title: E47KO_liver_untreated_rep3 [GAR1571]

status: Public on Nov 30 2018

type: SRA

city: Neuherberg

first: Henriette

last: Uhlenhaut

state: Munich

address: Ingolstaedter Landstr 1

department: HDC

country: Germany

institute: Helmholtz

description:
GAR1571
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice

library_source: transcriptomic

data_processing:
The reads were mapped to the mouse genome mm10 (Ensembl build 38.91) and reads per gene counted using STAR version 2.4.2a and/or HTSeq-cout version 0.7.0. Raw count data is available as _STAR_count.txt or _STARReadsPerGene.out.tab. See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
Counts were filtered for their expression strength by selecting only genes with counts above 25th percentile as expressed. Gene count normalization and differential expression analysis was performed with DESeq2. See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (build 38.91). See: https://github.com/FranziG/E47KO-liver for all the codebooks and scripts.
Genome_build: mm10
Supplementary_files_format_and_content: *_unfiltered.txt files contain the unfiltered results from the DESeq2 analysis for differential expression on E47-/- versus E47+/+ or Albcre/+;E47fl/fl versus  Alb+/+;E47fl/fl, respectively.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Mice were housed in a controlled SPF facility with a 12 hr dark/light cycle in groups of 4 animals per cage. The cages were individually ventilated and the room was kept at 23°C with constant humidity. They were fed ad libitum with regulator chow diet. Mice were sacrificed by cervical dislocation and the liver was immediately snap-frozen in liquid nitrogen.

extract_protocol:
For longterm Cort-treated liver tissue and longterm Dex-treated liver, skeletal muscle and white adipose tissue, RNA was extracted using the Qiazol protocol. For acute Dex-injected liver tissue RNA was extracted using the RNeasy minikit (Qiagen). All samples were DNAse-treated using the Ambion DNase I kit (Thermo Fisher Scientific).
The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies). Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) or unstranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: GR-ligand (dexamethasone or corticosterone) was supplemented in the drinking water of mice for 3 consecutive weeks. Mice had free access to water and food for the entire treatment period. For the acute response, mice were injected with 1mg/kg Dex and sacrificed 1 hour later with free access to food and water the entire time.

tag: strain background

tag: Sex

value: male

tag: genotype/variation

tag: diet

value: chow

tag: treatment

value: none (untreated)

tag: sacrifice condition

value: untreated

tag: tissue

value: liver tissue

tag: library

value: stranded


title: wildtype_liver_untreated_rep5 [GAR1573]

description:
GAR1573
PolyA RNA-Seq from liver tissue of untreated male, E47+/+  C57BL/6 mice


title: E47KO_liver_untreated_rep4 [GAR1572]

description:
GAR1572
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice


title: wildtype_liver_untreated_rep4 [GAR1570]

description:
GAR1570
PolyA RNA-Seq from liver tissue of untreated male, E47+/+  C57BL/6 mice


title: E47KO_liver_untreated_rep6 [GAR1575]

description:
GAR1575
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice


title: E47KO_liver_untreated_rep5 [GAR1574]

description:
GAR1574
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice


title: wildtype_liver_untreated_rep3 [GAR1569]

description:
GAR1569
PolyA RNA-Seq from liver tissue of untreated male, E47+/+  C57BL/6 mice


title: E47KO_liver_untreated_rep2 [GAR1568]

description:
GAR1568
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice


title: wildtype_liver_untreated_rep1 [GAR1480]

description:
GAR1480
PolyA RNA-Seq from liver tissue of untreated male, E47+/+  C57BL/6 mice


title: wildtype_liver_1hDex_rep3 [GAR1220]

description:
GAR1220
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Alb+/+;E47fl/fl  C57BL/6 mice

value: Dexamethasone was injected by i.p.  (1mg/kg)

value: sacrificed after 1 h  treatment of Dexamethasone


title: E47KO_liver_untreated_rep1 [GAR1479]

description:
GAR1479
PolyA RNA-Seq from liver tissue of untreated male, E47-/-  C57BL/6 mice


title: wildtype_liver_untreated_rep2 [GAR1482]

description:
GAR1482
PolyA RNA-Seq from liver tissue of untreated male, E47+/+  C57BL/6 mice


title: AlbCreE47KO_liver_1hDex_rep3 [GAR1221]

description:
GAR1221
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Albcre/+;E47fl/fl C57BL/6 mice


title: AlbCreE47KO_liver_1hDex_rep2 [GAR1219]

description:
GAR1219
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Albcre/+;E47fl/fl C57BL/6 mice


title: wildtype_liver_1hDex_rep2 [GAR1217]

description:
GAR1217
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Alb+/+;E47fl/fl C57BL/6 mice


title: wildtype_liver_3weeksCort_rep4 [GAR0894]

description:
GAR0894
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47+/+ C57BL/6 mice

value: 3 weeks 100 ug/ml concentration corticosterone in drinking water

value: sacrificed after GTT


title: AlbCreE47KO_liver_1hDex_rep1 [GAR1218]

description:
GAR1218
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Albcre/+;E47fl/fl  C57BL/6 mice


title: wildtype_liver_1hDex_rep1 [GAR1216]

description:
GAR1216
PolyA RNA-Seq from liver tissue of 1h Dexamethason-treated male, Alb+/+;E47fl/+  C57BL/6 mice


title: wildtype_liver_3weeksCort_rep3 [GAR0893]

description:
GAR0893
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47+/+  C57BL/6 mice


title: E47KO_liver_3weeksCort_rep2 [GAR0888]

description:
GAR0888
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47-/- C57BL/6 mice


title: E47KO_liver_3weeksCort_rep4 [GAR0892]

description:
GAR0892
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47-/- C57BL/6 mice


title: E47KO_liver_3weeksCort_rep3 [GAR0891]

description:
GAR0891
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47-/- C57BL/6 mice


title: wildtype_liver_3weeksCort_rep1 [GAR0886]

description:
GAR0886
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47+/+  C57BL/6 mice


title: wildtype_liver_3weeksCort_rep2 [GAR0890]

description:
GAR0890
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47+/+  C57BL/6 mice


title: wildtype_aE2A_rep1

description: GR ChIP-Seq in livers from untreated, wildtype, male C57BL/6J mice at ZT10

library_source: genomic

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Reads of two replicates were downsampled to same unique read pair number to account for libary size effects in peak calling and make wildtype and E47-/- samples comparable. GR CHIP-Seq was downsampled to 18mio read pairs per sample. E2A ChIP-Seq samples were downsampled to 22mio unique read pairs per sample.
Peaks  were  called  using  MACS2 version  2.1.0 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10
Supplementary_files_format_and_content: The .bed files containing the peak positions were generated with MACS2 version 2.1.0. The .tab files contain annotated peaks.

molecule: genomic DNA

source_name: liver tissue

extract_protocol:
ChIP was performed as previously described (Quagliarini et al., 2018) with minor changes for pellet preparation. Mouse livers were harvested, snap-frozen and homogenized in lysis buffer (10mM Hepes-KOH, 10mM KCL, 5mM MgCl2, 0.5mM DTT) using the TissueLyser (Qiagen) with steel beads. Lysates were passed through a cell strainer and cross-linked in 1% formaldehyde for 15 min followed by quenching with 0.2 M glycine solution for 5 min.
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: untreated

tag: strain

tag: antibody

value: E2A (sc-349; LOT:C1115; SantaCruz)

tag: time of day

value: ZT 10

tag: genotype


title: E47KO_liver_3weeksCort_rep1 [GAR0887]

description:
GAR0887
PolyA RNA-Seq from liver tissue of 3 weeks Corticosterone-treated male, E47-/- C57BL/6 mice


title: wildtype_aGR_rep2

value: Glucocorticoid Receptor (24050-1-AP; Proteintech)


title: wildtype_aE2A_rep2

description: GR ChIP-Seq in livers from untreated, male, E47-/- C57BL/6J mice at ZT10


title: wildtype_aGR_rep1


title: BY4742.caff [45]

city: Cambridge

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description: Total RNA was harvested at O.D. 0.4.

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the yeast reference genome transcripts (downloaded from the SGD database) using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Differential gene expression analysis between each strain and S288C was performed using DESeq2 v 3.8.
Genome_build: R64-2-1 2014_11_18 (SGD database)
Supplementary_files_format_and_content: Tab-delimited text files with the “kallisto_” prefix report the reads counts for each transcript, as well as the TPM values.
Supplementary_files_format_and_content: Comma-separated text files with the “deseq_” prefix report the differential gene expression between each strain and the reference in the same growth condition.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast strain culture

growth_protocol: Samples were grown in synthetic defined media until an O.D. concentration of 0.4.

extract_protocol:
Total RNA was extracted using the MasterPure Yeast RNA purification Kit (Biozym, Epicentre).
The samples were quality tested on the Fragment analyzer (AATi/Agilent) using the Standard sensitivity RNA kit (AATi/Agilent), 600 ng of total RNA was used for library preparation. The libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) using a Beckman Fxp liquid handler system.

treatment_protocol: Half of the samples were exposed for 4 hours to caffeine with 20mM concentration.

tag: growth condition

value: Synthetic defined media + caffeine 20mM


title: Y55.caff [47]

description: Total RNA was harvested at O.D. 0.4.


title: UWOPS87_2421.caff [48]

description: Total RNA was harvested at O.D. 0.4.


title: YPS606.caff [46]

description: Total RNA was harvested at O.D. 0.4.


title: UWOPS87_2421 [44]

description: Total RNA was harvested at O.D. 0.4.

value: Synthetic defined media


title: Y55 [43]

description: Total RNA was harvested at O.D. 0.4.


title: BY4742 [41]

description: Total RNA was harvested at O.D. 0.4.


title: UWOPS87_2421.caff [40]

description: Total RNA was harvested at O.D. 0.4.


title: CLJ3-RNA1

city: Grenoble

first: Ina

last: Attrée

address: 17 avenue des Martyrs

department: Laboratory Biology of Cancer and Infection

country: France

institute: Biosciences and Biotechnology Institute of Grenoble

data_processing:
For each replicate, raw RNA-Seq read trimmings to remove low quality sequences (limit = 0.05) and ambiguous nucleotides (maximum two nucleotides allowed) were done in CLC Genomics Workbench 9.0.
The trimmed reads were mapped to the CLJ1 genome using the RNA-Seq analysis tool in CLC Genomics Workbench 9.0.
Total number of reads mapped to each genes were exported to be used as the raw count data.
Genome_build: GCA_003032395.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa CLJ3

growth_protocol: Bacteria were grown at 37°C in liquid Lysogeny Broth (LB) medium (10 g/L Bacto tryptone, 5 g/L yeast extract, 10 g/L NaCl) with agitation until the cultures reached an optical density at 600 nm (OD600) of 1.0.

extract_protocol:
The total RNA for RNA-Seq was prepared as described in Han, K., Tjaden, B. and Lory, S. (2016) GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation. Nature microbiology, 2, 16239. Two bacterial cultures were treated independently.
The preparations of the Illumina libraries and sequencing were done by standard procedures at the Biopolymer Facility, Harvard Medical School, Boston, USA.

tag: clone

value: clinical isolate

tag: clone id

tag: culture


title: Y55.caff [39]

description: Total RNA was harvested at O.D. 0.4.


