title: wt_YPD_48h_H3_2_no-spike-in


title: ATAC-Seq of control treated arr1,10,12 roots; replicate 2

status: Public on Sep 27 2018

type: SRA

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 4144 Genome Sciences Building

department: Biology

country: USA

institute: University of North Carolina

description: TypeB

library_source: genomic

data_processing:
All datasets were trimmed using the BBDuk tool from the BBMap 37.50 package with the following parameters 'k=13 ktrim=r'.
The trimmed ATAC-Seq reads were then mapped to the Arabidopsis genome (TAIR10) using bowtie 1.2.0 with the following parameters '-X 1000 -v 2'. These parameters keep unique aligning fragments with lengths up to 1000 bps and reads can have up to 2 mismatches.
The resulting SAM file containing mapped reads was converted to BAM format, sorted, indexed, and processed to remove duplicate and organellar reads using Samtools 1.5.
To normalize and visualize the datasets, the BAM files were converted to bigwig using the bamCoverage function within deepTools 2.5.2 with a bin size of 10 bp and normalized to 1x sequencing depth of the genome size of Arabidopsis (150 M).
The findPeaks script within HOMER 4.9.2 was used to call peaks on ATAC datasets with the following options '-region -size 200 -minDist 202 -gsize 135000000 -tbp 0', which allows for peak calling of variable lengths greater than 200 bps.
To do differential accessible region analysis of ATAC datasets, diffReps, a perl script, was used with the following parameters '-ns b -mo n -me nb'. These parameters find broadly enriched regions (Z-score cutoff = 2) greater than 200 bps using a negative binomial test to test for significance.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak files are in BED format, which includes genomic coordinates for called peaks. Genome browser tracks are in BIGWIG format. Identified differential ATAC regions are in BED format, which includes the genomic coordinates for these regions.
There are processed data files for merged ATAC-seq replicates on the series record:
Roots_NaOH_Merged.bw: ATAC-Seq of control treated roots; merged reps
Roots_BA_Merged.bw: ATAC-Seq of BA treated roots; merged reps
Shoots_NaOH_Merged.bw: ATAC-Seq of control treated shoots; merged reps
Shoots_BA_Merged.bw: ATAC-Seq of BA treated shoots; merged reps
TypeB_NaOH_Merged.bw: ATAC-Seq of control treated arr1,10,12 roots; merged reps
TypeB_BA_Merged.bw: ATAC-Seq of BA treated arr1,10,12 roots; merged reps
Roots_WT_All_diffRepsFC1.2.bed: Differential_ATAC_Regions
Shoots_WT_All_diffRepsFC1.2.bed: Differential_ATAC_Regions

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: arr1,10,12 roots treated for 45 with control

extract_protocol:
For ATAC-Seq, crude nuclei were harvested on sucrose cushions and sorted by DAPI-staining and FANS.
For ATAC-Seq, the libraries were created by incubating nuclei with hyperactive Tn5 transposase and fragmented DNA was barcoded with indexing primers by PCR, as described by Buenrostro, et al., 2013.

treatment_protocol: Tissue were treated for 45 minutes with vehicle control or 5uM BA in MS liquid media.

tag: tissue

value: Roots

tag: treatment

value: Control

tag: replicate number

value: Rep 2

tag: genotype


title: axo2.D4

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

library_source: transcriptomic

data_processing:
"freeIbis" was used for C1 and SmartSeq2 sample data as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.) Cellranger, version 2.0.0, as part of the 10x Genomics analysis pipeline was used to call bases for 10x experiments.
"leeHom" was used to trim adapters and merge Illumina sequencing reads for C1 and SmartSeq2 sample data. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to trim adapters for 10x experiments.
"deML" was used for robust demultiplexing of Illumina sequences for C1 and SmartSeq2 sample data using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to demultiplex reads.
Reads were aligned against the axolotl transcriptome (www.axolotl-omics.org, Download: 2015-07-29) using kallisto (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) for C1 and SmartSeq 2 sample data or using STAR (Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.) implemented in 10x' cell ranger software, version 2.0.0, for 10x data.
Transcript Per Million (TPM) values were computed using kallisto for C1 and SmartSeq2 samples. (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) Cellranger, version 2.0.0, implemented in the 10x Genomics analysis pipeline was used to obtain bam alignment files and gene count (UMI) matrices.
Gene expression values of different isoforms of the same gene were summed using custom Perl scripts.
Genome_build: Axolotl transcriptome (Am_2.2)
Supplementary_files_format_and_content: Master data frame including cell ID, cell type, timepoint, gene ID, and TPM values for each single cell.

