep Kit

value: brain

tag: protocol

value: Nano


title: subject ID 13629-0 at diease time point 2_Male, a T1D control and 0.7830253yrs old_450K array [3998909079_R04C01]

value: peripheral blood sample


title: Chx10-Cre Rb1/p107/Hells-2 [tumor RNA-seq]

data_processing:
Illumina Casava software used for basecalling
Sequencing reads were aligned to the mouse reference genome (GRCm38, ENSEMBL v.92) using STAR (v2.5.2a)
Each read pair was allowed a maximum number of mismatches of 10. Each read was allowed a maximum number of multiple alignments of 3.
Gene counts for each sample were produced using HTSeq (v0.6.1p1)
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files

source_name: Chx10-Cre Rb1/p107/Hells_tumor

extract_protocol:
Total RNA was isolated using the RNA Micro Kit (Qiagen).
500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA fragmentation through the adenylation of end-repaired cDNA fragments and cleanup (TruSeq Stranded mRNA, Illumina). The collected sample was cleaned with AMPure XP beads (Beckman Coulter) and eluted in 20 μl of 10 mM Tris buffer, pH 8, 0.1% Tween 20.500 ng of total RNA was used to create the RNA-seq library following the manufacturer’s protocol from purification, mRNA

tag: strain background

tag: tissue type

value: tumor

tag: tumor type

value: retinoblastoma


title: Chx10-Cre Rb1/p107-1 [tumor RNA-seq]

source_name: Chx10-Cre Rb1/p107_tumor

value: Chx10-Cre Rb1/p107


title: Chx10-Cre Rb1/p107/Hells-1 [tumor RNA-seq]


title: Chx10-Cre Rb1/p107/Hells-3 [tumor RNA-seq]


title: Chx10-Cre Rb1/p107-2 [tumor RNA-seq]


title: Chx10-Cre Rb1/p107-3 [tumor RNA-seq]


title: subject ID 20770-0 at diease time point 2_Male, a T1D case and 0.7748118yrs old_450K array [3998909068_R01C02]

value: T1D case


title: EE_nipnip2_2_IP


title: subject ID 14179-0 at diease time point 5_Male, a T1D control and 7.3292266yrs old_450K array [3998909068_R05C01]


title: Nano OF3 mouse


title: Nano OF2 mouse


title: subject ID 14179-0 at diease time point 4_Male, a T1D control and 4.1505818yrs old_450K array [3998909068_R04C01]


title: MV1

city: San Francisco

first: Nadia

last: Roan

state: California

address: 1650 Owens Street

institute: University of California at San Francisco

description:
MV1
processed data file:  Normalized_counts_MV.xlsx

data_processing:
Trimmed reads were aligned to the Genome Reference Consortium Human Build 38 reference genome (GenBank Assembly Accession: GCA_000001405.15) using TopHat2 v2.1.0 with the following parameters: global alignment, no mismatch in the 20 base pair seed, up to two mismatches in the read, library type fr – unstranded, and mate inner distance 50. Aligned reads were filtered by removing reads with low mapping quality (below 20) and keeping singletons.
Filtered reads were annotated to the Genome Reference Consortium Human Build 38 reference transcriptome (RefSeq Assembly Accession: GCF_000001405.26) using the Partek E/M annotation model (Partek Flow, build version 5.0.16.1128) with the following parameters: junction reads required to match introns (set to true), strict paired-end compatibility not required (set to false), and strand specificity not required (set to false). Filtered reads were normalized using TPM (Transcripts Per Kilobase Million). Low expressing transcripts were removed, with lowest maximum coverage set to 1.0.
Differential gene expression was calculated by ANOVA in a paired test (paired on donor ID), by using treatment as the fixed factor and ID as the random factor. Differentially expressed transcripts were identified based on fold change (³ ± 1.5), with significance level set at P < 0.05.
Genome_build: Genome Reference Consortium Human Build 38 reference genome (GenBank Assembly Accession: GCA_000001405.15)
Supplementary_files_format_and_content: Excel files include counts normalized by transcripts per killobase million (TPM) + 1E-4.

source_name: MV

growth_protocol: eSF and endometrial epithelial cells (eEC) were isolated from endometrial biopsies from women of reproductive age undergoing benign gynecologic procedures and maintained in vitro.

extract_protocol:
Total RNA was extracted from eSF or eEC cultures (1 μg of total RNA from each sample) using the High Pure RNA Isolation kit (Roche) according to the manufacturer’s protocol. Quality of isolated RNA was confirmed using Nanodrop for RNA purity (OD 260/280) and Bioanalyzer (Agilent) for RNA integrity. RNA samples with an RNA Integrity Number (RIN) > 6 were used for library preparation for mRNA sequencing.
All RNA sequencing (RNAseq) procedures were performed by Novogene. Library preparation was performed using 1 μg of total RNA from each sample with the NEBNext Ultra RNA Library Prep Kit (New England BioLabs, Inc.). Briefly, polyadenylated (polyA) RNAs were selected using NEBNext Magnetic Oligo d(T)25 Beads (New England BioLabs, Inc.). Following polyA selection, RNA was fragmented and primed for first-strand cDNA synthesis, followed by second-strand synthesis. Double stranded cDNA was purified using Agencourt AMPure XP Beads (Beckman Coulter), the fragments were end-repaired, 3' adenylated, and NEBNext Adaptor with hairpin loop structure (Illumina) was ligated to prepare for hybridization. cDNA fragments ~350 bp in length were selected using the Agencourt AMPure XP system (Beckman Coulter) and PCR amplification was performed to create the final cDNA library.
Paired-end RNAseq, at >20 million reads per sample was sequenced on an Illumina HiSeq platform (Illumina), per the manufacturer’s instructions.

treatment_protocol: Endometrial SF were seeded into 24-well plates and cultured in SCM until confluent, while eEC glands were seeded into 24-well, thin layer Corning Matrigel Matrix Plates (VWR) and cultured in KSFM until domes were apparent. Cells were treated for 6 h at 37°C as follows: 1) with media alone, 2) with 1% SP, 3) with 1% SP pretreated for 20 h at 37°C, 4) with 100 mg/ml peptides, 5) with 100 mg/ml amyloids, or 6) with 0.1 Eu/ml LPS (equivalent to the levels of LPS present in 1% SP, as determined by LAL endotoxin analysis). In a separate set of experiments, cells were treated with as follows: 1) with media alone, 2) with 1% reconstituted SP, or 3) with 1% of the MV-enriched fraction. Cultured cells were harvested and RNA was isolated, as detailed below.

