title: wde GLKD RNA-seq 2

description: processed data file: DifferentialAnalysis.txt

data_processing:
Reads were aligned to the Drosophila genome (UCSC dm6) using TopHat and reported as FPKM
Differential analysis was completed using CuffDiff
Genes with at least a 2 fold change over wild type with a False Discovery Rate of < 5% were considered significant
Genome_build: dm6
Supplementary_files_format_and_content: Aligned reads were processed to wig files using bamtowig

source_name: wde GLKD_ovaries

growth_protocol: Flies were grown on standard growth media at 25 degrees Celcius for wild type at 29 degrees Celcius for setdb1 GLKD and hp1a GLKD. wde GLKD flies were raised at 18 degrees Celcius and switched to 29 degrees Celcius for 2 days post eclosion

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) methods
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit

value: 2 days


title: hp1a GLKD RNA-seq 1

status: Public on Sep 07 2018

type: SRA

city: Boston

first: Mitzi

middle: I

last: Kuroda

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Brigham and Women's Hospital/Harvard Medical School

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

source_name: hp1a GLKD_ovaries

tag: full genotype

tag: age

value: 3-5 days

tag: tissue

value: ovaries


title: Buspirone·HCl [HI.3146.003.BioO_1.52]

city: Cambridge

first: Hualin

last: Xi

address: 1 portland st

institute: Pfizer

data_processing:
Sequenced by Illumina HiSeq 2500 at the McGill Innovation Centre.
RNA-seq reads were alligned to mm10 using Star v2.4.0
Read counts were summarized to gene-level by the feature count module of Subread package (version 1.4.6).
All samples passed quality control based on post-alignment metrics using RSeQC (version 2.6.1).
Genes that had raw counts = 0 and/or cpm<1 across all 227 samples were excluded from the final results.
Normalization was performed using limma/EdgeR package (version 3.10.5). Briefly, two levels of normalization were performed to adjust for: 1) library size; 2) mean-variance heteroscedasticity. The trimmed mean of M-values (TMM) method was used to calculate a weighted trimmed mean across all samples.
Mean-variance relationship was estimated by the voom module. Principle component analysis (PCA) was calculated to check for systemic bias across samples. The top 4 principle components were removed, and the resultant residuals were used for subsequent analysis. Robust z-scores were calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: count and rpkm

organism: Mus musculus

source_name: Cerebral Cortex

growth_protocol: Briefly, dissociated cerebral cortices from embryonic day 16.5 filial 1 progeny of a FVB/N x C3B6F1 were cultured in Neurobasal medium containing B27 supplement (2%), GlutaMAX (2%), 100 I.U./mL penicillin, and 100 μg/mL streptomycin. Cultures were grown in 6-well plates at a density of one million cells per well.

extract_protocol:
RNA was isolated from cortical cultures using the NucleoSpin RNA kit (Macherey-Nagel). Purity and concentration of total RNA was tested by Nanodrop analysis while the RNA integrity number (RIN) of each total RNA sample was determined using the Agilent RNA 6000 nano kit and the Agilent 2100 Bioanalyzer.
Complementary DNA (cDNA) libraries were created using the KAPA Biosystems Stranded mRNA-Seq kit from high-quality RNA samples (RIN≥8). Chemical fragmentation was performed per kit specifications to generate an average fragment size 200-300bps (confirmed by Agilent DNA 1000 kit). NEXTflex™ RNA-Seq barcode adapters were ligated onto fragmented RNA samples and adapter ligated libraries were amplified by polymerase chain reaction (PCR) for 10 cycles.

treatment_protocol: Briefly, cerebrocortical cultures (DIV21) in 6-well plates were treated for 8 hours with vehicle (0.2% DMSO) or one of the 218 BBB-penetrant drugs used for the screen. Drug concentrations are provided as part of the Neuron Screen Database.

tag: cell type

value: Primary Cerebrocortical Cultures

tag: days in vitro

tag: strain

value: F1 embryo FVBN(F)xC3B6F1(M)

tag: agent

value: Buspirone·HCl


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time00

city: Berkeley

first: Leon

last: Chan

state: California

address: 628 Barker Hall UC Berkeley

department: Molecular Cell Biology

institute: UC Berkeley

data_processing:
reads aligned with Tophat
reads assembled and quantified with Cufflinks
Genome_build: W303_ALAV00000000_2012_SGD
Supplementary_files_format_and_content: fpkm_tracking files generated with Cufflinks

organism: Saccharomyces cerevisiae

source_name: gcn2∆ cells

growth_protocol: cells grown overnight and backdiluted and grown at least two doublings and never over OD = 0.7

extract_protocol:
hot phenol extraction followed by another phenol extraction followed by a chloroform extraction
BioO NEXTflex® Rapid Directional RNA-Seq Library Prep Kit

treatment_protocol: 4-thiouracil labeling, see associated publication

tag: genotype/variation

tag: growth phase

value: exponential growth

tag: time point


title: Betamethasone [HI.3147.005.BioO_1.51]

value: Betamethasone


title: wde GLKD RNA-seq 1


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time20

value: mock


title: ko.infected.r5

type: RNA

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: replicate 5

hyb_protocol: For each sample, 300 ng of total RNA was amplified using the Total prep RNA amplification kit (Illumina), quantified using the Qubit and analysed by Agilent 2100 Bioanalyzer.  Amplified cDNA (1500 ng) samples were hybridized to microarray slides at 58 °C for 14–20 h with Illumina MOUSE WG-6 V2.0 Beadarrays according to the manufacturer’s protocols at the High Throughput Screening facility of the Francis Crick institute

scan_protocol: iScan system, Illumina

data_processing: Detection pvalues were calculated from the idat files using Limma's detectionPvalues function within R.  Data were subsequently background corrected and quantile normalized using Limma's neqc function with default settings.

label: biotin

source_name: IFNA Receptor knock-out mouse injected with 105 Plasmodium berghei ANKA infected red blood cells

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

growth_protocol: Female C57BL/6 wildtype and IFNA Receptor knock-out (Muller et al 1992 Science, 264 1918) mice aged 6–10 weeks, obtained from the Biological Research Facility, Mill Hill, Francis Crick Institute, were housed conventionally with sterile bedding, food and irradiated water, with a 12 h light/dark cycle, and injected with 105 Plasmodium berghei ANKA infected red blood cells intraperitoneally. Parasitemia was monitored daily by Giemsa-stained thin blood films. Neurological complications typical of ECM, including ruffled fur, hunching, loss of equilibrium, partial paralysis, coma, loss of body weight and drop of temperature.   Methods are described in detail in described in Capuccini et al 2016, Scientific Reports, 6:39258

extract_protocol: Total RNA from approximately 10e5 sorted microglia cells was isolated using Ribopure (Ambion). RNA concentration was determined by Qubit fluorometric quantitation with  HS assay kit (ThermoFisher Scientific). The quality of RNA analysed on the Agilent 2100 Bioanalyzer; only samples with a RIN score above 8.50 were used for microarray analysis.

treatment_protocol: Brains were isolated in cold HBSS buffer (without Ca++ and Mg++), and enzymatically digested using a Neural Tissue Dissociation Kit (P) (Milteny Biotec) according to the manual. Digested brain samples were re-suspended in 4.5 ml of Percoll (GE Healthcare) 75% (in PBS) in a 15ml tube, on which 9.5ml of Percoll (37% in HBSS) was overlayed. After centrifugation at 800 g for 20 minutes at 4 °C without brake, the ring on the top of the upper layer containing myelin and debris was removed, and the ring between the phases 70% and 37% containing brain cells was collected and washed with PBS. Isolated microglia were incubated with Fc Receptor block (BD) for 15 minutes followed by 1h staining at 4 °C with Zombie, UV™ Fixable Viability kit (Biolegend) and combinations of fluorophore conjugated antibodies: APC-conjugated anti-CD11b, PE-conjugated-CD45, APCCy7- conjugated-Ly6C, pacific blue-cojugated-H-2Kb (Biolegend). Cells were then washed and resuspended in PBS containing 2% FCS. Cells sorting was performed on MoFlo XDP (Beckman coulter).Ghe purified microglia were collectd directly into TRIreagent (Ambion) and stored at −80 °C.  To access the purity of microglia, 50,000 to 100,000 cells were acquired on a BD LSR-Fortessa X-20 flow cytometer and analysed using FlowJoX (Treestar)

tag: genotype

value: IFNA Receptor knock-out

tag: Sex

value: female

tag: background strain

value: brain

value: microglia

tag: treatment

value: Intraperitoneal injection with 105 Plasmodium berghei ANKA infected red blood cells


title: Allopurinol [HI.3146.003.BioO_6.50]

value: Allopurinol


title: setdb1 GLKD RNA-seq 2

source_name: setdb1 GLKD_ovaries


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time15


title: 13Clamp

city: Bayreuth

first: Tillmann

last: Lueders

state: Bayern

address: Dr.-Hans-Frisch-Straße 1-3

department: Lehrstuhl Ökologische Mikrobiologie (ÖMIK)

country: Germany

institute: Universitaet Bayreuth

description:
otu_table_filtered.biom (and text version otu_table_filtered.txt)
KEGG_relative.megan
KEGG_functional.txt

data_processing:
Primary image processing was performed on the NextSeq500 instrument using Real Time Analysis 2.0 Software (RTA). The Illumina Sequence Analysis Viewer (SAV) 1.9.1. was used for imaging and evaluation of the sequencing run performance.
Primary data analysis, including demultiplexing, was performed using the bcl2fastq 2.0 software package.
Sequencing adapters were removed and paired-end reads merged using Adapterremoval with default settings except: trim ambiguous bases (N) at 5'/3' termini , trim bases at 5'/3' termini with quality scores ≤ 15 and minimum read length of 50.
RNA was sorted into 16S, 23S, and non-rRNA using SortmeRNA v2 and Silva databases. 16S and non-rRNA reads were then processed separately.
Non-rRNA tags were compared against the NCBI-nr, COG, and KEGG v58.1 databases using DIAMOND. Annotations were analyzed using MEGAN 5.
16S OTU assignment was performed using QIIME v1.9.1. Preprocessing was performed with commands split_libraries_fastq.py (quality=2, p=0.01), truncate_reverse_primer.py, identify_chimeric_seqs.py (method: usearch61), and filter_fasta.py. OTU calling was performed using the Silva database release 123 using pick_open_reference_otus.py (97 % similarity) and filter_otus_from_otu_table.py .
16S: Silva database release 123. Functional transcripts: KEGG datavase v58.1
16S: the biom file is the output from OTU assignment with QIIME and contains non-normalized read counts of each OTU. Functional transcripts: the megan file can be imported into MEGAN 5 and contains relativized read counts for each non-rRNA at all levels in the KEGG hierarchy. The text file is an output from MEGAN and includes each functional transcript with its KEGG ID number and relativized read counts from each sample.
Supplementary_files_format_and_content: otu_table_filtered.biom (and .txt version)
Supplementary_files_format_and_content: KEGG_relative.megan (megan file, compatible with MEGAN5)
Supplementary_files_format_and_content: KEGG_functional.txt

organism: aquifer metagenome

source_name: Aquifer sediment (Environmental microbial community)

extract_protocol:
RNA was extracted with the Powersoil RNA isolation kit from QIAgen. Heavy (representing microbes that metabolized toluene) and light (microbes that did not metabolize toluene) RNA was separated by isopycnic centrifugation. Additionally, subsamples of RNA from Heavy and Light fractions underwent linear amplification with the MessageAmp II Bacteria kit from Thermofisher to compare the effects of amplification against unamplified samples.
Libraries were produced according to manufacturer instruction using the Illumina TruSeq® Stranded mRNA HT kit.