molecule: total RNA

organism: Ambystoma mexicanum

source_name: Stage 44 forelimb limb bud

extract_protocol:
Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v2 Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.

treatment_protocol: no connective tissue enrichment

tag: sc-rna-seq method

value: Fluidigm C1

tag: development stage

value: stage 44 limb bud


title: ATAC-Seq of BA treated roots; replicate 1

source_name: Roots treated for 45 minutes with benzyl adenine

value: BA

value: Rep 1


title: axo2.D8


title: wt_YPD_48h_H3_1_no-spike-in

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
All reads had poor qualities and read-through adapter contamination removed with Trim Galore (v0.4.2) in default mode prior to mapping.
ChIP-Seq reads were aligned using Bowtie 2 (v2.3.2) with default parameters.
RNA-Seq reads were mapped to genome R64-2-1 using HISAT2 v2.0.5 (parameters: --sp 1000,1000 ). BAM files were imported into Seqmonk v0.39.0 and normalised based on the number of reads mapping to the antisense strand of annotated open reading frames, excluding the rDNA locus and the mtDNA.
Genome_build: R64-2-1
ChIP-Seq report: Quantitated ChIP-Seq data files are tab delimited SeqMonk reports containing the following columns: 1) Probe (chromosomal location), 2) Chromosome, 3) Start, 4) End, 5-30) raw read count 1 kb tiles
Quantitated RNA-Seq data files are tab delimited SeqMonk reports containing the following relevant columns: (1) CDS name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (8) Description (Ensembl); (12-13) log2 RPKM value

organism: Saccharomyces cerevisiae

source_name: Mother Enrichment Project diploid

growth_protocol: Cells were inoculated in 4ml YPD and grown for 6-8 hours then diluted in 25ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml. If required, cells were labelled (see below), then cells were inoculated in YPD at 2x104 cells/ml containing 5µg/ml ampicillin (Melford A0104) and 1µM β-estradiol (Sigma E2758).

extract_protocol:
Percoll gradients (1 for 7.5 hr or 2 for 24/48 hr timepoints) were formed by vortexing 1.16ml Percoll (Sigma P1644) with 42µl 5M NaCl, 98 µl water in 2ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Cells were defrosted on ice, re-suspended in ~250 µl cold PBSE per gradient and layered on the pre-formed gradients. Gradients were centrifuged for 20 min at 1,000 g, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g to pellet the cells, which were then re-suspended in 1ml PBSE per timepoint (re-uniting samples split across two gradients). 25 µl Streptavidin magnetic beads were added (Miltenyi Biotech 1010007) and cells incubated for 30 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 8 ml cold PBSE and eluted with 1ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. Final elution was to 1.5 ml tubes (Treff 1130153). 50 µl cells were set aside for quality control, while the remainder were pelleted by centrifugation and processed directly for ChIP.  Cells were re-suspended in 50 μl cold CLB (50mM HEPES pH 7.0, 14mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, cOmplete Protease Inhibitors (Roche 1836170)) with 50 µl zirconium beads and lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater then decanted to a Covaris 520045 microTUBE and topped up to 130 µl with CLB. Sonication was performed on a Covaris 220: Duty Factor 5 %, PIP 130 W, 900s, 200 cycles per burst, 8.9 ºC. Samples were decanted to a 1.5 ml tube and Covaris tube washed with CLB and combined to give 180 μl total volume, which was centrifuged 5 min top speed at 4 ºC and the pellet discarded. Lysate was pre-cleared by incubation with 10μl of pre-equilibrated Protein-G magnetic beads (Life Technologies 10004D), then 30 μl set aside for total DNA extraction and 50 μl used per immunoprecipitation (IP). Antibodies were added at 1:50 dilution (rabbit anti-H3, CST 2650 or rabbit anti-H3K4me3, CST 9751), one IP was processed without antibody, and IPs were incubated over night at 4 ºC on a wheel.   10μl pre-equilibrated protein-G beads in 25μl CLB were added to each IP and incubated 2-3 hrs at 4 ºC on a wheel. Beads were then washed once each at room temperature for 5 minutes on a wheel with: CLB, CLB with 0,5 M NaCl, wash buffer (10 mM Tris pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), TE, then eluted overnight at 65 ºC with 200 μl elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS). Input samples were diluted to 200 μl with TE, treated with 1 μl 1 mg/ml RNase A at 37 ºC for 1 hour then incubated overnight at 65 ºC. Input and IP samples were treated with 1 μl proteinase K for 2 hours at 55 ºC, then purified by phenol:chloroform extraction, precipitated and re-suspended in 5 μl TE.
libraries were synthesised using a NEBNext DNA Ultra II kit (NEB E7645) with modifications: Concentration of DNA was increased by reducing the volumes of the end repair and ligation steps 5-fold, with reagent quantities reduced in kind. After clean-up with 0.9x AMPure beads, PCR in 50 μl volumes according to manufacturer’s instructions. Libraries were purified with 0.9x AMPure beads and eluted in 30μl, then a size selection was performed by incubating first with 18μl AMPure beads, discarding the beads then purifying the remaining DNA from the supernatant with an additional 9 μl AMPure beads.

