title: hyphae_48 hrs_DMSO rep 2

city: Madison

first: Jae-Hyuk

last: Yu

state: Wisconsin

address: 1550 LInden Dr.

department: Bacteriology

institute: UW-Madison

description: DMSO rep 2

data_processing:
The fastQC program was used to verify raw data quality of the Illumina reads.
The A. nidulansFGSC4 genome and gene annotations (A_nidulans_FGSC_A4_version_s10-m03-r08_features.gff) were downloaded from AspGD and used for mapping.
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread, with majority of the reads aligned to the genome. The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were generated using the featureCounts tool from Subread, with of reads assigned to genes overall.
The raw counts data were normalized using voom method from the R Limma package, then used for differential expression analysis.
For transcripts assembly, Cufflinks program was used to assemble transcripts from RNA-Seq reads for each sample, and cuffmerge command from cufflinks was used to merge the transcripts from all samples into a single set of genes and transcripts. The gene annotation from AspGD was provided as reference in the process and included in the final assembly.
Supplementary_files_format_and_content: relative expression between treatment (BaP) and control (DMSO), micrscoft excel CSV

organism: Aspergillus nidulans FGSC A4

source_name: Hyphae

growth_protocol: 10^6 spores/mL were incubated in 1% glucose minimal media at 37C at 220 rpm for 18 hours (timepoint 0) then hyphal pellets were washed and transferred to 0.1% minimal media and corresponding treatment and incubated at 37C at 220 rpm for designated timepoint

extract_protocol:
Hyphae samples were collected, squeezed dried and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol, silica/zirconia beads in a minibeadbeater, and precipitation with isopropanol. mRNA was extracted from total RNA using polyA selection, followed by RNA fragmentation
Strand specific library was constructed by first-strand cDNA synthesis using random primers, followed by sample cleanup and the second-strand synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to the cDNA fragments followed by ligation of the adapters. Final cDNA library was obtained by further purification and enrichment with PCR, and the quality was checked using Bioanalyzer 2100

treatment_protocol: 200 µL 100 mM benzo(a)pyrene in DMSO to final concentration 200 µM or equal volume control DMSO

tag: strain

value: FGSC A4

value: Hyphae

tag: treatment

value: DMSO

tag: treatment time

value: 48 hrs


title: Eff_IV_Kpos_rep4_A9436

status: Public on Jul 10 2018

type: RNA

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan-SQ

data_processing: Raw data filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio, cutoff is 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: CD4+Foxp3-CD44hi cells sorted from lung

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

growth_protocol: Six to twelve week old male and female C57BL/6[TgH]EGFP:Foxp3 mice were obtained through a supply contract between the NIAID/NIH and Taconic Farms

extract_protocol: The RNA was isolated using the Direct-zol RNA kit (Zymoresearch, Irvine, CA) following manufacturer’s instructions

treatment_protocol: For mouse Mtb infections, animals were exposed to ~100 CFU of Mtb H37Rv strain using an aerosol inhalation exposure system (Glas-Col, LLC, Terre Haute, IN).  Dose calculations were measured by serial dilutions of lung homogenates on 7H11 agar plates supplemented with oleic acid-albumin-dextrose-catalase (Difco, Detroit, MI) immediately post exposure. Effector CD4 T cells were isolated from the lungs of Mtb infected Foxp3-EGFP mice on day 28 post-infection after administration of anti-CD45 at 2μg per mouse by intravenous injection 3 minutes prior to euthanasia.  The lungs were harvested, minced, placed into RPMI containing 1 mg/ml Collagenase D (Roche-Diagnostics, Indianapolis, IN), 1 mg/ml hyaluronidase, 50 U/ml DNase I and 1 mM aminoguanidine (all from Sigma-Aldrich, St. Louis, MO), and incubated at 37°C for 45 minutes with shaking.  The lungs were passed through a 100μm cell strainer, and washed with PBS containing 20% fetal bovine serum (FBS).  The lymphocytes were isolated by centrifugation through a density gradient of 37% Percoll from GE Healthcare Bio-Sciences (Uppsala, Sweden).  The red blood cells were lysed with ACK lysis buffer (KD Medical, Columbia MD), and the cells were counted.  The cells were stained with anti-CD4 (1:100), CD44 (1:100), and KLRG1 (1:100) for 30 minutes at 4°C, and then washed twice with PBS + 1% FBS. The cells were stained with a viability dye Fixable Viability Dye eFluor 780 from eBioscience Inc. (San Diego, CA) for 20 minutes at 4°C, and then washed twice with PBS + 1% FBS.  The cells were gated on live CD4+Foxp3-CD44hi cells were sorted into four populations: KLRG1-ivCD45dim, KLRG1-ivCD45+, KLRG1+ivCD45dim, and KLRG1+ivCD45+ on a BD Aria sorter (double check the sorter in 1E08).   The cells were collected in PBS + 1% FBS, and centrifuged.  The cell pellets were lysed in Trizol, and stored at -80°C until RNA isolation.  This was repeated for five independent experiments, pooling the lungs of 15 to 25 mice for each sort.

tag: sort fraction

value: effector

tag: pulmonary compartment

value: intravascular

tag: klrg1 marker

tag: experimental replicate


title: hyphae_48 hrs_DMSO rep 1

type: SRA

description: DMSO rep 1

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: hyphae_48 hrs_benzo(a)pyrene rep 3

description: benzo(a)pyrene rep 3

value: 200 µM benzo(a)pyrene


title: hyphae_48 hrs_benzo(a)pyrene rep 2

description: benzo(a)pyrene rep 2


title: Nve_PA_Kneg_rep3_A9434

value: naive

value: parchyma


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 77 F1]

city: Athens

first: Mandi

middle: M.

last: Murph

state: GA

address: 250 West Green Street, Room 312

department: Pharmaceutical & Biomedical Sciences

institute: University of Georgia

description:
Tumor 77 F1
Experimental Group 2

data_processing:
Normalization of raw Ct values from qRT-PCR was performed using Exiqon's recommended software, GenEx, according to instructions provided: http://www.biomcc.com/genex-download.html
Both plates (total of ~750 microRNAs and spike in microRNA controls) were calibrated to each other. Experimental groups with greater than 50% missing data were removed from analysis, as were any microRNAs that were considered outliers within their experimental groups, resulting in 373 microRNAs for further analysis.
All data was normalized to miR-16-5p, a microRNA widely regarded as a control microRNA, and also to the Wildtype group which was considered the control group.
Data was automatically calculated by software to result in relative ratios of experimental groups with respect to the control groups and all data was graphed using GraphPad Prism for publication purposes.

label: SYBR Green

source_name: Transgenic AT-ATX mouse (with tumor) serum

label_protocol: cDNA was used to perform quantitative real-time PCR using SYBR Green and Exiqon's ExiLENT SYBR Green Master Mix and Exiqon's Ready-to-use Serum microRNA PCR Panels I and II plates. PCR was run for 40 cycles.

extract_protocol:
Blood was collected from mice upon necropsy and centrifuged at 4000rpm for 3 minutes prior to serum collection.
50uL serum was used to extract total RNA using Exiqon's RNA Isolation Kit, and cDNA was subsequently made with total RNA using the Exiqon Universal cDNA Synthesis Kit II.

value: Serum

tag: genotype/variation

value: Transgenic AT-ATX

tag: disease status

value: Spontaneous tumor(s)


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 65 F6]

description:
Tumor 65 F6
Experimental Group 2


title: SRV-0007

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

description:
RSEM processed, expected count values, found in column 4 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt

data_processing:
De novo assembly of RNA-Seq isotigs was accomplished using Trinity’s three-stage protocol (Inchworm, Chrysalis, and Butterfly).
RSEM was used for count estimation with default parameters
Expected counts were extracted in a matrix file format from the RSEM output.

organism: Ambystoma maculatum

source_name: mid-zeugopod whole tissue

extract_protocol:
Mid-zeugopod amputations were conducted on all animals. Exactly 1mm distal most tissue was collected immediately after amputation (0hpa) and 24 hpa. Whole RNA tissue was extracted using the TruSeq RNA library prep kit from Illumina.
HudsonAlpha Institute for Biotechnology generated the RNA-Seq data by preparing cDNA libraries and sequencing approximately 50,000,000 100 bp read pairs per sample.

value: mid-zeugopod

tag: time post amputation (hpa)

tag: size of tissue collection


title: Eff_IV_Kneg_rep2_A9428


title: Nve_PA_Kneg_rep2_A9429


title: HeLa_RNAseq

city: Beijing

first: Liu

last: Fenglin

address: Courtyard 1, Beichen West Road

country: China

institute: Chinese Academy of Sciences

data_processing:
library strategy: RNase-seq
Illumina Casava1.7 software used for basecalling.
GWPBS-Cap-seq reads and MNase-seq reads were aligned to the hg19 genome assembly using the SOAP2 aligner, allowing up to 2 mismatches.
For GWPBS-Cap-seq, The resulting sequence read distribution was used to identify peaks. This was done by first separating forward (W) and reverse (C) strands, then connecting successive overlapping sequences on the W or C strand into continuous regions, and finally selecting the overlapping regions between the W and C strand. All these overlapping regions are considered to be peak regions. For MNase-seq, the peak calling procedure was finished with SICER (spatial clustering approach for the identification of ChIP-enriched regions) with a window size of 200 bp.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include peak information for each GWPBS-Cap group, MNase-seq group and FPKM values for each gene in Hela cells.

organism: Homo sapiens

growth_protocol: HeLa cells (from ATCC) were cultured in DMEM (HyClone, SH30243.01) supplemented with 10% FBS (Hyclone, SH30084.03) and 100 U ml-1 penicillin-streptomycin (HyClone, SV30010) and maintained in a incubator at 37˚C and 5% CO2.