title: YPS606 [42]

description: Total RNA was harvested at O.D. 0.4.


title: CLJ3-RNA2


title: CLJ1-RNA2

source_name: P. aeruginosa CLJ1


title: YPS606.caff [38]

description: Total RNA was harvested at O.D. 0.4.


title: BY4742.caff [37]

description: Total RNA was harvested at O.D. 0.4.


title: AZA010

type: RNA

city: La Jolla

first: Samuel

last: Danziger

state: CA

address: 10300 Campus Point Dr

country: USA

institute: Celgene

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5, Cy3

organism: Homo sapiens

source_name: AML Cell Line

label_protocol: Standard Illumina Protocol

growth_protocol: AML193, HL60, KG1a, and HNT34 cells were cultured in RPMI SILAC media (Thermo FisherScientific; Waltham, MA) containing L-[12C6,14N2]lysine and L-[12C6,14N4]arginine (light label)

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Cells were treated with vehicle (DMSO)or 0.5 μM AZA daily for 3 days. Cells were cultured for another 4 days in drug-free media

tag: cell line

tag: drug treatment

value: vehicle


title: AZA007

value: 0.5uM AZA


title: AZA004


title: AZA013


title: AZA009


title: AZA011


title: AZA002


title: Y55.caff [31]

description: Total RNA was harvested at O.D. 0.4.


title: CLJ1-RNA1


title: AZA014


title: BY4742.caff [29]

description: Total RNA was harvested at O.D. 0.4.


title: NHA KO 4

type: genomic

city: Chicago

first: Yanrong

last: Ji

state: IL

address: Arthur J. Rubloff Building, 750 North Lake Shore Drive, 11th Floor

department: Feinberg School of Medicine

institute: Northwestern University

description: immortalized cell line

hyb_protocol: standard Illumina Protocol

scan_protocol: standard Illumina Protocol

data_processing:
R software (version 3.4.3) Bioconductor package minfi
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: brain astrocytes

label_protocol: standard Illumina Protocol

growth_protocol: NHA Control and KO cells were grown to confluency in 15 cm dishes. They were then trypsinized, counted, and collected.

extract_protocol: gDNA was then extracted using the Blood & Cell Culture DNA Mini Kit from Qiagen following the manufacturer's protocol

treatment_protocol: No treatments were applied

tag: cell type

value: astrocytes

value: IDH3a KO

value: brain


title: AZA012


title: UWOPS87_2421 [28]

description: Total RNA was harvested at O.D. 0.4.


title: AZA016


title: AZA006


title: AZA008


title: UWOPS87_2421.caff [32]

description: Total RNA was harvested at O.D. 0.4.


title: Y55 [27]

description: Total RNA was harvested at O.D. 0.4.


title: AZA005


title: AZA015


title: NHA Control 4

description: immortalized cell line

value: wild type


title: YPS606.caff [30]

description: Total RNA was harvested at O.D. 0.4.


title: BY4742 [25]

description: Total RNA was harvested at O.D. 0.4.


title: NHA KO 3

description: immortalized cell line


title: YPS606 [34]

description: Total RNA was harvested at O.D. 0.4.


title: BY4742 [33]

description: Total RNA was harvested at O.D. 0.4.


title: ONS_AH017

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

institute: Oxford University

description: Poly-A selected RNA

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version HD 3.4.0.38  Demux of files and FastQ preparation by BcltoFastq 2.17.1.14  Reads were mapped to GRCh38 human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.88.chr.gtf) using STAR aligner  BAM files were merged across sequencing lanes and sorted using SAMtools  Features were counted using HTSeq with the intersection not empty strategy  All reads overlapping annotations: RefSeq (Pruitt et al., 2014), XenoRefSeq, ENSEMBL genes (Harrow et al., 2012) were discarded. We then used the remaining subset of RNA-seq reads in order to identify islands of expression outside known gene models (continuously expressed regions) using a coverage window approach. Workflow generally described in (Cabili et al., 2011; Gerstein et al., 2014; Ilott and Ponting, 2013) with modifications to produce annotations at the gene level. Doing this we get a non-redundant annotation of unique genes of LncRNAs suitable for count based DE analysis (Anders et al., 2015; Love et al., 2014). The concept of islands of expression (I.o.E) is described in (Gerstein et al., 2014). Coverage cut-off has been set as in (Cabili et al., 2011) Only properly paired and uniquely mapped reads were selected. We selected splicing junctions covered with > 2 reads. We discarded all reads overlapping know gene models. We then used the remaining subset of RNA-seq reads to identify I.o.E outside known gene models using a coverage window approach. We selected continuous regions above the coverage threshold of more than a read-mate length to ensure that overlapping read-mates would not artificially increase coverage. I.o.E were collapsed and clustered as co-overlapping features connected by splicing junctions. In each cluster consensus introns were calculated by the relative frequency of each discrete segment of a set of splicing junctions. We then subtracted the genomic intervals of these consensus introns from the genomic intervals of the grouped (I.o.E) to reconstruct full length putative LncRNAs. We included putative LncRNAs in this novel annotation only if they were present in all replicates a biological condition or strain. Annotations were exported in the Gene Transfer Format (GTF). Subsequently we filtered out transcripts with length < 200 bp and we used CPAT (Wang et al., 2013) to assess coding potential. The pipeline was scripted in R using bioconductor (Gentleman et al., 2004) packages and custom scripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files *res*.csv include DESeq2 results for both ENSEMBL genes (ens_genes_res) and novel LncRNAs (lncs_res). CSV files *toc*.csv include read-pairs counts calculated using HTSeq. GTF files Novel_LncRNAs_*.gtf included gene models of novel LncRNAs.
Supplementary_files_format_and_content: TOC.csv: abundance measurements in IPSC and IPS derived sensory neurons

source_name: SENSORY NEURONS

growth_protocol: Induced pluripotent stem cell generation NHDF1 (from 44-year-old female) was reprogrammed with Yamanaka retroviruses SOX2, KLF4, OCT3/4, c-MYC and NANOG (Takahashi et al., 2006), and has previously been described (Hartfield et al., 2014). AD2-01 (from 51-year-old male) (Buskin et al., in preparation) and AD4-01 (from 68-year-old male) (Melguzo et al, in preparation) were reprogrammed using the CytoTune™-iPS Reprogramming Kit (ThermoFisher). The fibroblasts to generate AD2-01 and AD4-01 were obtained from a commercial source (Lonza, CC-2511). CytoTune-iPS reprogramming was performed as directed by the manufacturer’s instructions (ThermoFisher). The CytoTune reprogramming kit contains four Sendai virus-based reprogramming vectors each capable of expressing one of the four Yamanaka factors (KLF4, OCT3/4, SOX2 and c-MYC). Briefly, after fibroblast transduction with the four Sendai virus-based reprogramming vectors, cells are cultured for 5-6 days, with medium changes every other day (DMEM, high glucose (Sigma), 10% FBS (ThermoFisher), 1% Pen/Strep (100x, ThermoFisher), 200mM L-glutamine (Sigma), 1% non-essential amino acids (ThermoFisher)). The transduced fibroblasts are then passaged using 0.05% Trpsin-EDTA onto pre-prepared feeder layer plates containing mitotically inactivated mouse embryonic fibroblasts (MEF). 3-4 weeks after transduction, colonies should have grown to an appropriate size to allow for manual picking. Using an inverted microscope, a single colony displaying iPSC morphology is cut into 5-6 pieces using a 25 gauge needle, transferred into iPS media (KO-DMEM (ThermoFisher), 25% Knock Serum Replacement (ThermoFisher), 1% nonessential amino acids (100x, ThermoFisher), 200mM L- glutamine (Sigma), 1% Pen/Strep (100x, ThermoFisher), 8 ng/ml human FGF2 (Miltenyi Biotec)) and plated onto pre-prepared MEF plates. Colonies are allowed to attach for 48 hours, and thereafter medium changes are performed daily. iPSCs were adapted to feeder-free conditions onto Matrigel (Scientific Laboratory Supplies)-coated plates in mTeSR1 medium (ScienCell). Bulk passaging was by 0.5 mM ethylenediaminetetraacetic acid (EDTA) to make large-scale, quality-controlled stocks that were cryopreserved in liquid nitrogen. The number of feeder-free passages was kept to a minimum. When selecting iPSCs from frozen stocks for differentiation, vials with the same passage number were selected for each cell line throughout all experiments performed in this study. The iPSC lines AD2-01 and AD4-01 were obtained through the IMI/EU sponsored StemBANCC consortium via the Human Biomaterials Resource Centre, University of Birmingham, UK (http://www.birmingham.ac.uk/facilities/hbrc). All iPSC lines were subject to strict quality control checks before the initiation of differentiation. Quality control checks of this line included: tests for Sendai virus clearance, fluorescence-activated cell sorting (FACS) for pluripotency markers, genomic integrity checks and embryoid body tri-lineage differentiation experiments. Cells are also confirmed as negative for Mycoplasma before cryopreservation. Sensory neuron differentiation For neuronal differentiation, iPSCs were passaged onto Matrigel®-coated six-well plates using TrypLE express (ThermoFisher Scientific) and maintained in mTeSR1 supplemented with 10 μM ROCK inhibitor (ScienCell). Twenty-four hours after plating, the medium was exchanged to mouse embryonic fibroblast (MEF) conditioned medium (ScienCell) supplemented with 10 ng/ml human recombinant FGF2. Cells were allowed to expand on MEF-conditioned medium until ∼50% confluent, at which time differentiation was started according to Chambers et al. (2012). Briefly, medium was exchanged to knockout serum replacement (KSR) medium containing; knockout-DMEM, 15% knockout-serum replacement, 1% GlutaMAX™, 1% non-essential amino acids, 100 μM β-mercaptoethanol, 1% antibiotic/antimycotic (ThermoFisher Scientific), supplemented with the SMAD inhibitors SB431542 (Sigma, 10 μM) and LDN-193189 (Stratech, 100 nM). The medium was gradually transitioned from KSR medium to N2 medium (Neurobasal® medium, 2% B27 supplement, 1% N2 supplement, 1% GlutaMAX™, 1% antibiotic/antimycotic) (ThermoFisher Scientific) over an 11-day period. On Day 2, the small molecules CHIR99021 (Apollo Scientific, 3 μM), SU5402 (R&D Systems, 10 μM) and DAPT (Sigma, 10 μM) were also added. SMAD inhibitors were removed from the media from Day 6 onwards. On Day 11, the now immature neurons were replated onto Matrigel®-coated coverslips (25 000 cells per 13 mm coverslip) in 100% N2 medium containing human recombinant NGF, GDNF, BDNF, NT3 (all at 25 ng/ml, PeproTech) and 10 μM ROCK inhibitor. CHIR99021 (3 μM) was included in the medium until Day 14, and laminin (1 μg/ml, ThermoFisher Scientific) was supplemented into the medium from Day 20 onwards. Medium changes were performed twice weekly after replating. Cytosine β-D-arabinofuranoside (AraC, 2 μM, Sigma) was included in the medium for 24 h following replating to remove the few non-neuronal dividing cells remaining in the culture. This differentiation resulted in a completely pure neuronal culture with extensive arborized neurites by 3 weeks after the end of the small inhibitor stage. Ethics statement Human iPSC lines used in this study were derived from human skin biopsy fibroblasts, following signed informed consent. Three control cells lines were used in this study – AD2-01, AD4-01 and NHDF1. NHDF1 were reprogrammed with approval from research ethics committee: National Health Service, Health Research Authority, NRES Committee South Central, Berkshire, UK (REC 10/H0505/71).