value: Endometrium

tag: cell type

value: Endometrial stromal fibroblast

tag: sample group

value: MV


title: Recon_SP3

description:
Recon_SP3
processed data file:  Normalized_counts_MV.xlsx


title: MV2

description:
MV2
processed data file:  Normalized_counts_MV.xlsx


title: Recon_SP2

description:
Recon_SP2
processed data file:  Normalized_counts_MV.xlsx


title: MV3

description:
MV3
processed data file:  Normalized_counts_MV.xlsx


title: Mock1

description:
Mock1
processed data file:  Normalized_counts_MV.xlsx

source_name: Mock

value: Mock


title: Mock3

description:
Mock3
processed data file:  Normalized_counts_MV.xlsx


title: Recon_SP1

description:
Recon_SP1
processed data file:  Normalized_counts_MV.xlsx


title: EE_wt_3_IP

tag: age


title: eEC_SP_deplete_3

description:
eEC_SP_deplete_3
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrial epithelial cell


title: EE_wt_1_IP


title: subject ID 14179-0 at diease time point 3_Male, a T1D control and 3.1129363yrs old_450K array [3998909068_R03C01]

value: Male

value: T1D control


title: eEC_SP_deplete_2

description:
eEC_SP_deplete_2
processed data file:  Normalized_counts_eEC.xlsx


title: EE_nipnip2_3_input

description:
5` independent small RNA-seq
NRDE3:FLAG_IP
input_embryo_rawcounts.csv
input_embryo_rawcounts_TE.csv

value: embryo


title: Control OF5 mouse

tag: strain

value: Control


title: eEC_SP_deplete_1

description:
eEC_SP_deplete_1
processed data file:  Normalized_counts_eEC.xlsx


title: Control OF3 mouse


title: Mock2

description:
Mock2
processed data file:  Normalized_counts_MV.xlsx


title: subject ID 00180-0 at diease time point 3_Female, a T1D case and 6.2861054yrs old_450K array [3998909038_R06C02]

source_name: T1D case_Female_time point 3

value: Female


title: eEC_SP_3

description:
eEC_SP_3
processed data file:  Normalized_counts_eEC.xlsx


title: EE_wt_3_input

value: FLAG

value: anti-FLAG M2


title: Control OF2 mouse

value: brain


title: subject ID 30541-0 at diease time point 5_Female, a T1D case and 13.9685147yrs old_450K array [3998909038_R03C02]

source_name: T1D case_Female_time point 5

value: peripheral blood sample


title: subject ID 30541-0 at diease time point 3_Female, a T1D case and 7.2142368yrs old_450K array [3998909038_R02C02]


title: genomic DNA from distal femur trabecular bone Ptro03

description: medial condyle distal femur trabecular bone from chimpanzee

value: male

tag: age (years)

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: eEC_SP_1

description:
eEC_SP_1
processed data file:  Normalized_counts_eEC.xlsx

tag: tissue

tag: cell type

tag: sample group


title: Control OF1 mouse

tag: strain

tag: protocol


title: eEC_SP_2

description:
eEC_SP_2
processed data file:  Normalized_counts_eEC.xlsx


title: aa_3_heavy_stauro

city: sherbrooke

first: Mustafa

last: Malik Ghulam

state: quebec

address: 3201 rue mignault

country: Canada

institute: university of sherbrooke

data_processing:
TrimmomaticPE: Started with arguments: -phred33 R1.fastq.gz R2.fastq.gz R1.trimmed.paired.fastq.gz R1.trimmed.unpaired.fastq.gz R2.trimmed.paired.fastq.gz R2.trimmed.unpaired.fastq.gz ILLUMINACLIP:Adapters-PE_NextSeq.fa:2:12:10:8:true TRAILING:30
STAR --runMode genomeGenerate --genomeDir genome/ --genomeFastaFiles Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.all.fa --sjdbGTFfile Saccharomyces_cerevisiae.R64-1-1.90.gtf --sjdbOverhang 75
STAR --runMode alignReads --genomeDir genome/ --readsFilesIn R1.trimmed.paired.fastq.gz R2.trimmed.paired.fastq.gz --readsFilesCommand zcat --outReadsUnmapped Fastx --outFilterType BySJout --outStd Log --outSAMunmapped None --outSAMtype BAM SortedByCoordinate
Rsubread featureCounts(Aligned.sortedByCoord.out.bam, genome=Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.all.fa, annot.ext=Saccharomyces_cerevisiae.R64-1-1.90.gtf, isGTFAnnotationFile=TRUE, GTF.featureType="exon", GTF.attrType="gene_id",countChimericFragments=FALSE, largestOverlap=FALSE, isPairedEnd=TRUE, useMetaFeatures=TRUE, requireBothEndsMapped=TRUE, strandSpecific=2, minOverlap=10, autosort=TRUE, allowMultiOverlap=FALSE, reportReads=TRUE, juncCounts=FALSE,fraction=FALSE, countMultiMappingReads=FALSE)
Genome_build: Saccharomyces_cerevisiae.R64-1-1
Supplementary_files_format_and_content: comma-separated-value (csv) files holding the name of every gene and their abundance value for each sample (CPM or TPM)

organism: Saccharomyces cerevisiae

source_name: ul30aa strain #3

growth_protocol: Cells grown in Yc media at 30°C with or without staurosporine treatment

extract_protocol:
RNA was extracted from cultures growing in exponential phase. Total RNA was extracted from the culture. Light and heavy fractions RNA were purified after polysome fractionation
RNA libraries were prepared using NEBNExt Poly(A) mRNA Isolation Module and NEBNExt Ultra II Directional RNA Library Prep Kit

tag: background

value: BY background

value: ul30aa strain #3

tag: growth protocol

value: grown to log phase in synthetic minimal media with staurosporine

tag: rna fraction

value: RNA from heavy polysome fractions (Poly2+Poly3), polyA enriched, fragmented (200nt)


title: CIE vapor, ethanol drinker, mouse 12, medial prefrontal cortex

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, medial prefrontal cortex

tag: vapor treatment

value: CIE

tag: drinking treatment

value: Drinker

tag: brain region

value: prefrontal cortex

tag: Sex


title: CIE vapor, ethanol drinker, mouse 4, medial prefrontal cortex


title: YA_nip3_qe17_3

description:
5` independent small RNA-seq
YA_rawcounts.csv
YA_rawcounts_TEs.csv

source_name: whole animal

tag: age

value: adult


title: Nano OF1 mouse

value: Nano


title: subject ID 30541-0 at diease time point 2_Female, a T1D case and 1.2292950yrs old_450K array [3998909038_R01C02]

source_name: T1D case_Female_time point 2

tag: subject id

tag: disease time point

tag: t1d status

value: T1D case


title: eEC_peptide_3

description:
eEC_peptide_3
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrium

value: Endometrial epithelial cell


title: EE_wt_1_input

description:
5` independent small RNA-seq
input_embryo_rawcounts.csv
input_embryo_rawcounts_TE.csv

value: embryo


title: subject ID 14179-0 at diease time point 2_Male, a T1D control and 0.8323066yrs old_450K array [3998909068_R02C01]

value: Male

value: T1D control


title: YA_nip3_qe17_2


title: eEC_peptide_2

description:
eEC_peptide_2
processed data file:  Normalized_counts_eEC.xlsx


title: EE_nipnip2_2_input

tag: ip tag

value: FLAG

tag: antibody

value: anti-FLAG M2


title: subject ID 37997-0 at diease time point 5_Male, a T1D control and 15.9479808yrs old_450K array [3998909038_R05C01]