treatment_protocol: 0.25x107 cells per sample were harvested by centrifugation (15 s at 13,000 g), washed twice with 125µl PBS and re-suspended in 125µl of PBS containing ~3mg/ml Biotin-NHS (Sigma B1022 or Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125µl PBS and re-suspended in YPD. For 7.5 hr time points, cells were inoculated in 15ml YPD + 5µg/ml ampicillin and grown for 2 hours before addition of 1µM β-estradiol (Sigma E2758). For 24 and 48 hr time points, cells were directly inoculated in 125ml YPD containing 5µg/ml ampicillin and 1mm β-estradiol. For 24/48 hr time points, no contamination of labelled non-aged cells was observed by bud scar staining as these cells presumably lyse, and this strategy helped keep the culture density low (cultures did not exceed 0.75x107 cells/ml in 48 hr). Cells were harvested by centrifugation for 1 min, 4600 rpm in 15/50 ml tubes and immediately fixed by resuspension in 70% ethanol and storage at -80°C. Alternatively, formaldehyde (Thermo 11586711) was added to 1% and cells incubated at room temperature for 15 min before quenching with 125 mM glycine, harvested by centrifugation as above and washed three times with PBS before freezing on N2 and storage at -80°.

tag: strain

value: Mother Enrichment Project diploid

tag: age

value: 48 hour

tag: chip antibody

value: Cell Signalling Technologies, 2650


title: wt_YPD_7.5h_H3_1_no-spike-in

value: 7.5 hour


title: axo2.D12


title: wt_YPD_24h_TOTAL_3_no-spike-in

value: 24 hour


title: axo2.D11


title: wt_YPD_24h_TOTAL_2_no-spike-in


title: ATAC-Seq of control treated roots; replicate 3

source_name: Roots treated for 45 minutes with control

value: Rep 3


title: axo2.D9


title: ATAC-Seq of control treated roots; replicate 2


title: axo2.C4


title: ATAC-Seq of control treated roots; replicate 1


title: wt_YPD_24h_H3K4me3_3_no-spike-in

value: Cell Signalling Technologies, 9751


title: HN019_LOG_32_1

city: Madison

first: Wesley

middle: w.

last: Morovic

state: WI

address: 3329 Agriculture Dr.

department: Genomics & Microbiome Science

institute: DuPont Nutrition & Health

description: Method described in ISO (2010). "ISO 10932:2010 (IDF 223:2010). Milk and milk products -- Determination of the minimal inhibitory concentration (MIC) of antibiotics applicable to bifidobacteria and non-enterococcal lactic acid bacteria (LAB)." Int. Organ. Stand. (ICS: 67.100.01.): 1–31.