extract_protocol: RNA was extracted according to the hybrid method of combined phenol extraction (TriPure, Roche) and column purification (High Pure RNA tissue Kit, Roche) (Bartus et al., 2016). The concentration of RNA in the samples was measured using a nanodrop and proved sufficient for sequencing. According to the hybrid method, DRG tissue was first homogenized in TriPure and then mixed with chloroform, following the phenol extraction method. After centrifuging the aqueous liquid, which stays on the top of the tube and contains the nucleic acids, was removed. This solution was then subjected to the column purification method. Following this protocol, the clear aqueous liquid was placed in Roche High Pure RNA tissue Kit columns and washed several times in order to purify the RNA. RNA was then extracted with the mRNeasy kit and all samples were subjected to on-column DNAse digestion in order to prevent genomic contamination i.e. presence of DNA in the RNA samples. RNA libraries were prepared for sequencing using standard Illumina protocols. Second strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing over eight lanes of a flow cell.

tag: genome build

tag: condition

value: Differentiated sensory neurons late plus serum


title: ONS_NHDF

description: Poly-A selected RNA


title: UWOPS87_2421 [36]

description: Total RNA was harvested at O.D. 0.4.


title: Wildtype_repeat 2

city: WUHAN

first: Tingting

last: Liu

address: Shizishan Street

department: College of Plant Science and Technology

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling
small RNA sequencing reads were aligned to Brassica napus genome using SOAP version 2,20
the raw reads were filtered to remove low quality reads, adaptor sequences, <18nt and >30nt reads and other containments using the Fastx-toolkit pipeline 146
the expression level of each miRNA was normalized using fragments per kilobase million (FPKM) methods,  according to Chepelev et al., Nucleic Acids Research, 2009. After that, DESeq package in R was used to identify differentially expressed miRNAs.
Genome_build: Brassica napus
Supplementary_files_format_and_content: abundance measurements of known and novel miRNAs

organism: Brassica napus

source_name: stem epidermis

extract_protocol:
Stem epidremis were peeled from glossy and wildtype materials.Total RNA was extracted by using TRIzol reagent
RNA from three individuals were mixed together with equal quantity. Then 18-30nt length small RNA were isolated from four total RNA libraries by size fractionation with 15% polyacrylamide gel, and ligated with 5’-RNA and 3’RNA adapters. Second, reverse transcription PCR using Super-Script II Reverse Transcriptase was used to create cDNA constructs based on two adapters, followed by PCR amplified

value: stem epidermis

tag: developmental stage

value: seedling

tag: age

value: 4 weeks after cultivation

value: wildtype


title: ONS_AD2

description: Poly-A selected RNA


title: YPS606 [26]

description: Total RNA was harvested at O.D. 0.4.


title: ON_AD3

description: Poly-A selected RNA

value: Differentiated sensory neurons late


title: NHA KO 1

description: immortalized cell line

tag: tissue


title: N2_NHDF

description: Poly-A selected RNA

value: Differentiated sensory neurons


title: ON_NHDF

description: Poly-A selected RNA


title: ON_AD2

description: Poly-A selected RNA


title: NHA KO 2

description: immortalized cell line


title: Wildtype_repeat 1


title: Glossy_repeat 2

value: glossy mutant


title: NHA Control 1

description: immortalized cell line


title: N2_AH017

description: Poly-A selected RNA


title: N2_AD3

description: Poly-A selected RNA


title: AZA001


title: N2_AD2

description: Poly-A selected RNA


title: AZA003


title: NHA Control 3

description: immortalized cell line


title: N1_NHDF

description: Poly-A selected RNA


title: N1_AH017

description: Poly-A selected RNA


title: N1_AD3

description: Poly-A selected RNA


title: N1_AD2

description: Poly-A selected RNA


title: ONS_AD3

description: Poly-A selected RNA


title: NHA Control 2

description: immortalized cell line


title: Glossy_repeat 1


title: iPSC_AD3

description: Poly-A selected RNA

source_name: AD3 IPSC

value: IPSC


title: iPSC_AH017

description: Poly-A selected RNA

source_name: AH017 IPSC


title: CLI-012

city: Greenville

first: Joseph

middle: M.

last: McClung

state: NC

address: 115 Heart Drive East Carolina Heart Institute

department: Physiology

institute: East Carolina University

description: Ryan et al. TMM_normalized_reads_count_per_million.txt

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
The gene expression level was estimated using RSEM v1.2.15.(54) TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program
Genes showing altered expression with p < 0.05 and more than 1.5-fold changes were considered differentially expressed. Adjusted p values were also calculated assuming FDR = 0.05. Goseq was used to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: text file with normalized reads

source_name: gastrocnemius muscle biopsy

extract_protocol:
percutaneous muscle biopsy was performed and sampels was flash frozen in liquid nitrogen.  Total RNA was extracted using Qiagen Rneasy Midi Kits per manufacturer instructions.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly(A) selected kit with 201-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNA as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer. 150 bp paired end reads were sequenced on Illumina HighSeq 4000 (Illumnia Inc., San Diego, CA).

value: gastrocnemius muscle

tag: diagnosis

value: Critical limb ischemia


title: CLI-009


title: CLI-010


title: CLI-016


title: CLI-013


title: CLI-014


title: CLI-015


title: iPSC_NHDF

description: Poly-A selected RNA

source_name: NHDF IPSC


title: CLI-007


title: CLI-006


title: CLI-011


title: iPSC_AD2

description: Poly-A selected RNA

source_name: AD2 IPSC


title: CLI-005


title: CLI-003


title: GBT24h [A24]

first: Eileen

last: McNeill

address: Wellcome Trust Centre for Human Genetics, Roosevelt Drive

department: Radcliffe Department of Medicine

institute: University of Oxford

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Chips were scanned with Illumina BeadArray Reader; GenomeStudio V2010.1 (Illumina Inc) was used for data extraction.

data_processing: Raw data were processed and analysed using R/BioConductor (R version 2.14). Data underwent variance stabilization and normalization (VSN) algorithm using the 'vsn' package (Huber et al., Bioinformatics, 2002), and the 'limma' package (Ritchie et al., Nucleic Acids Res, 2015) was used to perform comparisons between genotypes at each time point to identify significantly differentially expressed genes (at 5% false discovery rate).

label: biotin

source_name: BMDM, GCHfl/fl, t=24hrs

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

growth_protocol: Bone marrow was obtained by flushing the femur and tibia of adult female mice with PBS. A single cell suspension was prepared by passing the bone marrow through a 70 µm cell strainer. Cells were then cultured in 10 cm non-tissue culture treated dishes for 7 days in DMEM:F12 (Invitrogen) supplemented with 100 U/ml penicillin and 100 ng/ml streptomycin (Sigma), 10% (v/v) fetal bovine serum (PAA Laboratories), 5 mM L-glutamine (Sigma) and 10% (v/v) L929 conditioned medium at 37°C and 5% CO2. The resulting bone marrow-derived macrophages (BMDM) were plated at 1x10^6/ml in OPTIMEM supplemented with 0.2% low endotoxin BSA into 6 well plates.

extract_protocol: Cells were scraped directly into mirVana Total RNA Isolation Kit lysis buffer (Cat# AM1560). Total RNA was isolated using the standard kit protocol, prior to elution into water. The resulting RNA was quantified using a Nanodrop spectrophometer and underwent further QC using an Agilent Tapestation to assess concentration and RNA integrity.

treatment_protocol: After 2 hours serum starvation, the cells were stimulated with LPS (Sigma) in the presence of 10ng/ml interferon-gamma (Peprotech EC). Cells were incubated at 37°C and 5% CO2 for up to 24 hours. Samples were harvested just prior to stimulation (t=0) and after 2, 8 or 24 hours of stimulation.

tag: animal id

tag: strain/background

tag: genotype/variation

value: GCHfl/fl

tag: gender

value: Female

value: Adult

value: Bone marrow-derived macrophages

tag: treatment

value: LPS in the presence of interferon-gamma

tag: timepoint

value: 24 hrs


title: CLI-002


title: GAT24h [A23]

source_name: BMDM, GCHfl/flTie2cre, t=24hrs


title: GAT24h [A19]


title: GAT24h [A22]


title: Y55 [35]

description: Total RNA was harvested at O.D. 0.4.

tag: strain

tag: growth condition

value: Synthetic defined media


title: CLI-008


title: CLI-001


title: IC-H455R

value: Intermittent claudicant


title: IC-H446R


title: IC-H437L


title: IC-H397L


title: CLI-004


title: IC-H380L


title: IC-H376R


title: IC-H326L


title: IC-H287R


title: GBT8h [A18]

source_name: BMDM, GCHfl/fl, t=8hrs

value: 8 hrs


title: IC-H276L


title: IC-H271R


title: GBT24h [A20]


title: GAT8h [A16]

source_name: BMDM, GCHfl/flTie2cre, t=8hrs


title: IC-H267R


title: IC-H309R


title: GBT24h [A21]


title: GAT8h [A17]


title: GAT2h [A7]

source_name: BMDM, GCHfl/flTie2cre, t=2hrs

value: 2 hrs


title: IC-H269R


title: GBT2h [A12]

source_name: BMDM, GCHfl/fl, t=2hrs


title: GAT8h [A13]


title: GAT2h [A10]


title: GBT2h [A9]


title: GAT0h [A1]

source_name: BMDM, GCHfl/flTie2cre, t=0hrs

value: 0 hrs


title: GAT0h [A5]


title: GBT8h [A14]


title: IC-H251L


title: GAT2h [A11]


title: GBT0h [A3]

source_name: BMDM, GCHfl/fl, t=0hrs


title: IC-H231L


title: GAT0h [A4]


title: GBT8h [A15]


title: GBT0h [A6]


title: GBT2h [A8]


title: GBT0h [A2]


title: IC-H228R


title: IC-H221L


title: IC-H222R


title: IC-H218R


title: HA-026

value: Healthy Adult


title: IC-H227R


title: HA-024


title: HA-25


title: HA-019


title: HA-23


title: HA-022


title: IR3-CD19

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

description: Gene expression in CD19+ B cells in Incomplete Remission patient number 3.