extract_protocol:
For GWPBS-Cap samples, lysates were washed by cold NaCl Buffer containing different concentrations (50 mM,100 mM, 200 mM, 400 mM, 1000 mM or 2000 mM) of NaCl. After 2 hours’ rotation, nuclei were pelleted and resuspended in the same cold NaCl Buffer. Formaldehyde solution were added to cross-link protein and DNA and the complexes were sheared by sonication. Supernatants containing the solubilized chromatin DNA: protein complexes were clarified and added TCEP to reduce disulfide bonds of proteins. These complexes were isolated with active Amine-coated beads through sulfo-SMCC. For MNase-seq samples, lysates were clarified from MNase treated nuclei. For RNA-seq samples, total RNA was extracted using TRIzol and an aliquot of the RNA was reversed transcribed.
For GWPBS-Cap samples, DNA was end-repaired using T4 Polynucleotide Kinase. Phosphorylated 5' ends were treated with Lambda exonuclease and 3' single-stranded Sp6 adapters were ligated using T4 RNA Ligase 1. The DNA was extracted and double-stranded DNA was built using Klenow Fragment. DNA was added A-tail using dATP and Klenow Fragment (3'→5' exo-) and T7 double-stranded adapters were ligated to ends of DNA using T4 DNA Ligase. After adapter ligation DNA was PCR amplified with Sp6 and T7 primers for 20 cycles and library fragments of 80~120 bp (insert plus PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured and the paired-end sequencing was performed on Illumina Hiseq 4000 platform. For MNase-seq samples, The extracted 147 bp DNA bands were separated on agarose gel. The library  preparation and the high-throughput sequencing was performed on Illumina HiSeq 4000 platform. For RNA-seq samples, RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer cells


title: hyphae_48 hrs_DMSO rep 3

description: DMSO rep 3


title: Transgenic AT-ATX mouse; no tumors [Nontumor 87 F4]

description:
Nontumor 87 F4
Experimental Group 1

source_name: Transgenic AT-ATX mouse (no tumor) serum

value: No tumors


title: Eff_PA_Kpos_rep2_A9425


title: sham-24h-1 (exosomal RNA)

city: Baltimore

first: Lin

last: Zou

address: 20 Penn Street, HSF II-GS003C

department: Anesthesiology

institute: University of Maryland School Of Medicine

hyb_protocol: For each sample, FirePlex Particles (35 μl) are added to a well of 96-well flitler plate and fitlered. Three additional wells for no-sample controls are also prepared. Next, 25  μl of Hybridization Buffer is added to each well followed by 25  μl sample. The plate is incubated at 37oC for 60 minutes while shaking at 750 rpm

scan_protocol: Particles are scanned on an EMD Milipore Guava 8HT or 6HT flow cytometter

data_processing:
The flow cytometer output was analyzed with the FirePlexTM Analysis Wrokbench software, avaialble on the Abcam website at www.abcam.com/FireflyAnalysisSoftware, and R.
[normalization method applied to the signal intensity data]:
A geNorm-like algorithm is applied to the data in order to select the three most appropriate miRNAs for normalization in the experiment. To improve the likelihood of identifying three appropriate normalization candidates, several miRNA targets identified by others [Chen et al] and by Abcam in an independent analysis are automatically included in the fixed panels. The miRNAs selected for normalization of the current samples are: hsa-let-7i-5p, hsa-mir-20a-5p, hsa-miR-29a-3p.
Chen X., Liang H., Guan D., Wang C., Hu X., et al. (2013) A Combination of Let-7d, Let-7g and Let-7i Serves as a Stable Reference for Normalization of Serum microRNAs. PLoS ONE 8(11): e79652.

label: Fireplex

source_name: plasma exosome

label_protocol: Oligonucleotide adapters are ligated to each end of the hybridized miRNA to serve as PCR priming sites. Labelled miRNAs are dehybridized from particles and undergo one-step RT-PCR with a biotinlyated primer.

extract_protocol: Exosome was purfied from plasam via ultracentrifuge. RNA was extracted for plasma exosome using miRNeasy Micro Kit (Qiagen)

tag: genotype

value: WT

tag: disease state

value: control

tag: rna source

value: plasma exosome

tag: gender

value: Male

tag: time

value: 24 hours post-surgery


title: hyphae_24 hrs_DMSO rep 3

description: DMSO rep 3

tag: strain

value: FGSC A4

value: Hyphae

tag: treatment

value: DMSO

tag: treatment time

value: 24 hrs


title: Eff_PA_Kpos_rep1_A9420

tag: sort fraction

value: effector

tag: pulmonary compartment

value: parchyma

tag: klrg1 marker


title: Transgenic AT-ATX mouse; no tumors [Nontumor 87 F1]

description:
Nontumor 87 F1
Experimental Group 1

tag: tissue

value: Serum

tag: genotype/variation

value: Transgenic AT-ATX


title: Calf 35 P5 Organoids

city: Edinburgh

first: Neil

last: Mabbott

state: Midlothian

address: Easter Bush

country: United Kingdom

institute: The Roslin Institute & Royal (Dick) School of Veterinary Sciences, University of Edinburgh

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-011_TP-D5-002

data_processing:
Sequenced reads were checked for read quality using FastQC
Pseudoaligner Kallisto (v 0.43.1) was used to measure transcript abundance level by aligning the reads against transcripts from Bos Taurus UMD3.1.1 assembly
The abundance value in Transcripts per million (TPM) was aggregated from each sample into one table and log2 transformed for downstream analysis.
Genome_build: Bos Taurus UMD3.1.1
Supplementary_files_format_and_content: Tab-delimited files include TPM and estimated count for each sample

organism: Bos taurus

source_name: Bovine intestinal crypts

growth_protocol: To prepare organoids, 200 bovine intestinal crypts in 100 µl advanced DMEM/F12 medium were added to 150 μl of BD Growth Factor Reduced Matrigel Matrix (BD Biosciences, UK) and 50 μl droplets added to wells of a pre-warmed 24-well plate (Nunc, ThermoFisher Scientific). The crypts/organoids were maintained in 700 μl of IntestiCult Organoid Growth Medium (STEMCELL Technologies, UK) containing 50 μg/ml gentamicin, 100 mM Y-27632 (Cambridge Bioscience, UK), 5mM LY2157299 (Cambridge Bioscience) and 100mM SB202190 (Enzo Life Sciences, UK) at 37°C in a 5% CO2/air atmosphere.

extract_protocol:
To extract RNA from the organoid cultures, organoids were treated with 1.0 ml Corning Cell Recovery Solution (Corning) and incubated for 1 h at 4ºC with constant shaking at 120 rpm.   The suspension was then centrifuged at 1,200 x g for 5 min, and the pellet washed twice in 1.0 ml ice-cold PBS.  The pellet was then lysed in 600 µl of the RLT buffer (Qiagen, Germany) containing 10 µg/ml 2-mercaptoethanol (Sigma-Aldrich, UK), and homogenized using a Qiashredder homogenizer (Qiagen).  Total RNA was then extracted using a RNeasy mini kit (Qiagen) according to the manufacturer’s instructions which included a DNase digestion step to remove genomic DNA.  The RNA was eluted into RNase-free water. 3 µg of RNA (10 wells) was used for RNA seq.
7 libraries were prepared using the TruSeq stranded total RNA-seq library preparation kit (Illumina) with one round of RiboZero Gold treatment
The libraries were pooled and the pool was sequenced on 3 lanes on a HiSeq 4000 instrument with 150-base paired end reads to a depth of 147-191M read pairs per sample.

value: Bovine intestinal organoids

tag: passage number


title: Calf 35 P4 Organoids

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-010_TP-D5-002


title: Transgenic AT-ATX mouse; no tumors [Nontumor 85 F2]

description:
Nontumor 85 F2
Experimental Group 1

tag: disease status


title: hyphae_24 hrs_DMSO rep 1

description: DMSO rep 1


title: Eff_IV_Kpos_rep1_A9421

value: intravascular

tag: experimental replicate


title: Calf 35 P3 Organoids

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-009_TP-D5-002

tag: cell type


title: Transgenic AT-ATX mouse; no tumors [Nontumor 85 F1b]

description:
Nontumor 85 F1b
Experimental Group 1


title: hyphae_24 hrs_benzo(a)pyrene rep 2

description: benzo(a)pyrene rep 2

value: 200 µM benzo(a)pyrene


title: hyphae_24 hrs_benzo(a)pyrene rep 3

description: benzo(a)pyrene rep 3


title: Calf 35 P2 Organoids

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-010_TP-D5-001


title: Transgenic AT-ATX mouse; no tumors [Nontumor 81 F3]

description:
Nontumor 81 F3
Experimental Group 1

value: No tumors


title: hyphae_24 hrs_benzo(a)pyrene rep 1

description: benzo(a)pyrene rep 1


title: hyphae_48 hrs_benzo(a)pyrene rep 1

description: benzo(a)pyrene rep 1

value: 48 hrs


title: Transgenic AT-ATX mouse; no tumors [Nontumor 77 F5]

description:
Nontumor 77 F5
Experimental Group 1


title: Calf 35 P0 Organoids

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-011_TP-D5-001


title: hyphae_24 hrs_DMSO rep 2

description: DMSO rep 2


title: Calf 35 P1 Organoids

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-012_TP-D5-001


title: hyphae_6 hrs_DMSO rep 3

description: DMSO rep 3

value: 6 hrs


title: wildtype FVB/N mouse; healthy [Wildtype F4]

description:
Wildtype F4
Control

source_name: Wildtype mouse serum

value: Wildtype

value: Healthy


title: SRV-0028

description:
RSEM processed, expected count values, found in column 7 of processed data file
AAND_RNASEQ_EXPCOUNT.txt

organism: Ambystoma andersoni

value: mid-zeugopod

tag: time post amputation (hpa)

tag: size of tissue collection


title: wildtype FVB/N mouse; healthy [Wildtype F2]

description:
Wildtype F2
Control


title: hyphae_6 hrs_DMSO rep 1

description: DMSO rep 1

value: FGSC A4


title: SRV-0026

description:
RSEM processed, expected count values, found in column 5 of processed data file
AAND_RNASEQ_EXPCOUNT.txt


title: hyphae_6 hrs_benzo(a)pyrene rep 3

description: benzo(a)pyrene rep 3

value: Hyphae


title: hyphae_6 hrs_benzo(a)pyrene rep 2

description: benzo(a)pyrene rep 2


title: hyphae_6 hrs_DMSO rep 2

description: DMSO rep 2

value: DMSO


title: Calf 35 Crypts

description: 170526_K00166_0220_BHJW72BBXX_*_TP-D7-009_TP-D5-001

value: Bovine intestinal crypts


title: wildtype FVB/N mouse; healthy [Wildtype F1]

description:
Wildtype F1
Control


title: hyphae_0 hrs rep 3

description: none rep 3


title: hyphae_6 hrs_benzo(a)pyrene rep 1

description: benzo(a)pyrene rep 1


title: SRV-0025

description:
RSEM processed, expected count values, found in \column 4 of processed data file
AAND_RNASEQ_EXPCOUNT.txt


title: SRV-0024

description:
RSEM processed, expected count values, found in column 3 of processed data file
AAND_RNASEQ_EXPCOUNT.txt


title: hyphae_0 hrs rep 1

description: none rep 1


title: hyphae_0 hrs rep 2

description: none rep 2


title: Transgenic AT-ATX mouse; no tumors [Nontumor 15 F1]

description:
Nontumor 15 F1
Experimental Group 1


title: SRV-0027

description:
RSEM processed, expected count values, found in column 6 of processed data file
AAND_RNASEQ_EXPCOUNT.txt


title: NEBNext.Lab2.SynthA

status: Public on Jul 09 2018

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

molecule: other

organism: synthetic construct

source_name: Synthetic smallRNA; Ratiometric Pool A

extract_protocol:
The RNA sample was provided as a single aliquot containing all the synthetic RNAs. 10 femtomoles of the RNA pool was used as input for each library.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.