source_name: T1D control_Male_time point 5

tag: tissue

value: peripheral blood sample


title: aa_3_total_stauro

value: BY background

value: ul30aa strain #3

value: Total RNA, polyA enriched, fragmented (200nt)


title: aa_3_light_stauro

value: grown to log phase in synthetic minimal media with staurosporine

value: RNA from light polysome fractions (40S+60S+80S), polyA enriched, fragmented (200nt)


title: subject ID 37997-0 at diease time point 4_Male, a T1D control and 9.9822040yrs old_450K array [3998909038_R04C01]

source_name: T1D control_Male_time point 4


title: bb_3_total_stauro

source_name: ul30bb strain #3

value: ul30bb strain #3


title: genomic DNA from distal femur trabecular bone Ptro01

source_name: distal femur trabecular bone from chimpanzee

value: unknown

tag: age (years)

value: medial condyle distal femur trabecular bone

tag: femur length (mm)

tag: bicondylar femur length (mm)

tag: maximum femur length (mm)

tag: superior shaft width (mm)

tag: superior shaft depth (mm)

tag: middle shaft width (mm)

tag: middle shaft depth (mm)

tag: inferior shaft width (mm)

tag: inferior shaft depth (mm)

tag: head height (mm)

tag: head length (mm)

tag: head width (mm)

tag: anatomical neck length (mm)

tag: anatomical neck height (mm)

tag: anatomical neck depth (mm)

tag: biomechanical neck length (mm)

tag: proximal width (mm)

tag: lesser trochanter to head (mm)

tag: lesser trochanter to neck (mm)

tag: lesser to greater trochanter (mm)

tag: medial condyle height (mm)

tag: medial condyle depth (mm)

tag: medial condyle width (mm)

tag: lateral condyle height (mm)

tag: lateral condyle depth (mm)

tag: lateral condyle width (mm)

tag: intercondylar notch width (mm)

tag: intercondylar notch depth (mm)

tag: bicondylar width (mm)


title: eEC_peptide_1

description:
eEC_peptide_1
processed data file:  Normalized_counts_eEC.xlsx

tag: tissue

tag: cell type

tag: sample group


title: subject ID 37997-0 at diease time point 3_Male, a T1D control and 8.9883641yrs old_450K array [3998909038_R03C01]

source_name: T1D control_Male_time point 3

tag: subject id

tag: disease time point

tag: age

tag: Sex

tag: t1d status


title: YA_nip2nip3_3

value: adult


title: eEC_Mock_3

description:
eEC_Mock_3
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrium


title: YA_nip2nip3_2


title: WT_3_total_stauro

source_name: wild type strain #3

tag: background

tag: strain

value: wild type strain #3

tag: growth protocol

tag: rna fraction


title: subject ID 37997-0 at diease time point 2_Male, a T1D control and 1.2977413yrs old_450K array [3998909038_R02C01]

source_name: T1D control_Male_time point 2


title: YA_nip3_qe17_1


title: eEC_Mock_1

description:
eEC_Mock_1
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrial epithelial cell


title: subject ID 00884-0 at diease time point 4_Female, a T1D case and 1.9849418yrs old_450K array [3999120164_R05C02]

source_name: T1D case_Female_time point 4

value: Female

value: T1D case


title: aa_2_heavy_stauro

source_name: ul30aa strain #2

value: ul30aa strain #2

value: RNA from heavy polysome fractions (Poly2+Poly3), polyA enriched, fragmented (200nt)


title: subject ID 00902-0 at diease time point 5_Male, a T1D control and 1.4784394yrs old_450K array [3999120164_R04C02]

value: Male

value: T1D control

value: peripheral blood sample


title: aa_2_total_stauro

value: BY background

value: Total RNA, polyA enriched, fragmented (200nt)


title: eEC_Mock_2

description:
eEC_Mock_2
processed data file:  Normalized_counts_eEC.xlsx


title: YA_wt_3


title: eEC_LPS_3

description:
eEC_LPS_3
processed data file:  Normalized_counts_eEC.xlsx


title: YA_wt_1


title: eEC_LPS_1

description:
eEC_LPS_1
processed data file:  Normalized_counts_eEC.xlsx


title: WT_2_total_stauro

source_name: wild type strain #2

value: wild type strain #2

value: grown to log phase in synthetic minimal media with staurosporine


title: bb_2_total_stauro

source_name: ul30bb strain #2

value: ul30bb strain #2


title: subject ID 00600-0 at diease time point 5_Male, a T1D case and 2.0506502yrs old_450K array [3999120164_R02C02]

source_name: T1D case_Male_time point 5


title: eEC_amyloid_3

description:
eEC_amyloid_3
processed data file:  Normalized_counts_eEC.xlsx


title: subject ID 00600-0 at diease time point 4_Male, a T1D case and 1.8015058yrs old_450K array [3999120164_R01C02]

source_name: T1D case_Male_time point 4


title: subject ID 00884-0 at diease time point 5_Female, a T1D case and 2.9514031yrs old_450K array [3999120164_R06C02]

source_name: T1D case_Female_time point 5


title: aa_3_heavy_untreated

source_name: ul30aa strain #3

value: ul30aa strain #3

value: grown to log phase in synthetic minimal media


title: eEC_amyloid_2

description:
eEC_amyloid_2
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrium


title: aa_3_light_untreated

value: RNA from light polysome fractions (40S+60S+80S), polyA enriched, fragmented (200nt)


title: YA_nip2nip3_1

source_name: whole animal

value: adult


title: eEC_LPS_2

description:
eEC_LPS_2
processed data file:  Normalized_counts_eEC.xlsx

value: Endometrial epithelial cell


title: aa_2_light_stauro


title: subject ID 00690-0 at diease time point 5_Male, a T1D control and 1.4291581yrs old_450K array [3999120164_R06C01]


title: eEC_amyloid_1

description:
eEC_amyloid_1
processed data file:  Normalized_counts_eEC.xlsx


title: subject ID 00539-0 at diease time point 5_Male, a T1D case and 2.1054073yrs old_450K array [3999120164_R04C01]

value: T1D case


title: eSF_SP_deplete_2

description:
eSF_SP_deplete_2
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrial stromal fibroblast


title: eSF_SP_deplete_3

description:
eSF_SP_deplete_3
processed data file:  Normalized_counts_eSF.xlsx


title: subject ID 00539-0 at diease time point 4_Male, a T1D case and 0.5859001yrs old_450K array [3999120164_R03C01]


title: bb_3_total_untreated

value: ul30bb strain #3


title: WT_3_total_untreated

value: wild type strain #3


title: subject ID 00625-0 at diease time point 5_Male, a T1D control and 2.0041068yrs old_450K array [3999120164_R02C01]

value: Male

value: T1D control


title: ATF7+/+ from F0 pLPD rep8

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

country: Japan

institute: RIKEN

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-8

hyb_protocol: Samples are hybridized to the Mouse Gene 1.0 ST Array (Affymetrix) according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G according to the manufacturer's instructions..