treatment_protocol: Each microcosm consisted of a 100 ml serum bottle with 5 g (wet weight) sediment material, 50 ml artificial groundwater medium, and 5 µL of non-labeled  (12C) or fully labelled (13 463 C7) toluene with a N2/CO2 (80/20, v/v) headspace. Microcosms were incubated at 16 °C with 145 rpm rotary shaking. Dissolved oxygen levels were maintained between 0 and 0.5 mg/L by daily replenishment with air injected through a 0.2 µm filter.

tag: geographic location

value: Siklos, Hungary

value: Linear amplification

tag: density

value: Light

tag: microcosm set

value: Labeled (13C-toluene)


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time10


title: setdb1 GLKD RNA-seq 1

tag: full genotype

value: 3-5 days

value: ovaries


title: ko.infected.r4

description: replicate 4


title: ko.infected.r1

description: replicate 1


title: ko.infected.r3

description: replicate 3


title: ko.infected.r2

description: replicate 2


title: Pramipexole Dihydrochloride Monohydrate [HI.3146.002.BioO_4.48]

value: Primary Cerebrocortical Cultures

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Pramipexole Dihydrochloride Monohydrate


title: 13CHamp

value: Heavy


title: wild type RNA-seq 2

source_name: wild type_ovaries

value: yw

tag: age

value: 0-24 hours


title: Oseltamivir Phosphate [HI.3146.002.BioO_3.47]

value: Oseltamivir Phosphate


title: wild type RNA-seq 1

tag: tissue


title: 12CLamp

value: Control (12C-toluene)


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time05

value: exponential growth

value: mock


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time30


title: Granisetron·HCl [HI.3146.002.BioO_2.46]

tag: cell type

value: Granisetron·HCl


title: gcn2∆_exponential_growth_mock_treated_mRNA_decay_profile_time00


title: 12CHamp

value: Siklos, Hungary


title: 13CLunamp

value: No linear amplification


title: Fosinopril·Na [HI.3147.004.BioO_6.45]

tag: days in vitro

value: Fosinopril·Na


title: Acyclovir [HI.3146.003.BioO_5.49]

tag: strain

value: Acyclovir


title: 13CHunamp

value: Labeled (13C-toluene)


title: Dolasetron [HI.3147.004.BioO_5.44]

tag: agent

value: Dolasetron


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time20

source_name: wild-type cells

tag: genotype/variation

value: wild-type

value: hippuristanol


title: Anastrozole [HI.3146.001.BioO_4.43]

value: Primary Cerebrocortical Cultures

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Anastrozole


title: 12CLunamp

value: Light


title: N37_2

city: Irene

first: Dina

middle: Alida

last: Linde

state: Gauteng

address: Olifantsfontein road

department: Animal Breeding and Genetics

country: South Africa

institute: Agricultural research council

description:
processed data file:
HENLEN_raw_counts.tab; HEBHEN_raw_counts.tab

data_processing:
sequence reads were trimmed with the slidding window technique (4:10) from Trimmomatic and quality was checked using fastqc
Salmon was then used to align the reads and assemble the transcripts
DESeq2 was then used to determine the differential expression
Genome_build: UDM3.1.1
Supplementary_files_format_and_content: tab delimited files with the raw counts from the differential expression

organism: Bos taurus

source_name: Nguni_High Energy Diet_longissimus dorsi

growth_protocol: Feedlot trial: animals were fed for 120 days

extract_protocol:
Longissimus dorsi samples were removed, flash frozen on in liquid Nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used.
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Nguni and Bonsmara bulls received either a low energy diet (10.9 MJ ME/kg) of a high energy diet (12.0 MJ ME/kg) as feed

tag: breed

value: Sanga breed, Nguni

tag: diet

value: High Energy Diet

value: Longissimus dorsi


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time30

tag: growth phase

value: exponential growth

tag: time point


title: N14_3


title: Letrozole [HI.3146.001.BioO_3.42]

value: Letrozole


title: N14_2


title: N37_1


title: N37_3


title: 12CHunamp

value: Siklos, Hungary

value: Heavy

value: Control (12C-toluene)


title: Celecoxib [HI.3122.008.BioO_2.41]

value: Celecoxib


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time15


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time10


title: N14_1


title: wild-type_exponential_growth_hippuristanol_treated_t00_total_mRNA_seq


title: Glyburide [HI.3122.008.BioO_1.40]

value: Glyburide


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time05


title: ko.infected.r6

description: replicate 6

tag: genotype

value: IFNA Receptor knock-out

tag: Sex

value: female

tag: background strain

value: brain

value: microglia

value: Intraperitoneal injection with 105 Plasmodium berghei ANKA infected red blood cells


title: wild-type_exponential_growth_hippuristanol_treated_mRNA_decay_profile_time00

value: wild-type

value: hippuristanol


title: Diazoxide [HI.3122.008.BioO_6.39]

value: Primary Cerebrocortical Cultures

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Diazoxide


title: N1_2

description:
processed data file:
HENLEN_raw_counts.tab; LEBLEN_raw_counts.tab

source_name: Nguni_Low Energy Diet_longissimus dorsi

value: Sanga breed, Nguni

value: Low Energy Diet

value: Longissimus dorsi


title: wild-type_exponential_growth_cycloheximide_treated_t00_total_mRNA_seq

value: exponential growth

value: cycloheximide


title: Sulindac [HI.3122.007.BioO_4.37]

value: Sulindac


title: N215_3


title: N1_1


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time20


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time30


title: Zafirlukast [HI.3122.008.BioO_5.38]

value: Zafirlukast


title: Rivastigmine Tartrate [HI.3122.007.BioO_3.36]

value: Rivastigmine Tartrate


title: Pioglitazone·HCl [HI.3122.007.BioO_2.35]

value: Pioglitazone·HCl


title: N215_2


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time15


title: N215_1


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time10


title: Cetirizine 2HCl [HI.3122.007.BioO_1.34]

value: Cetirizine 2HCl


title: N11_3

value: High Energy Diet


title: N1_3


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time05


title: Simvastatin [HI.3147.004.BioO_3.32]

value: Simvastatin


title: Rifampin [HI.3147.004.BioO_4.33]

value: Rifampin


title: N11_2


title: N11_1


title: wild-type_exponential_growth_DMSO_treated_t00_total_mRNA_seq

value: wild-type

value: DMSO


title: N008_3


title: Meloxicam [HI.3122.006.BioO_6.31]

value: Primary Cerebrocortical Cultures

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Meloxicam


title: Ketoprofen [HI.3122.006.BioO_5.30]

value: Ketoprofen


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time30


title: N008_2

value: Sanga breed, Nguni

value: Longissimus dorsi


title: H37Rv_0.006BTZ043_D1_rep4

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/sturkarslan/DuffyNGS, and https://github.com/sturkarslan/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis H37Rv

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of BTZ043 (0μM, 0.006μM) (as indicated in each sample title).

tag: drug dose

tag: days post drug


title: H37Rv_0.006BTZ043_D1_rep2


title: H37Rv_0.006BTZ043_D1_rep3


title: H37Rv_0.006BTZ043_D1_rep1


title: Moxifloxacin·HCl [HI.3122.006.BioO_4.29]

value: Moxifloxacin·HCl


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time20

value: exponential growth


title: N008_1


title: Tranylcypromine Hemisulfate [HI.3122.006.BioO_3.28]

value: Tranylcypromine Hemisulfate


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time15


title: N39_1

value: Low Energy Diet


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time10


title: Captopril [HI.3147.003.BioO_2.27]

value: Captopril


title: wild-type_exponential_growth_cycloheximide_treated_mRNA_decay_profile_time00

value: cycloheximide


title: H37Rv_0BTZ043_D1_rep4

value: 0 μM


title: H37Rv_0BTZ043_D1_rep2


title: H37Rv_0BTZ043_D1_rep3


title: Bumetanide [HI.3122.005.BioO_2.26]

value: Bumetanide


title: hp1a GLKD RNA-seq 2

tag: full genotype

value: 3-5 days

value: ovaries


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time05

value: wild-type

value: DMSO


title: wild-type_exponential_growth_DMSO_treated_mRNA_decay_profile_time00


title: N35_3

value: High Energy Diet


title: H37Rv_0BTZ043_D1_rep1


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time55


title: Felodipine [HI.3122.005.BioO_6.24]

value: Primary Cerebrocortical Cultures

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Felodipine


title: Dexamethasone [HI.3122.005.BioO_1.25]

value: Dexamethasone


title: N35_2

value: Sanga breed, Nguni

value: Longissimus dorsi


title: N35_1


title: H37Rv_0.006BTZ043_D0_rep3


title: N33_3


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time40

value: exponential growth


title: N33_2

value: Low Energy Diet


title: H37Rv_0.006BTZ043_D0_rep2


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time30


title: H37Rv_0.006BTZ043_D0_rep1


title: N33_1


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time20


title: Verapamil·HCl [HI.3122.005.BioO_5.23]

value: Verapamil·HCl


title: Nimodipine [HI.3147.003.BioO_1.22]

value: Nimodipine


title: Diltiazem·HCl [HI.3147.003.BioO_5.20]

value: Diltiazem·HCl


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time15


title: H37Rv_0BTZ043_D0_rep2

value: 0 μM


title: N31_2


title: N289_3


title: N289_1


title: Galantamine·HBr [HI.3147.002.BioO_4.19]

value: Galantamine·HBr


title: H37Rv_0P218_D0_rep4

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of P218 (0μM, 0.1μM) (as indicated in each sample title).

tag: p218 dose


title: H37Rv_0BTZ043_D0_rep1


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time05


title: N26_3

tag: tissue


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time00


title: Metformin·HCl [HI.3122.004.BioO_4.18]

tag: cell type

value: Metformin·HCl


title: wild-type_exponential_growth_replicate2_t00_total_mRNA_seq

value: wild-type


title: wild-type_exponential_growth_replicate1_no_polyA_selection_mRNA_decay_profile_time10


title: H37Rv_0P218_D0_rep3


title: Tizanidine·HCl [HI.3122.004.BioO_3.16]

tag: days in vitro

value: Tizanidine·HCl


title: Carvedilol [HI.3147.002.BioO_3.17]

tag: strain

value: Carvedilol


title: H37Rv_0P218_D0_rep2


title: Guanfacine·HCl [HI.3147.002.BioO_2.15]

value: Primary Cerebrocortical Cultures

tag: agent

value: Guanfacine·HCl


title: Nifedipine [HI.3147.003.BioO_6.21]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Nifedipine