data_processing:
Paired-end reads were imported and mapped to the B. lactis Bl-04 genome (NC_012814.1) using the “Geneious for RNA” Mapper with default settings in Geneious v. 11.0.4
Transcript levels in the resulting assemblies were calculated using the “Calculate Expression Levels” function, which enabled the comparison of replicates and experiments using the “Compare Expression Levels” with the DESeq2 method and parametric fit type.
The assemblies were exported as BAM files and imported into ArrayStar v. 1.2 (DNAStar, Madison, WI), processed using QSeq, and normalized by reads per kilobase of transcript per million mapped reads (RPKM).
Regression analyses of the RNA data were made in ArrayStar software using the Student’s t-test with FDR correction. Statistical analyses between sets of samples were analyzed using DESeq2 method as above. Differences in expression were considered significant if the Absolute Confidence (-Log10 adjusted p-value) was +1.00, and the Log2 ratio was at + 1.00, representing p < 0.05 and a > 2x fold change, respectively, after normalization.
Genome_build: CP001515
.bam sequence alignment using Geneious v. 11.0.4
Supplementary_files_format_and_content: raw counts

organism: Bifidobacterium animalis subsp. lactis

source_name: Bacterial culture

extract_protocol:
After reaching early log phase, cells were centrifuged for 10 min. at 4,063 x g. The supernatant was removed and 1 mL of TRIzol (p/n: 15596026, Thermo) was added. The pellet was re-suspended by vortexing and the tubes were immediately frozen at -80°C. The cell pellets were later thawed, transferred to a Lysing Matrix B 2mL tube (p/n: 116911050, MPBio, Santa Ana, CA), and disrupted using a Mini-Beadbeater. The lysate was subjected to a chloroform organic extraction and followed by purification using RNeasy Mini Kit (p/n: 74104, Qiagen, Hilden, Germany).
Quality checks and quantifications of the isolated RNA were carried out on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Ribosomal RNA was removed prior to library construction using Ribo-Zero rRNA Removal Kit Gram-Positive Bacteria (p/n: MRZGP126, Illumina). Stranded cDNA libraries were prepared using TruSeq Stranded mRNA Kit (p/n: 20020594, Illumina), quantitated by Agilent TapeStation, pooled quimolarly, and sequenced on one flowcell lane for 75 cycles using paired-end 75 basepair sequencing on Illumina 2500 HiSeq Rapid Cluster Kit v. 2 (p/n: PE-402-4002, Illumina) and HiSeq Rapid SBS Kit v. 2 (p/n: FC-402-4021, Illumina).

treatment_protocol: Tetracycline exposure

tag: tetracycline conc.

value: 32 ug/mL

tag: growth condition

value: LOG (ISO method undiluted)


title: HN019_LOG_32_2

growth_protocol: Method described in ISO (2010). "ISO 10932:2010 (IDF 223:2010). Milk and milk products -- Determination of the minimal inhibitory concentration (MIC) of antibiotics applicable to bifidobacteria and non-enterococcal lactic acid bacteria (LAB)." Int. Organ. Stand. (ICS: 67.100.01.): 1–31.


title: wt_YPD_24h_H3_3_no-spike-in


title: wt_YPD_24h_H3K4me3_2_no-spike-in


title: axo2.D6


title: axo2.C3


title: Bl-04_LOG_32_2


title: B316-3-Pectin

city: Palmerston North

first: Nikola

last: Palevich

state: Manawatu

address: Tennent Drive, Agresearch, Grasslands

country: New Zealand

institute: AgResearch

description:
NC_014387_Pectin_transcripts.txt
NC_014388_Pectin_transcripts.txt
NC_014389_Pectin_transcripts.txt
NC_014390_Pectin_transcripts.txt

data_processing:
Sequence data from BGI had been filtered using DynamicTrim (Cox MP, Peterson DA, Biggs PJ. 2010) to remove reads containing: ≥ 10% unreadable bases, ≥ 20% low quality (≥ Q20) bases, any reads with a quality score ≤ Q28, adapter contamination or duplicate read pairs, and quality of the sequence data before analysis was assessed using FastQC (Andrews S, 2010).
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences.
Reference-based transcriptome assembly and differential expression between mono- and co-culture growth of B. hungatei MB2003 and B. proteoclasticus B316T on xylan and pectin conditions separately was performed using Rockhopper (Tjaden B. 2015) with default parameters.
Genome_build: CP017831
Genome_build: CP017830
Genome_build: CP017832
Genome_build: CP017833
Genome_build: CP001810
Genome_build: CP001811
Genome_build: CP001812
Genome_build: CP001813
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Butyrivibrio proteoclasticus