tag: lab

value: NEBNext

tag: pool

value: SynthA


title: 4N_B.Lab5.SynthA


title: 4N_B.Lab5.SynthB

source_name: Synthetic smallRNA; Ratiometric Pool B

value: SynthB


title: NEBNext.Lab2.SynthB


title: NEBNext.Lab5.SynthEQ

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Mature miRNA Read Counts: Tab-delimited text files contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Mapped Calibrator Counts: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

source_name: Synthetic smallRNA; Equimolar Pool

value: SynthEQ


title: NEBNext.Lab5.SynthB


title: NEBNext.Lab5.SynthA


title: TruSeq.LAB6.SynthEdit1

description:
POOL3-TS-KW-A_S25
POOL3-TS-KW-B_S26
POOL3-TS-KW-C_S27
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

data_processing:
Trim adapters: cutadapt 1.9.1 with Python 2.7.10; TruSeq Parameters: -a TGGAATTCTCGGGTGCCAAGG -g GTTCAGAGTTCTACAGTCCGACGATC -m 16 –trim-n; NEBNext Parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g GTTCAGAGTTCTACAGTCCGACGATC -m 16 –trim-n; 4N_B Parameters: -a NNNNTGGAATTCTCGGGTGCCAAGGC -g GTTCAGAGTTCTACAGTCCGACGATNNNN -m 16 –trim-n
Align to editing pool sequences: bowtie2 (Version 2.3.0);parameters:-p 1 --mm --trim5 4 -x editing_pool_sequences --non-deterministic --time --local -D 15 -R 3 -N 0 -L 8 -i S,1,0.50 --norc
Filter MAPQ > 10: samtools (version 1.2) using htslib (version 1.2.1).
Tabulate 0 mismatch alignments by aligned sequence, start position and quality score.
Supplementary_files_format_and_content: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt: Supplementary file contains the combined output from tabulating 0 mismatch alignments.

source_name: Synthetic small RNA; Editing Pool 1%

extract_protocol:
The RNA sample was provided as a single aliquot containing all the synthetic RNAs. 10 femtomoles of the RNA pool was used as input for each library.
Library construction protocols varied by sample (See lib.method.detail sample characteristic). TruSeq and NEBNext use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_B is an in-house protocol using 5' and 3' adapters with 4N randomized terminal nucleotides.

value: TruSeq

tag: percent editing expected


title: TruSeq.LAB6.SynthEdit5

description:
POOL4-TS-KW-A_S28
POOL4-TS-KW-B_S29
POOL4-TS-KW-C_S30
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

source_name: Synthetic small RNA; Editing Pool 5%


title: TruSeq.LAB6.SynthEdit100

description:
POOL6-TS-KW-A_S34
POOL6-TS-KW-B_S35
POOL6-TS-KW-C_S36
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

source_name: Synthetic small RNA; Editing Pool 100%


title: 4N_B.Lab5.SynthEQ


title: OGG1 inhibitor + TNFa

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description:
Test
Female+male (50%-50%)
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For normalization, the average of five housekeeping genes (Gusb, Hprt, Hsp90ab1, Gapdh, Actb) were used.
Target gene signals normalized to housekeeping genes; 2^-delta CT, where delta CT = (Ct Target − Ct HKG)]
The web-based software package automatically performs all delta delta Ct based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change data file reports test/control (i.e., Solvent/OGG1 inhibitor/TNFa challenge) ratios.

source_name: Lung lysate

label_protocol: PCR assays were performed using the Mouse Inflammatory Cytokines & Receptors PCR array PAMM-011Z (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the Superscript® III First Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Solvent, OGG1 inhibitor (30 mg per kg) was administered intra-peritoneally, challenge of lungs was performed by administration of TNFa via  intranasal route.

tag: strain

value: Balbc J

value: lung

tag: age

value: 8 weeks

tag: Sex

value: pooled male and female


title: 4N_B.Lab6.SynthA


title: TruSeq.LAB6.SynthEdit0.1

description:
POOL2-TS-KW-A_S22
POOL2-TS-KW-B_S23
POOL2-TS-KW-C_S24
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

source_name: Synthetic small RNA; Editing Pool 0.1%


title: TruSeq.LAB6.SynthEdit50

description:
POOL5-TS-KW-A_S31
POOL5-TS-KW-B_S32
POOL5-TS-KW-C_S33
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

source_name: Synthetic small RNA; Editing Pool 50%


title: NEBNext.Lab2.SynthEQ


title: TruSeq.LAB6.SynthEdit0

description:
POOL1-TS-KW-A_S19
POOL1-TS-KW-B_S20
POOL1-TS-KW-C_S21
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt

source_name: Synthetic small RNA; Editing Pool 0%


title: NEBNext.Lab1.SynthEQ


title: 4N_B.Lab6.SynthB


title: TruSeq.LAB5.SynthEdit1

description:
POOL1-TS-MT-1_S85521_ATTCCT
POOL1-TS-MT-2_S85522_CAAAAG
POOL1-TS-MT-3_S85523_CAACTA
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB5.SynthEdit5

description:
POOL5-TS-MT-1_S85524_CACCGG
POOL5-TS-MT-2_S85525_CACGAT
POOL5-TS-MT-3_S85526_CACTCA
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB5.SynthEdit0.1

description:
POOL01-TS-MT-1_S85518_GGTAGC
POOL01-TS-MT-2_S85519_ACTGAT
POOL01-TS-MT-3_S85520_ATGAGC
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.Lab6.SynthEQ


title: TruSeq.LAB5.SynthEdit50

description:
POOL50-TS-MT-1_S85527_CAGGCG
POOL50-TS-MT-2_S85528_CATGGC
POOL50-TS-MT-3_S85529_CATTTT
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: SRV-0023

description:
RSEM processed, expected count values, found in column 2 of processed data file
AAND_RNASEQ_EXPCOUNT.txt


title: TruSeq.LAB5.SynthEdit0

description:
POOL0-TS-MT-1_S85515_GTTTCG
POOL0-TS-MT-2_S85516_CGTACG
POOL0-TS-MT-3_S85517_GAGTGG
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit5

description:
POOL4-TS-DG-A_S10_R1_001
POOL4-TS-DG-B_S11_R1_001
POOL4-TS-DG-C_S12_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit100

description:
POOL6-TS-DG-A_S28_R1_001
POOL6-TS-DG-B_S29_R1_001
POOL6-TS-DG-C_S30_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit50

description:
POOL5-TS-DG-A_S25_R1_001
POOL5-TS-DG-B_S26_R1_001
POOL5-TS-DG-C_S27_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit0

description:
POOL1-TS-DG-A_S1_R1_001
POOL1-TS-DG-B_S2_R1_001
POOL1-TS-DG-C_S3_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit0.1

description:
POOL2-TS-DG-A_S4_R1_001
POOL2-TS-DG-B_S5_R1_001
POOL2-TS-DG-C_S6_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit5

description:
POOL4-NEB-KW-A_S10
POOL4-NEB-KW-B_S11
POOL4-NEB-KW-C_S12
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit50

description:
POOL5-NEB-KW-A_S13
POOL5-NEB-KW-B_S14
POOL5-NEB-KW-C_S15
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit1

description:
POOL3-NEB-KW-A_S7
POOL3-NEB-KW-B_S8
POOL3-NEB-KW-C_S9
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit100

description:
POOL6-NEB-KW-A_S16
POOL6-NEB-KW-B_S17
POOL6-NEB-KW-C_S18
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB2.SynthEdit1

description:
POOL3-TS-DG-A_S7_R1_001
POOL3-TS-DG-B_S8_R1_001
POOL3-TS-DG-C_S9_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: TruSeq.LAB5.SynthEdit100

description:
POOL100-TS-MT-1_S85530_CCAACA
POOL100-TS-MT-2_S85531_CGGAAT
POOL100-TS-MT-3_S85532_CTAGCT
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit0

description:
POOL1-NEB-KW-A_S1
POOL1-NEB-KW-B_S2
POOL1-NEB-KW-C_S3
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit100

description:
POOL100-NEB-MT-A_Sample85391
POOL100-NEB-MT-B_Sample85392
POOL100-NEB-MT-C_Sample85393
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit1

description:
POOL3-NEB-DG-A_S17_R1_001
POOL3-NEB-DG-B_S18_R1_001
POOL3-NEB-DG-C_S33_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit50

description:
POOL5-NEB-DG-A_S21_R1_001
POOL5-NEB-DG-B_S22_R1_001
POOL5-NEB-DG-C_S35_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit5

description:
POOL4-NEB-DG-A_S19_R1_001
POOL4-NEB-DG-B_S20_R1_001
POOL4-NEB-DG-C_S34_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit100

description:
POOL6-NEB-DG-A_S23_R1_001
POOL6-NEB-DG-B_S24_R1_001
POOL6-NEB-DG-C_S36_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit0

description:
POOL0-NEB-MT-A_Sample85376
POOL0-NEB-MT-B_Sample85377
POOL0-NEB-MT-C_Sample85378
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit50

description:
POOL50-NEB-MT-A_Sample85388
POOL50-NEB-MT-B_Sample85389
POOL50-NEB-MT-C_Sample85390
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit0.1

description:
POOL01-NEB-MT-A_Sample85379
POOL01-NEB-MT-B_Sample85380
POOL01-NEB-MT-C_Sample85381
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit0

description:
POOL1-NEB-DG-A_S13_R1_001
POOL1-NEB-DG-B_S14_R1_001
POOL1-NEB-DG-C_S31_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit50

description:
POOL5-4N-KW-A_S49
POOL5-4N-KW-B_S50
POOL5-4N-KW-C_S51
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB2.SynthEdit0.1

description:
POOL2-NEB-DG-A_S15_R1_001
POOL2-NEB-DG-B_S16_R1_001
POOL2-NEB-DG-C_S32_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit1

description:
POOL1-NEB-MT-A_Sample85382
POOL1-NEB-MT-B_Sample85383
POOL1-NEB-MT-C_Sample85384
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit100

description:
POOL6-4N-KW-A_S52
POOL6-4N-KW-B_S53
POOL6-4N-KW-C_S54
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit1

description:
POOL3-4N-KW-A_S43
POOL3-4N-KW-B_S44
POOL3-4N-KW-C_S45
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit5

description:
POOL4-4N-KW-A_S46
POOL4-4N-KW-B_S47
POOL4-4N-KW-C_S48
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB5.SynthEdit50

description:
POOL50-4N-MT-A_Sample85370
POOL50-4N-MT-B_Sample85371
POOL50-4N-MT-C_Sample85372
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit0.1

description:
POOL2-4N-KW-A_S40
POOL2-4N-KW-B_S41
POOL2-4N-KW-C_S42
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB6.SynthEdit0

description:
POOL1-4N-KW-A_S37
POOL1-4N-KW-B_S38
POOL1-4N-KW-C_S39
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB5.SynthEdit1

description:
POOL1-4N-MT-A_Sample85364
POOL1-4N-MT-B_Sample85365
POOL1-4N-MT-C_Sample85366
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB5.SynthEdit5

description:
POOL5-NEB-MT-A_Sample85385
POOL5-NEB-MT-B_Sample85386
POOL5-NEB-MT-C_Sample85387
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: NEBNext.LAB6.SynthEdit0.1

description:
POOL2-NEB-KW-A_S4
POOL2-NEB-KW-B_S5
POOL2-NEB-KW-C_S6
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB5.SynthEdit100