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time55

tag: genotype/variation


title: H37Rv_0P218_D0_rep1


title: H37Rv_0BTZ043_D0_rep3


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time50


title: H37Rv_0.1P218_D0_rep4


title: B199_2

description:
processed data file:
HEBLEB_raw _counts.tab; HEBHEN_raw_counts.tab

source_name: Bonsmara_High Energy Diet_longissimus dorsi

tag: breed

value: Sanga-related breed, Bonsmara

value: High Energy Diet


title: B199_3

tag: diet

value: Longissimus dorsi


title: Escitalopram  [HI.3147.002.BioO_1.14]

value: Escitalopram


title: B199_1


title: Sildenafil Citrate [HI.3122.004.BioO_2.13]

value: Sildenafil Citrate


title: H37Rv_0.1P218_D0_rep3


title: B300_1


title: N26_2

value: Sanga breed, Nguni

value: Low Energy Diet


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time35

tag: growth phase

value: exponential growth


title: Clemastine Fumarate [HI.3122.003.BioO_6.11]

value: Clemastine Fumarate


title: B178_1

description:
processed data file:
HEBLEB_raw _counts.tab; LEBLEN_raw_counts.tab

source_name: Bonsmara_Low Energy Diet_longissimus dorsi


title: B208_1


title: H37Rv_0.1P218_D0_rep2


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time40

tag: time point


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time30


title: H37Rv_0.1P218_D0_rep1


title: Famotidine [HI.3122.003.BioO_5.10]

value: Famotidine


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time25

value: wild-type


title: Imipramine·HCl [HI.3122.003.BioO_4.9]

value: Imipramine·HCl


title: Lovastatin [HI.3122.004.BioO_1.12]

value: Lovastatin


title: H37Rv_0P218_D1_rep4

value: 0 μM


title: H37Rv_0P218_D1_rep3


title: B72_1


title: B72_2


title: H37Rv_0P218_D1_rep2


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time20


title: Aminophylline  [HI.3122.003.BioO_3.8]

value: Primary Cerebrocortical Cultures

value: Aminophylline


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time15


title: Riluzole·HCl [HI.3122.002.BioO_2.7]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Riluzole·HCl


title: H37Rv_0P218_D1_rep1


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time45


title: B29_2

value: Sanga-related breed, Bonsmara


title: B29_3

value: Longissimus dorsi


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time10


title: Memantine·HCl [HI.3122.002.BioO_1.6]

value: Memantine·HCl


title: H37Rv_0.1P218_D1_rep4


title: B29_1


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time05


title: Zolmitriptan [HI.3122.002.BioO_6.5]

value: Zolmitriptan


title: H37Rv_0.1P218_D1_rep3


title: B126_2


title: Naltrexone·HCl [HI.3122.002.BioO_5.4]

value: Naltrexone·HCl


title: wild-type_exponential_growth_replicate1_t00_total_mRNA_seq


title: H37Rv_0.1P218_D1_rep1


title: Pindolol [HI.3122.001.BioO_4.3]

value: Pindolol


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time55

value: exponential growth


title: B126_1

value: Low Energy Diet


title: Betaxolol·HCl [HI.3122.001.BioO_3.2]

value: Betaxolol·HCl


title: B51_3


title: H37Rv_0CLA_D1_rep3

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of clarithromycin (0μM, 20μM) (as indicated in each sample title).

tag: clarithromycin dose


title: Rosiglitazone  [HI.3122.001.BioO_2.1]

value: Rosiglitazone


title: B51_2


title: H37Rv_0CLA_D1_rep1


title: B51_1


title: H37Rv_0CLA_D1_rep2


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time40

value: wild-type


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time45


title: H37Rv_20CLA_D1_rep3

value: 20 μM


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time35


title: H37Rv_20CLA_D1_rep2


title: B126_3


title: wild-type_exponential_growth_replicate2_mRNA_decay_profile_time00


title: H37Rv_0.1P218_D1_rep2


title: H37Rv_20CLA_D1_rep1


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time30


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time25


title: B25_1

value: High Energy Diet


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time50


title: H37Rv_0CLA_D0_rep3

value: 0 μM


title: mouse blood NK cells from mouse group 3

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

description: Sample 6m

data_processing:
Cell Ranger software (v1.3.1)
Reads were first simultaneously aligned with the mm10 and GRch38 genomes, with CellRanger software (v1.3.1), for their assignment as murine or human sequences. Species assignments were improved by  individual alignment with the mm10 and GRch38 sequences, resulting in two clusters, one for each species. Finally, we took the intersection between the corresponding clusters of the two alignments and we removed cells identified as doublets (within a range of 1.5 to 3.8%).
Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed, and cells expressing more than 2500 genes.
Cells with more than 0.05% of mitochondrial-associated genes among their expressed genes were also removed.
Genome_build: GRch38 and mm10
Supplementary_files_format_and_content: csv files (gene/cell matrix)

molecule: polyA RNA

source_name: Normal blood mouse NK cells

extract_protocol:
10x Genomics Chromium Single-Cell 3’ v2 protocol
Single-cell RNAseq

value: blood

value: NK cells


title: H37Rv_0CLA_D0_rep2


title: B11_3


title: mouse blood NK cells from mouse group 1

description: Sample 4m


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time15


title: B11_1


title: H37Rv_0CLA_D0_rep1


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time20


title: mouse spleen NK cells from mouse group 3

description: Sample 3m

source_name: Normal spleen mouse NK cells

value: spleen


title: B6_3

value: Sanga-related breed, Bonsmara


title: mouse blood NK cells from mouse group 2

description: Sample 5m


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time05


title: mouse spleen NK cells from mouse group 2

description: Sample 2m


title: H37Rv_20CLA_D0_rep2


title: B25_3

value: Longissimus dorsi


title: B6_2


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time00


title: H37Rv_20CLA_D0_rep3


title: B25_2


title: mouse spleen NK cells from mouse group 1

description: Sample 1m


title: H37Rv_20CLA_D0_rep1


title: B6_1


title: B11_2


title: wild-type_exponential_growth_replicate1_mRNA_decay_profile_time10


title: PBMC-Exposed-BiolRep53

status: Public on Sep 06 2018

first: Cliona

last: McHale

state: CA

address: 384 Li Ka Shing Center

department: School of Public Health

institute: University of California Berkeley

hyb_protocol: Digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. 300ng of each RNA sample was added to the CodeSet in hybridization buffer and incubated at 65°C for 16 hours. 12 samples were processed per cartridge. Each cartridge was subjected to a 3 hour automated processing  on the Prep Station

scan_protocol: Data Collection was carried out in theGEN2 nCounterTM Digital Analyzer. Digital images were processed and the barcode counts are tabulated in a comma separated value (CSV) format. Raw target counts were collected using the NanoString data collection software, nSolver.

data_processing: Six positive control probes (POS A-F) and their corresponding RNA targets at various concentrations from 128 fM to 0.5 fM were included in the assay to account for systematic variation introduced by pipetting, sample purification, and imaging. Negative control probes (with no corresponding targets, NEG A-H) were included to control for non-specific background noise, i.e. non-specific carryover of reporter probes. The raw target counts were background corrected, normalized to the mean of the positive control probes for each assay, and then normalized to the geometric mean of the reference genes (B2M, PGK1, and RPLP0). nSolver computes a normalization factor for each assay based on the average of positive control counts for the whole data set. NanoString recommends that for optimal results positive control normalization factors range between 0.3 and 3.0 for all assays.

label: fluorescent (reporter probe); biotin (capture probe)

organism: Homo sapiens

source_name: PBMC,  Benzene-Exposed

label_protocol: RNA is not labeles

extract_protocol: The PBMC fraction, consisting of lymphocytes, monocytes, and some platelets, was isolated in the field using Ficoll-Paque (Amersham, Piscataway, NJ). One to five million PBMCs were added to 1 mL RLT buffer (Qiagen, Valencia, CA) containing 1% β-mercaptoethanol. Samples were transported on dry ice and stored at -70 degrees pending extraction.RNA was isolated by the mirVanaTM miRNA isolation kit (Applied Biosystems, Austin, TX)

treatment_protocol: Subjects were Chinese factory workers occupationally exposed to benzene or were non-pexposed controls.

value: PBMC

tag: exposure category

value: Benzene-Exposed, <1ppm

tag: age(years)

tag: Sex

value: Female

tag: current smoker

value: No

tag: batch processed


title: PBMC-Control-BiolRep31

source_name: PBMC, Nonexposed Control

value: Control-non-exposed

value: Male

value: Yes


title: PBMC-Exposed-BiolRep52

value: Benzene-Exposed, 5-10ppm


title: PBMC-Control-BiolRep6-TecRepB


title: PBMC-Exposed-BiolRep50


title: PBMC-Control-BiolRep32


title: PBMC-Exposed-BiolRep51


title: PBMC-Control-BiolRep33


title: PBMC-Exposed-BiolRep57


title: PBMC-Exposed-BiolRep54


title: PBMC-Exposed-BiolRep56


title: corpuscallosum_remyel_rep4

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Gene expression

hyb_protocol: The Cy3-labeled samples were hybridized for 17 hours at 65°C to Agilent Whole Mouse Genome Microarray (G4122F, 4x44K) in a rotating Agilent hybridization oven.

scan_protocol: The arrays were scanned with an Agilent DNA Microarray Scanner BA.

data_processing: Signal quantification was carried out by Feature Extraction (ver. 11.0.1.1) using default parameters (protocol: GE1_1100_Jul11 and Grid: 014868_D_F_20120131  ). Image Analysis Software and data were further analyzed by Genespring GX10.0.