data_processing:
The obtained data were converted to binary file using R, affxparser, and analyzed using the Expression Console software (Affymetrix). GSM2656114, GSM2656115 and GSM2656116 were used as wild-type from F0 pCD rep6, 7 and 8, respectively. Normalization was performed using the RMA algorithm. Signal intensities of hybridization control were ommited for downstream analysis.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps
Normalized signal intensity exported from Expression Console software.

source_name: ATF7+/+, F1 liver, pLPD

label_protocol: cDNA is labeled using by WT terminal labeling kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: Median lobe of liver was collected from F1 male or female mouse at three weeks age.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: F0 male mice were treated by control diet or low protein diet at 3-12 weeks age.

tag: paternal diet

value: paternal low protein diet

tag: genotype

value: F1 liver


title: LLC/luc BM2nd

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

country: Taiwan

institute: NHRI

hyb_protocol: operated by Genetech Biotech Co., Ltd

scan_protocol: operated by Genetech Biotech Co., Ltd

data_processing: quantile normalized (GenomeStudio 2011.1)

source_name: NSCLC_osteotropic subline

label_protocol: operated by Genetech Biotech Co., Ltd

growth_protocol: DMEM containing 10% FBS, 1% PSG

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit

tag: strain background

value: osteotropic Lewis Lung carcinoma cells

tag: cell subtype

value: in vivo selection 2nd generation


title: aa_2_light_untreated

value: BY background

value: ul30aa strain #2


title: subject ID 00748-0 at diease time point 5_Male, a T1D case and 11.3347023yrs old_450K array [3999120156_R06C02]

value: peripheral blood sample


title: aa_2_heavy_untreated

value: grown to log phase in synthetic minimal media

value: RNA from heavy polysome fractions (Poly2+Poly3), polyA enriched, fragmented (200nt)


title: eSF_SP_deplete_1

description:
eSF_SP_deplete_1
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrium


title: LLC/luc BM1st

value: in vivo selection 1st generation


title: LLC/luc P

source_name: NSCLC_parental cell

value: parental cell line


title: aa_3_total_untreated

value: ul30aa strain #3

value: Total RNA, polyA enriched, fragmented (200nt)


title: subject ID 00748-0 at diease time point 4_Male, a T1D case and 7.8576318yrs old_450K array [3999120156_R05C02]

value: T1D case


title: aa_2_total_untreated


title: bb_2_total_untreated

value: ul30bb strain #2


title: eSF_SP_1

description:
eSF_SP_1
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrial stromal fibroblast


title: subject ID 00748-0 at diease time point 3_Male, a T1D case and 5.9931554yrs old_450K array [3999120156_R04C02]

source_name: T1D case_Male_time point 3

value: Male


title: subject ID 00585-0 at diease time point 5_Female, a T1D control and 9.7111567yrs old_450K array [3999120156_R03C02]

source_name: T1D control_Female_time point 5

value: Female

value: T1D control


title: subject ID 00625-0 at diease time point 4_Male, a T1D control and 0.7693361yrs old_450K array [3999120164_R01C01]

source_name: T1D control_Male_time point 4


title: WT_2_total_untreated

value: wild type strain #2


title: eSF_peptide_3

description:
eSF_peptide_3
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pLPD rep7

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-7

value: paternal low protein diet

value: F1 liver


title: ATF7+/+ from F0 pLPD rep5

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-5


title: bb_3_heavy_stauro

source_name: ul30bb strain #3

value: BY background

value: ul30bb strain #3

value: grown to log phase in synthetic minimal media with staurosporine


title: eSF_SP_2

description:
eSF_SP_2
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrium


title: bb_3_light_stauro

value: RNA from light polysome fractions (40S+60S+80S), polyA enriched, fragmented (200nt)


title: subject ID 00585-0 at diease time point 3_Female, a T1D control and 6.6338125yrs old_450K array [3999120156_R01C02]

source_name: T1D control_Female_time point 3

value: peripheral blood sample


title: eSF_SP_3

description:
eSF_SP_3
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pLPD rep6

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-6


title: subject ID 00902-0 at diease time point 4_Male, a T1D control and 0.8049281yrs old_450K array [3999120164_R03C02]


title: eSF_peptide_1

description:
eSF_peptide_1
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pLPD rep4

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-4


title: ATF7+/+ from F0 pLPD rep2

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-2


title: ATF7+/+ from F0 pLPD rep3

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-3


title: eSF_Mock_3

description:
eSF_Mock_3
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pLPD rep1

description:
Whole gene expression data from liver in ATF7+/+_LPD
ATF7+/+_LPD-1


title: ATF7+/+ from F0 pCD rep8

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-8

source_name: ATF7+/+, F1 liver, pCD

value: paternal control diet


title: subject ID 38100-0 at diease time point 5_Female, a T1D case and 7.4880219yrs old_450K array [3999120156_R06C01]


title: WT_3_heavy_stauro

source_name: wild type strain #3

value: wild type strain #3

value: RNA from heavy polysome fractions (Poly2+Poly3), polyA enriched, fragmented (200nt)


title: eSF_Mock_2

description:
eSF_Mock_2
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pCD rep7

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-7


title: WT_3_light_stauro


title: subject ID 00585-0 at diease time point 4_Female, a T1D control and 7.6687201yrs old_450K array [3999120156_R02C02]

source_name: T1D control_Female_time point 4


title: subject ID 38100-0 at diease time point 4_Female, a T1D case and 0.8021903yrs old_450K array [3999120156_R05C01]

source_name: T1D case_Female_time point 4

value: T1D case


title: bb_3_heavy_untreated

value: grown to log phase in synthetic minimal media


title: ATF7+/+ from F0 pCD rep6

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-6


title: eSF_Mock_1

description:
eSF_Mock_1
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrial stromal fibroblast


title: subject ID 00756-0 at diease time point 3_Female, a T1D case and 2.6748802yrs old_450K array [3999120148_R06C01]

source_name: T1D case_Female_time point 3

value: Female


title: bb_3_light_untreated


title: subject ID 28245-0 at diease time point 5_Male, a T1D control and 7.4086242yrs old_450K array [3999120156_R03C01]

source_name: T1D control_Male_time point 5

value: Male

value: T1D control


title: WT_3_heavy_untreated


title: eSF_LPS_3

description:
eSF_LPS_3
processed data file:  Normalized_counts_eSF.xlsx


title: WT_3_light_untreated


title: ATF7+/+ from F0 pCD rep5

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-5


title: subject ID 00997-0 at diease time point 5_Male, a T1D case and 11.3702943yrs old_450K array [3999078044_R03C01]

source_name: T1D case_Male_time point 5


title: subject ID 00567-0 at diease time point 3_Male, a T1D control and 2.0971937yrs old_450K array [3999120148_R02C01]

source_name: T1D control_Male_time point 3


title: eSF_LPS_1

description:
eSF_LPS_1
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pCD rep3