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan resolution 5µm).

data_processing: The scanned images were analyzed with Feature Extraction Software 13 (Agilent) using quantile normalization and baseline transformation on median of all samples.

source_name: CD19+ B cells, Incomplete Remission

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng of total starting RNA.

extract_protocol: ARN extraction was performed using PicoPure® RNA Isolation Kit according to the manufacturer instructions (Applied Biosystems).

treatment_protocol: PBMCs were extracted from whole blood using Ficoll-Paque (GE Healthcare Lifescience). Fluorescence-assisted cell sorting was used to isolate CD4+ and CD19+ cells (BD FACSAria, BD Biosciences).

tag: disease state

value: Pemphigus

tag: remission

value: Incomplete

value: CD19+ B cells

tag: patient number


title: HA-017

value: gastrocnemius muscle


title: IR2-CD19

description: Gene expression in CD19+ B cells from Incomplete Remission patient number 2.

tag: cell type


title: HA-016


title: IR1-CD19

description: Gene expression in CD19+ B cells from Incomplete Remission patient number 1.

value: Male


title: CR3-CD19

description: Gene expression in CD19+ B cells from Complete Remission patient number 3.

source_name: CD19+ B cells, Complete Remission

value: Complete


title: HA-010


title: HA-013


title: CR2-CD19

description: Gene expression in CD19+ B cells from Complete Remission patient number 2.


title: CR1-CD19

description: Gene expression in CD19+ B cells from Complete Remission patient number 1.


title: IR4-CD4

description: Gene expression in CD4+ T cells from Incomplete Remission patient number 4.

source_name: CD4+ T cells, Incomplete Remission

value: CD4+ T cells


title: HA-009


title: HA-012


title: HA-005


title: HA-003


title: CR3-CD4

description: Gene expression in CD4+ T cells from Complete Remission patient number 3.

source_name: CD4+ T cells, Complete Remission

value: Female


title: ON_AH017

description: Poly-A selected RNA

source_name: SENSORY NEURONS

tag: genome build

tag: cell line

tag: condition

value: Differentiated sensory neurons late


title: CR1-CD4

description: Gene expression in CD4+ T cells from Complete Remission patient number 1.


title: IR1-CD4

description: Gene expression in CD4+ T cells from Incomplete Remission patient number 1.


title: CR2-CD4

description: Gene expression in CD4+ T cells from Complete Remission patient number 2.


title: GCHfl/fl_Tie2cre_Control_rep4

hyb_protocol: Fragmented sscDNA were hybridized using the Affymetrix GeneTitan instrument using the Hyb-Wash-Scan protocol according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the Affymetrix GeneTitan instrument using the Hyb-Wash-Scan protocol according to the manufacturer's instructions.

data_processing: The CEL files were processed using Affymetrix Expression Console to generate RMA-normalized data values and further data analysis was performed in R (3.2.5) using the 'limma' BioConductor package (Ritchie et al., Nucleic Acids Res 43(7), e47, 2015). Exploratory data analysis revealed an unexpected separation of the treated samples into 2 distinct clusters (each of mixed genotypes); despite extensive checks and investigations the source of this variation was unclear and it was treated as a 'batch' effect in downstream analyses.

source_name: BMDM, GCHfl/flTie2cre, uninfected

label_protocol: The Affymetrix Genechip WTPlus Reagent Kit was used according to the manufacturer's instructions to produce biotin labelled sscDNA

growth_protocol: Bone marrow was obtained by flushing the femur and tibia of adult female mice with PBS. A single cell suspension was prepared by passing the bone marrow through a 70 µm cell strainer. Cells were then cultured in 10 cm non-tissue culture treated dishes for 7 days in DMEM:F12 (Invitrogen) supplemented with 100 U/ml penicillin and 100 ng/ml streptomycin (Sigma), 10% (v/v) fetal bovine serum (PAA Laboratories), 5 mM L-glutamine (Sigma) and 10% (v/v) L929 conditioned medium at 37°C and 5% CO2.  The resulting bone marrow dervied macrophages (BMDM) were plated at 1x10^6/ml in OPTIMEM supplemented with 0.2% low endotoxin BSA into 6 well plates.

extract_protocol: Cells were scraped directy into mirVana Total RNA Isolation Kit lysis buffer (Cat# AM1560).  Total RNA was isolated using the standard kit protocol, prior to elution into water.  The resulting RNA was quantified using a Nanodrop spectrophometer and underwent further QC using an Aglient Tapestation to assess concentation and RNA integrity.

treatment_protocol: After 2 hours serum starvation the cells were infected with BCG (Pasteur) at a multiplicity of infection of 1:1 in the presence of 10ng/ml interferon gamma, or left uninfected.  Cells were incubated at 37°C and 5% CO2 for 24 hours.

value: Bone Marrow Derived Macrophages

tag: genotype

tag: infection

value: uninfected


title: GCHfl/fl_Tie2cre_BCG_rep1

source_name: BMDM, GCHfl/flTie2cre, BCG infected

value: BCG infected in the presence of interferon gamma


title: GCHfl/fl_Control_rep1

source_name: BMDM, GCHfl/fl, uninfected

value: GCHfl/fl


title: GCHfl/fl_Control_rep2


title: HA-002

source_name: gastrocnemius muscle biopsy

tag: tissue

tag: diagnosis


title: NET_H2O_r2_1

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
anti-pol II mNET-seq
NET_H2O_r2.F.bw
NET_H2O_r2.R.bw

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the Lexogen small RNA-seq kit (#052)

treatment_protocol: Uninduced control cells

tag: growth conditions

value: DMEM 10% FCS, +hygromycin, +blasticidin

tag: antibody

value: Mouse 8WG16 anti-pol II (Thompson et al, 1990)

tag: molecule

value: Nascent RNA


title: NET_H2O_r1_1

description:
anti-pol II mNET-seq
NET_H2O_r1.F.bw
NET_H2O_r1.R.bw


title: NET_H2O_r1_2


title: NET_Dox_r1_1

description:
anti-pol II mNET-seq
NET_Dox_r1.F.bw
NET_Dox_r1.R.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline


title: NET_Dox_r1_2


title: GRO_H2O_r2_2

description:
IP of BrU-labeled nascent RNA
GRO_H2O_r2.F.bw
GRO_H2O_r2.R.bw

extract_protocol:
BrU-labeled RNA was isolated by IP
20-50ng of RNA was used with the Lexogen small RNA-seq kit (#052)

value: Mouse B44 anti-BrU


title: GCHfl/fl_Control_rep4


title: NET_Dox_r2_1

description:
anti-pol II mNET-seq
NET_Dox_r2.F.bw
NET_Dox_r2.R.bw


title: GCHfl/fl_BCG_rep1

source_name: BMDM, GCHfl/fl, BCG infected


title: GCHfl/fl_Tie2cre_BCG_rep4


title: GRO_H2O_r2_1


title: GCHfl/fl_BCG_rep2


title: GCHfl/fl_BCG_rep3


title: GRO_Dox_r2_2

description:
IP of BrU-labeled nascent RNA
GRO_Dox_r2.F.bw
GRO_Dox_r2.R.bw


title: GRO_Dox_r2_1


title: GRO_H2O_r1_2

description:
IP of BrU-labeled nascent RNA
GRO_H2O_r1.F.bw
GRO_H2O_r1.R.bw


title: GCHfl/fl_Tie2cre_Control_rep1


title: GRO_Dox_r1_2

description:
IP of BrU-labeled nascent RNA
GRO_Dox_r1.F.bw
GRO_Dox_r1.R.bw


title: GCHfl/fl_Tie2cre_BCG_rep2


title: polII_H2O_DRB5m_2

description:
Chromatin IP of RNA pol II
polII_H2O_DRB5m.bw

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min

value: DMEM 10% FCS, +hygromycin, +blasticidin, +DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: Genomic DNA


title: GCHfl/fl_Tie2cre_Control_rep3


title: GCHfl/fl_Tie2cre_BCG_rep3


title: iNOS-KO_BCG_rep4

source_name: BMDM,  Nos2-/-, BCG infected


title: polII_H2O_DRB20m_2

description:
Chromatin IP of RNA pol II
polII_H2O_DRB20m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min


title: GCHfl/fl_Tie2cre_Control_rep2


title: iNOS-KO_BCG_rep2


title: iNOS-KO_Control_rep4

source_name: BMDM,  Nos2-/-, uninfected


title: iNOS-KO_Control_rep1


title: iNOS-KO_Control_rep3


title: GCHfl/fl_BCG_rep4


title: iNOS-KO_BCG_rep3


title: C57bl6/J_Control_rep2

source_name: BMDM, C57bl6/J, uninfected


title: iNOS-KO_Control_rep2


title: C57bl6/J_Control_rep4


title: C57bl6/J_Control_rep3


title: GRO_Dox_r1_1


title: polII_H2O_DRB10m_2

description:
Chromatin IP of RNA pol II
polII_H2O_DRB10m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min


title: GRO_H2O_r1_1


title: C57bl6/J_BCG_rep2

source_name: BMDM, C57bl6/J, BCG infected


title: iNOS-KO_BCG_rep1


title: C57bl6/J_BCG_rep1


title: C57bl6/J_BCG_rep4


title: C57bl6/J_Control_rep1


title: polII_Dox_DRB20m_2

description:
Chromatin IP of RNA pol II
polII_Dox_DRB20m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 20 min

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB


title: polII_Dox_DRB0m_2

description:
Chromatin IP of RNA pol II
polII_Dox_DRB0m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs


title: polII_H2O_DRB0m_2

description:
Chromatin IP of RNA pol II
polII_H2O_DRB0m.bw

treatment_protocol: Uninduced control cells were treated with 100 uM DRB for 3 hrs


title: polII_Dox_DRB5m_2

description:
Chromatin IP of RNA pol II
polII_Dox_DRB5m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 5 min


title: polII_Dox_DRB10m_2

description:
Chromatin IP of RNA pol II
polII_Dox_DRB10m.bw

treatment_protocol: TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min


title: C57bl6/J_BCG_rep3


title: MALME3M_NT-shRNA (1)

city: Fort Worth

first: Yu-Chieh

last: Wang

state: TX

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

description:
SAMPLE 17
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were filtered for detection P value <0.01 in GenomeStudio (Illumina, Hayward, CA), and normalized using the LUMI package with RSN (Robust spline normalization) algorithm in R.

source_name: MALME3M, no knockdown

extract_protocol: RNA was extracted with Ambion MirVana Isolation Kit

tag: shRNA-mediated knockdown

value: control

value: no knockdown


title: COLO829_NT-shRNA (2)

description:
SAMPLE 20
replicate 2

source_name: COLO829, no knockdown


title: SK-MEL-2_NT-shRNA (2)

description:
SAMPLE 24
replicate 2

source_name: SK-MEL-2, no knockdown


title: UACC257_shRNA645 (2)

description:
SAMPLE 14
replicate 2

source_name: UACC257, knockdown


title: UACC257_NT-shRNA (1)

description:
SAMPLE 21
replicate 1

source_name: UACC257, no knockdown


title: MALME3M_NT-shRNA (2)

description:
SAMPLE 18
replicate 2


title: COLO829_shRNA645 (2)

description:
SAMPLE 12
replicate 2

source_name: COLO829, knockdown


title: UACC257_NT-shRNA (2)

description:
SAMPLE 22
replicate 2


title: UACC257_shRNA645 (1)

description:
SAMPLE 13
replicate 1


title: NHA KO 5

description: immortalized cell line

data_processing:
RNA sequencing data was preprocessed using RSEM software package (version 1.3.0) with in-built STAR alignment tool (version 2.5.2)
Raw sequence reads were examined for quality using Fastqc and adapter sequences and low-quality bases were trimmed using Trimmomatic.
The reads were then aligned to human reference genome (GRCh37 assembly) using STAR and RSEM was used for quantification of gene abundance estimates.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include estimated counts from RSEM

source_name: brain astrocytes

growth_protocol: Cells were grown in their full media  till confluency, at which point the cells were trypsinized, counted, collected.