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 4

label_protocol: Labeling and hybridization of total RNA were performed according to the manufacturer’s protocol with no modification.

extract_protocol: The affected areas of corpus callosum was punched out and RNA was extracted by the RNeasy micro Kit (Qiagen, Valencia, CA). The quantity and quality of total RNA was assessed by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively. Only those samples that gave >8.0 for RNA integrity number, showed a clear gel image and no DNA contamination was observed on the histogram were used for microarray experiments.

treatment_protocol: To induce demyelination, cuprizone (CPZ) was administrated for four weeks orally. The powdered standard chow was mixed with 0.2-0.4% CPZ. After 4 weeks, treatment with cuprizone diet was stopped. Remyelination was induced by four weeks feeding with CPZ followed by regular diet. Control mice were kept on a normal diet.

value: corpus callosum

tag: gender

value: male

tag: treatment

value: normal diet after completion cuprizone treatment for 4 weeks


title: corpuscallosum_remyel_rep1

description: Gene expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 1

tag: tissue


title: PBMC-Exposed-BiolRep55

tag: cell type


title: corpuscallosum_remyel_rep6

description: Gene expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 6


title: corpuscallosum_untreated_rep3

description: Gene expression

source_name: Corpus callosum, healthy untreated controls, replicate 3

value: untreated


title: corpuscallosum_remyel_rep5

description: Gene expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 5


title: corpuscallosum_remyel_rep2

description: Gene expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 2


title: corpuscallosum_4weeks_demyel_rep4

description: Gene expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 4

value: cuprizone treatment for 4 weeks


title: PBMC-Exposed-BiolRep48


title: corpuscallosum_4weeks_demyel_rep3

description: Gene expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 3


title: PBMC-Exposed-BiolRep49


title: corpuscallosum_4weeks_demyel_rep1

description: Gene expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 1


title: corpuscallosum_2weeks_demyel_rep2

description: Gene expression

source_name: Corpus callosum, demyelinated, after 2 weeks treatment by cuprizone, replicate 2

value: cuprizone treatment for 2 weeks


title: corpuscallosum_4weeks_demyel_rep2

description: Gene expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 2


title: corpuscallosum_untreated_rep2

description: Gene expression

source_name: Corpus callosum, healthy untreated controls, replicate 2


title: corpuscallosum_2weeks_demyel_rep3

description: Gene expression

source_name: Corpus callosum, demyelinated, after 2 weeks treatment by cuprizone, replicate 3


title: corpuscallosum_remyel_rep3

description: Gene expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by regular diet, replicate 3


title: corpuscallosum_2weeks_demyel_rep1

description: Gene expression

source_name: Corpus callosum, demyelinated, after 2 weeks treatment by cuprizone, replicate 1


title: corpuscallosum_untreated_rep1

description: Gene expression

source_name: Corpus callosum, healthy untreated controls, replicate 1


title: PBMC-Exposed-BiolRep46

source_name: PBMC,  Benzene-Exposed


title: PBMC-Exposed-BiolRep47


title: PBMC-Exposed-BiolRep43


title: PBMC-Exposed-BiolRep42

value: Benzene-Exposed, >10ppm


title: PBMC-Control-BiolRep29

source_name: PBMC, Nonexposed Control


title: PBMC-Exposed-BiolRep44


title: PBMC-Exposed-BiolRep39


title: PBMC-Exposed-BiolRep38


title: PBMC-Exposed-BiolRep35


title: PBMC-Exposed-BiolRep37


title: PBMC-Exposed-BiolRep34


title: PBMC-Exposed-BiolRep36


title: PBMC-Control-BiolRep28


title: PBMC-Exposed-BiolRep41


title: PBMC-Control-BiolRep26


title: PBMC-Control-BiolRep25


title: PBMC-Control-BiolRep24


title: PBMC-Exposed-BiolRep32


title: PBMC-Exposed-BiolRep33


title: PBMC-Exposed-BiolRep27


title: PBMC-Exposed-BiolRep28


title: PBMC-Exposed-BiolRep17-TechRepB


title: PBMC-Control-BiolRep30


title: PBMC-Exposed-BiolRep31


title: PBMC-Exposed-BiolRep30


title: PBMC-Exposed-BiolRep26


title: PBMC-Exposed-BiolRep40


title: PBMC-Control-BiolRep27


title: PBMC-Exposed-BiolRep45


title: PBMC-Exposed-BiolRep29


title: PBMC-Control-BiolRep22


title: PBMC-Control-BiolRep23


title: PBMC-Control-BiolRep21


title: PBMC-Exposed-BiolRep25


title: PBMC-Control-BiolRep20


title: PBMC-Exposed-BiolRep22


title: PBMC-Exposed-BiolRep24


title: PBMC-Exposed-BiolRep23


title: PBMC-Exposed-BiolRep20


title: PBMC-Control-BiolRep16


title: PBMC-Exposed-BiolRep21


title: PBMC-Control-BiolRep9-TechRepB


title: PBMC-Control-BiolRep18


title: PBMC-Exposed-BiolRep1-TechRepB


title: BSF_0148_C6GU0ANXX_8_24h7

city: vienna

first: Peter

last: Petzelbauer

address: Währinger Gürtel

department: Dermatology

country: Austria

institute: Medical University Vienna

data_processing:
fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (version 0.11.5) was used to check the quality of reads
Reads were mapped to mouse genome reference (mm9) using gsnap (version 2013-05-09) with the non-default parameter: max-mismatches (−m) 10.
For Expression quantification and differential expression analysis counted reads were mapped to each gene (counts) using HTSeq-count (version 0.5.4p3) with parameters: --stranded=no, -a 19 and a mouse GTF file downloaded from UCSC.
Differential expression (DE) analysis was performed using DESeq2 (version 1.14.1) package in R.
Genome_build: mm9
Supplementary_files_format_and_content: Differential expression (DE) analysis; RefSeq, baseMean, log2FoldChange, lfcSE,  stat,  pvalue, padj, description,  external_gene_name_ entrezgene, raw_counts, normalized_counts

source_name: bypass grafts

growth_protocol: 8-10 week old, male C57BL/6J mice were housed for 2 weeks on a light/dark (12-hour/12-hour) cycle at 24°C and received food and water ad libitum before experimentation.

extract_protocol:
Frozen tissue was thawed, placed in Quiagen RLT lysis buffer (+DTT) and subjected to tissue homogenization utilizing a bead mill. Afterwards, samples were processed utlizing the quiagen RNeasy micro kit and the corresponding isolation protocol.
Sequencing libraries were prepared by the Core Facility Genomics at the Medical University of Vienna using the SMARTer Ultra Low Input RNA for Illumina Sequencing in combination with the Low Input Library Prep Kit (Promega). Libraries were sequenced on the Illumina HiSeq 2000 platform in the 50 bp SR Modus.

treatment_protocol: Bypass grafting was performed as described previously by Zou et al. (Mouse model of venous bypass graft arteriosclerosis. The American journal of pathology. 1998;153(4):1301-10. doi: 10.1016/S0002-9440(10)65675-1). After indicated re-perfusion times, the bypass grafts were explanted, placed in RNA later and snap frozen in liquid nitrogen, followed by storage at -80°C until further processing.

tag: perfusion time

tag: strain

tag: age

value: 10-12 week old

value: vena cava  as carotid artery bypass graft


title: 70_mEC_Stretch_1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tsv format containing edgeR differential expression results along with RPKM values

source_name: Stretched

growth_protocol: Once isolated, primary murine sinusoidal endothelial cells were cultured in endothelial cell media supplemented with fetal bovine serum.

extract_protocol:
Primary murine sinusoidal endothelial cells were isolated from mice using an immunomagnetic bead isolation protocol.
TruSeq

treatment_protocol: Cyclic stretch was applied with a Flexcell device at 4% stretch, 1 Hz.

value: Sinusoidal endothelial cells

value: Liver


title: 71_mEC_Stretch_2


title: PBMC-Exposed-BiolRep14

value: PBMC

value: Benzene-Exposed, <1ppm

value: Female


title: PBMC-Exposed-BiolRep18

value: Male

value: No


title: 68_mEC_Control_3

source_name: Control (Unstretched)


title: PBMC-Exposed-BiolRep17-TechRepA


title: 69_mEC_Control_4


title: PBMC-Exposed-BiolRep15

value: Yes


title: 72_mEC_Stretch_4


title: PBMC-Exposed-BiolRep13


title: PBMC-Exposed-BiolRep19


title: PBMC-Exposed-BiolRep16

value: Benzene-Exposed, 5-10ppm


title: BSF_0148_C6GU0ANXX_8_24h6

value: male


title: PBMC-Control-BiolRep15-TechRepB

value: Control-non-exposed


title: PBMC-Control-BiolRep19


title: 67_mEC_Control_2


title: BSF_0148_C6GU0ANXX_8_24h10


title: BSF_0148_C6GU0ANXX_7_6h19


title: BSF_0148_C6GU0ANXX_8_24h1


title: BSF_0148_C6GU0ANXX_7_6h16


title: PBMC-Control-BiolRep15-TechRepA


title: PBMC-Exposed-BiolRep12


title: ATAC-seq_P7_Kidney_EC_R2

city: Baltimore

first: Mark

middle: F

last: Sabbagh

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: ATAC-seq.bed.tar

library_source: genomic

data_processing:
We aligned ATAC-seq data using Bowtie2 (Version 2.3.2 -t -X 2000 --no-mixed --no-discordant) and then removed duplicate reads (picard MarkDuplicates).  Peaks were called using MACS2 (Version 2.1.1.20160309 callpeak --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits) (Zhang et al., 2008).
genome build: mm10
Supplementary_files_format_and_content: bed file with called peaks (in tar archive on series record) and narrowPeak and bigwig files

molecule: genomic DNA

source_name: P7 GFP-positive sorted cells from Kidney (vascular ECs)

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
For ATAC-seq, ~50,000 GFP-positive FACS-sorted cells were resuspended in ice-cold lysis buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 0.1% Igepal CA-630) and immediately centrifuged at 500 x g for 10 minutes at 4° Celsius to prepare nuclei.  The resulting nuclear pellet was resuspended in a 50 ul reaction volume in Tn5 transposase and transposase reaction buffer (FC-121-1030, Illumina Inc., San Diego, CA) and the tagmentation reaction was continued for 30 minutes at 37° Celsius.
Tagmented DNA was purified using QIAGEN MinElute GelExtraction kit (28604, Qiagen). ATAC-seq libraries were PCR amplified for 11 cycles. Agencourt AMPure XP beads (A63880, Beckman Coulter) were used to purify ATAC-seq libraries, which were then paired-end sequenced for 36 cycles on a NextSeq500.

tag: strain/genotype

value: Kidney

tag: cell-type

value: Vascular endothelial cells


title: PBMC-Control-BiolRep17


title: PBMC-Control-BiolRep12


title: PBMC-Control-BiolRep13


title: ATAC-seq_P7_Kidney_EC_R1

description: ATAC-seq.bed.tar


title: PBMC-Control-BiolRep14


title: BSF_0148_C6GU0ANXX_7_6h15


title: ATAC-seq_P7_Liver_EC_R2

description: ATAC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from Liver (vascular ECs)


title: ATAC-seq_P7_Brain_EC_R1

description: ATAC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from brain (vascular ECs)

value: Brain


title: ATAC-seq_P7_Lung_EC_R1

description: ATAC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from Lung (vascular ECs)

value: Lung


title: ATAC-seq_P7_Brain_EC_R2

description: ATAC-seq.bed.tar


title: ATAC-seq_P7_Lung_EC_R2

description: ATAC-seq.bed.tar


title: RNA-seq_P7_Kidney_GFPpos_R2

data_processing:
Three different sets of RNA-seq data were generated from papain dissociated P7 Tie2-GFP brain, liver, lung, and kidney: (1) total tissue; (2) GFP-negative FACS-sorted cells; and (3) GFP-positive FACS-sorted cells.  RNA-seq was also performed on cultured primary brain ECs.  RSEM version 1.3.0 (Li and Dewey, 2011) was used to align reads with Bowtie2 to the mm10/GRCm38 genome and calculate transcript expression using Ensembl annotation (rsem-calculate-expression --bowtie2 --estimate-rspd --append-names --output-genome-bam --sort-bam-by-coordinate).  Differentially expressed genes were identified using EBSeq version 1.18.0 (Leng and Kendziorski, 2015).
genome build: mm10
Supplementary_files_format_and_content: text file with gene abundances and bigwig

extract_protocol:
RNA was extracted from an aliquot of dissociated tissue prior to filtering and antibody staining and from GFP-positive and GFP-negative FACS sorted cells using the RNeasy Micro Plus kit (74034, QIAGEN, Venlo, Netherlands).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.). Cultured brain EC RNA-seq libraries were paired-end sequenced for 36 cycles on a NextSeq500.