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-3


title: eSF_LPS_2

description:
eSF_LPS_2
processed data file:  Normalized_counts_eSF.xlsx


title: eSF_amyloid_3

description:
eSF_amyloid_3
processed data file:  Normalized_counts_eSF.xlsx


title: subject ID 00997-0 at diease time point 4_Male, a T1D case and 2.7296372yrs old_450K array [3999078044_R02C01]

source_name: T1D case_Male_time point 4


title: bb_2_heavy_stauro

source_name: ul30bb strain #2

value: ul30bb strain #2


title: subject ID 00973-0 at diease time point 4_Female, a T1D control and 2.8254620yrs old_450K array [3999078044_R01C01]


title: bb_2_light_stauro


title: eSF_amyloid_1

description:
eSF_amyloid_1
processed data file:  Normalized_counts_eSF.xlsx


title: WT_2_heavy_stauro

source_name: wild type strain #2

value: wild type strain #2


title: eSF_amyloid_2

description:
eSF_amyloid_2
processed data file:  Normalized_counts_eSF.xlsx


title: ATF7+/+ from F0 pCD rep4

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-4

value: F1 liver


title: subject ID 00709-0 at diease time point 5_Female, a T1D case and 5.8781656yrs old_450K array [3999002104_R05C02]

source_name: T1D case_Female_time point 5


title: WT_2_light_stauro

value: BY background


title: subject ID 00709-0 at diease time point 4_Female, a T1D case and 2.0041068yrs old_450K array [3999002104_R04C02]


title: ATF7+/+ from F0 pCD rep1

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-1


title: bb_2_heavy_untreated


title: subject ID 00929-0 at diease time point 5_Female, a T1D control and 4.5037645yrs old_450K array [3999002104_R03C02]


title: 41B_15926_2W_PBMC

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm.
Normalized expression (normalized read counts) was obtained with DESeq2 v1.22.1.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis.
Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer’s instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample.
Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.

tag: set

value: B

tag: siv genotype

value: nef

value: PBMC

tag: timepoint (weeks)

tag: infection status


title: 42B_15899_2W_PBMC

tag: subject id

tag: tissue


title: ATF7+/– from F0 pLPD rep5

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-5

source_name: ATF7+/–, F1 liver, pLPD

value: paternal low protein diet


title: bb_2_light_untreated

value: RNA from light polysome fractions (40S+60S+80S), polyA enriched, fragmented (200nt)


title: ATF7+/– from F0 pLPD rep6

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-6


title: subject ID 00929-0 at diease time point 4_Female, a T1D control and 2.0150582yrs old_450K array [3999002104_R02C02]

data_processing:
SeSAMe (v1.0.0) pipeline was used to normalize data (via Noob), perform dye bias correction and perform probe specific QC (via pOOBAH).
ComBat was used to adjust for batch effects were batch was considered to be plate and row position combination
Filtered probes with a small Beta range (range < 0.05), those with known SNPs in the CpG site, and those located on the sex chromosomes
Mvalues.normalized.*.txt contains methylation M-value

extract_protocol: Standard Illumina Protocol

tag: disease time point

tag: age

value: peripheral blood sample


title: 64A_14875_2W_PBMC

value: A


title: 40B_2746_2W_PBMC


title: WT_2_heavy_untreated

value: RNA from heavy polysome fractions (Poly2+Poly3), polyA enriched, fragmented (200nt)


title: ATF7+/– from F0 pLPD rep7

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-7


title: subject ID 00929-0 at diease time point 3_Female, a T1D control and 1.3032170yrs old_450K array [3999002104_R01C02]

tag: Sex

tag: t1d status


title: ATF7+/+ from F0 pCD rep2

description:
Whole gene expression data from liver in ATF7+/+_CD
ATF7+/+_CD-2

value: paternal control diet


title: ATF7+/– from F0 pLPD rep4

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-4


title: eSF_peptide_2

description:
eSF_peptide_2
processed data file:  Normalized_counts_eSF.xlsx

value: Endometrium

tag: cell type

value: Endometrial stromal fibroblast

tag: sample group


title: subject ID 00635-0 at diease time point 5_Female, a T1D case and 5.7604381yrs old_450K array [3999002104_R06C01]

value: Female

value: T1D case


title: WT_2_light_untreated

tag: background

tag: strain

tag: growth protocol

value: grown to log phase in synthetic minimal media

tag: rna fraction


title: ATF7+/– from F0 pLPD rep8

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-8

tag: paternal diet

tag: genotype


title: 14A_2503_2W_PBMC

tag: set

tag: siv genotype


title: ATF7+/– from F0 pLPD rep3

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-3


title: ATF7+/– from F0 pLPD rep2

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-2


title: Nano human

source_name: HEK 293T

tag: cell line

value: HEK 293T

tag: protocol

value: Nano


title: subject ID 00635-0 at diease time point 4_Female, a T1D case and 3.2553046yrs old_450K array [3999002104_R05C01]

tag: subject id

tag: tissue


title: subject ID 00635-0 at diease time point 3_Female, a T1D case and 1.2648871yrs old_450K array [3999002104_R04C01]

tag: disease time point

tag: age


title: Control human

value: Control


title: Control

city: Rio de Janeiro

first: Cíntia

middle: Barros

last: Santos-Rebouças

state: RIO DE JANEIRO

address: Rua São Francisco Xavier, 524 - PHLC - sala 501F - Maracanã

department: Department of Genetics

country: Brazil

institute: State University of Rio de Janeiro

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR.
The quantification of reads were obtained by HTSeq v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: Blood

extract_protocol:
Total RNA samples were extracted from peripheral blood stored in RNAlater solution (Thermo Fisher Scientific Inc.) with RiboPure blood kit (Ambion, USA). Total RNA was purified using poly-T oligo-attached magnetic beads with rRNA removal Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). One ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: female

value: whole blood

tag: ethinicity

value: caucasian


title: Individual_II.3


title: ATF7+/– from F0 pCD rep7

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-7

source_name: ATF7+/–, F1 liver, pCD

value: F1 liver


title: ATF7+/– from F0 pCD rep8

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-8


title: 15A_2583_2W_PBMC

value: nef

value: PBMC

tag: timepoint (weeks)

tag: infection status


title: E4_S12

city: Canberra

first: Thomas

last: Preiss

state: Acton

address: 31 Garran Road

department: Genome Science

institute: Australian National University, John Curtin School of Medical Research

data_processing:
library strategy: bisulfite RNA-seq
low quality bases and adaptors were trimmed using Trimmomatic v0.36 (ILLUMINCLIP:Adapter.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50)
in silico converted reads (C-to-T of forward and G-to-A of reverse) were aligned to the in silico converted hg38 reference genome using meRanTK; unquely mapping reads were retained and replaced by the original unconverted read
read counts were obtained using mpileup in samtools and non-conversion sites called using a custom script with parameters ‘-minBQ 30 --overhang 6’ to mask non-converted sites at the terminal 6nt of each read.
reads with more than three unconverted cytosines were removed from mapping and sites called again
sites were subjected to signal-to-noise ratio filtering and only sites with 80% C+T, 30 read coverage, minimum of 5 non-converted C depth were retained. For transcriptome-wide detection, an 10% non-converison average across the triplicates was required
Genome_build: hg38
Supplementary_files_format_and_content: excel file listing genome coordinates of non-converted sites, read coverage, C and T count, non-conversion level and annotation of sites according to UCSC v28

source_name: HeLa_heavy polysomal region

growth_protocol: 6x106 HeLa cells were cultured in DMEM supplemented with 5% FBS and 2mM L-glutamine until 70% confluent

extract_protocol:
Cell lysates were cleared and polysome gradients obtained by sucrose density centrfugation. Samples were fractionated and RNA isolated by ethanol precipitation and subsequent trizol extraction of pellets
Libraries were prepared using 10ug of total RNA per sample according to the Illumina TruSeq Stranded Total RNA Library Kit including a bisulfite conversion step following rRNA depletion.