extract_protocol:
RNA was extracted according to the Qiagen RNeasy manufacturer's protocol
RNA-SEQ libraries were generated using Illumina TruSEQ mRNA stranded kits using the Illumina provided protocol
Libraries were quantitated using an Agilent bio-analyzer and the pooled libraries were sequenced using an Illumina HiSEQ4000 using Illumina reagents and protocols

treatment_protocol: No treatments were done

value: astrocytes

value: IDH3a KO

value: brain


title: COLO829_NT-shRNA (1)

description:
SAMPLE 19
replicate 1


title: SK-MEL-2_shRNA645 (2)

description:
SAMPLE 16
replicate 2

source_name: SK-MEL-2, knockdown


title: SK-MEL-2_NT-shRNA (1)

description:
SAMPLE 23
replicate 1


title: MALME3M_shRNA645 (1)

description:
SAMPLE 9
replicate 1

source_name: MALME3M, knockdown


title: COLO829_shRNA645 (1)

description:
SAMPLE 11
replicate 1


title: SK-MEL-2_shRNA647 (2)

description:
SAMPLE 8
replicate 2


title: COLO829_shRNA647 (2)

description:
SAMPLE 4
replicate 2


title: UACC257_shRNA647 (1)

description:
SAMPLE 5
replicate 1


title: SK-MEL-2_shRNA647 (1)

description:
SAMPLE 7
replicate 1


title: MALME3M_shRNA645 (2)

description:
SAMPLE 10
replicate 2


title: NHA KO 2

description: immortalized cell line


title: UACC257_shRNA647 (2)

description:
SAMPLE 6
replicate 2


title: 48h salt-treatedroots rep2

city: Qingdao

last: Chen

address: wannianquan road

institute: Shandong Peanut Research Institute

description: This sample is of 48h salt treated roots of peanut huayu19. It is the second of three wild-type biological replicates used in this experiment.

hyb_protocol: Labeled samples were dried and redissolved in the hybridization solution, DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Hybridization was performed at 42℃ for 14h with NimbleGen Hybridization System, Array were washed in wash buffer I and II and III supplied by NimbleGen,and dried in NimbleGen Microarray Dryer.

scan_protocol: After hybridizations, microarrays were scanned using the Roche NimbleGen MS200 scanner and the data of obtained images were extracted with NimbleScan software at CapitalBio Corporation.

data_processing: Normalization was performed using RMA (Robust Multichip Analysis) method and further analysis was performed with SAM (Significance Analysis of Microarrays) software (Tusher et al. 2001).

organism: Arachis hypogaea

source_name: salt-treated roots

label_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 µg amplified RNA was mixed with 4 µg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 µL of 4×first-strand buffer, 2 µL of 0.1M DTT, and 1.5 µL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 µL. The cDNA was mixed with 4 µg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 µL Klenow buffer, dNTP, and Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 µM dATP, 240 µM dGTP, 240 µM dTTP, 120 µM dCTP, and 40 µM Cy-dCTP. 1.2 µL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Peanut seeds were germinated in a mixture of nutrient-rich soil and vermiculite (2:1) and grown under conditions of 16/8 h and 28/22°C of light/dark.

extract_protocol: Total RNA was isolated from samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA samples were purified with a NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany). RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantified spectrophotometrically. All RNA was stored at –80°C until further analysis.

treatment_protocol: For the NaCl treatments, the roots of ten seedlings grown in soil were pulled out carefully to avoid injury, flushed carefully to remove all soil and then dipped into 200 mM NaCl solution. The roots were collected at 0 h, 3 h and 48 h. The 3- and 48-h points were chosen in order to capture early responsive genes and late responsive genes, respectively, according to reports by Lee et al. (2005) and Kreps et al. (2002). All the samples were immediately frozen in liquid nitrogen and then stored at -80℃ until required.

tag: genoytpe

value: wild-type

tag: strain

value: peanut huayu 19

value: root


title: 48h salt-treatedroots rep1

description: This sample is of 48h salt treated roots of peanut huayu19. It is the first of three wild-type biological replicates used in this experiment.


title: NHA KO 1

description: immortalized cell line


title: NHA Control 4

description: immortalized cell line

value: wild type


title: NHA Control 3

description: immortalized cell line


title: 48h salt-treatedroots rep3

description: This sample is of 48h salt treated roots of peanut huayu19. It is the third of three wild-type biological replicates used in this experiment.


title: 3h salt-treatedroots rep2

description: This sample is of 3h salt treated roots of peanut huayu19. It is the second of three wild-type biological replicates used in this experiment.


title: P. involutus T4 3

city: Lund

first: Anders

last: Tunlid

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

description: Prolonged glucose depletion

data_processing:
FastQC (ver. 0.11.2) (Andrews, 2010) was used for quality control of raw RNA-Seq reads and ribosomal RNA-like sequences were removed using riboPicker (standalone ver. 0.4.3, SILVA database ver. 119) (Schmieder et al., 2012). RNA-Seq reads were aligned to the transcriptome using TopHat2 (ver. 2.0.13) (Kim et al., 2013) with Bowtie2 (ver. 2.2.3.0) (Langmead et al., 2012) and the following parameters: -T -x 1 -I 5000 --library-type 'fr-firststrand'  SAMtools (ver. 0.1.19) (Li et al., 2009) was used to sort and convert the BAM files to SAM files. Transcript abundances were measured as read counts in CDS using htseq-count (ver. 0.6.1) (Anders et al., 2015) with the following parameters: -s 'reverse' -t 'CDS' -i 'gene_id' -m 'intersection-nonempty'   Genes with mean count below 11 across all samples were removed. Read count normalization factors were calculated for each fungus using EDASeq (ver. 2.8.0) with 50 strata and full quantile normalization to correct for transcript length and G/C-content within each sample (Risso et al., 2011), and combined with sample size factors to adjust for different sequencing depths using DESeq2 (ver. 1.14.1) (Love et al., 2014). Principal component analysis (PCA) was performed on normalized and regularized log-transformed (DESeq2) RNAseq data blinded to the experimental design for quality assurance.
Genome_build: Paxillus involutus ATCC 200175 v1.0 (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html)
Genome_build: Laccaria bicolor v2.0 (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html)
Supplementary_files_format_and_content: The tab-delimited Lac_rawCounts.tab and Pax_rawCounts.tab files contain the Joint Genome Institute (JGI) gene model names and raw read counts for each sample.
Supplementary_files_format_and_content: The tab-delimited Lac_normalizationFactors.tab and Pax_normalizationFactors.tab files contain the matrix of normalization factors for each gene and sample. Used in DESeq2 with the raw counts file to correct for gene-specific effects and sample-specific sequencing depths. For correct dispersion estimation the matrix of normalization factors needs first to be scaled to geometric mean near 1 for each row (gene) for correct dispersion estimation (see DESeq2::normalizationFactors).
Supplementary_files_format_and_content: The tab-delimited Lac_rlog_normalizedCounts.tab and Pax_rlog_normalizedCounts.tab files contain the gene model names and DESeq2 regularized log (rlog) transformed normalized counts for each sample.

organism: Paxillus involutus

source_name: Mycelium

growth_protocol: Cultures of P. involutus (Batsch Fr., strain ATCC 200175) and L. bicolor (strain Maire P.D.Orton) were grown in petri dishes on a glass bead layer containing liquid minimum Melin-Norkrans (MMN) medium for 9 and 18 days, respectively. The medium was replaced with MMN medium without N to induce an N-deprived mycelium.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with the RLC buffer and on-column DNase treatment, according to the manufacturer’s instructions. Total RNA was eluted in H2O.
After reverse transcription into double-stranded cDNA and barcoding by means of the massively parallel signature sequencing protocol, libraries were sequenced (RNA-Seq) using a HiSeq2000 instrument (Illumina Inc.) in single-read mode and with a read length of 50 bp (IGA Technology Services, Italy; www.igatechnology.com).

treatment_protocol: After 24 h of nitrogen starvation, the mycelium was washed with sterile water and the SOM extract was added. The extract was supplemented with glucose to a final concentration similar to that in the MMN medium (Rineau et al., 2012). For the production om extract forest litter material was collected from the upper 10-cm soil layer in a 61-year-old Norway spruce stand growing in a N-poor site in central Sweden (soil pH, 5.0) and was extracted using hot water.

value: Batsch Fr., ATCC 200175

tag: days

tag: time point

tag: biological replicate


title: MALME3M_shRNA647 (2)

description:
SAMPLE 2
replicate 2


title: P. involutus T4 2

description: Prolonged glucose depletion


title: COLO829_shRNA647 (1)

description:
SAMPLE 3
replicate 1


title: 3h salt-treatedroots rep1

description: This sample is of 3h salt treated roots of peanut huayu19. It is the first of three wild-type biological replicates used in this experiment.


title: MALME3M_shRNA647 (1)

description:
SAMPLE 1
replicate 1


title: NHA KO 3

description: immortalized cell line

tag: cell type


title: untreated roots rep3

description: This sample is of untreated roots of peanut huayu19. It is the third of three wild-type biological replicates used in this experiment.

source_name: untreated roots


title: NHA Control 2

description: immortalized cell line


title: WT1

city: Houston

first: Shiyang

last: Song

state: Texas

address: 2111 Holly Hall ,Apt.2206

department: Medicine

institute: Baylor College of Medicine

data_processing:
raw sequence reads from each biological replicate of total RNA were first aligned to the UCSC mm10 genome with Tophat v2.1.0 using default parameters.
HTSeq was used to obtain read counts from the aligned reads.
DESeq2 (version 1.8.2) was used to normalized the read counts and perform differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table include p value and adjust p value for each sample

source_name: tibialis anterior muscle

extract_protocol:
Tibialis anterior muscle were removed, flash frozen on dry ice.Total mRNA was extracted with TRIzol reagent followed by RNeasy mini columns (Qiagen).
RNA libraries were prepared for sequencing using standard protocols

value: tibialis anterior muscle

tag: age

value: 21 weeks


title: NS-DADm1

value: NS-DADm


title: WT3


title: NS-DADm3


title: WT2


title: NS-DADm2


title: untreated roots rep2

description: This sample is of untreatedroots of peanut huayu19. It is the second of three wild-type biological replicates used in this experiment.


title: 3h salt-treatedroots rep3

description: This sample is of 3h salt treated roots of peanut huayu19. It is the third of three wild-type biological replicates used in this experiment.


title: untreated roots rep1

description: This sample is of untreated roots of peanut huayu19. It is the first of three wild-type biological replicates used in this experiment.


title: P. involutus T3 3

description: Glucose depletion


title: NHA Control 1

description: immortalized cell line


title: P. involutus T4 1

description: Prolonged glucose depletion


title: P. involutus T3 2

description: Glucose depletion


title: P. involutus T3 1

description: Glucose depletion


title: SK-MEL-2_shRNA645 (1)

description:
SAMPLE 15
replicate 1

tag: cell line


title: P. involutus T2 3

description: Ammonium depletion


title: SAMPLE 442_Memory Th1-90

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

country: Japan

institute: Chiba University

description: Memory Th1

data_processing: raw data was collected from the Fluidigm Real-Time PCR Analysis software single cell data could be furthor analized in R software with the Package SINGuLAR™ 3.0

label: Eva Green

source_name: primary CD4 T cells from spleen

label_protocol: qRT-PCR was performed on the 96.96 IFC using the pre-amplified product on the Fluidigm Biomark platform according to the manufacture's instructions

extract_protocol: single cells were lysed and preamplified with the kit (CellsDirect™ One-Step qRT-PCR Kit, Thermo, 11753100)

treatment_protocol: Memory Th1 cells from the spleen were purified using cell sorter.