title: BSF_0148_C6GU0ANXX_8_1h8

value: 10-12 week old


title: ATAC-seq_P7_Liver_EC_R1

description: ATAC-seq.bed.tar


title: PBMC-Exposed-BiolRep9


title: BSF_0148_C6GU0ANXX_8_1h2

value: vena cava  as carotid artery bypass graft


title: PBMC-Exposed-BiolRep11


title: BSF_0148_C6GU0ANXX_7_6h14


title: PBMC-Exposed-BiolRep10


title: BSF_0148_C6GU0ANXX_7_6h20


title: PBMC-Exposed-BiolRep8


title: RNA-seq_P7_Kidney_GFPpos_R1


title: PBMC-Exposed-BiolRep7


title: ATAC-seq_P7_Brain_EC_R3

description: ATAC-seq.bed.tar


title: RNA-seq_P7_Kidney_GFPneg_R2

source_name: P7 GFP-negative sorted cells from Kidney

value: Non-endothelial


title: RNA-seq_P7_Kidney_GFPneg_R1


title: BSF_0148_C6GU0ANXX_7_ControlIVC4

source_name: vena cava

value: Control

value: vena cava  as control


title: BSF_0148_C6GU0ANXX_8_1h12


title: RNA-seq_P7_Lung_GFPpos_R2


title: RNA-seq_P7_Kidney_TotalTissue_R1

source_name: P7 dissociated Kidney

value: Whole tissue


title: RNA-seq_P7_Kidney_TotalTissue_R2


title: PBMC-Control-BiolRep11

value: PBMC


title: BSF_0148_C6GU0ANXX_7_ControlIVC3


title: PBMC-Control-BiolRep9-TechRepA

value: Male


title: RNA-seq_P7_Lung_GFPneg_R1

source_name: P7 GFP-negative sorted cells from Lung


title: PBMC-Control-BiolRep10


title: RNA-seq_P7_Lung_GFPpos_R1


title: BSF_0148_C6GU0ANXX_7_ControlIVC1


title: RNA-seq_P7_Liver_GFPpos_R2

value: Liver


title: RNA-seq_P7_Liver_GFPpos_R1


title: RNA-seq_P7_Liver_GFPneg_R2

source_name: P7 GFP-negative sorted cells from Liver


title: RNA-seq_P7_Lung_GFPneg_R2


title: RNA-seq_P7_Lung_TotalTissue_R1

source_name: P7 dissociated Lung


title: PBMC-Control-BiolRep8

value: Female

value: No


title: RNA-seq_P7_Lung_TotalTissue_R2


title: BSF_0148_C6GU0ANXX_8_1h17

value: male


title: PBMC-Control-BiolRep7

value: Control-non-exposed


title: RNA-seq_P7_Liver_GFPneg_R1


title: PBMC-Control-BiolRep6-TecRepA

value: Yes


title: NNK3_50d

city: Miami

first: Nagaraj

last: Nagathihalli

state: Florida

address: 1550 NW 10th Ave

department: Surgery

institute: University of Miami

data_processing:
Sequencing was performed in two multiplexed lanes of 100-bp single-end sequencing, which resulted in 75 million mappable reads per lane. Subsequent analysis was performed on the GALAXY open platform using the Tuxedo Tools analysis suite.
After aligning RNA-Seq reads to a reference genome  using TopHat, the transcript assembly and abundance estimates of transcripts in fragments per kilobase of exon per million fragments mapped (FPKM) were performed by Cufflinks.
Additional filtering removed any transcripts with <0.5 FPKM value.
Significant differences in total gene and transcript expression, splice site, transcription start site (TSS) and promoter usage were determined using a false discovery rate (FDR)-adjusted P-value (q-value) in Cuffdiff, with q value) in Cuffdiff, with  the Tuxedo Tools analysis suwas performed using PANTHER tools
Ingenuity analysis was performed
Genome_build: GRch37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values done using Cufflinks

extract_protocol:
Total RNA was isolated from PanIN cells using RNeasy Plus Mini Kit. Samples were processed for RNA-seq using standard methods on the Illumina HiSeq 2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PanIN cells were treated with NNK for 5 and 50 days

tag: genotype

value: LSL-KrasG12D/+; Pdx1Cre/+

value: Pancreas

value: PanIN cells

tag: agent

value: NNK

tag: time


title: NNK2_50d


title: RNA-seq_P7_Liver_TotalTissue_R2

source_name: P7 dissociated Liver


title: PBMC-Exposed-BiolRep6

tag: exposure category

value: Benzene-Exposed, <1ppm


title: RNA-seq_P7_Brain_GFPpos_R2

value: Brain

value: Vascular endothelial cells


title: NNK1_50d


title: PBMC-Exposed-BiolRep5

value: Benzene-Exposed, 5-10ppm

tag: age(years)


title: BSF_0148_C6GU0ANXX_7_ControlIVC2

value: Control

value: 10-12 week old

value: vena cava  as control


title: Untreated3_50d

value: control


title: RNA-seq_P7_Brain_GFPneg_R2

source_name: P7 GFP-negative sorted cells from brain

tag: Sex

value: Male

value: Non-endothelial


title: RNA-seq_P7_Brain_TotalTissue_R1

source_name: P7 dissociated brain

value: Whole tissue


title: RNA-seq_P7_Brain_GFPpos_R1


title: RNA-seq_P7_Brain_TotalTissue_R2


title: PBMC-Exposed-BiolRep3

source_name: PBMC,  Benzene-Exposed

value: PBMC

tag: current smoker

value: No


title: NNK3_5d

value: LSL-KrasG12D/+; Pdx1Cre/+


title: KO Rep1_IL4

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description:
29_KO_IL4
KO_IL4_1

data_processing:
#genome alignment: tophat2 -p 16 -g 1
#counting reads: featureCounts -t exon -g gene_id -a mm9.gtf
#DGE with edgeR
Genome_build: mm9
Supplementary_files_format_and_content: normlized FPKM of all samples

growth_protocol: Control and PPARgMKO mice were injected with 3% thioglycollate into the peritoneal cavity. 4 days post injection the ellicited macrophages were harvested and cultured overnight in DMEM.

extract_protocol:
After treatment, cells were immediately lysed in trizol and RNA purified with RNeasy RNA isolation kit according to the manufacturers instructions.  Illumina Truseq Stranded RNA Total RNA library prep kit was used with 1ug RNA of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After overnight culture, macrophages were untreated or treated with 20ng/mL IL4, or 1uM Rosi or equal volume of DMSO as vehicle control.

tag: strain background

value: 8.5 weeks

tag: genotype/variation

value: PPARgammaMPKO


title: KO Rep4_IL4

description:
32_KO_IL4
KO_IL4_4


title: KO Rep2_IL4

description:
30_KO_IL4
KO_IL4_2


title: Untreated2_50d

value: Pancreas

value: PanIN cells


title: RNA-seq_P7_Brain_GFPneg_R1

value: Brain


title: Untreated1_50d


title: PBMC-Exposed-BiolRep1-TechRepA

value: Benzene-Exposed, <1ppm

value: Female

tag: batch processed


title: WT Rep4_IL4

description:
28_Control_IL4
Control_IL4_4


title: NNK2_5d

tag: tissue

value: NNK


title: KO Rep3_IL4

description:
31_KO_IL4
KO_IL4_3

tag: cell type


title: PBMC-Exposed-BiolRep2


title: PBMC-Control-BiolRep5

source_name: PBMC, Nonexposed Control

value: Control-non-exposed

value: Yes


title: WT Rep3_IL4

description:
27_Control_IL4
Control_IL4_3

value: control


title: RNA-seq_P7_Liver_TotalTissue_R1

value: Male

value: Liver


title: WT Rep2_IL4

description:
26_Control_IL4
Control_IL4_2


title: PBMC-Control-BiolRep4


title: NNK1_5d


title: WT Rep1_IL4

description:
25_Control_IL4
Control_IL4_1


title: PBMC-Exposed-BiolRep4

value: Benzene-Exposed, 5-10ppm


title: KO Rep3_Rosi

description:
24_KO_Rosi
KO_Rosi_3


title: Untreated3_5d


title: PBMC-Control-BiolRep3

value: PBMC


title: KO Rep2_Rosi

description:
23_KO_Rosi
KO_Rosi_2


title: KO Rep1_Rosi

description:
22_KO_Rosi
KO_Rosi_1


title: Untreated2_5d


title: PBMC-Control-BiolRep2

value: No


title: WT Rep4_Rosi

description:
20_Control_Rosi
Control_Rosi_4


title: WT Rep2_Rosi

description:
18_Control_Rosi
Control_Rosi_2


title: WT Rep1_Rosi

description:
17_Control_Rosi
Control_Rosi_1


title: KO Rep2_DMSO

description:
14_KO_DMSO
KO_DMSO_2


title: PBMC-Control-BiolRep1-TechRepB


title: KO Rep4_DMSO

description:
16_KO_DMSO
KO_DMSO_4


title: WT Rep3_Rosi

description:
19_Control_Rosi
Control_Rosi_3


title: Untreated1_5d

value: LSL-KrasG12D/+; Pdx1Cre/+


title: WT Rep4_DMSO

description:
12_Control_DMSO
Control_DMSO_4

value: 8.5 weeks


title: KO Rep3_DMSO

description:
15_KO_DMSO
KO_DMSO_3

value: PPARgammaMPKO


title: WT Rep3_DMSO

description:
11_Control_DMSO
Control_DMSO_3


title: PBMC-Control-BiolRep1-TechRepA


title: KO Rep1_DMSO

description:
13_KO_DMSO
KO_DMSO_1


title: WT-28-1: treated

city: Shanghai

first: Feng

last: Liu

address: 600 Yishan Road

department: Department of Otolaryngology-Head and Neck Surgery

country: China

institute: Shanghai JiaoTong University Affiliated Sixth People's Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged mouse pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value. miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Genome_build: mm8

source_name: lung tissues from Mtb H37Rv infected C57B/6 mice

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: C57B/6 mice were infected with Mtb H37Rv (CFU=200) for 28 days

value: Lung


title: WT-28-3: treated


title: WT Rep1_DMSO

description:
9_Control_DMSO
Control_DMSO_1


title: WT-28-2: treated


title: WT Rep2_DMSO

description:
10_Control_DMSO
Control_DMSO_2


title: WT-0-2: input

source_name: lung tissues from uninfected C57B/6 mice


title: KO Rep4

description:
8_KO
KO_4


title: WT-0-3: input


title: KO Rep3

description:
7_KO
KO_3


title: WT-0-1: input


title: KO Rep1

description:
5_KO
KO_1


title: KO Rep2

description:
6_KO
KO_2


title: S4h3: treated

source_name: peritoneal macrophages from Mtb H37Rv infected C57B/6 mice

growth_protocol: Peritoneal macrophages were isolated from C57BL/6 mice, and grown in RPMI1640 medium containing 10% FBS in 37℃ with 5% CO2.

treatment_protocol: Peritoneal macrophages were infected with Mtb H37Rv at MOI5 for 4 hours.