treatment_protocol: Cells were incubated with 0.1mg/ml cycloheximide for 3 minutes prior to lysate preparation

value: HeLa

tag: cell type

value: cervical cancer cells

tag: polysomal fraction

value: Replicate E-Polysome Fraction 4

tag: translation state

value: heavy polysomal region


title: subject ID 00710-0 at diease time point 5_Male, a T1D control and 4.2026010yrs old_450K array [3999002104_R03C01]

value: Male

tag: t1d status

value: T1D control

value: peripheral blood sample


title: subject ID 00710-0 at diease time point 3_Male, a T1D control and 1.4154689yrs old_450K array [3999002104_R01C01]


title: subject ID 00133-0 at diease time point 5_Female, a T1D case and 14.6748802yrs old_450K array [3998909018_R06C02]

value: Female

value: T1D case


title: ATF7+/– from F0 pCD rep5

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-5

tag: paternal diet

value: paternal control diet

tag: genotype


title: E3_S11

source_name: HeLa_light polysomal region

value: Replicate E-Polysome Fraction 3

value: light polysomal region


title: ATF7+/– from F0 pCD rep6

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-6


title: subject ID 00133-0 at diease time point 3_Female, a T1D case and 10.7268994yrs old_450K array [3998909018_R04C02]


title: 14B_15926_minus4W_PBMC

tag: set

value: B

tag: siv genotype

value: uninfected


title: subject ID 00544-0 at diease time point 5_Male, a T1D control and 16.1533196yrs old_450K array [3998909018_R03C02]


title: 15B_15899_minus4W_PBMC


title: ATF7+/– from F0 pLPD rep1

description:
Whole gene expression data from liver in ATF7+/–_LPD
ATF7+/–_LPD-1

value: paternal low protein diet

value: F1 liver


title: C4_S8

tag: cell line

value: Replicate C-Polysome Fraction 4


title: E1_S9

source_name: HeLa_small ribosomal subunit

value: HeLa

value: Replicate E-Polysome Fraction 1

value: small ribosomal subunit


title: 13B_2746_minus4W_PBMC

tag: subject id

value: nef

value: PBMC


title: subject ID 00710-0 at diease time point 4_Male, a T1D control and 2.1765914yrs old_450K array [3999002104_R02C01]

source_name: T1D control_Male_time point 4

value: Male

value: T1D control

tag: tissue


title: ATF7+/– from F0 pCD rep4

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-4


title: ATF7+/– from F0 pCD rep3

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-3


title: ATF7+/– from F0 pCD rep1

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-1


title: subject ID 00544-0 at diease time point 4_Male, a T1D control and 13.1279945yrs old_450K array [3998909018_R02C02]

tag: disease time point

value: peripheral blood sample


title: E2_S10

source_name: HeLa_large ribosomal subunit and monosome

value: cervical cancer cells

value: Replicate E-Polysome Fraction 2

value: large ribosomal subunit and monosome


title: ATF7+/– from F0 pCD rep2

description:
Whole gene expression data from liver in ATF7+/–_CD
ATF7+/–_CD-2

value: paternal control diet


title: C2_S6

value: Replicate C-Polysome Fraction 2


title: subject ID 00544-0 at diease time point 3_Male, a T1D control and 12.1122519yrs old_450K array [3998909018_R01C02]

tag: age


title: subject ID 00133-0 at diease time point 4_Female, a T1D case and 12.5530459yrs old_450K array [3998909018_R05C02]

source_name: T1D case_Female_time point 4

tag: Sex

value: Female

value: T1D case


title: wild-type from F0 pLPD rep8

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-8

source_name: wild-type, F1 liver, pLPD

value: paternal low protein diet

value: wild-type

value: F1 liver


title: subject ID 01002-0 at diease time point 5_Male, a T1D case and 6.6529774yrs old_450K array [3998909018_R06C01]

source_name: T1D case_Male_time point 5


title: wild-type from F0 pLPD rep7

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-7


title: subject ID 01002-0 at diease time point 4_Male, a T1D case and 2.1574264yrs old_450K array [3998909018_R05C01]

source_name: T1D case_Male_time point 4


title: B4_S4

value: HeLa

value: Replicate B-Polysome Fraction 4

value: heavy polysomal region


title: C1_S5

value: Replicate C-Polysome Fraction 1

value: small ribosomal subunit


title: B3_S3

value: Replicate B-Polysome Fraction 3

value: light polysomal region


title: subject ID 01002-0 at diease time point 3_Male, a T1D case and 0.8049281yrs old_450K array [3998909018_R04C01]

source_name: T1D case_Male_time point 3

value: Male

value: peripheral blood sample


title: subject ID 00402-0 at diease time point 5_Male, a T1D control and 9.2347707yrs old_450K array [3998909018_R03C01]

source_name: T1D control_Male_time point 5

value: T1D control


title: wild-type from F0 pLPD rep3

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-3


title: wild-type from F0 pLPD rep6

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-6


title: subject ID 00402-0 at diease time point 4_Male, a T1D control and 3.4661191yrs old_450K array [3998909018_R02C01]


title: C3_S7

value: cervical cancer cells

value: Replicate C-Polysome Fraction 3


title: Glu-free-CTCF-ChIP-seq_2

city: Gainesville

first: Jianrong

last: Lu

state: FL

address: 2033 Mowry RD

department: Biochemistry and Molecular Biology

institute: University of Florida

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences
ChIP-seq reads were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: hg19
Supplementary_files_format_and_content: bed files including peaks for ChIP-seq

source_name: Breast cancer cells

growth_protocol: MCF7 cells were cultured on Eagle's Minimum Essential Medium with 10% FBS.

extract_protocol:
ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF antibody (Cell Signaling Technology, Cat: #3418S).
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MCF7 cells were Treated with normal and glucose free medium.