source_name: Cultured cells

growth_protocol: B. hungatei MB2003 and B. proteoclasticus B316T were cultured anaerobically under a CO2 atmosphere at 39 ºC in pre-warmed RM02 medium supplemented with 0.5% (w/v) cellobiose. Culture purity was verified via wet mounts and Gram staining. Cells were sub-cultured two times consecutively in triplicate with the respective growth media to ensure complete adaptation to the carbohydrate growth source. The optical density (OD) at 600 nm wavelength was monitored using an Ultrospec 1100 Pro Spectrophotometer (GE Healthcare) over a period of 24 h. At mid-log phase of growth (OD600nm = 0.4), cell counts of each mono-culture were quantified using a Petroff-Hausser chamber (Hausser Scientific)  to the manufacturer’s instructions. Cell density-equilibrated cultures were sub-cultured into 70 mL pre-warmed RM02 media with 0.5% (v/v) inoculum and supplemented with either 0.5% (w/v) of xylan from oat spelts (Sigma-Aldrich) or pectin isolated from apple (Sigma-Aldrich) as the main carbohydrate source. For the mono-cultures, B316T or MB2003 were inoculated separately into the media and for the co-culture samples, 0.25% (v/v) inocula of each equilibrated culture was added. Inoculations were done in triplicate per organism (or co-culture) and harvested after 12 h of growth.

extract_protocol:
RNA was extracted using a modified version of a liquid N2 and grinding method. Briefly, 10 g of each frozen culture sample was combined with two volumes of RNA Bacterial Protect Reagent (Qiagen). The thawed sample was centrifuged at 15,000 × g for 10 min at 4 ºC and cell pellet resuspended in 1 mL of Extraction buffer A (200 mM NaCl, 20 mM EDTA), 420 µL of 20% (w/v) SDS and 1 mL of a mixture of phenol: chloroform: isoamyl alcohol solution. The cells were disrupted by five rounds of bead-beating using a Mini-Beadbeater-96 (BioSpec) for 4 min at full speed. An equal volume of isopropanol and 0.1 volume of 3 M sodium acetate (pH 5.5) were added, gently mixed and stored at -20 ºC overnight (54). The cell pellets were ethanol precipitated, followed by DNase treatment using the Baseline-ZERO DNase (Epicentre Technologies) kit and RNA was purified using the MEGAClear kit (Thermo Fisher Scientific), based on the manufacturer’s instructions. RNA yield and quality were assessed using the Bioanalyzer 2100 with a RNA 6000 Nano Assay reagent kit from Agilent (Santa Clara, CA), and stored at -85 ºC. RNA was sequenced on the Illumina HiSeq 2000 platform at the Beijing Genomics Institute, BGI (Shenzen, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Bacterial cultures were snap-frozen with liquid N2 immediately upon collection and stored at -85 ºC.

tag: growth phase

value: Stationary phase

tag: growth environment

value: Anaerobic - Mono-culture

tag: growth substrate

value: Pectin


title: axo2.C2


title: wt_YPD_24h_H3_2_no-spike-in


title: B316-2-Pectin


title: axo2.C1


title: Bl-04_LOG_32_1


title: Co-culture-3-Pectin

description:
CP017831_Pectin_transcripts.txt
CP017830_Pectin_transcripts.txt
CP017832_Pectin_transcripts.txt
CP017833_Pectin_transcripts.txt
NC_014387_Pectin_transcripts.txt
NC_014388_Pectin_transcripts.txt
NC_014389_Pectin_transcripts.txt
NC_014390_Pectin_transcripts.txt

organism:
Butyrivibrio proteoclasticus
Butyrivibrio hungatei

value: Anaerobic - Co-culture


title: axo2.B7

value: Fluidigm C1


title: B316-1-Pectin


title: Co-culture-2-Pectin


title: ATAC-Seq of control treated roots; replicate 4

value: Roots

value: Control

value: Rep 4


title: B316-3-Xylan

description:
NC_014387_Xylan_transcripts.txt
NC_014388_Xylan_transcripts.txt
NC_014389_Xylan_transcripts.txt
NC_014390_Xylan_transcripts.txt