value: BALB/c

value: spleen

value: CD4 T cells


title: SAMPLE 441_Memory Th1-89

description: Memory Th1


title: SAMPLE 445_Memory Th1-93

description: Memory Th1


title: SAMPLE 444_Memory Th1-92

description: Memory Th1


title: SAMPLE 443_Memory Th1-91

description: Memory Th1


title: SAMPLE 440_Memory Th1-88

description: Memory Th1


title: SAMPLE 439_Memory Th1-87

description: Memory Th1


title: SAMPLE 438_Memory Th1-86

description: Memory Th1


title: SAMPLE 435_Memory Th1-83

description: Memory Th1


title: SAMPLE 436_Memory Th1-84

description: Memory Th1


title: SAMPLE 434_Memory Th1-82

description: Memory Th1


title: SAMPLE 432_Memory Th1-80

description: Memory Th1


title: SAMPLE 433_Memory Th1-81

description: Memory Th1


title: SAMPLE 430_Memory Th1-78

description: Memory Th1


title: P. involutus T2 1

description: Ammonium depletion


title: P. involutus T1 2

description: Active growth


title: P. involutus T1 3

description: Active growth


title: P. involutus T1 1

description: Active growth


title: P. involutus T2 2

description: Ammonium depletion


title: SAMPLE 426_Memory Th1-74

description: Memory Th1


title: SAMPLE 429_Memory Th1-77

description: Memory Th1


title: SAMPLE 425_Memory Th1-73

description: Memory Th1


title: SAMPLE 427_Memory Th1-75

description: Memory Th1


title: SAMPLE 428_Memory Th1-76

description: Memory Th1


title: SAMPLE 437_Memory Th1-85

description: Memory Th1


title: SAMPLE 424_Memory Th1-72

description: Memory Th1


title: SAMPLE 431_Memory Th1-79

description: Memory Th1


title: SAMPLE 423_Memory Th1-71

description: Memory Th1


title: SAMPLE 419_Memory Th1-67

description: Memory Th1


title: SAMPLE 418_Memory Th1-66

description: Memory Th1


title: SAMPLE 417_Memory Th1-65

description: Memory Th1


title: SAMPLE 416_Memory Th1-64

description: Memory Th1


title: SAMPLE 420_Memory Th1-68

description: Memory Th1


title: SAMPLE 422_Memory Th1-70

description: Memory Th1


title: SAMPLE 414_Memory Th1-62

description: Memory Th1


title: SAMPLE 413_Memory Th1-61

description: Memory Th1


title: SAMPLE 408_Memory Th1-56

description: Memory Th1


title: SAMPLE 409_Memory Th1-57

description: Memory Th1


title: SAMPLE 421_Memory Th1-69

description: Memory Th1


title: SAMPLE 411_Memory Th1-59

description: Memory Th1


title: SAMPLE 406_Memory Th1-54

description: Memory Th1


title: SAMPLE 405_Memory Th1-53

description: Memory Th1


title: SAMPLE 407_Memory Th1-55

description: Memory Th1


title: SAMPLE 410_Memory Th1-58

description: Memory Th1


title: SAMPLE 404_Memory Th1-52

description: Memory Th1


title: SAMPLE 402_Memory Th1-50

description: Memory Th1


title: SAMPLE 403_Memory Th1-51

description: Memory Th1


title: SAMPLE 412_Memory Th1-60

description: Memory Th1


title: 1461_96h_N: NK cells from donor 2 treated under normoxia for 96H

city: Genova

first: Davide

last: Cangelosi

address: Via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: NK cells from healthy donors  were isolated from PB mononuclear cells using RosetteSep NK Cell Enrichment Cocktail (StemCell Technologies, 15025 Vancouver, Canada), according to a protocol approved by the Regional Ethics Committee for Human Experimentation, Written informed consent was obtained from all the subjects enrolled in the study in adherence with the Declaration of Helsinki. Only preparations displaying more than 95% of CD56+ CD3- CD14- NK cells were selected for the experiments. After isolation, NK cells were cultured for the indicated time points in RPMI 1640 (Lonza Verviers, Belgium) supplemented with 10% Fetal Bovine Serum (FBS, Voden Medical S.p.a. Meda MB, Italy), antibiotic mixture (0.05 mg/mL penicillin, 0.05 mg/mL streptomycin Lonza, Verviers, Belgium), and 100 U/mL recombinant human IL-2 (Proleukin, Novartis Basilea, Switzerland) at 2X 106cells/mL in round bottom 96-well microtiter plates. The cultures were performed either under normoxic conditions in a humidified incubator containing 20% O2, 5% CO2, and 75% N2 or under hypoxic conditions. Hypoxic conditions were obtained by culturing cells in a sealed anaerobic workstation incubator (Ruskinn, INVIVO2 400, CARLI Biotec, Roma, Italy), incorporating a gas mixing system (Ruskinn Gas Mixer Q) and flushed with a mixture of 1% O2, 5% CO2, and 94% N2.

hyb_protocol: Fragmented cRNA was hybridized on the Affymetrix HG-U133 plus 2.0 GeneChips (Genopolis Corporation, Milano) containing 54,000 probe sets (coding for 47,000 transcripts and variants, including 38,500 unique human genes) on a single array. Chips were stained with streptavidin-phycoerythrin (Invitrogen Life Technologies, Milano) as described.

scan_protocol: GeneChips were scanned using  an Affymetrix GeneChip Scanner 3000.

data_processing: Data were processed by RMA normalization utilizing the ‘Affy’ R package. Probesets with an Absent call in all samples were filtered out. Statistical analysis using paired t test was performed to identify differentially expressed genes. We corrected the p value for multiple hypothesis testing by Benjamini-Hochberg method to false discovery rate control. Only gene differences that passed the test at a confidence level of 95% (P<0.05) and a false discovery rate of 0.05% were considered significant. Fold-change (FC) was calculated as the ratio between the average expression level under hypoxia and normoxia. Genes were defined as being differentially regulated by hypoxia if they exhibited more than 2-fold increase in gene expression or down-regulated if they showed less than 0.5-fold change compared with normoxic cultures. We converted the Affymetrix probe sets into the corresponding gene symbol by Netaffx tool. When multiple probe sets were associated with the same gene symbol, the probe set with the highest expression signal was considered. Biological processes were assessed by DAVID Gene Ontology (GO) enrichment analysis (http://david.niaid.nih.gov). The significant  GO terms were defined as p value <0.05 and FDR <0.05.

source_name: Human NK cells under normoxic conditions

label_protocol: The RNA was  reverse-transcribed into double-stranded cDNA on a GeneAmp PCR System 2700 thermal cycler (Applied Biosystems, Milano) using the one-cycle cDNA synthesis kit (Affymetrix, Milano). cDNA derived from three donors/time point was purified and biotin labeled using the GeneChip IVT kit (Affymetrix). Labeled cRNA was fragmented according to Affymetrix’s instructions.

extract_protocol: Total RNA was purified from different donor-derived NK cells using the RNeasy MiniKit from Qiagen (Milano, Italy). RNA was controlled for integrity by nanoelectrophoresis with an Agilent 2100 Bioanalyzer  (Agilent Technologies Europe, Waldbroon, Germany),  quantified by spectrophotometry using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, USA).

value: Blood

value: Natural killer (NK) cells


title: 1461_96h_H: NK cells from donor 2 treated under hypoxia for 96H

source_name: Human NK cells under hypoxic conditions

treatment_protocol: After isolation, NK cells were cultured for the indicated time points in RPMI 1640 (Lonza Verviers, Belgium) supplemented with 10% Fetal Bovine Serum (FBS, Voden Medical S.p.a. Meda MB, Italy), antibiotic mixture (0.05 mg/mL penicillin, 0.05 mg/mL streptomycin Lonza, Verviers, Belgium), and 100 U/mL recombinant human IL-2 (Proleukin, Novartis Basilea, Switzerland) at 2X 106cells/mL in round bottom 96-well microtiter plates. The cultures were performed either under normoxic conditions in a humidified incubator containing 20% O2, 5% CO2, and 75% N2 or under hypoxic conditions. Hypoxic conditions were obtained by culturing cells in a sealed anaerobic workstation incubator (Ruskinn, INVIVO2 400, CARLI Biotec, Roma, Italy), incorporating a gas mixing system (Ruskinn Gas Mixer Q) and flushed with a mixture of 1% O2, 5% CO2, and 94% N2.


title: 2339_96h_N: NK cells from donor 3 treated under normoxia for 96H


title: 643_96h_H: NK cells from donor 1 treated under hypoxia for 96H


title: 2339_96h_H: NK cells from donor 3 treated under hypoxia for 96H


title: 643_96h_N: NK cells from donor 1 treated under normoxia for 96H


title: 3010_16h_H: NK cells from donor 3 treated under hypoxia for 16H


title: 3010_16h_N: NK cells from donor 3 treated under normoxia for 16H


title: SAMPLE 401_Memory Th1-49

description: Memory Th1


title: SAMPLE 398_Memory Th1-46

description: Memory Th1


title: SAMPLE 400_Memory Th1-48

description: Memory Th1


title: SAMPLE 399_Memory Th1-47

description: Memory Th1


title: SAMPLE 397_Memory Th1-45

description: Memory Th1


title: SAMPLE 396_Memory Th1-44

description: Memory Th1


title: SAMPLE 394_Memory Th1-42

description: Memory Th1


title: SAMPLE 395_Memory Th1-43

description: Memory Th1


title: SAMPLE 393_Memory Th1-41

description: Memory Th1


title: SAMPLE 415_Memory Th1-63

description: Memory Th1


title: SAMPLE 391_Memory Th1-39

description: Memory Th1


title: SAMPLE 392_Memory Th1-40

description: Memory Th1


title: SAMPLE 390_Memory Th1-38

description: Memory Th1


title: 403_16h_H: NK cells from donor 1 treated under hypoxia for 16H


title: SAMPLE 389_Memory Th1-37

description: Memory Th1


title: 780_16h_H: NK cells from donor 2 treated under hypoxia for 16H


title: SAMPLE 388_Memory Th1-36

description: Memory Th1


title: SAMPLE 386_Memory Th1-34

description: Memory Th1


title: SAMPLE 387_Memory Th1-35

description: Memory Th1


title: 403_16h_N: NK cells from donor 1 treated under normoxia for 16H


title: SAMPLE 384_Memory Th1-32

description: Memory Th1


title: SAMPLE 380_Memory Th1-28

description: Memory Th1


title: SAMPLE 382_Memory Th1-30

description: Memory Th1


title: SAMPLE 385_Memory Th1-33

description: Memory Th1


title: X10cc [B cells treated in Vivo]

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Gene expression data from B cells from blood of RR-MS female patient after six months of GA treatment in vivo.

hyb_protocol: Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix Gene-Chip Human Genome HG-U133A_2 for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: B cells, from the patients treated after six months of GA treatment in vivo.