description:
POOL100-4N-MT-A_Sample85373
POOL100-4N-MT-B_Sample85374
POOL100-4N-MT-C_Sample85375
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB5.SynthEdit5

description:
POOL5-4N-MT-A_Sample85367
POOL5-4N-MT-B_Sample85368
POOL5-4N-MT-C_Sample85369
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB5.SynthEdit0

description:
POOL0-4N-MT-A_Sample85358
POOL0-4N-MT-B_Sample85359
POOL0-4N-MT-C_Sample85360
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit5

description:
POOL4-4N-DG-A_S47_R1_001
POOL4-4N-DG-B_S48_R1_001
POOL4-4N-DG-C_S49_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit100

description:
POOL6-4N-DG-A_S53_R1_001
POOL6-4N-DG-B_S54_R1_001
POOL6-4N-DG-C_S55_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit0

description:
POOL1-4N-DG-A_S37_R1_001
POOL1-4N-DG-B_S38_R1_001
POOL1-4N-DG-C_S39_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit50

description:
POOL5-4N-DG-A_S50_R1_001
POOL5-4N-DG-B_S51_R1_001
POOL5-4N-DG-C_S52_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit0.1

description:
POOL2-4N-DG-A_S40_R1_001
POOL2-4N-DG-B_S42_R1_001
POOL2-4N-DG-C_S43_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: 4N_B.LAB2.SynthEdit1

description:
POOL3-4N-DG-A_S44_R1_001
POOL3-4N-DG-B_S45_R1_001
POOL3-4N-DG-C_S46_R1_001
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: P4-A

city: Innsbruck

first: Fabian

last: Guggenberger

state: Tirol

address: Anichstrasse 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

description: Patient 4 group A

data_processing:
Illumina paired-end reads of 75 bases were trimmed by removing the TrueSeq adapter sequences using Trimmomatic (v.0.33)
Subsequently, the reads were mapped to the human reference genome build hg38 and the Homo sapiens GENCODE v23 annotation and in parallel to build mm10 with GENCODE vM8 annotation file, using with the RNA-seq aligner STAR (v2.4.2a) in 2-pass mode.
Aligned reads were assigned to human or mouse using the disambiguate algorithm (v1.0)
Raw counts were add-up with the summarizeOverlaps function from the Bioconductor Genomic Alignments package (v1.14.0) using union mode
Genes were called differentially expressed with a generalized linear model using a negative binomial distribution with patient number as factor.  DESeq2 (v1.16.1) performed the calculations. We applied a Wald-test to identify statistical significant differently expressed genes of 0 vs 0.5 and 1 Gy samples. P-values were adjusted using Benjamini Hochberg calculation and a threshold value was set to p-adjusted value of < 0.01.
Counts were normalized with blind variance stabilizing log2 transformation function of DESeq2, and the differentially expressed genes were selected to calculate scaled gene-wise values (Z-score). We clustered the scaled values hierarchically with complete linkage using Euclidean distances and plotted in a heat map with pheatmap package (v1.0.8).
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) gene enrichment analyses were carried out as described previously [Meinders et al., 2015]. We used R(v 3.4.0) for statistics and visualization of the data.
Genome_build: mm10
Supplementary_files_format_and_content: CPMs

source_name: Prostate

growth_protocol: Primary cells were isolated from prostate tissue by collagenase digestion, were seeded onto collagen I coated culture flask and were co-cultured with cell-cycle arrested murine feeder cells (STO cellline, 10^5 cells per cm2). Primary cultures were splitted (approx. 1:3) when reaching about 80% confluecy after feeder cells being washed away. Primary cell medium: Keratinocyte-SFM medium supplemented with 5 µg/l epidermal growth factor and 50 mg/l  bovine pituitary extract (Thermo Fisher Scientific (Gibco), Waltham, USA),), 1x antibiotic/antimitotic (Invitrogen, Carlsbad, USA), 2 ng/ml leukemia inhibitory factor (Merck Millipore, Billerica, USA), 100 ng/ml cholera toxin (Sigma, St. Louis, USA), 2 ng/ml stem cell factor (Merck Millipore), 1 ng/ml granulocyte-macrophage colony-stimulating factor (Merck Millipore) and 5 µM rock inhibitor Y-27632 (ENZO Life Sciences, Farmingdale, USA).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden Germany) following manufacurers protocol.
Illumina stranded TruSeq RNA library including poly(A) enrichment: (1) Quality control of total RNA samples, (2) poly(A) enrichment, (3) cDNA synthesis an Illumina Library preparation, (4) Equimolar pooling according to library quantification measurements;

treatment_protocol: We irradiated PrEPs with either 0.5 or 1 Gy including untreated control group for a total of 20 times (5 times a week for 4 weeks). Cells were allowed to recover/expand for one week before a final radiation of 1 Gy was delivered to all groups.

value: Prostate primary basal cells

tag: pathology

value: benign

tag: individual

value: Patient 4

tag: treatment

value: group A


title: P4-B

description: Patient 4 group B

value: group B


title: 4N_B.LAB5.SynthEdit0.1

description:
POOL01-4N-MT-A_Sample85361
POOL01-4N-MT-B_Sample85362
POOL01-4N-MT-C_Sample85363
Processed data file: ALL_MT_DG_KW_q10_from_trim4NBowtie.txt


title: P4-CTRL

description: Patient 4 control

value: control


title: P3-CTRL

description: Patient 3 control

value: Patient 3


title: Day 8 of iPSC-EC Differentiation

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
Cell Ranger v1.1
Seurat
Genome_build: hg19
Supplementary_files_format_and_content: gene read counts in TXT format; cell name includes cell barcode and differentiation day
R object includes cell barcodes, differentiation day, cell cluster, raw read counts, normalized gene expression.

source_name: Endothelial cell

growth_protocol: Human induced pluripotent stem cells subjected to endothelial cell differentiation were isolated at day 8 and 12 of differentiation.

extract_protocol:
Live cells were trysinized and single cell capture was performed with 3' V1 chemistry per manufacturer's instructions from 10X Genomics (Pleasanton, CA).
Libraries were prepared per manufacturer's instructions from 10X Genomics (Pleasanton, CA).

tag: differentiation days

value: Day 8

value: iPSC-EC


title: Day 12 of iPSC-EC Differentiation

value: Day 12


title: P2-A

description: Patient 2 group A

value: Patient 2


title: P1-B

description: Patient 1 group B

value: Patient 1


title: P2-CTRL

description: Patient 2 control


title: P2-B

description: Patient 2 group B


title: Muscle RYGB 9weeks4

city: Jerusalem

first: Danny

last: Ben-Zvi

state: Israel

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description:
MR3
Roux4
processed data file: Muscle_63_processed

data_processing:
StarAligner was used for allignment, http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635)
Counts were aggregated to genes using HTSeq-count (http://bioinformatics.oxfordjournals.org/content/31/2/166)
RSeqQC was used for quality control
Genome_build: Mus_musculus.GRCm38

source_name: Skeletal muscle_sham_9 weeks

growth_protocol: High fat diet

extract_protocol:
RNA later or liquid nitrogen (adipose tissue), followed by rneasy (Qiagen) kit. Mice were sacrificed at 10am after fasting. Intestinal villi were scraped using a cell scraper after 5 minutes in ice-cold EDTA
PrepX

treatment_protocol: RYGB/Shamsurgery, followed by liquid elemental diet

tag: mouse status

value: diet-induced obese

value: male

tag: surgery

value: Roux en Y Gastric Bypass (RYGB)

tag: tissue

value: Gastroscnemius skeletal musle


title: patients 5,6 (pooled) baseline

description: P1_2 1 baseline

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed  using Affymetrix default analysis settings.

source_name: Jejunum_during RYGB

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Obese patients undergoing RYGB surgery and followup biopsy

extract_protocol: RNeasy mini kit (Qiagen) per manufacturer instruction. RIN score>8.0

treatment_protocol: Biopsy was flash frozen

tag: patients status

value: Obese patients undergoing RYGB surgery

tag: patients id

value: patients 5,6 (pooled)

tag: time point

value: during RYGB

value: jejunum


title: patients 7,8 (pooled) 1 month

description: P3_4 1 baseline

source_name: Jejunum_1 month after RYGB

value: patients 7,8 (pooled)

value: 1 month after RYGB


title: patients 3,4 (pooled) baseline

description: P7_8 1 month

value: patients 3,4 (pooled)


title: patients 9,10 (pooled) 1 month

description: P7_8 1 baseline

value: patients 9,10 (pooled)


title: NEBNext.Lab5.PlasmaPool

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15. No spike-in sequences were provided for plasma pool samples. For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Processed data files are tab-delimited text files that contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.

source_name: Human Plasma Pool; 11 healthy individuals

extract_protocol:
Whole blood was collected from 11 healthy male participants, and was processed to separate and collect the plasma. Blood was collected in K2EDTA vacutainer tubes, inverted 8-10 times and centrifuged at 500xg for 10 minutes at room temperature. The plasma layer was then transferred to a fresh 15ml tube and centrifuged at 2500 xg for 10 minutes at room temperature. The top 80% of the plasma was transferred to a fresh 15ml tube. 5x volumes of QIAzol Lysis reagent was added to 1.2 ml of the plasma. RNA was extracted using the miRNeasy kit.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.

value: Plasma

tag: disease status

value: Healthy

value: Male

tag: age range

value: 21-45 years

value: NEBNext

value: PlasmaPool


title: NEBNext.Lab2.PlasmaPool

tag: lab

tag: pool


title: patients 7,8 (pooled) baseline

description: P5_6 1 baseline


title: NEBNext.Lab1.PlasmaPool


title: Muscle RYGB 9weeks2

description:
MR2
Roux2
processed data file: Muscle_63_processed

tag: strain

value: diet-induced obese

value: male


title: patients 5,6 (pooled) 1 month

description: P9_10 1 month


title: patients 9,10 (pooled) baseline

description: P9_10 1 baseline


title: 4N_B.Lab6.PlasmaPool


title: patients 3,4 (pooled) 1 month

description: P5_6 1 month


title: patients 1,2 (pooled) 1 month

description: P1_2 1 month

value: patients 1,2 (pooled)


title: patients 1,2 (pooled) baseline

description: P3_4 1 month

value: Obese patients undergoing RYGB surgery


title: P3-A

description: Patient 3 group A

tag: cell type

value: Prostate primary basal cells

value: benign

value: Patient 3

value: group A


title: Muscle RYGB 9weeks1

description:
MR1
Roux1
processed data file: Muscle_63_processed

tag: Sex

value: Roux en Y Gastric Bypass (RYGB)