value: Human-derived breast cancer cells

tag: tissue source

value: mammary gland

tag: growth media

value: glucose free medium

tag: chip antibody

value: CTCF antibody (Cell Signaling Technology, Cat:#3418S)


title: B1_S1

tag: cell type

value: Replicate B-Polysome Fraction 1


title: B2_S2

value: HeLa

tag: polysomal fraction

value: Replicate B-Polysome Fraction 2

value: large ribosomal subunit and monosome


title: WT-CTCF-ChIP-seq_2

value: normal medium


title: subject ID 00950-0 at diease time point 4_Female, a T1D case and 0.8405202yrs old_450K array [3998909017_R06C02]

value: Female

value: T1D case


title: wild-type from F0 pLPD rep2

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-2

value: paternal low protein diet

value: wild-type

value: F1 liver


title: WT-CTCF-ChIP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (single end)
ChIP-seq reads were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files includes peaks for ChIP-seq

tag: cell types

tag: protocol

tag: antibody

value: CTCF antibody

tag: antibody vendor

value: Cell Signaling Technology

tag: antibody catalogy no


title: subject ID 00824-0 at diease time point 4_Male, a T1D control and 0.8213552yrs old_450K array [3998909017_R04C02]

value: Male

tag: t1d status

value: T1D control

value: peripheral blood sample


title: subject ID 00824-0 at diease time point 5_Male, a T1D control and 10.0889801yrs old_450K array [3998909017_R05C02]


title: subject ID 36336-0 at diease time point 5_Male, a T1D case and 14.7186858yrs old_450K array [3998909017_R03C02]


title: Glu-free-CTCF-ChIP-seq

value: Human-derived breast cancer cells

value: mammary gland

tag: cell line

value: glucose free medium


title: wild-type from F0 pLPD rep1

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-1

tag: paternal diet

tag: genotype


title: human kidney sample 3

city: Baltimore

first: Theresa

last: Hodges

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Illumina reads from Human and Mouse were aligned to their target reference genome using TopHat version 1.4.0.
Gene-level read counts were produced by HTseq (version 0.4.7). DESeq (version 1.1.10) was used to determine gene-level differential expression.
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Expression estimates in the form of Fragments per Kilobase of exon per Million bases mapped (FPKM) were calculated by Cufflinks version 1.3.0. Isoform-level differential expression was determined using Cuffdiff (version 1.3.0).
Genome_build: human build = GRCh37; mouse build = GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts generated for each sample using HTSeq

source_name: kidney

extract_protocol:
Total RNA extracted from snap frozen kidneys
RIN = 8.6
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: kidney

tag: tissue section

value: cortex

tag: source of tissue

value: post-mortem sample


title: wild-type from F0 pCD rep7

description:
Whole gene expression data from liver in WT_CD
WT_CD-7

source_name: wild-type, F1 liver, pCD

value: paternal control diet


title: wild-type from F0 pLPD rep4

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-4


title: wild-type from F0 pCD rep5

description:
Whole gene expression data from liver in WT_CD
WT_CD-5


title: wild-type from F0 pCD rep6

description:
Whole gene expression data from liver in WT_CD
WT_CD-6


title: subject ID 36336-0 at diease time point 4_Male, a T1D case and 1.3032170yrs old_450K array [3998909017_R02C02]

tag: subject id

tag: disease time point

tag: age

tag: Sex


title: subject ID 00402-0 at diease time point 3_Male, a T1D control and 2.1519507yrs old_450K array [3998909018_R01C01]

source_name: T1D control_Male_time point 3


title: subject ID 20228-0 at diease time point 5_Male, a T1D control and 14.7761807yrs old_450K array [3998909017_R06C01]


title: wild-type from F0 pLPD rep5

description:
Whole gene expression data from liver in WT_LPD
WT_LPD-5


title: wild-type from F0 pCD rep4

description:
Whole gene expression data from liver in WT_CD
WT_CD-4


title: wild-type from F0 pCD rep8

description:
Whole gene expression data from liver in WT_CD
WT_CD-8


title: wild-type from F0 pCD rep2

description:
Whole gene expression data from liver in WT_CD
WT_CD-2


title: wild-type from F0 pCD rep3

description:
Whole gene expression data from liver in WT_CD
WT_CD-3


title: 24B_15899_2W_LN

source_name: Lymph Node MNCs

tag: set

value: B

tag: siv genotype

value: nef

value: LN

tag: timepoint (weeks)

tag: infection status


title: ChIP-seq of EGL43 (GFP tagged) in wild-type, replicate 2

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

data_processing:
ChIP-seq reads were aligned to the ce11/WBcel235 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
ChIP-seq reads were normalized using BEADS algorithm (Cheung et al, 2011).
ChIP-seq signals were exported to bigWig tracks.
Genome_build: ce11/WBcel235
Genome_build: ftp://hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: "spknorm" scores in bigWig tracks represent spike-in normalised values in linear scale

growth_protocol: Synchronized populations of L3 larvae containing the endogenous EGL-43::GFP reporter (genotype zh136[egl-43::gfp]) were obtained by bleaching gravid adults to release the embryos and letting the L1 larvae hatch in M9 buffer overnight at 20°C. The following day,  L1 larvae  were incubated at 25°C for 27 hours until they reached the L3 stage. The L3 larvae were isolated by  sucrose-floatation, washed with PBS containing protease inhibitors and frozen by dripping the concentrated solution of larvae into liquid nitrogen.

extract_protocol: Chromatin immunoprecipitations and library preparations were conducted as in (McMurchy et al., 2017), using formaldehyde and EGS as fixatives and the anti-GFP antibody ab290 (Abcam) to precipitate chromatin-bound EGL-43::GFP.

value: larvae

tag: strain

tag: Stage

tag: chip antibody

value: anti-GFP

tag: chip antibody supplier

value: Abcam

tag: chip antibody catalog#


title: subject ID 20228-0 at diease time point 4_Male, a T1D control and 0.8213552yrs old_450K array [3998909017_R05C01]

city: Aurora

first: Lauren

last: Vanderlinden

address: 13001 E. 17th Place, Mail Stop B119

tag: t1d status


title: subject ID 00409-0 at diease time point 5_Male, a T1D case and 11.9479808yrs old_450K array [3998909017_R04C01]

value: T1D case

tag: tissue


title: 23B_15926_2W_LN


title: human kidney sample 4

extract_protocol:
Total RNA extracted from snap frozen kidneys
RIN = 8.1
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue section

value: whole kidney

value: from normal part of renal carcinoma


title: ChIP-seq of EGL43 (GFP tagged) in wild-type, replicate 1


title: wild-type from F0 pCD rep1

description:
Whole gene expression data from liver in WT_CD
WT_CD-1

tag: paternal diet

tag: genotype

value: wild-type

value: F1 liver


title: 22B_2746_2W_LN

tag: subject id


title: subject ID 00409-0 at diease time point 4_Male, a T1D case and 0.7720739yrs old_450K array [3998909017_R03C01]

tag: disease time point

tag: age

value: Male

value: peripheral blood sample


title: 21B_15934_2W_LN

tag: set

value: wt


title: human kidney sample 2

extract_protocol:
Total RNA extracted from snap frozen kidneys
RIN = 8
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: cortex