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

growth_protocol: B cells were purified from PBMCs by negative selection using MACS Human B cell isolation kit II using CD19+ (expressed from early pro-B cell stage to B cell lymphoblast stage) and CD20+ (expressed on plasma cells) microbeads according to manufacturer's instructions (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: B cells were counted, harvested and centrifugated at 4000g x 4 min and immediately cryopreserved at -80C° before RNA extraction. Total RNAs from extracted from B cells from all patients, treated or not with GA for 6 hours in vitro, and before and after six months of GA treatment in vivo. RNA were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with TRIzol reagent (Ambion) according to manufacture procedure. All experimental protocols were approved by the local ethical review committees.

treatment_protocol: The purified cells, were analyzed using a FACS Calibur (BD Biosciences, CA, USA) to confirm the purity of cells (>98%). Cells at baseline were divided in two group. One underwent RNA extraction together with B cells from SM patients treated for six months with GA and the second group was cultured (1 × 10^6 cells/ml) in six-well plates (Becton-Dickinson; Falcon) with RPMI-1640 medium supplemented with 100 UI/ml penicillin, 100 μg/ml streptomycin (Life Technologies) and 5% autologous serum. Cultured cells were treated in vitro or not with 100ug/ml GA for six hours in a humidified atmosphere containing 5% CO2 at 37C°.

value: blood

tag: patient id

value: B cells

tag: Sex

value: female

value: Relapsing-Remitting Multiple Sclerosis (RR-MS)

tag: patient age

value: 30-35 years


title: SAMPLE 378_Memory Th1-26

description: Memory Th1

tag: tissue


title: SAMPLE 377_Memory Th1-25

description: Memory Th1


title: SAMPLE 375_Memory Th1-23

description: Memory Th1


title: X11cc [B cells treated in Vivo]

tag: diagnosis


title: X13c [B cells treated in Vivo technical replicate 1]


title: 780_16h_N: NK cells from donor 2 treated under normoxia for 16H


title: SAMPLE 379_Memory Th1-27

description: Memory Th1


title: SAMPLE 383_Memory Th1-31

description: Memory Th1


title: X12cc [B cells treated in Vivo technical replicate 2]


title: SAMPLE 381_Memory Th1-29

description: Memory Th1


title: X12c [B cells treated in Vivo technical replicate 1]


title: SAMPLE 373_Memory Th1-21

description: Memory Th1


title: SAMPLE 376_Memory Th1-24

description: Memory Th1


title: SAMPLE 372_Memory Th1-20

description: Memory Th1


title: SAMPLE 370_Memory Th1-18

description: Memory Th1


title: X9cc [B cells treated in Vivo]


title: X8c [B cells treated in Vivo technical replicate 1]


title: X8cc [B cells treated in Vivo technical replicate 2]


title: X13cc [B cells treated in Vivo technical replicate 2]


title: X5bb [B cells treated in Vitro technical replicate 2]

description: Gene expression data from B cells from a patient treated with GA  six hours in vitro

source_name: B cells isolated by peripheral blood mononuclear cells (PBMCs) treatment with GA six hours in vitro


title: SAMPLE 368_Memory Th1-16

description: Memory Th1


title: SAMPLE 369_Memory Th1-17

description: Memory Th1


title: X5b [B cells treated in Vitro technical replicate 1]


title: SAMPLE 371_Memory Th1-19

description: Memory Th1


title: SAMPLE 367_Memory Th1-15

description: Memory Th1


title: SAMPLE 374_Memory Th1-22

description: Memory Th1


title: SAMPLE 366_Memory Th1-14

description: Memory Th1


title: X7b [B cells treated in Vitro]


title: SAMPLE 361_Memory Th1-9

description: Memory Th1


title: SAMPLE 362_Memory Th1-10

description: Memory Th1


title: SAMPLE 364_Memory Th1-12

description: Memory Th1


title: SAMPLE 363_Memory Th1-11

description: Memory Th1


title: SAMPLE 365_Memory Th1-13

description: Memory Th1


title: X4bb [B cells treated in Vitro technical replicate 2]


title: SAMPLE 359_Memory Th1-7

description: Memory Th1


title: SAMPLE 360_Memory Th1-8

description: Memory Th1


title: SAMPLE 357_Memory Th1-5

description: Memory Th1


title: SAMPLE 358_Memory Th1-6

description: Memory Th1


title: X4b [B cells treated in Vitro technical replicate 1]


title: SAMPLE 355_Memory Th1-3

description: Memory Th1


title: SAMPLE 354_Memory Th1-2

description: Memory Th1


title: X6b [B cells treated in Vitro]


title: SAMPLE 352_Effector Th1 (ACC1 KO-93)

description: Effector Th1

source_name: cultured primary CD4 T cells from spleen

treatment_protocol: Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-12) for 5 days in vitro.


title: SAMPLE 353_Memory Th1-1

description: Memory Th1


title: SAMPLE 356_Memory Th1-4

description: Memory Th1


title: SAMPLE 349_Effector Th1 (ACC1 KO-90)

description: Effector Th1


title: SAMPLE 350_Effector Th1 (ACC1 KO-91)

description: Effector Th1


title: SAMPLE 351_Effector Th1 (ACC1 KO-92)

description: Effector Th1


title: X5aa [CTL, technical replicate 2]

description: Gene expression data from B cells from a patient not treated with GA

source_name: B cells isolated by peripheral blood mononuclear cells (PBMCs) not treated


title: X1b [B cells treated in Vitro technical replicate 1]


title: X1bb [B cells treated in Vitro technical replicate 2]


title: X2b [B cells treated in Vitro technical replicate 1]


title: X7aa [CTL, technical replicate 1]


title: EpiSC #1_rep1

city: Bunkyo-ku

first: Shin

last: Kobahashi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Epigenetics

institute: Tokyo Medical & Dental University, Medical Research Institute

description: passage 9

hyb_protocol: Cy3-labeled RNA probes were hybridized to a whole mouse genome DNA oligo microarray (4 × 44K, Agilent) for 16 hours at 65°C according to the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner at a 5 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. We average the expression values of the multiple probe sets representing the same gene. The gene expression levels of the EpiSCs were normalized by the total expression levels of all the autosomal genes.

source_name: EpiSC clone#1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified by RNAeasy column (QIAGEN).

treatment_protocol: EpiSCs  were treated with trypsin and collected.

tag: genotype

value: wildtype

tag: gender

tag: genetic background


title: SAMPLE 348_Effector Th1 (ACC1 KO-89)

description: Effector Th1


title: SAMPLE 347_Effector Th1 (ACC1 KO-88)

description: Effector Th1


title: SAMPLE 346_Effector Th1 (ACC1 KO-87)

description: Effector Th1


title: SAMPLE 345_Effector Th1 (ACC1 KO-86)

description: Effector Th1


title: X6aa [CTL, technical replicate 2]


title: X6a [CTL, technical replicate 1]


title: SAMPLE 338_Effector Th1 (ACC1 KO-79)

description: Effector Th1


title: Control

city: NANJING

first: MIN

last: HUANG

state: JIANGSU

address: 300 GUANGZHOU ROAD

department: Geriatrics

institute: The First Hospital Affiliated to Nanjing Medical University

description: neonatal rat ventricular cardiomyocytes transfected with corresponding empty vector

hyb_protocol: The labeled cRNAs were hybridized to Agilent Whole Rat Genome Microarray (Agilent, 4×44 K) using an Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the manufacturer’s protocol.

scan_protocol: The processed slides were scanned with an Agilent DNA microarray scanner (Agilent p/n G2565BA).

data_processing: The raw gene expression data were extracted from Agilent Feature Extraction Software (version 11.0.1.1) and imported into Agilent GeneSpring GX software (version12.1) for further analysis.

organism: Rattus norvegicus

source_name: cardiomyocytes

label_protocol: A total of 1 µg RNA from each group was linearly amplified and labeled with Cy3-UTP.

growth_protocol: The neonatal rat ventricular cardiomyocytes were cultured at 37 °C in a 5% CO2 incubator.

extract_protocol: A pool containing equivalent amounts of mixed cardiomyocytes for each group was prepared and purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Neonatal rat ventricular cardiomyocytes were transfected either with the expression vector for 11β-HSD1 or co-treated with overexpression 11β-HSD1 vector and 11β-HSD1 inhibitor BVT.2733, or transfected with corresponding empty vector.

tag: developmental stage

value: neonatal

value: ventricular cardiomyocytes

tag: treatment

value: control


title: PVN of control rat

city: Meguro-ku

first: Fumiko

last: Mori

address: 4-6-1 Komaba

department: Research Center for Advanced Science and Technology

institute: University of Tokyo

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Rat Gene Expression Microarray 4x44K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: paraventricular nucleus of male offspring (control mother)

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: strain

value: Sprague Dawley

value: male

value: Paraventricular nucleus


title: SAMPLE 341_Effector Th1 (ACC1 KO-82)

description: Effector Th1

value: BALB/c


title: HSD1+BVT

description: neonatal rat ventricular cardiomyocytes co-treated with overexpression 11β-HSD1 vector and 11β-HSD1 inhibitor BVT.2733


title: SAMPLE 342_Effector Th1 (ACC1 KO-83)

description: Effector Th1

value: spleen


title: SAMPLE 344_Effector Th1 (ACC1 KO-85)

description: Effector Th1

value: CD4 T cells


title: SAMPLE 343_Effector Th1 (ACC1 KO-84)

description: Effector Th1


title: X2bb [B cells treated in Vitro technical replicate 2]


title: SAMPLE 339_Effector Th1 (ACC1 KO-80)

description: Effector Th1


title: X4a [CTL, technical replicate 1]


title: X5a [CTL, technical replicate 1]


title: SAMPLE 340_Effector Th1 (ACC1 KO-81)

description: Effector Th1


title: HSD1

description: neonatal rat ventricular cardiomyocytes transfected with the expression vector for 11β-HSD1


title: Muscle_post_11

city: Kanoya

first: Eri

last: Miyamoto-Mikami

state: Kagoshima

address: 1 Shiromizu

department: Department of Sports and Life Science

institute: National Institute of Fitness and Sports in Kanoya

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 16 hr at 45C on the Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G according to the Affymetrix® GeneChip® Command Console® User Manual.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software and RMA normalization was conducted.

source_name: vastus lateralis muscle, after HIIT

label_protocol: Biotinylated cDNA were prepared using GeneChip® WT PLUS Reagent Kit according to the GeneChipR WT PLUS Reagent Kit User Manual from 500 ng total RNA.

extract_protocol: Total RNA was isolated from muscle biopsy samples using the miRNeasy® Mini Kit (Qiagen, Hilden, Germany) accoding to the manufacturer's instructions.