value: Gastroscnemius skeletal musle


title: Muscle RYGB 9weeks3

description:
MR4
Roux3
processed data file: Muscle_63_processed


title: 4N_B.Lab5.PlasmaPool


title: P1-CTRL

description: Patient 1 control

tag: pathology

value: Patient 1

value: control


title: P1-A

description: Patient 1 group A

tag: individual


title: Muscle sham 9weeks4

description:
MW3
sham4
processed data file: Muscle_63_processed

value: Sham


title: Muscle sham 9weeks3

description:
MW15
sham3
processed data file: Muscle_63_processed


title: Muscle sham 9weeks1

description:
MW11
sham1
processed data file: Muscle_63_processed


title: Liver RYGB 9weeks4

description:
LR4
Roux4
processed data file: Liver_63_processed

source_name: Liver_RYGB_9 weeks

value: Liver


title: Liver RYGB 9weeks3

description:
LR3
Roux3
processed data file: Liver_63_processed


title: Liver RYGB 9weeks2

description:
LR2
Roux2
processed data file: Liver_63_processed


title: Liver RYGB 9weeks5

description:
LR5
Roux5
processed data file: Liver_63_processed


title: Liver RYGB 9weeks1

description:
LR1
Roux1
processed data file: Liver_63_processed


title: Liver sham 9weeks1

description:
LW11
sham1
processed data file: Liver_63_processed

source_name: Liver_sham_9 weeks


title: Liver sham 9weeks2

description:
LW14
sham2
processed data file: Liver_63_processed


title: Liver sham 9weeks3

description:
LW15
sham3
processed data file: Liver_63_processed


title: WAT RYGB 9weeks4

description:
WR4
Roux4
processed data file: WAT_63_processed

source_name: Subcutanous white adipose tissue_RYGB_9 weeks

value: Subcutaneous white adopse tissue


title: WAT sham 9weeks3

description:
WW14
sham3
processed data file: WAT_63_processed

source_name: Subcutanous white adipose tissue_sham_9 weeks


title: WAT sham 9weeks1

description:
WW11
sham1
processed data file: WAT_63_processed


title: WAT sham 9weeks4

description:
WW15
sham4
processed data file: WAT_63_processed


title: WAT RYGB 9weeks2

description:
WR2
Roux2
processed data file: WAT_63_processed


title: Muscle sham 9weeks2

description:
MW12
sham2
processed data file: Muscle_63_processed


title: WAT sham 9weeks5

description:
WW3
sham5
processed data file: WAT_63_processed


title: Jejunum sham 9weeks 2

description:
JW12
sham2
processed data file: Jejunum_63_processed

source_name: Jejunal villi_sham_9 weeks

value: Jejunum


title: Ileum sham 9weeks1

description:
IW11
sham1
processed data file: Ileum_63_processed

source_name: Ileal villi_sham_9 weeks

value: Ileum


title: Jejuum RYGB 9weeks 1

description:
JR1
Roux1
processed data file: Jejunum_63_processed

source_name: Jejunal villi_RYGB_9 weeks

value: diet-induced obese


title: Ileum RYGB 9weeks1

description:
IR2
Roux1
processed data file: Ileum_63_processed

source_name: Ileal villi_RYGB_9 weeks

value: male


title: WAT sham 9weeks2

description:
WW12
sham2
processed data file: WAT_63_processed


title: Jejunum sham 9weeks 3

description:
JW14
sham3
processed data file: Jejunum_63_processed


title: Jejuum RYGB 9weeks 4

description:
JR5
Roux4
processed data file: Jejunum_63_processed


title: WAT RYGB 9weeks3

description:
WR3
Roux3
processed data file: WAT_63_processed


title: Jejuum RYGB 9weeks 3

description:
JR4
Roux3
processed data file: Jejunum_63_processed


title: Jejunum sham 9weeks 5

description:
JW3
sham5
processed data file: Jejunum_63_processed


title: Ileum sham 9weeks4

description:
IW15
sham4
processed data file: Ileum_63_processed


title: Jejunum sham 9weeks 1

description:
JW11
sham1
processed data file: Jejunum_63_processed


title: WAT RYGB 9weeks1

description:
WR1
Roux1
processed data file: WAT_63_processed


title: Ileum sham 9weeks5

description:
IW3
sham5
processed data file: Ileum_63_processed


title: Jejuum RYGB 9weeks 2

description:
JR2
Roux2
processed data file: Jejunum_63_processed


title: Ileum RYGB 9weeks2

description:
IR5
Roux2
processed data file: Ileum_63_processed


title: Ileum sham 9weeks3

description:
IW14
sham3
processed data file: Ileum_63_processed


title: Jejunum sham 9weeks 4

description:
JW15
sham4
processed data file: Jejunum_63_processed


title: Liver sham 9weeks4

description:
LW3
sham4
processed data file: Liver_63_processed


title: Duodenum RYGB 9weeks 4

description:
DR5
Roux4
processed data file: Duodenum_63_processed

source_name: Duodenal villi_RYGB_9 weeks

value: Duodenum


title: Duodenum RYGB 9weeks 2

description:
DR3
Roux2
processed data file: Duodenum_63_processed


title: Duodenum RYGB 9weeks 3

description:
DR4
Roux3
processed data file: Duodenum_63_processed


title: Ileum sham 9weeks2

description:
IW12
sham2
processed data file: Ileum_63_processed


title: Duodenum RYGB 9weeks 1

description:
DR2
Roux1
processed data file: Duodenum_63_processed


title: Duodenum sham 9weeks 5

description:
DW3
sham5
processed data file: Duodenum_63_processed

source_name: Duodenal villi_sham_9 weeks


title: Duodenum sham 9weeks 2

description:
DW12
sham2
processed data file: Duodenum_63_processed


title: Duodenum sham 9weeks 4

description:
DW15
sham4
processed data file: Duodenum_63_processed


title: Duodenum sham 9weeks 3

description:
DW14
sham3
processed data file: Duodenum_63_processed


title: Muscle sham 9days 3

description:
MS3
Sham3
TEEMt0827_CTGAAGCT-CCTATCCT_L003
processed data file: muscle_9_processed.txt

data_processing:
StarAligner was used for allignment, http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635)
Counts were aggregated to genes using HTSeq-count (http://bioinformatics.oxfordjournals.org/content/31/2/166)
RSeqQC was used for quality control
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Skeletal muscle_Sham

extract_protocol:
RNA later or liquid nitrogen (adipose tissue), followed by rneasy (Qiagen) kit. Mice were sacrificed at 10am after fasting. Intestinal villi were scraped using a cell scraper after 5 minutes in ice-cold EDTA
Illumina TruSeq Stranded mRNA library kit

treatment_protocol: RYGB/Sham surgery, followed by liquid elemental diet for 9 days, and transfer back to high fat diet


title: Muscle RYGB 9days 2

description:
MR2
Roux2
TEEMt0825_ATTCAGAA-GGCTCTGA_L002
processed data file: muscle_9_processed.txt

source_name: Skeletal muscle_RYGB

value: Roux en Y Gastric Bypass (RYGB) surgery


title: Muscle RYGB 9days 3

description:
MR3
Roux3
TEEMt0836_TCCGCGAA-GGCTCTGA_L004
processed data file: muscle_9_processed.txt


title: Muscle sham 9days 4

description:
MS4
Sham4
TEEMt0831_TAATGCGC-GGCTCTGA_L003
processed data file: muscle_9_processed.txt


title: Duodenum sham 9weeks 1

description:
DW11
sham1
processed data file: Duodenum_63_processed


title: Liver RYGB 9days 1

description:
LR1
Roux1
TEEMt0083_ATTACTCG-CAGGACGT_L002
processed data file: liver_9_processed


title: Muscle sham 9days 2

description:
MS2
Sham2
TEEMt0826_GAATTCGT-GGCTCTGA_L002
processed data file: muscle_9_processed.txt


title: Muscle sham 9days 1

description:
MS1
Sham1
TEEMt0823_GAATTCGT-CCTATCCT_L002
processed data file: muscle_9_processed.txt


title: Muscle RYGB 9days 1

description:
MR1
Roux1
TEEMt0824_GAGATTCC-GGCTCTGA_L002
processed data file: muscle_9_processed.txt


title: Liver RYGB 9days 4

description:
LR4
Roux4
TEEMt0095_GAGATTCC-ATAGAGGC_L004
processed data file: liver_9_processed


title: Liver RYGB 9days 3

description:
LR3
Roux3
TEEMt0094_GAGATTCC-TATAGCCT_L004
processed data file: liver_9_processed


title: WAT RYGB 9days 4

description:
WR4
Roux4
TEEMt0882_GAATTCGT-TAATCTTA_L006
processed data file: WAT_9_processed.txt

source_name: Subcutanous white adipose tissue_RYGB


title: WAT RYGB 9days 2

description:
WR2
Roux2
TEEMt0870_TCCGGAGA-AGGCGAAG_L005
processed data file: WAT_9_processed.txt


title: WAT RYGB 9days 3

description:
WR3
Roux3
TEEMt0876_GAGATTCC-TAATCTTA_L005
processed data file: WAT_9_processed.txt


title: Liver RYGB 9days 2

description:
LR2
Roux2
TEEMt0091a_CGCTCATT-ATAGAGGC_L003
processed data file: liver_9_processed


title: Muscle RYGB 9days 4

description:
MR4
Roux4
TEEMt0837_TCTCGCGC-GGCTCTGA_L004
processed data file: muscle_9_processed.txt


title: Liver sham 9days 4

description:
LS4
Sham4
TEEMt0089_TCCGGAGA-GTACTGAC_L003
processed data file: liver_9_processed


title: Liver sham 9days 1

description:
LS1
Sham1
TEEMt0081_ATTACTCG-AGGCGAAG_L004
processed data file: liver_9_processed


title: Liver sham 9days 2

description:
LS2
Sham2
TEEMt0084_ATTACTCG-GTACTGAC_L002
processed data file: liver_9_processed


title: Liver sham 9days 3

description:
LS3
Sham3
TEEMt0085_TCCGGAGA-AGGCGAAG_L003
processed data file: liver_9_processed


title: WAT RYGB 9days 1

description:
WR1
Roux1
TEEMt0869_ATTACTCG-AGGCGAAG_L001
processed data file: WAT_9_processed.txt


title: WAT sham 9days 4

description:
WS4
Sham4
TEEMt0881_ATTCAGAA-TAATCTTA_L006
processed data file: WAT_9_processed.txt

source_name: Subcutanous white adipose tissue_Sham


title: WAT sham 9days 3

description:
WS3
Sham3
TEEMt0873_ATTACTCG-TAATCTTA_L004
processed data file: WAT_9_processed.txt


title: Liver tissue from Canertinib treated MET KO mice at Day 10 after start of canertinib in diet

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

description: Gene expression data at Day 10 in [delta MET + EGFRi] mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: [delta MET + EGFRi] mice liver tissue Day 10

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

growth_protocol: Following systemic inhibition of MET-EGFR,  liver tissues harvested at Day 7 and 10

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

treatment_protocol: METfl/fl: TamCre+/+ mice were injected i.p. for five consecutive days with tamoxifen (100 μl of a 10 mg/ml solution in corn oil) to delete exon 16 of MET. Control group consisted of littermates injected with vehicle (corn oil) only. EGFR was inhibited in delta MET mice by adding Canertinib (EGFRi) in the diet with the aim of administrating 80 mg/kg/day.  Canertinib diet was initiated 4 days after completion of tamoxifen treatment. Microarray analysis was performed on RNAs isolated from pooled liver samples from the control and [delta MET + EGFRi] groups at Day 7 and 10 after start of Canertinib treatment.