value: Peritoneal Macrophages


title: WT Rep4

description:
4_Control
Control_4


title: WT Rep3

description:
3_Control
Control_3


title: WT Rep1

description:
1_Control
Control_1


title: WT Rep2

description:
2_Control
Control_2


title: S4h2: treated


title: S0h3: input

source_name: peritoneal macrophages from uninfected C57B/6 mice


title: S0h2: input


title: 1702_PC_neg [RNA-Seq]

city: Atlanta

first: Jeremy

middle: Matthew

last: Boss

state: Georgia

address: 1510 Clifton Rd NE, Room 3120

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the HOMER package v4.8.2.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing mRNA/cell (FPKM normalized to ERCC spike-in transcripts) normalized read counts for each sample.

source_name: spleen

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
All RNA from 50,000 cells per sample was used as input for the KAPA Biosystems Stranded mRNA-seq kit with polyA selection beads.

treatment_protocol: Three days following LPS stimulation, cells were FACS-purified from the spleens of wild-type and LSD1-knockout mice.

value: Plasmablasts

tag: gender

value: female

tag: sorting markers

value: spleen

tag: stimulation

value: LPS

tag: lsd1 status

value: wild-type


title: 1701_PC_pos [RNA-Seq]

tag: strain

value: knockout


title: 1699_PC_pos [RNA-Seq]


title: 1703_PC_pos [RNA-Seq]


title: 1698_PC_neg [RNA-Seq]


title: S0h1: input


title: 1703_nB_pos [RNA-Seq]

value: naive B cells


title: Muscle_Meishan_5-months_7

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

country: Japan

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

hyb_protocol: Hybridization was carried out using Gene Expression Hybridization kit (Agilent) in SureHyb Hybridization chambers. Each array slide was washed with Gene Expression Wash Pack (Agilent).

scan_protocol: Microarray slides were scanned at 5 microns/pixel resolution using Agilent DNA Microarray Scanner G2505B.

data_processing: Microarray images were analyzed with Agilent Feature Extraction Software (ver. 9.5) using the GE2-v5_95_Feb07 FE extraction protocol.

organism: Sus scrofa

label_protocol: Quick Amp Labeling Kit (Agilent)

growth_protocol: All animals were fed a diet according to the Japanese Feeding Standard for Swine.

extract_protocol: Rneasy Midi Kit (QIAGEN)

treatment_protocol: All animals were handled humanely under the guidelines of the Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO).

value: Skeletal muscle

tag: breed

value: LWD x Meishan (LWDM)

tag: age

value: LWD


title: 1701_nB_pos [RNA-Seq]


title: Muscle_Meishan_5-months_6

value: Liver


title: Muscle_Meishan_5-months_4


title: Muscle_Meishan_5-months_5


title: WT_pool [ChIP-seq]

data_processing:
All the reads were aligned to mouse genome, mm9, using Bowtie with option (--best --strata --fullref -m 1 -k 1).
All the redundant tags were eliminated except one per each genomic position before downstream analysis.
Peak calling was done using Homer and 1 rpm cutoff was further applied for peak tag counts within 200bp window.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig of called WT peaks

growth_protocol: Control and PPARgMKO mice were injected with 3% thioglycollate into the peritoneal cavity. 4 days post injection the ellicited macrophages were harvested and cultured overnight in DMEM

extract_protocol:
ChIP was performed as described previously (Steger et al., 2008) using PPARγ (Santa Cruz) antibody
ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina

value: control

tag: chip antibody

value: anti-PPARγ (H100), Santa Cruz, sc7196x, K1010


title: Muscle_Meishan_5-months_1


title: Muscle_Meishan_5-months_2


title: Muscle_Meishan_5-months_3


title: Muscle_Landrace_5-months_8

value: LWD x Landrace (LWDL)


title: S4h1: treated


title: 1699_nB_pos [RNA-Seq]


title: 1702_nB_neg [RNA-Seq]


title: KO_pool [ChIP-seq]

description: only used as input for background removal

value: 8.5 weeks

value: PPARG KO


title: Muscle_Landrace_5-months_6


title: 1700_nB_neg [RNA-Seq]


title: 1700_PC_neg [RNA-Seq]


title: 1703_PC_pos [ATAC-Seq]

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample, peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rpm) using R/Bioconductor

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
10,000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).


title: 1698_nB_neg [RNA-Seq]


title: DMSO [GRO-seq]

data_processing:
library strategy: GRO-seq
adapter and poly-A sequence were trimmed off from the raw tags, then remaining tags were converted into FASTA format before alignment. Trimmed tags were aligned to the mouse genome, mm9, using Bowtie with the following options: inputs were in FASTA format (-f), three mismatches were allowed for each tags (-v 3), and only uniquely mapped tags were retained (-m 1).
All the alignments were adjusted to 50bp by extending toward 3'-end if their size is shorter than that to make libraries comparable.  For stack-height profiles, all the replicates for each condition were pooled. genomeCoverageBed in bedtools was used first to make bedGraph files for plus and minus strands separately, where minus strand values were converted into negative ones.
All the bedGraph files were then converted into bigWig files using bedGraphToBigWig utility.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: DMSO

growth_protocol: Mice were injected with 3% thioglycollate into the peritoneal cavity. 4 days post injection the ellicited macrophages were harvested and cultured overnight in DMEM.

extract_protocol:
Cells were washed twice with ice-cold PBS, then swelled in swelling buffer (10mM Tris pH 7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice. Cells were centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, then resuspended in freezing buffer (50mM Tris pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). Nuclei were counted, pelleted, and 5 x 106 nuclei were resuspended in 100ul freezing buffer. For each library, run-on was performed on 4 tubes of 5 x 106 nuclei.   For the run-on, cells were mixed with an equal volume of run-on buffer (10mM Tris pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% Sarkosyl, 500uM ATP, GTP and Br-UTP, 2uM CTP) and incubated for 5 min at 30°C. Nuclear RNA was extracted with TRIzol (Invitrogen) and precipitated with NaCl and ethanol overnight. The pellet was resuspended in water and the RNA was DNase treated (Ambion) for 30 min. RNA was hydrolyzed using fragmentation reagents (Ambion) for 13 min at 70°C and purified through a Micro Bio-Spin p-30 column (Bio-Rad) according to manufacturer's instructions. RNA was treated with 1.5ul T4 polynucleotide kinase (New England Biolabs) for 1h at 37°C, then with an additional 1l for 1h more. RNA was denatured for 5 min at 65°C.   Anti-BrU agarose beads (Santa Cruz) were rotated for 1h in blocking buffer (0.5xSSPE, 1mM EDTA, 0.05% Tween-20, 0.1% PVP, and 1mg/ml BSA). Run-on RNA was rotated with beads for 1h, followed by washes twice in binding buffer (0.5xSSPE, 1mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2SSPE, 1mM EDTA, 0.05% Tween-20), once in high salt buffer (0.5x SSPE, 1mM EDTA, 0.05% Tween-20, 15mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrU-labeled RNA was eluted from the beads four times for 15 min with 10% elution buffer pre-heated to 42°C. RNA was ethanol-precipitated overnight.
Precipitated RNA was resuspended in water, denatured, and treated with poly(A)-polymerase (NEB) for 30 min at 37°C. cDNA synthesis was performed as described previously (Wang et al, Nature 2011) using oNTI223 primer ((5'-pGATCGTCGGACTGTAGAACTCT;CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3') where the p indicates 5' phosphorylation, indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. The reaction was treated with  3 ul exonuclease I (Fermentas) for 15 min at 37°C, followed by 2 ul 1M NaOH for 20 min at 98°C, and neutralized with 1ul 2M HCl. cDNA was run on 10% TBE-urea gel, then products were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated in ethanol overnight.   First-strand cDNA was circularized with CircLigase (Epicentre), denatured for 10 min at 80°C, and relinearized with APE I (NEB). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit, according to manufacturer's instructions. The oligonucleotide primers oNTI200 (5'-CAAGCAGAAGACGGCATA-3') and oNTI201 (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3') were used for amplification. The PCR product was run on a 10% TBE gel and eluted as before. Libraries were sequenced on an Illumina hi-Seq2000 with sequencing primer 5'CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3'.

treatment_protocol: After overnight culture, macrophages were untreated or treated with  1uM Rosi or equal volume of DMSO as vehicle control.

value: WT


title: Rosi [GRO-seq]

source_name: Rosi


title: 1701_PC_pos [ATAC-Seq]

value: Plasmablasts


title: Muscle_Landrace_5-months_4

value: female


title: Muscle_Landrace_5-months_7


title: Muscle_Landrace_5-months_5


title: Muscle_Landrace_5-months_3


title: 1699_PC_pos [ATAC-Seq]

value: spleen


title: 1702_PC_neg [ATAC-Seq]

value: LPS


title: 1698_PC_neg [ATAC-Seq]

value: wild-type


title: 1699_nB_pos [ATAC-Seq]

value: knockout


title: 1701_nB_pos [ATAC-Seq]

value: naive B cells


title: Rosi-H [GRO-seq]

source_name: Rosi-H


title: 1702_nB_neg [ATAC-Seq]


title: Muscle_Landrace_5-months_1

value: Skeletal muscle


title: 1698_nB_neg [ATAC-Seq]


title: Muscle_Landrace_5-months_2


title: Muscle_Meishan_12-days_6

value: LWD x Meishan (LWDM)


title: 10xGenomics_SingleCell_RNA-seq_P7_Brain_GFPpos

data_processing:
scRNA-seq data were pre-processed using the cellranger pipeline (v2.0; 10x Genomics) with default settings. The normalized geneXcell matrix was used as input for the Monocle R/Bioconductor package (Trapnell et al., 2014). Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis (Monocle). Briefly, high-dispersion genes were identified as those genes with a residual greater than 1 * the estimated mean-variance split using the `estimateDispersions` method in Monocle. Non-endothelial-specific transcripts in the high-dispersion gene set, defined as transcripts enriched >2-fold by bulk RNA-seq in the FACS-purified GFP-negative fraction compared to the GFP-positive fraction, likely derived from high-abundance transcripts released and solubilized by lysis of non-ECs during the preparation of the single cell suspension. 311 non-EC specific genes were excluded from the high-dispersion gene set and removed from subsequent analyses. For preliminary cell clustering, principal component analysis (PCA) was performed on the high-variance genes and components 2-10 were visualized in two dimensions using t-Distributed Stochastic Neighbor Embedding (t-SNE) (van der Maaten and Hinton, 2008; Krijthe, 2015, Macosko et al., 2015). Component 1 was excluded as it was determined to primarily reflect capture efficiency (num_genes_expressed). Initial clusters were identified from the 2D embedding using Mclust. To refine the list of genes contributing to the initial clustering, we performed a Monocle differential gene test with respect to cluster assignment, accounting for total mRNAs in both full and reduced models as well. The top 1200 genes with significant differential expression across clusters were then selected and used as input for a second PCA and components 2-8 were reduced into 2 dimensions using tSNE. Final cluster assignments were determined using Mclust on the updated 2D embedding. Clusters were annotated based on the expression of canonical EC subtype markers and a differential gene test between the subtypes was performed using the R package Monocle. The final six EC clusters conformed well to the expression patterns of known markers for arterial, venous, tip, capillary and mitotic cells. Cell trajectory analyses were carried out in Monocle on the same 1200 differentially expressed genes used for the second PCA.
genome build: mm10
Supplementary_files_format_and_content: tsv files with barcodes and genes and matrix with data. The "filtered" genes refer to reads that the 10X Genomics software reliably determines as coming from cells whereas the "raw" genes includes background reads as well. The filtered set was used in the analysis.