value: vastus lateralis muscle

value: post


title: X4aa [CTL, technical replicate 2]

value: blood


title: PVN of Dex-treated rat

source_name: paraventricular nucleus of male offspring (dex-treated mother)

value: dexamethasone at the third trimester


title: X2a [CTL, technical replicate 1]

value: B cells

value: female


title: Muscle_post_7


title: Muscle_post_10


title: SAMPLE 337_Effector Th1 (ACC1 KO-78)

description: Effector Th1


title: Muscle_post_9


title: SAMPLE 335_Effector Th1 (ACC1 KO-76)

description: Effector Th1


title: Muscle_post_8


title: SAMPLE 330_Effector Th1 (ACC1 KO-71)

description: Effector Th1


title: X2aa [CTL, technical replicate 2]

value: Relapsing-Remitting Multiple Sclerosis (RR-MS)

value: 30-35 years


title: SAMPLE 333_Effector Th1 (ACC1 KO-74)

description: Effector Th1


title: SAMPLE 334_Effector Th1 (ACC1 KO-75)

description: Effector Th1


title: SAMPLE 331_Effector Th1 (ACC1 KO-72)

description: Effector Th1


title: SAMPLE 332_Effector Th1 (ACC1 KO-73)

description: Effector Th1


title: SAMPLE 336_Effector Th1 (ACC1 KO-77)

description: Effector Th1


title: adjacent tissues 10N H3K27Ac_IP

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

description: H3K27Ac enriched DNA

data_processing:
Basecalls performed using bcl2fastq2-2.18
Reads were aligned to the hg19 genome assembly using Novoalign V3.02.07 with parameters: -F ILM1.8 -o SAM -r None
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using in house R scripts

source_name: Thyroid

growth_protocol: Retrospective surgical human specimens from thyroidectomy

extract_protocol:
Chromatin Immunopreciptation (ChIP) with fresh frozen tissue was previously described (Hahn MA, Li AX, Wu X, et al: Loss of the polycomb mark from bivalent promoters leads to activation of cancer-promoting genes in colorectal tumors. Cancer Res 74:3617-3629, 2014)
Enriched thyroid DNA fraction was repaired and linker ligated by using by using KAPA Hyper Prep Kit (KAPA biosystems). Further, DNA amplified by using Phusion® High-Fidelity DNA Polymerase (NEB) and sequenced on  an HiSeq2500 Illumina instrument and aligned to the human genome at the City of Hope Integrative Genomics Core

value: adjacent thyroid tissue


title: X1a [CTL, technical replicate 1]


title: X1aa [CTL, technical replicate 2]


title: SAMPLE 329_Effector Th1 (ACC1 KO-70)

description: Effector Th1


title: SAMPLE 328_Effector Th1 (ACC1 KO-69)

description: Effector Th1


title: SAMPLE 327_Effector Th1 (ACC1 KO-68)

description: Effector Th1


title: adjacent tissues 7N H3K27Ac_IP

description: H3K27Ac enriched DNA


title: Muscle_post_6


title: SAMPLE 323_Effector Th1 (ACC1 KO-64)

description: Effector Th1


title: SAMPLE 324_Effector Th1 (ACC1 KO-65)

description: Effector Th1


title: SAMPLE 321_Effector Th1 (ACC1 KO-62)

description: Effector Th1


title: Muscle_post_5


title: Muscle_post_4


title: EpiSC #2_rep1

description: passage 9

source_name: EpiSC clone#2

value: wildtype


title: Muscle_post_2


title: SAMPLE 326_Effector Th1 (ACC1 KO-67)

description: Effector Th1


title: SAMPLE 322_Effector Th1 (ACC1 KO-63)

description: Effector Th1


title: SAMPLE 325_Effector Th1 (ACC1 KO-66)

description: Effector Th1


title: Muscle_pre_11

source_name: vastus lateralis muscle, before HIIT

value: pre


title: SAMPLE 316_Effector Th1 (ACC1 KO-57)

description: Effector Th1


title: SAMPLE 317_Effector Th1 (ACC1 KO-58)

description: Effector Th1


title: SAMPLE 312_Effector Th1 (ACC1 KO-53)

description: Effector Th1


title: SAMPLE 313_Effector Th1 (ACC1 KO-54)

description: Effector Th1


title: SAMPLE 319_Effector Th1 (ACC1 KO-60)

description: Effector Th1


title: SAMPLE 320_Effector Th1 (ACC1 KO-61)

description: Effector Th1


title: Muscle_post_3


title: SAMPLE 314_Effector Th1 (ACC1 KO-55)

description: Effector Th1


title: SAMPLE 315_Effector Th1 (ACC1 KO-56)

description: Effector Th1


title: SAMPLE 311_Effector Th1 (ACC1 KO-52)

description: Effector Th1


title: SAMPLE 307_Effector Th1 (ACC1 KO-48)

description: Effector Th1


title: SAMPLE 306_Effector Th1 (ACC1 KO-47)

description: Effector Th1


title: SAMPLE 310_Effector Th1 (ACC1 KO-51)

description: Effector Th1


title: SAMPLE 308_Effector Th1 (ACC1 KO-49)

description: Effector Th1


title: Muscle_pre_10


title: SAMPLE 305_Effector Th1 (ACC1 KO-46)

description: Effector Th1


title: Muscle_post_1


title: Muscle_pre_9


title: SAMPLE 309_Effector Th1 (ACC1 KO-50)

description: Effector Th1


title: Muscle_pre_8


title: SAMPLE 301_Effector Th1 (ACC1 KO-42)

description: Effector Th1


title: SAMPLE 302_Effector Th1 (ACC1 KO-43)

description: Effector Th1


title: SAMPLE 303_Effector Th1 (ACC1 KO-44)

description: Effector Th1


title: SAMPLE 318_Effector Th1 (ACC1 KO-59)

description: Effector Th1


title: Muscle_pre_6


title: Muscle_pre_7


title: Muscle_pre_5


title: Muscle_pre_4


title: Muscle_pre_1


title: Muscle_pre_2


title: SAMPLE 299_Effector Th1 (ACC1 KO-40)

description: Effector Th1


title: SAMPLE 298_Effector Th1 (ACC1 KO-39)

description: Effector Th1


title: Muscle_pre_3


title: SAMPLE 304_Effector Th1 (ACC1 KO-45)

description: Effector Th1


title: SAMPLE 294_Effector Th1 (ACC1 KO-35)

description: Effector Th1


title: SAMPLE 296_Effector Th1 (ACC1 KO-37)

description: Effector Th1


title: SAMPLE 295_Effector Th1 (ACC1 KO-36)

description: Effector Th1


title: SAMPLE 297_Effector Th1 (ACC1 KO-38)

description: Effector Th1


title: SAMPLE 293_Effector Th1 (ACC1 KO-34)

description: Effector Th1


title: SAMPLE 291_Effector Th1 (ACC1 KO-32)

description: Effector Th1


title: SAMPLE 290_Effector Th1 (ACC1 KO-31)

description: Effector Th1


title: SAMPLE 292_Effector Th1 (ACC1 KO-33)

description: Effector Th1


title: SAMPLE 289_Effector Th1 (ACC1 KO-30)

description: Effector Th1


title: SAMPLE 288_Effector Th1 (ACC1 KO-29)

description: Effector Th1


title: SAMPLE 300_Effector Th1 (ACC1 KO-41)

description: Effector Th1


title: SAMPLE 287_Effector Th1 (ACC1 KO-28)

description: Effector Th1


title: SAMPLE 286_Effector Th1 (ACC1 KO-27)

description: Effector Th1


title: SAMPLE 285_Effector Th1 (ACC1 KO-26)

description: Effector Th1


title: SAMPLE 278_Effector Th1 (ACC1 KO-19)

description: Effector Th1


title: SAMPLE 282_Effector Th1 (ACC1 KO-23)

description: Effector Th1


title: SAMPLE 279_Effector Th1 (ACC1 KO-20)

description: Effector Th1


title: SAMPLE 280_Effector Th1 (ACC1 KO-21)

description: Effector Th1


title: SAMPLE 281_Effector Th1 (ACC1 KO-22)

description: Effector Th1


title: SAMPLE 275_Effector Th1 (ACC1 KO-16)

description: Effector Th1


title: SAMPLE 273_Effector Th1 (ACC1 KO-14)

description: Effector Th1


title: SAMPLE 274_Effector Th1 (ACC1 KO-15)

description: Effector Th1


title: SAMPLE 276_Effector Th1 (ACC1 KO-17)

description: Effector Th1


title: SAMPLE 284_Effector Th1 (ACC1 KO-25)

description: Effector Th1


title: SAMPLE 283_Effector Th1 (ACC1 KO-24)

description: Effector Th1


title: SAMPLE 271_Effector Th1 (ACC1 KO-12)

description: Effector Th1


title: SAMPLE 272_Effector Th1 (ACC1 KO-13)

description: Effector Th1


title: SAMPLE 269_Effector Th1 (ACC1 KO-10)

description: Effector Th1


title: SAMPLE 270_Effector Th1 (ACC1 KO-11)

description: Effector Th1


title: SAMPLE 277_Effector Th1 (ACC1 KO-18)

description: Effector Th1


title: SAMPLE 268_Effector Th1 (ACC1 KO-9)

description: Effector Th1


title: SAMPLE 266_Effector Th1 (ACC1 KO-7)

description: Effector Th1


title: SAMPLE 267_Effector Th1 (ACC1 KO-8)

description: Effector Th1


title: Batf3-/-_Irf8VENUS+_CD24+_3

city: St Louis

first: Theresa

last: Murphy

state: MO

address: 4940 Parkview Place

institute: washington university school of medicine

description: 24562 3ko 24 venus+

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip Mouse Gene 2.0 ST Array (Affymetrix).

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner.

data_processing:
Expression values were analyzed after RMA background correction and quantile normalization using ArrayStar software (DNASTAR)
program-name = ArrayStar
program-version = 5.1.0.114
affymetrix-algorithm-name = RMA
affymetrix-algorithm-version = 1.0
affymetrix-algorithm-param-Background correction method = RMA Background Correction
affymetrix-algorithm-param-Normalization method = Quantile
affymetrix-algorithm-param-Summarization method = Median polish

label: Biotin

source_name: Batf3-/-_Irf8VENUS+_CD24+_sorted DC1

label_protocol: Target preparation was performed using the GeneChip WT Pico Kit (Affymetrix).

growth_protocol: Mice were bred and maintained in a specific pathogen-free animal facility according to institutional guidelines and under approved protocols.

extract_protocol: Total RNA was isolated from cells using an RNAqueous-Micro Kit (Ambion).

treatment_protocol: Spleens were minced and digested with Collagenase B and DNAse 1. After ACK lysis, splenocytes were labeled with antibodies and DC1 cells were sorted as B220- SiglecH- CD11c+ MHCII+ CD172a+ XCR1+ and/or CD24+.

tag: strain background

tag: genotype/variation

value: sorted DC1


title: Batf3-/-_Irf8VENUS+_CD24+XCR1+_2

description: 26536_182 3ko pos 24


title: Batf3-/-_Irf8VENUS+_CD24+XCR1+_1

description: 26537_161 3ko pos 24


title: WT_Irf8VENUS+_CD24+XCR1+_2

description: 26535_195 wt pos 24

source_name: WT_Irf8VENUS+_CD24+XCR1+_sorted DC1


title: SAMPLE 265_Effector Th1 (ACC1 KO-6)

description: Effector Th1


title: WT_Irf8VENUS+_CD24+XCR1+_1

description: 26534_192 wt pos 24


title: WT_Irf8VENUS-_CD24+XCR1+_2

description: 26532_145 wt neg 24

source_name: WT_Irf8VENUS-_CD24+XCR1+_sorted DC1


title: SAMPLE 264_Effector Th1 (ACC1 KO-5)

description: Effector Th1


title: WT_Irf8VENUS+_CD24+_3

description: 24561 WT 24 venus+

source_name: WT_Irf8VENUS+_CD24+_sorted DC1


title: SAMPLE 263_Effector Th1 (ACC1 KO-4)

description: Effector Th1


title: WT_Irf8VENUS-_CD24+XCR1+_1

description: 26533_143 wt neg 24