tag: genotype

tag: group

value: delta MET + EGFRi

value: Day 10


description:
Gene expression data at Day 10 in Control mice
Liver tissue  from corn oil treated MET flox mice at Day 10 after completion of 4-day resting period  post-corn oil treatment

source_name: Control mice liver tissue Day 10


title: WAT sham 9days 2

description:
WS2
Sham2
TEEMt0872_GAGATTCC-AGGCGAAG_L005
processed data file: WAT_9_processed.txt

tag: mouse status


description:
Gene expression data at Day 7 in Control mice
Liver tissue  from corn oil treated MET flox mice at Day 7 after completion of 4-day resting period  post-corn oil treatment

source_name: Control mice liver tissue Day 7

value: Day 7


title: Liver tissue from Canertinib treated MET KO mice at Day 7 after start of canertinib in diet

description: Gene expression data at Day 7 in [delta MET + EGFRi] mice

source_name: [delta MET + EGFRi] mice liver tissue Day 7


title: Ileum RYGB 9days 2

description:
IR2
Roux2
TEEMt0810_AGCGATAG-TATAGCCT_L001
processed data file: Ileum_9_processed.txt

source_name: Ileal villi_RYGB

tag: surgery


title: Ileum RYGB 9days 1

description:
IR1
Roux1
TEEMt0809_TCTCGCGC-TATAGCCT_L001
processed data file: Ileum_9_processed.txt

tag: tissue


title: Ileum RYGB 9days 3

description:
IR3
Roux3
TEEMt0818_TCCGCGAA-ATAGAGGC_L001
processed data file: Ileum_9_processed.txt


title: Ileum RYGB 9days 4

description:
IR4
Roux4
TEEMt0821_TCTCGCGC-ATAGAGGC_L001
processed data file: Ileum_9_processed.txt


title: Ileum sham 9days 4

description:
IS4
Sham4
TEEMt0813_CTGAAGCT-TATAGCCT_L003
processed data file: Ileum_9_processed.txt

source_name: Ileal villi_Sham


title: Ileum sham 9days 1

description:
IS1
Sham1
TEEMt0808_GAGATTCC-ATAGAGGC_L002
processed data file: Ileum_9_processed.txt


title: Ileum sham 9days 5

description:
IS5
Sham5
TEEMt0816_CTGAAGCT-ATAGAGGC_L003
processed data file: Ileum_9_processed.txt


title: Jejuum RYGB 9days  3

description:
JR3
Roux3
TEEMt0029_CGCTCATT-ATAGAGGC_L001
processed data file: Jejunum_9_processed.txt

source_name: Jejunal villi_RYGB


title: NEBNext.Lab1.SynthB

source_name: Synthetic smallRNA; Ratiometric Pool B

value: NEBNext

value: SynthB


title: NEBNext.Lab1.SynthA

source_name: Synthetic smallRNA; Ratiometric Pool A

value: SynthA


title: WAT sham 9days 1

description:
WS1
Sham1
TEEMt0871_CGCTCATT-AGGCGAAG_L005
processed data file: WAT_9_processed.txt


title: Ileum RYGB 9days 5

description:
IR5
Roux5
TEEMt0822_AGCGATAG-ATAGAGGC_L001
processed data file: Ileum_9_processed.txt


title: Jejuum RYGB 9days  2

description:
JR2
Roux2
TEEMt0026_CGGCTATG-TATAGCCT_L002
processed data file: Jejunum_9_processed.txt


title: Ileum sham 9days 3

description:
IS3
Sham3
TEEMt0812_GAATTCGT-ATAGAGGC_L002
processed data file: Ileum_9_processed.txt


title: M.quadriceps_mLFD_08

city: Wageningen

first: Evert

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 4*44K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). All Cy3-labeled samples  were used for the reference pool.

extract_protocol: Total RNA was isolated from quadriceps muscle using Trizol isolation, quantified using Nanodrop (IsoGen Life Science) and qualified using Agilent RNA 6000 Nano kit (BioAnalyzer; Agilent).

treatment_protocol: Starting three days prior to mating, female C57BL/6J mice (8 weeks old) received either a semisynthetic low-fat (LF; 10% energy from fat, 23% energy from protein, 67% energy from carbohydrates) or HF diet (40% energy from fat, 23% energy from protein, 37% energy from carbohydrates) diet during pregnancy and lactation (mLFD and mHFD, resp.). For mating, two females were introduced to one male for two weeks and subsequently individually caged. The litter size was adjusted to 5–7 pups, with no more than four siblings finally present in one group. Mice were kept in a light- and temperature-controlled facility at 22°C with a 12 h light-12 h dark cycle. After weaning, mLF and mHF male offspring were single caged and received LF until the end of the study at 6 weeks of age. All mice were sacrificed after 2 h of fasting using isoflurane and cervical dislocation.

tag: gender

tag: age

value: 6 weeks old

value: M. quadriceps

tag: maternal diet

value: mLFD

source_name: reference pool

tag: reference pool composition


title: hsfa2 seedlings, primed and triggered, biological rep2

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

description: hsfa2 (P+T) rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were RMA normalized using GeneSpring 11.5.1.

organism: Arabidopsis thaliana

source_name: hsfa2 whole seedling of 7-d-old plants subjected to primed and triggered treatment

growth_protocol: The seeds were sowed on 0.5X MS medium containing 1% sucrose, then treated at 4°C for 3 d for synchronized germination and grown at 22°C with 16 h of light (120 mmol m-2 s-1) daily.

extract_protocol: Total RNA was extracted using RNeasy RNA extraction kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Naïve treatment: the seedlings were kept at normal growth condition without heat stress; Primed treatment: 4-d-old seedlings were treated at 37 °C for 1 h then at normal growth condition for 3 d before sample collection; Triggered treatment: 7-d-old seedlings were treated at 37 °C for 1 h before sample collection; Primed and triggered treatment: 4-d-old seedlings were treated at 37 °C for 1 h, transferred to normal growth condition for 3 d, treated at 37 °C for 1 h again before sample collection.  For heat stress treatment, the seedlings were incubated at 37°C for 1 h in a water bath.

tag: ecotype background

tag: genotype/variation

value: 7 days

value: whole seedling

tag: subjected to

value: primed and triggered treatment


title: hsfa2 seedlings, primed and triggered, biological rep1

description: hsfa2 (P+T) rep1


title: M.quadriceps_mHFD_10

tag: strain

value: mHFD

value: samples were pooled on a equimolar basis


title: M.quadriceps_mHFD_09

value: male


title: hsfa2 seedlings, naïve, biological rep2

description: hsfa2 (N) rep2

source_name: hsfa2 whole seedling of 7-d-old plants subjected to naïve treatment

value: naïve treatment


title: hsfa2 seedlings, triggered, biological rep2

description: hsfa2 (T) rep2

source_name: hsfa2 whole seedling of 7-d-old plants subjected to triggered treatment

value: triggered treatment


title: hsfa2 seedlings, triggered, biological rep1

description: hsfa2 (T) rep1


title: M.quadriceps_mLFD_10


title: Jejuum RYGB 9days  1

description:
JR1
Roux1
TEEMt0018_TCTCGCGC-TATAGCCT_L001
processed data file: Jejunum_9_processed.txt

value: diet-induced obese

value: Roux en Y Gastric Bypass (RYGB) surgery

value: Jejunum


title: M.quadriceps_mLFD_09


title: Jejunum sham 9days  4

description:
JS4
Sham4
TEEMt0024_CGCTCATT-TATAGCCT_L001
processed data file: Jejunum_9_processed.txt

source_name: Jejunal villi_Sham

value: Sham


title: hsfa2 seedlings, naïve, biological rep1

description: hsfa2 (N) rep1


title: Jejunum sham 9days  3

description:
JS3
Sham3
TEEMt0020_CGGCTATG-ATAGAGGC_L001
processed data file: Jejunum_9_processed.txt


title: Jejunum sham 9days  2

description:
JS2
Sham2
TEEMt0019_AGCGATAG-TATAGCCT_L001
processed data file: Jejunum_9_processed.txt


title: Jejunum sham 9days  1

description:
JS1
Sham1
TEEMt0016_TAATGCGC-GGCTCTGA_L001
processed data file: Jejunum_9_processed.txt


title: M.quadriceps_mHFD_08


title: Wild-type seedlings, primed and triggered, biological rep3

description: Wt (P+T) rep3

source_name: Wild type whole seedling of 7-d-old plants subjected to primed and triggered treatment

value: wild type (Col-0)


title: Duodenum RYGB 9days  2

description:
DR2
Roux2
TEEMt0039_ATTCAGAA-ATAGAGGC_L002
processed data file: Duodenum_9_processed.txt

source_name: Duodenal villi_RYGB

value: Duodenum


title: Duodenum RYGB 9days  3

description:
DR3
Roux3
TEEMt0040_GAATTCGT-ATAGAGGC_L002
processed data file: Duodenum_9_processed.txt


title: Duodenum RYGB 9days  1

description:
DR1
Roux1
TEEMt0032_ATTCAGAA-TATAGCCT_L002
processed data file: Duodenum_9_processed.txt


title: M.quadriceps_mLFD_07

value: 6 weeks old


title: M.quadriceps_mHFD_07

value: M. quadriceps


title: Duodenum sham 9days  3

description:
DS3
Sham3
TEEMt0035_AGCGATAG-TAATCTTA_L002
processed data file: Duodenum_9_processed.txt

source_name: Duodenal villi_Sham


title: M.quadriceps_mHFD_06


title: Duodenum sham 9days  4

description:
DS4
Sham4
TEEMt0036_GAATTCGT-TATAGCCT_L002
processed data file: Duodenum_9_processed.txt


title: Wild-type seedlings, primed and triggered, biological rep1

description: Wt (P+T) rep1


title: Wild-type seedlings, primed and triggered, biological rep2

description: Wt (P+T) rep2


title: Duodenum sham 9days  2

description:
DS2
Sham2
TEEMt0034_AGCGATAG-GGCTCTGA_L002
processed data file: Duodenum_9_processed.txt


title: Wild-type seedlings, triggered, biological rep2

description: Wt (T) rep2

source_name: Wild type whole seedling of 7-d-old plants subjected to triggered treatment


title: M.quadriceps_mLFD_06

value: mLFD


title: Wild-type seedlings, primed, biological rep2

description: Wt (P) rep2

source_name: Wild type whole seedling of 7-d-old plants subjected to primed treatment

value: 7 days

value: primed treatment


title: Wild-type seedlings, triggered, biological rep3

description: Wt (T) rep3

value: whole seedling


title: Duodenum sham 9days  1

description:
DS1
Sham1
TEEMt0031_AGCGATAG-ATAGAGGC_L002
processed data file: Duodenum_9_processed.txt


title: Wild-type seedlings, primed, biological rep1

description: Wt (P) rep1


title: M.quadriceps_mLFD_04


title: M.quadriceps_mLFD_05


title: Wild-type seedlings, triggered, biological rep1

description: Wt (T) rep1


title: Wild-type seedlings, naïve, biological rep1

description: Wt (N) rep1

source_name: Wild type whole seedling of 7-d-old plants subjected to naïve treatment


title: Wild-type seedlings, naïve, biological rep2

description: Wt (N) rep2


title: M.quadriceps_mHFD_05

value: mHFD


title: M.quadriceps_mHFD_04

value: samples were pooled on a equimolar basis


title: M.quadriceps_mLFD_03

value: male


title: M.quadriceps_mLFD_02


title: M.quadriceps_mHFD_03


title: Wild-type seedlings, naïve, biological rep3

description: Wt (N) rep3

value: naïve treatment


title: non_GVHD_PN7

status: Public on Jul 08 2018

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

description:
test
non_GVHD_PN7

data_processing:
ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).