source_name: P7 GFP-positive sorted cells from brain (vascular ECs)

extract_protocol:
FACS purified GFP-postive P7 brain ECs from a Tie2-GFP mouse were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol.  In brief, papain-dissociated ECs were sorted into 0.4% BSA–DPBS, and approximately 10,000 FACS-purified singlet brain ECs were added to the channel with a final recovery rate of 4,257 cells.
ECs were then partitioned into gel beads in emulsion in the GemCode instrument for cell lysis and barcoded oligo-DT priming and reverse transcription of poly-adenylated RNA.  This was followed by PCR amplification, shearing, and 5′ adaptor and sample index attachment.  Libraries were sequenced on an Illumina HiSeq 2500.

tag: strain/genotype

value: Male

value: Brain

tag: cell-type

value: Vascular endothelial cells


title: DSMO-H [GRO-seq]

source_name: DSMO-H


title: 1700_PC_neg [ATAC-Seq]


title: 1700_nB_neg [ATAC-Seq]


title: tumor1_Input

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

country: Canada

institute: UHN

data_processing:
MeRIP-seq reads were aligned to the hg38 genome assembly using STAR2 version 2.4.2a. For the pair-end read mates were pooled and treated as single-end reads.
m6A peaks were called using MeTpeak
Genome_build: hg38
Supplementary_files_format_and_content: BED file for m6A peak

source_name: Lung Adenocarcinorma Primary Tumor

growth_protocol: Human lung cancer cell line A549 was maintained in RPMI-1640 medium with 10% fetal bovine serum.

extract_protocol:
Total RNA from cells in culture was extracted using Trizol reagent (Thermo Fisher Scientific, Waltham, MA), and then treated with DNase I (04 716 728 001, Roche Diagnostics, Indianapolis, IN) for 20 min at 37°C to remove DNA contamination.
RNA libraries were prepared  using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian.

value: Lung Adenocarcinorma Primary Tumor

tag: merip-seq antibody


title: tumor2_IP

value: anti-m6A(ABE572, Millipore)


title: Rosi-H-2 [GRO-seq]

value: 8.5 weeks


title: Millipore-500ng_Input_Rep2

source_name: A549 cell line

value: A549 cell line


title: 1703_nB_pos [ATAC-Seq]


title: Millipore-500ng_IP_Rep2


title: Millipore-500ng_Input_Rep1


title: Muscle_Meishan_12-days_4

tag: Sex

value: Liver

value: LWD


title: Muscle_Meishan_12-days_3

value: female


title: MII 120115_02 SPIA

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64 (SPIA libraries) & v2.7.6 (SoLo libraries)
Hisat2  to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: raw counts

organism: Macaca mulatta

source_name: MII Oocyte

growth_protocol: Control ovarian stimulation protocol (COS) was used for the collection of oocytes. Rhesus macaques were observed daily for signs of menses. Within day 1-4 of menses, animals were administered an intramuscular injection of recombinant macaque FSH (r-mFSH; National Hormone and Peptide Program, A. F. Parlow, UCLA) twice daily for a total of 7 days. On day 8 a subset of animals was used for collection of GV oocytes and another subset of animals were administrated an intramuscular injection of 1000 IU of human chorionic gonadotropin (hCG; LaJ olla Discount Pharmacy, La Jolla, CA). On day 9, ultrasound-guided needle aspiration of follicles was used for the collection of oocytes. Oocytes were observed for maturation status for both normal GV and MII, and FTM oocytes.

extract_protocol:
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA).  After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011).  After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.
SoLo libraries: cDNA libraries were produced with Nugen Ovation SoLo RNA-Seq(NuGEN, San Carlos, CA). After bead purification, the cDNA was processed: end repair, adaptor ligation and first round library amplification and purification. Then 20 ng of each library was used for the remainder of library preparation, which included use of InDA-C primers for rRNA depletion, as well as 2nd round library amplification and purification steps. SoLo Custom R1 primer was used instead of a standard Illumina R1 sequencing primer for the sequencing of the libraries.

value: oocyte

tag: developmental stage

value: MII

tag: library processing kit

value: SPIA


title: MII 120115_01 SPIA


title: MII 111815_02 SPIA


title: Millipore-500ng_IP_Rep1


title: tumor2_Input


title: tumor1_IP


title: MII 110515_02 SPIA


title: Muscle_Meishan_12-days_1


title: Muscle_Meishan_12-days_5


title: MII 021916_02 SPIA


title: MII 021916_01 SPIA


title: Muscle_Meishan_12-days_2


title: Muscle_Landrace_12-days_3

value: LWD x Landrace (LWDL)


title: Muscle_Landrace_12-days_5


title: Muscle_Landrace_12-days_2


title: Muscle_Landrace_12-days_4


title: Muscle_Meishan_f85-days_5


title: Muscle_Landrace_12-days_1


title: Muscle_Meishan_f85-days_6


title: Muscle_Meishan_f85-days_3


title: Muscle_Meishan_f85-days_2


title: MII 020516_05 SPIA


title: MII 020516_06 SPIA


title: D2_NoStim_ReAmp

city: San Francisco

first: Eric

last: Shifrut

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

description: Reamplification of U6 transrcipts w/ CellBC and UMI

data_processing:
Fastq files from 10x library were processed with Cell Ranger 2.0, using default parameters.
(1) For U6 reamplification sample, Read2 fastq files were match to U6 TGGAAAGGACGAAACACCG using matchPattern (ShortRead R package), (2) Cell BC for matched R2 reads was extracted from R1 files.
No technical replicates in this dataset. D1 and D2 are two unrelated human donors, which we consider as biological replicates. The ReAmp fastq files are targeted amplicon re-sequencing of the sgRNA transcripts captured in the 10x pipeline. The design for the re-amplification is unchanged from 10x V2:    Read 1 (26bp): Cell Barcode (16bp) - UMI (8bp)  Index read (8bp): i7 index   Read 2 (58bp): 3' end of the captured polyA transcripts, for successful amplicons should start  the U6 sequence TTGTGGAAAGGACGAAACACCG.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, tar file contains matrix.mtx, barcodes.tsv and genes.tsv, output from CellRanger 2.0, post QC filter. These have UMI counts for all genes and cell barcodes identified.

source_name: CD8+ T cells

growth_protocol: Cells were infected with the library, electroporated with Cas9 protein and Puro selected.

extract_protocol:
ChromiumTM Single Cell 3’ v2 Protocol (CG00052)
ChromiumTM Single Cell 3’ v2 Protocol (CG00052)

treatment_protocol: Two conditions: with TCR stimulus or without.

value: CD8+ T cells

tag: agent


title: D1_Stim_ReAmp

value: TCR stimulation


title: D2_Stim_ReAmp


title: Muscle_Meishan_f85-days_4

tag: tissue

value: Skeletal muscle

value: LWD x Meishan (LWDM)


title: Muscle_Meishan_f85-days_1


title: Muscle_Landrace_f85-days_6


title: D2_NoStim_10x

description: raw data from Cell Ranger

tag: cell type


title: D2_Stim_10x

description: raw data from Cell Ranger


title: control diet offspring liver gene expression 2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
gene expression data of control diet pups liver
C57Bl6/J mice, 4–5 weeks old, were used. Female mice were divided in three groups that received one of three isocaloric diets, containing 6g% commercial oil of different origins as follows: soybean in control diet, coconut in SFA and flaxseed in ALA. Oleic acid in RD (42%), ALA in ALA diet (31.6%) and the saturated fatty acids in SFA diet (48.51%) were the predominant FA in the maternal diets. Males received regular chow diet except during the mating period during which they shared their female mates' diets. At all stages, the animals had free access to food and water and were kept in ventilated rooms under a light/dark cycle of 12h/12h. Within a day after birth, offspring's livers were excised and snap frozen in liquid nitrogen for further use.

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Probe-set analyses was performed. RMA normalization and summarization by mean, all were done by Partek Genomics suite (version 6.6)

source_name: 1 day C57Bl6/J mice offspring's liver

extract_protocol: Total RNA was isolated from frozen liver tissues (3 livers pooled samples for each condition, in duplicates). Perfect Pure RNA Tissue Kit (5Prime, Darmstadt, Germany) following the manufacturer’s instructions

tag: date

tag: sample type

value: Control liver

value: liver

tag: treatment

value: Control


title: Muscle_Landrace_f85-days_4


title: SFA diet offspring liver gene expression 2

description:
gene expression data of SFA diet pups liver
C57Bl6/J mice, 4–5 weeks old, were used. Female mice were divided in three groups that received one of three isocaloric diets, containing 6g% commercial oil of different origins as follows: soybean in control diet, coconut in SFA and flaxseed in ALA. Oleic acid in RD (42%), ALA in ALA diet (31.6%) and the saturated fatty acids in SFA diet (48.51%) were the predominant FA in the maternal diets. Males received regular chow diet except during the mating period during which they shared their female mates' diets. At all stages, the animals had free access to food and water and were kept in ventilated rooms under a light/dark cycle of 12h/12h. Within a day after birth, offspring's livers were excised and snap frozen in liquid nitrogen for further use.

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: SFA diet liver

value: SFA


title: ALA diet offspring liver gene expression 2

description:
gene expression data of ALA diet pups liver
C57Bl6/J mice, 4–5 weeks old, were used. Female mice were divided in three groups that received one of three isocaloric diets, containing 6g% commercial oil of different origins as follows: soybean in control diet, coconut in SFA and flaxseed in ALA. Oleic acid in RD (42%), ALA in ALA diet (31.6%) and the saturated fatty acids in SFA diet (48.51%) were the predominant FA in the maternal diets. Males received regular chow diet except during the mating period during which they shared their female mates' diets. At all stages, the animals had free access to food and water and were kept in ventilated rooms under a light/dark cycle of 12h/12h. Within a day after birth, offspring's livers were excised and snap frozen in liquid nitrogen for further use.