tag: source of tissue


title: subject ID 00604-0 at diease time point 5_Male, a T1D control and 11.4140999yrs old_450K array [3998909017_R02C01]

tag: Sex

value: T1D control


title: 20B_15925_2W_LN

value: B

tag: siv genotype

tag: timepoint (weeks)

tag: infection status


title: 19B_2729_2W_LN


title: subject ID 00604-0 at diease time point 4_Male, a T1D control and 0.7665982yrs old_450K array [3998909017_R01C01]


title: subject ID 00588-0 at diease time point 4_Male, a T1D case and 4.5968515yrs old_450K array [3998909016_R06C01]


title: 15B_15899_minus2W_LN

value: nef

value: uninfected


title: human kidney sample 1

extract_protocol:
Total RNA extracted from snap frozen kidneys
RIN = 7.3
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post-mortem sample


title: subject ID 00588-0 at diease time point 3_Male, a T1D case and 3.0581793yrs old_450K array [3998909016_R05C01]


title: 14B_15926_minus2W_LN

value: LN


title: 13B_2746_minus2W_LN


title: subject ID 00770-0 at diease time point 4_Male, a T1D control and 5.7303217yrs old_450K array [3998909016_R03C01]


title: 12B_15934_minus2W_LN


title: Serum_NC [NC029]

city: Catania

first: Marco

last: Ragusa

address: Via Santa sofia 87

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Purified and labeled target/probe complexes were hybridized to the manufactuer supplied cartridge, according to the manufactuer's instructions.

scan_protocol: The cartridges were digitally imaged and analyzed using the nCounter Digital Analyzer.

data_processing: Data analysis was performed using nSolver 3.0 software. Quality of raw data was assessed through an evaluation of imaging, binding density, positive control linearity and positive control limit of detection parameters. A code-set normalization was applied to minimize technical noise (variations in purification, binding, hybridization efficiency), according to the nSolver analysis software protocol.

label: color codes

label_protocol: RNA were hybridized to color codes and washed using a two step-magnetic bead method, according to the manufactuer's instructions.

extract_protocol:
Extraction of RNA was carried out from 800 μl of serum samples by using a Qiagen miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany), according to Qiagen Supplementary Protocol for purification of total RNA (including small RNAs) from serum and plasma.
MiRNA profiling was performed on 3 μl (approximately 150 ng) of isolated RNA of samples.

tag: subject status

value: unaffected controls (NC)

tag: gender

value: M

value: serum

tag: molecule subtype

value: circulating RNA


title: subject ID 00770-0 at diease time point 3_Male, a T1D control and 4.7173169yrs old_450K array [3998909016_R02C01]

institute: Colorado School of Public Health

tag: t1d status


title: Serum_NC [NC047]

tag: tissue


title: Serum_AC [AC007]

value: Arnold-Chiari (AC)


title: Serum_AC [AC003]


title: Serum_AC [AC009]

value: F


title: Serum_AC [AC010]


title: 11B_15925_minus2W_LN


title: subject ID 00770-0 at diease time point 2_Male, a T1D control and 0.9007529yrs old_450K array [3998909016_R01C01]

source_name: T1D control_Male_time point 2

value: Male


title: Ozone_repB_hyb2_green

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_4.txt
GS6M_O3-B2_Cy3

hyb_protocol: Hybridizations were performed on a rotative Agilent Hybridization Oven, for 17h at 65°C, 10g. Afterwards, slides were washed, dried, and scanned according to the manufacturer protocol

scan_protocol: Scanning was performed at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200.

data_processing: Statistical analyses were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. Data were normalized with the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple Granny Smith fruit peel, 6 months cold storage with enriched ozone atmosphere

label_protocol: 200 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5 mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France). After purification (NucleoSpin Gel and PCR Clean-up column kits, Macherey-Nagel, GmbH & Co. KG, Germany), labelled samples were combined as 30 pmol for each dye and co-hybridized on the array.

growth_protocol: Granny Smith apples were harvested from a commercial orchard at Imathia region (North Greece).

extract_protocol: Total RNA was extracted from 1 g of frozen fruit peel tissue ground in liquid nitrogen using two successive extraction procedures with a CTAB (cetyltrimethylammonium bromide) buffer (Gasic et al., 2004) and then a SSTE buffer (Chang et al., 1993) as described by Nobile et al., 2011 and Segonne et al., 2014.

treatment_protocol:
treatment 1: Harvested apples were treated with 1-MCP (1000 ppm for 24 h at 0 °C) according to manufacturer’s instructions (SmartFresh, AgroFresh Inc., Rohm and Haas, Spring House, USA) .
treatment 2: Cold storage atmosphere was enriched with O3 at 0.3 μL.L-1 (ozone generator model COM-AD-04 and ozone analyser model MP-6060, Anseros Klaus Nonnenmacher GmbH, Tübingen, Germany)
treatment 3: Storage in cold rooms at 0°C and 95% relative humidity (RH) for 6 months.

tag: organ

value: Fruit

value: Peel

tag: genetic background

value: Granny Smith

value: Wild-type

tag: tissue developmental stage

value: Harvested at physiological maturity (full ripe)

tag: treatment 1

tag: treatment 2

value: Enriched ozone atmosphere

tag: treatment 3

value: 6 months cold storage


title: Serum_TS [TS003]

value: Tourette syndromes (TS)

tag: age


title: 1-MCP & Ozone_repB_hyb2_red

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_4.txt
GS6M_MCPO3-B2_Cy5

source_name: Apple Granny Smith fruit peel, 1-MCP treated, 6 months cold storage with enriched ozone atmosphere

tag: genotype


title: Ozone_repA_hyb2_red

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_3.txt
GS6M_O3-A2_Cy5


title: Serum_ACTS [ACTS002]

value: ACTS


title: 1-MCP & Ozone_repA_hyb2_green

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_3.txt
GS6M_MCPO3-A2_Cy3


title: 1-MCP & Ozone_repA_hyb1_green

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_1.txt
GS6M_MCPO3-A1_Cy3


title: Control_repB_hyb3_green

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_2.txt
GS6M_Ctrl-B3_Cy3

source_name: Apple Granny Smith fruit peel, 6 months cold storage


title: subject ID 00588-0 at diease time point 2_Male, a T1D case and 1.0896646yrs old_450K array [3998909016_R04C01]

source_name: T1D case_Male_time point 2

tag: subject id

tag: disease time point

tag: Sex

value: T1D case

value: peripheral blood sample


title: Ozone_repB_hyb1_red

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_4.txt
GS6M_O3-B1_Cy5


title: subject ID 00947-0 at diease time point 4_Female, a T1D control and 1.2375086yrs old_450K array [3998909009_R02C02]

source_name: T1D control_Female_time point 4

value: Female

value: T1D control


title: Serum_AC [AC002]

value: serum

value: circulating RNA


title: 1-MCP & Ozone_repB_hyb1_red

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_2.txt
GS6M_MCPO3-B1_Cy5


title: Serum_TS [TS004]

value: F