label: TaqMan probe (FAM-MGB)

source_name: exosome

label_protocol: The RT reaction and pre-amplification step were set up according to the recommendations. MiRNAs were reverse transcribed with Megaplex Prime Pools (Human Pools A v2:1; Thermo Fisher Sciences). The miRNA expression profiles were determined with a TaqMan miRNA Array Human Card A (Thermo Fisher Sciences).

extract_protocol: Total RNA was isolated with the miRNeasy kit (Qiagen) from eight unselected healthy volunteers, five LA GVHD patients and five non-GVHD patients. The exosome pellets were dissolved by 700 μl of Qiazol. After a 5-min incubation, 1 μl of 1 nM ath-miR-159 (Hokkaido System Science) was added to aliquot followed by vortexing for 30 s and incubation for 5 min. Subsequent phenol extraction and filter cartridge was performed according to the manufacture’s instruction.

treatment_protocol: Plasma samples were harvested form 2ml of whole blood. Exosomes were extracted from 200 µL of plasma by using Total Exosome Isolation Reagent (Invitrogen).

tag: condition

value: plasma

tag: rna fraction

value: exosomal miRNA


title: non_GVHD_PN9

description:
test
non_GVHD_PN9


title: non_GVHD_PN6

description:
test
non_GVHD_PN6


title: M.quadriceps_mLFD_01


title: M.quadriceps_mHFD_01


title: non_GVHD_PN8

description:
test
non_GVHD_PN8


title: LA_GVHD_PN5

description:
test
LA_GVHD_PN5


title: LA_GVHD_PN2

description:
test
LA_GVHD_PN2


title: TLDA-235_NC8

description:
test
NC8

value: NC


title: LA_GVHD_PN1

description:
test
LA_GVHD_PN1


title: LA_GVHD_PN3

description:
test
LA_GVHD_PN3


title: M.quadriceps_mHFD_02


title: TLDA-234_NC7

description:
test
NC7


title: TLDA-233_NC6

description:
test
NC6


title: TLDA-232_NC5

description:
test
NC5


title: TLDA-231_NC4

description:
test
NC4


title: non_GVHD_PN10

description:
test
non_GVHD_PN10


title: Ileum sham 9days 2

description:
IS2
Sham2
TEEMt0811_ATTCAGAA-ATAGAGGC_L002
processed data file: Ileum_9_processed.txt

value: diet-induced obese

tag: Sex

value: Ileum


title: TLDA-140_NC2

description:
test
MC2


title: TLDA-139_NC1

description:
control sample for fold-change calculation
NC1


title: TLDA-230_NC3

description:
test
NC3


title: LA_GVHD_PN4

description:
test
LA_GVHD_PN4


title: breast cancer tissue B7

status: Public on Jul 07 2018

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

institute: Shantou University Medical College

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 11 tissue samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

source_name: breast tumor tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: breast cancer and non-tumor breast tissues

treatment_protocol: Tissues from surgury and promptly frozen in liquid nitrogen.

value: breast tumor

tag: subtype

value: Triple-negative breast cancer

value: female


title: breast cancer tissue B8


title: breast cancer tissue B10


title: breast cancer tissue A3

value: luminal A


title: breast cancer tissue B6


title: breast cancer tissue A4


title: mammary gland tissue C12

source_name: mammary gland tissue

value: mammary gland

value: non-tumor breast tissues


title: breast cancer tissue A1


title: mammary gland tissue C11


title: breast cancer cell S15

source_name: breast cancer cell

growth_protocol: Cells are cultured in EMEM containing 2 mM L-glutamine, 0.01 mg/mL bovine insulin (90%), fetal bovine serum (10%) and Earle’s BSS containing 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids and 1 mM sodium pyruvate.

treatment_protocol: Treated with Trizol for extraction

tag: cell line

value: breast cancer


title: mammary gland tissue C13


title: breast cancer cell S17

value: Tamoxifen-Resistant MCF-7 cell


title: breast cancer cell S14


title: breast cancer tissue A2


title: IRF9WT_HPOS_D4_3

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

source_name: splenic NK cells

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

tag: genotype

tag: replicate

value: HPOS


title: IRF9WT_HPOS_D4_2


title: IRF9KO_HPOS_D4_3


title: IRF9WT_HPOS_D4_1


title: IRF9WT_HPOS_D0_1


title: WT_monosome_2

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

institute: University of Liverpool

hyb_protocol: 600 ng of labeled cRNA was hybridized to Agilent Sureprint G3 Mouse whole-genome microarrays according to manufacturers instructions

scan_protocol: Agilent SureScan microarray scanner

data_processing: Microarray data were log2 transformed and normalized using quantile normalisation

label_protocol: Cy3 labeled cRNA was generated using the Agilent Low-Input QuickAmp Kit following the manufacturer’s instructions.

growth_protocol: Mice were housed in standard housing units, fed ab libitum with rodent laboratory chow. Mice were sacrificed by cervical dislocation, and skeletal muscle was immediately removed, cleaned of any excess fat or connective tissue, and flash frozen in liquid nitrogen

extract_protocol: Muscle lysate was layered on a 15%–50% linear sucrose gradient and centrifuged at 37,000 rpm for 170 min. The sucrose gradient was fractionated and UV absorption at 260 nm was recorded. RNA was precipitated by adding 2 volumes of 100% ethanol, redissolved in RNase-free water, and treated with phenol-chloroform. Sucrose fractions containing ≥2 polysomes were pooled for subsequent analysis. Total RNA was extracted from muscle using the methods of Caddick et al. (2006).

value: wt

value: Gastrocnemius

tag: rna source

value: monosome


title: WT_wholemuscle_3

source_name: Gastrocnemius_WT_whole muscle

tag: tissue

value: whole muscle


title: Het_wholemuscle_2

source_name: Gastrocnemius_Het_whole muscle

value: het


title: WT_monosome_1


title: Het_monosome_1


title: Soleus_Young_pair_2

data_processing: Microarray data were log2 transformed and normalized using loess (normalizeWithinArrays function in R package marrray) without background subtraction

label_protocol: Cy3 and Cy5-labeled cRNA was generated using the Agilent Low-Input QuickAmp Kit following the manufacturer’s instructions.

extract_protocol: Frozen soleus muscle was homogenized in RLT buffer (QIAGEN) with β-mercaptoethanol (1% v/v) using a Precellys-24 tissue homogenizer system (Precellys, UK). Each tissue lysate was centrifuged at 13,000 rpm for 10 min, and the supernatant was removed for RNA extraction. RNA was isolated using QIAGEN RNeasy columns following the manufacturer’s instructions. Sample purity was assessed by measuring absorbance at 260 and 280 nm using a NanoDrop spectrophotometer.

value: Het

value: Soleus

value: Young

value: WT


title: Het_wholemuscle_1


title: Het_wholemuscle_3


title: Het_monosome_3


title: Het_polysome_2

value: polysome


title: Soleus_Mature_pair_1

value: Mature


title: Soleus_Mature_pair_4


title: WT_wholemuscle_1


title: Soleus_Young_pair_1


title: Soleus_Mature_pair_3


title: Soleus_Mature_pair_2


title: Het_polysome_1


title: WT_wholemuscle_2


title: Soleus_Young_pair_4


title: WT_polysome_3


title: WT_polysome_2


title: Soleus_Young_pair_3


title: WT_polysome_1


title: Het_polysome_3


title: IRF9KO_HPOS_D0_1


title: IRF9KO_HPOS_D4_1


title: IFNARWT_HPOS_D2_002

description: IFNARKOChimera_MCMV_IfnarHpos_rawCounts_knownGene.txt

value: IFNARWT


title: IFNARWT_HPOS_D2_001


title: IRF9KO_HPOS_D4_2


title: IFNARWT_HPOS_D0_002


title: IFNARWT_HPOS_D0_001


title: IFNARKO_HPOS_D2_002

value: IFNARKO


title: IFNARKO_HPOS_D2_001


title: IFNARKO_HPOS_D0_002


title: IFNa_01

description: ExVivoCytokineStim_unstimIFNaonly_rawCounts_knownGene.txt

value: HPOSNEG

value: IFNa


title: aIRF9_IRF9WT_STIM_3_CHIP

description: Irf9_ChIP_peaklist_ZeroBasedCorrected.bed

library_source: genomic

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled. BED file consists of IDR-thresholded (IDR < 0.01) peak list.

molecule: genomic DNA

extract_protocol:
Protein was cross-linked to DNA with 1% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: antibody


title: aIRF9_IRF9WT_STIM_1_INPUT

value: Input


title: aIRF9_IRF9WT_STIM_1_CHIP


title: P50_WT_Dorsal_Dermis_RNAseq

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
For analysis, raw transcriptome sequence data were mapped to the mouse genome (GRCm38/mm9) using TopHat (v2.0.13) with default settings to produce a reference-guided transcript assembly.
Cufflinks (v2.2.1) was used to normalize expression levels for each sample to fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: GRCm38/mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: skin

extract_protocol:
Total RNA was isolated from FACS-purified cells lysed with Trizol (Life Techologies) followed by extraction using a direct-Zol RNA mini prep kit (Zymo research). For cDNA synthesis, equal amounts of RNA were added to re¬verse-transcriptase reaction mix (Vazyme, R222-01).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: skin

tag: cell type

value: dorsal dermal cells

tag: age

value: post natal day 50

value: Wt/Wt


title: P50_WT_Ear_Dermis_RNAseq

value: ear dermal cells


title: P50_Koa_Ear_Dermis_RNAseq

value: Wt/Koa


title: P50_Koa_Ear_Epidermis_RNAseq

value: ear epidermal cells


title: P50_WT_Ear_Epidermis_RNAseq


title: P50_WT_Dorsal_Epidermis_RNAseq

value: dorsal epidermal cells


title: P50-WT-Ear-Dermis-H3K27me3-0-merged_ChIPseq

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were filtered, and then de-barcoded. Low-quality ends were trimmed. Reads were then aligned to mouse genome (mm9) using Bowtie2.
Normalization among different samples was achieved using Homer with default settings and normalize reads for each sample to fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using Homer package.