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: ALA diet liver

value: ALA


title: Muscle_Landrace_f85-days_3

value: Liver

value: LWD


title: SFA diet offspring liver gene expression 1


title: D1_NoStim_ReAmp


title: Muscle_Landrace_f85-days_1

value: female


title: ALA diet offspring liver gene expression 1


title: Muscle_Landrace_f85-days_2


title: Muscle_Landrace_f85-days_5


title: Liver_Meishan_5-months_7


title: control diet offspring liver gene expression 1


title: Liver_Meishan_5-months_6


title: Liver_Meishan_5-months_5


title: Liver_Meishan_5-months_3


title: Liver_Meishan_5-months_2


title: Liver_Meishan_5-months_4


title: D1_NoStim_10x

description: raw data from Cell Ranger


title: D1_Stim_10x

description: raw data from Cell Ranger


title: nm1054 C57BL6/J Replicate 1

city: Sioux Falls

first: Lance

last: Lee

state: SD

institute: Sanford Research

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol. A total of 1,500 ng of labeled cRNA was hybridized overnight at 58°C onto the MouseWG-6 Expression BeadChip (Illumina, San Diego, CA) according to the manufacturer's instructions.

scan_protocol: Standard Illumina scanning protocol. Chips were developed with fluorolink streptavidin-Cy3 (GE Healthcare, Little Chalfont, UK) and scanned with an Illumina BeadArray Reader.

data_processing: Intensity values for each probe cell in the hybridized arrays were calculated by GenomeStudio software from Illumina, and flags were assigned to each probe set declaring a Present, Marginal, or Absent call.  Probe cell intensities were used to calculate an average intensity for each set of probe pairs representing a gene, which directly correlated with the amount of cRNA.  Gene expression data analysis and normalization were performed using the GeneSpring GX bioinformatics software from Agilent Technologies.  Quality control filtering was performed on the normalized intensity values, and genes were clustered into four group conditions (WT 129, nm1054 129, WT B6 and nm1054 B6).  Statistical analysis of gene expression was performed using unpaired t-test and the Benjamini Hochberg correction to determine a corrected (Corr) p value for each gene.  Statistical significance was set at fold change > 1.5 and p (Corr) < .05.

label: Biotin

source_name: Mouse brain

label_protocol: Labeled cRNA was prepared from 500 ng of total RNA using the Illumina RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Whole brains were dissected from P1 mice and lysed

extract_protocol: RNA was extracted with TRIzol and purified using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, Madison, WI) according to the manufacturer’s instructions.

treatment_protocol: Mice are wild type or homozygous for the heritable nm1054 mutation

value: 1 day

value: Brain

tag: genotype

value: nm1054 mutant


title: nm1054 C57BL6/J Replicate 3

description: Replicate 3

tag: strain


title: Striatum WT Biological Replicate 2

city: Edinburgh

first: Clare

last: Pridans

address: 47 Little France Crescent

department: University of Edinburgh

institute: Centre for Inflammation Research

description: Gene expression data from adult striatum

hyb_protocol: GeneTitan

scan_protocol: GeneChip Command Console

data_processing: CEL files were normalised (RMA) in R/Bioconductor.

organism: Rattus norvegicus

source_name: Striatum

label_protocol: GeneChip Whole Transcript Labeling Kit (Applied Biosystems)

extract_protocol: Trizol extraction of total RNA followed by purification with Rneasy Mini kit

value: Adult

value: Csf1r +/+

value: Female

value: DA/SD


title: Striatum HET Biological Replicate 2

value: Csf1r +/-


title: nm1054 C57BL6/J Replicate 2

description: Replicate 2


title: WT C57BL6/J Replicate 3

description: Replicate 3

value: wild type


title: WT C57BL6/J Replicate 2

description: Replicate 2


title: Liver_Landrace_5-months_6

tag: breed

value: LWD x Landrace (LWDL)


title: Striatum KO Biological Replicate 2

tag: age

value: Csf1r -/-


title: Liver_Landrace_5-months_5


title: Liver_Landrace_5-months_8


title: WT C57BL6/J Replicate 1

description: Replicate 1


title: Liver_Meishan_5-months_1

value: LWD x Meishan (LWDM)


title: nm1054 129S6/SvEvTac Replicate 3

description: Replicate 3


title: Liver_Landrace_5-months_7


title: nm1054 129S6/SvEvTac Replicate 2

description: Replicate 2


title: Striatum KO Biological Replicate 1


title: Liver_Landrace_5-months_4


title: Hippocampus WT Biological Replicate 2

description: Gene expression data from adult hippocampus

source_name: Hippocampus


title: Liver_Landrace_5-months_3


title: Hippocampus KO Biological Replicate 2


title: Liver_Landrace_5-months_2


title: Liver_Landrace_5-months_1


title: Liver_Meishan_12-days_6


title: WT 129S6/SvEvTac Replicate 1

description: Replicate 1


title: Striatum WT Biological Replicate 1


title: WT 129S6/SvEvTac Replicate 3

description: Replicate 3


title: WT 129S6/SvEvTac Replicate 2

description: Replicate 2


title: nm1054 129S6/SvEvTac Replicate 1

description: Replicate 1


title: Hippocampus HET Biological Replicate 2


title: Striatum HET Biological Replicate 1


title: Liver_Meishan_12-days_4


title: Liver_Meishan_12-days_3


title: Liver_Meishan_12-days_5


title: Liver_Meishan_12-days_2


title: Spleen WT Biological Replicate 2

description: Gene expression data from adult spleen

source_name: Spleen


title: Spleen KO Biological Replicate 2

description: Gene expression data from adult spleen


title: Hippocampus KO Biological Replicate 1


title: Hippocampus HET Biological Replicate 1


title: Liver_Meishan_12-days_1


title: Hippocampus WT Biological Replicate 1


title: A549.CTL.Sample1

city: Spokane

first: Bin

last: Shan

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed of sequencing adapters, primers, and low quality reads with autoadapt.pl 0.2 using default settings
Trimmed FASTQ files were aligned to HG19 using STAR 2.6.0c. Gene and isoform expression values were determined using RSEM 1.3.0 rsem-calculate-expression with “--star”, “--star-gzipped-read-file”, “--output-genome-bam”, and “-p 48” options
Genome_build: hg19
Supplementary_files_format_and_content: text file with expression signal in expected_count, TPM, FPKM

source_name: Lung cancer cell line

growth_protocol: H23 cells were cultured in RPM1640 with 10% FBS. A549 cells were cultured in DMEM with 10% FBS.

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: No treatment.

tag: cell line

value: Lung cancer cell line

value: Lung


title: Liver_Landrace_12-days_5

value: Liver


title: A549.CTL.Sample3


title: A549.CTL.Sample2


title: H23.CTL.Sample3


title: Liver_Landrace_12-days_4

value: LWD


title: Liver_Landrace_12-days_3

value: female


title: Spleen WT Biological Replicate 1

description: Gene expression data from adult spleen


title: Spleen HET Biological Replicate 1

description: Gene expression data from adult spleen


title: Liver_Landrace_12-days_1


title: H23.CTL.Sample2


title: H23.CTL.Sample1


title: A549.BLM.siRNA1.Sample1

growth_protocol: A549 cells were cultured in DMEM with 10% FBS.

extract_protocol:
Total cell RNA was extracted from the treated cells at 48 hrs after transfection using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: Bloom-specific siRNA and control siRNA were transfected into A549 cells using RNAiMAX.


title: A549.BLM.siRNA1.Sample3


title: Spleen KO Biological Replicate 1

description: Gene expression data from adult spleen


title: A549.BLM.siRNA1.Sample2


title: T47D.HOTAIR-N.siRNA.Sample3

source_name: T47D_HOTAIR-N siRNA

growth_protocol: T47D cells were cultured in RPM1640 with 10% FBS.

treatment_protocol: HOTAIR-N-specific siRNA and control siRNA were transfected into T47D cells using RNAiMAX.

value: Breast cancer cell line

tag: tissue type

value: Breast


title: Liver_Meishan_f85-days_6


title: Liver_Landrace_12-days_2


title: BMDM  Biological Replicate 2

description: Gene expression data from bone marrow derived macrophages

source_name: BMDM

value: Male

value: DA


title: Liver_Meishan_f85-days_5


title: Liver_Meishan_f85-days_3


title: Liver_Meishan_f85-days_2


title: Liver_Landrace_f85-days_6


title: Liver_Meishan_f85-days_4


title: A549.CTLsi.Sample1


title: Liver_Landrace_f85-days_3


title: Liver_Landrace_f85-days_4


title: BMDM  Biological Replicate 3

value: Adult

value: Csf1r +/+


title: A549.CTLsi.Sample3


title: A549.CTLsi.Sample2


title: Liver_Meishan_f85-days_1


title: T47D.HOTAIR-N.siRNA.Sample1


title: T47D.HOTAIR-N.siRNA.Sample2


title: Liver_Landrace_f85-days_5


title: T47D.CTLsi.Sample2

source_name: T47D_control siRNA


title: Spleen HET Biological Replicate 2

description: Gene expression data from adult spleen

value: Female

value: DA/SD


title: ELT3_DMSO_rep3

city: Memphis

first: Aristotelis

last: Astrinidis

state: TN

address: 50 N Dunlap

department: Pediatrics

institute: University of Tennessee Health Sciences Center

description: Gene expression data from rapamycin-sensitive cell line ELT3 (DMSO control)

hyb_protocol: Hybridization was performed using GeneChip WT PLUS Reagent Kit (Applied Biosystems).

scan_protocol: Microarrays were scanned on a GeneChip Scanner (Affymertrix) according to GeneChip WT PLUS Reagent Kit (Applied Biosystems).

data_processing: Data was normalized and log transformed using ThermoFisher TAC console with RMA.

source_name: ELT3 cell line

label_protocol: cDNA was labelled using GeneChip WT PLUS Reagent Kit (Applied Biosystems).

growth_protocol: Cells (200,000-400,000 per 100 mm cell culture plate) were grown in triplicate in 10 ml media (IIA complete media supplemented with 10% FBS) for 24 hours.

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

treatment_protocol: Rapamycin (10 ul from a stock of 20 mM in DMSO, final concentration 20 nM) or DMSO (10 ul) was added to the cultures, and cells were incubated for 24 hours.

value: DMSO


title: ELT3-RAPA_20nM_24h_rep1

description: Gene expression data from rapamycin-sensitive cell line ELT3 (rapamycin treatment)

value: Rapamycin 20 nM 24 h


title: T47D.CTLsi.Sample3


title: ELT3_DMSO_rep2


title: ELT3-245-RAPA_20nM_24h_rep3

description: Gene expression data from rapamycin-resistant cell line ELT3-245 (rapamycin treatment)

source_name: ELT3-245 cell line


title: ELT3-RAPA_20nM_24h_rep2


title: Liver_Landrace_f85-days_2

value: LWD x Landrace (LWDL)


title: Fat_Meishan_5-months_7

description: Biological replicate 7 of 7. Liver, Meishan crossbred pig, 5 months old.

value: Subcutaneous adipose tissue

value: LWD x Meishan (LWDM)


title: Liver_Landrace_f85-days_1


title: MII 120115_01 SOLO

value: oocyte

value: MII

value: SoLo


title: ELT3_DMSO_rep1


title: ELT3-RAPA_20nM_24h_rep3


title: Fat_Meishan_5-months_5

description: Biological replicate 5 of 7. Liver, Meishan crossbred pig, 5 months old.

value: female

value: Liver

value: LWD


title: T47D.CTLsi.Sample1

value: Breast cancer cell line

value: Breast


title: ELT3-245-RAPA_20nM_24h_rep1


title: ELT3-245_DMSO_rep1

description: Gene expression data from rapamycin-resistant cell line ELT3-245 (DMSO control)


title: Fat_Meishan_5-months_6

description: Biological replicate 6 of 7. Liver, Meishan crossbred pig, 5 months old.