extract_protocol:
~5-6 million dermal cells were fixed in 1% formaldehyde for 10 min at 37ºC. Crosslinked cells were lysed in lysis buffer (0.3% SDS, 50 mM Tris-HCl, pH=8.0, 20 mM EDTA, and freshly added protease inhibitors) on ice for 10 min, with vortexing every 2 min. Lysed samples were immediately subjected to 36 cycles of sonication at power 10 with a sonicator (Qsonica, Q700) to generate small chromatin fragments. 5 μg of the H3K27ac (ActiveMotif, 39133), and H3K27me3 (Millipore, 07-449), and CTCF (Thermal Fisher, PA5-17143), antibodies were used for immunoprecipitation.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)


title: P50-WT-Ear-Dermis-H3K27me3-2-merged_ChIPseq


title: P50-WT-Ear-Dermis-H3K27ac-1-merged_ChIPseq

value: H3K27ac (ActiveMotif, 39133)


title: P50-WT-Ear-Dermis-H3K27me3-1-merged_ChIPseq


title: P50-WT-Ear-Dermis-H3K27ac-0-merged_ChIPseq


title: P50-WT-Ear-Dermis-CTCF-2-merged_ChIPseq

value: CTCF (Thermal Fisher,PA5-17143)


title: P50-WT-Ear-Dermis-CTCF-1-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-H3K27me3-2-merged_ChIPseq


title: P50-WT-Ear-Dermis-H3K27ac-2-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-H3K27me3-0-merged_ChIPseq


title: IFNa_02

value: WT


title: aIRF9_IRF9WT_STIM_3_INPUT


title: aIRF9_IRF9WT_STIM_2_CHIP


title: P50-WT-Dorsal-Dermis-H3K27ac-1-merged_ChIPseq


title: aIRF9_IRF9WT_STIM_2_INPUT


title: P50-WT-Dorsal-Dermis-H3K27ac-2-merged_ChIPseq


title: P50-WT-Ear-Dermis-CTCF-0-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-H3K27ac-0-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-CTCF-1-merged_ChIPseq


title: P50-Koa-Ear-Dermis-H3K27me3-2-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-CTCF-0-merged_ChIPseq


title: P50-WT-Dorsal-Dermis-CTCF-2-merged_ChIPseq


title: P50-Koa-Ear-Dermis-H3K27me3-1-merged_ChIPseq


title: P50-Koa-Ear-Dermis-H3K27ac-2-merged_ChIPseq


title: P50-Koa-Ear-Dermis-H3K27ac-1-merged_ChIPseq


title: P50-Koa-Ear-Dermis-H3K27me3-0-merged_ChIPseq


title: P50-WT-Ear-Dermis-Hoxc4-ViewPoint-4Cseq

data_processing:
Library strategy: 4C
Basecalls performed using CASAVA version 1.4
Raw sequencing reads were trimmed using cutadapt, with 4C reading primer sequence and primary restriction site ligated to the 5' end.
The processed reads were aligned to the mouse reference genome (mm9) by bowtie with no mismatches and unique match allowed. Reads in a region directly surrounding the 2 kb up- and downstream viewpoint were excluded. A library file of fragments is generated based on the first and second restriction sites used for the 4C template preparation using a custom perl script.
A list of raw reads number per fragment was counted using aligned reads. Then the 4C signal was transformed to a binary value (0 or 1) for each fragment, depending on whether the normalized read count was below or above a certain threshold of 10 counts. Fragments that fulfill the threshold criteria are termed hits. Then the hit percentage of a window of 10 fragment was calculated as an estimate of the contact frequency.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig

extract_protocol: 4C experiment was conducted based on a previously-described protocol (Daan Noordermeer et al., 2011)


title: P50-Koa-Ear-Dermis-H3K27ac-0-merged_ChIPseq


title: P50-Koa-Ear-Dermis-Hoxc4-ViewPoint-4Cseq


title: P50-WT-Dorsal-Dermis-H3K27me3-1-merged_ChIPseq


title: Old mouse aorta scRNA-seq

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
BCL files were extracted from the sequencer and used as input for the Cell Ranger pipeline to generate the digital expression matrix.
Genome_build: Mus_musculus GRCm38.84 (from ENSEMBL - http://www.ensembl.org/Mus_musculus/Info/Annotation)
Supplementary_files_format_and_content: tab-delimited text files contains raw expression matrix, in which each column represents a cell, and each row represents a gene

source_name: Mouse Aorta

extract_protocol:
Isolation of endothelial cells from the aorta was performed by first dissecting the aorta free of adventitia and exposing the endothelium to the surface. After several washes with versine solution (REF), the endothelium was bathed in 1X trypsin solution and incubated for 10min at 37C. After this time and under the dissecting microscope the surface of the endothelium was gently removed with a small scalpel (microfeatherTM) and repeating pipetting to dissociate cell-cell junctions. The trypsin solution with released cells was placed  in a solution of 0.04% BSA and 0.01% FCS.
For the generation of single-cell GEMs a suspension of 8700 cells were loaded on a Chromium Single Cell Instrument (10x Genomics) with an estimated targeted cell recovery of ~5000 cells.  Single-cell RNAseq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics).

value: 18 months old

value: aorta


title: Young mouse aorta scRNA-seq

value: 8 weeks old


title: WT Vehicle rep 4

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Reads were aligned to the mouse GRCm38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples

source_name: Cecum

extract_protocol:
Ceca were dissected out, emptied of their content, flash frozen in liquid nitrogen, and RNA was prepared using Qiagen RNeasy Mini Kit.
Libraries were prepped using Illumina’s TruSeq Stranded mRNA HT kit according to manufacturer’s instructions, starting with 1ug of RNA

treatment_protocol: C57Bl/6 mice were treated for 30 days with a cocktail of antibiotics twice daily by oral gavage (AIMD) or water (vehicle).

value: Cecum

value: 20 weeks

tag: treatment

value: Vehicle


title: WT Vehicle rep 6


title: WT Vehicle rep 3


title: WT AIMD rep 7

value: AIMD


title: WT Vehicle rep 7


title: WT Vehicle rep 2


title: WT AIMD rep 6


title: WT Vehicle rep 1


title: WT AIMD rep 5


title: WT AIMD rep 3


title: WT Vehicle rep 8


title: WT AIMD rep 2


title: WT AIMD rep 1


title: WT Vehicle rep 5


title: 05_10_ant_bud_v-dsRNA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Asparagus dsRNA, 0.5 - 1.0 mm anthers (whole buds), BM14-182, Rnase V1

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043). Processed files for sRNA libraries were aligned to the Asparagus genome (v.1) using Bowtie (v0.12.8) with no allowed mismatches. Mapped sRNA reads were finally normalized to empirically derived, 30 s. Raw SMRT-sequencing data was pre-processed using the pbscript-tofu tool set (v2.3.0) from Pacific Biosciences using the default settings. The pre-processing included generation of subreads FASTA file using the RS_subreads protocol, followed by classification of reads to full-length and non-full-length categories, clustering of transcripts to consensus isoforms by ICE algorithm and final polishing by Quiver algorithm (min. accuracy = 0.99). For all downstream analysis, “high QV” transcript set generated from Quiver analyses was used. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”.For this, reads from paired-end libraries were first combined into two (FASTQ) files, one corresponding to left reads and other to right reads. Reads from the single-end libraries were then added to the combined left reads (FASTQ) file. These left and right reads files were used to generate a hybrid assembly with the default settings except for the minimum assembled contig length (set to 250 nt). ExN50 and the quality of assemblies was accessed as recommended in Trinity workflow. Transcripts from de novo assembly were annotated using Trinotate workflow with the default settings (https://trinotate.github.io/).
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts for sRNAs, FASTA files for SMRT-seq and FASTA files for Illumina mRNA seq. Since the mRNAseq and SMRT-seq samples were used for transcriptome assembly, there are no quantitative data for these samples. The transcriptome assembly made from the mRNA-seq samples is available on the series record.

organism: Asparagus officinalis

growth_protocol: Flowering Asparagus plants were harvested from T.S. Smith and Sons Farms (Bridgeville, Delaware)

extract_protocol:
Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Total RNA was isolated using the PureLink Plant RNA Reagent following the manufacturer’s instructions. Total RNA quality and quantity were assessed before proceeding to the next step.
Small RNAs (20 to 30 nt) were size selected in a 15% polyacrylamide/urea gel and libraries were constructed using the TruSeq Small RNA Prep Kit (Illumina, cat. # RS-200-0012). Small RNA libraries containing different index tags were pooled and sequenced on an Illumina HiSeq 2500 instrument at the Delaware Biotechnology Institute. The complete protocol for sRNA library preparation is described in Mathioni et al. (DOI: 10.1002/cppb.20043). RNA-seq libraries (for mRNA) were constructed using the TruSeq Stranded Total RNA Library Preparation Kit with Ribo-Zero Plant (Illumina, cat # RS-122-2401), and RNA was treated with DNase I (NEB, cat # M0303S) and then cleaned using the RNA Clean & Concentrator™-5 (Zymo Research, cat # R1015). Single Molecule Real Time (SMRT) sequencing libraries were prepared using protocol recommended by Pacific Biosciences for Isoform Sequencing using SageELF size selection system
Small RNA sequencing using Illumina single-end (1x50 bp) reads. Messenger RNA sequencing using Illumina single-end (2x150 bp) reads and Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts.

value: floral bud


title: 05_ant_bud_o-dsRNA

description: Asparagus dsRNA, <0.5 mm anthers (whole buds), BM14-181, Rnase ONE


title: 05_ant_bud_v-dsRNA

description: Asparagus dsRNA, <0.5 mm anthers (whole buds), BM14-181, Rnase V1


title: 05_10_ant_bud-dsRNA

description: Asparagus dsRNA, 0.5 - 1.0 mm anthers (whole buds), BM14-182, Rnase ONE


title: Asp_le-mRNA

description: Asparagus, cladophylls, BM14-72

source_name: Asparagus, cladophylls, BM14-72

value: leaf


title: WT AIMD rep 4


title: Primary cardiomyocytes-No LeTx-24h-rep4

city: El Paso

first: Lihong

last: Wu

address: MSB1, Room 3105,5001 El Paso Drive

department: Department of Biomedical Sciences, Paul L. Foster School of Medicine

institute: Texas Tech University Health Sciences Center El Paso

description: P-cardio-No LeTx-4

hyb_protocol: Samples were hybridized with GeneChip Mouse Transcriptome Arrays (Affymetrix) and scanned at the UTSW Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with Affymetrix Expression console software for background correction and normalization.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: PBS treated primary cardiomyocytes

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT plus reagent kit. (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted according to the manufacturer's instructions of Qiagen Rneasy MiNi Kit.

treatment_protocol: Primary cardiomyocytes were exposed to 2 µg/ml LeTx for 24h, with PBS as a negative control.

value: Balb/c

value: heart

value: primary cardiomyocytes

tag: exposed to

value: PBS (negative control) for 24hrs


title: Asp_0_5_ant_b-mRNA

description: Asparagus, <0.5 mm anthers (whole buds), BM14-181


title: Asp_1_ant_b-mRNA

description: Asparagus, 0.5 - 1.0 mm anthers (whole buds), BM14-182