value: Xylan


title: HN019_LOG_8_2

value: 8 ug/mL


title: axo2.D10

value: stage 44 limb bud


title: axo2.B3


title: HN019_LOG_8_1


title: Co-culture-1-Pectin


title: Bl-04_LOG_8_2


title: axo2.B11


title: B316-2-Xylan


title: Co-culture-3-Xylan

description:
CP017831_Xylan_transcripts.txt
CP017830_Xylan_transcripts.txt
CP017832_Xylan_transcripts.txt
CP017833_Xylan_transcripts.txt
NC_014387_Xylan_transcripts.txt
NC_014388_Xylan_transcripts.txt
NC_014389_Xylan_transcripts.txt
NC_014390_Xylan_transcripts.txt


title: B316-1-Xylan


title: Bl-04_LOG_8_1


title: axo2.B1


title: HN019_ISO_4_2

value: 4 ug/mL

value: ISO method


title: axo2.A7


title: Co-culture-1-Xylan


title: Co-culture-2-Xylan


title: MB2003-3-Pectin

description:
CP017831_Pectin_transcripts.txt
CP017830_Pectin_transcripts.txt
CP017832_Pectin_transcripts.txt
CP017833_Pectin_transcripts.txt

organism: Butyrivibrio hungatei


title: Bl-04_ISO_4_2


title: axo2.A2


title: axo2.A3


title: Ananascomosus_I377-T02_good

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
For each biological replicate of BS-seq data, bisulfite-converted reads were aligned to the pineapple reference genome using BSMAP v2.90. Four mismatches were allowed per 100-bp read length, and only uniquely mapped reads were kept. The conversion rate was calculated by one minus the global average methylation level of the chloroplast genome. For methylcytosine, only coverage more than three reads was used to calculate the weighted methylation level. Correlation between replicates was calculated using the average DNA methylation level of non-overlapping 100-bp windows, and the cor() function in R. Metaplots for both gene and TE regions were generated using the average DNA methylation level of three separate regions: the upstream region (100-bp bin size), gene body (20 proportional bins), and downstream region (100-bp bin size). Differentially methylated regions (DMRs) were defined as previously described.
RNA-seq reads were aligned to the pineapple reference genome by Tophat v2.1.0 with default parameters, and only uniquely mapped reads were kept. Expression value was quantified by Cufflinks as FPKM (fragments per kilobase per million mapped reads). Differentially expressed genes (DEGs) were identified by Cuffdiff v2.2.1 with default parameters.
genome build: http://pineapple.angiosperms.org/pineapple/html/download.html
Supplementary_files_format_and_content: For mRNA-seq, the format is "gene name, Green_FPKM, White_FPKM, Ave_FPKM". For BS-seq, the format is cytosine location and corresponding methyaltion as data process step.

organism: Ananas comosus

source_name: green tip of leaf

extract_protocol: DNA was extracted from ‘D’ leaf of pineapple (Ananas comosus var. comosus cultivar MD-2), and BS-seq libraries were prepared using the TruSeq Nano DNA LT kit (Illumina), as described previously. For each tissue type, two libraries corresponding to two biological replicates were sequenced on a HiSeq X Ten system (Illumina) to obtain paired-end 150-bp reads per the manufacturer’s instructions. Total RNA was extracted from the same tissue used for the BS-seq libraries, and RNA-seq libraries were prepared using the TruSeq Preparation Kit with polyA mRNA selection, per the manufacturer’s instructions (Illumina). Two libraries were pooled and sequenced to obtain paired-end 150-bp reads on the Illumina HiSeq X Ten system.

value: "D" leaf


title: Bl-04_ISO_4_1


title: Ananascomosus_I377-T04_good

source_name: white base of leaf


title: MB2003-2-Pectin


title: Ananascomosus_I377-T03_good


title: Ananascomosus_I378-J03_good

description: White_merge.C_coverage.wig.gz  White_merge.CG.wig.gz  White_merge.CHG.wig.gz  White_merge.CHH.wig.gz


title: axo2.A12


title: axo2.A10


title: MB2003-3-Xylan

description:
CP017831_Xylan_transcripts.txt
CP017830_Xylan_transcripts.txt
CP017832_Xylan_transcripts.txt
CP017833_Xylan_transcripts.txt


title: HN019_ISO_0_1

value: 0 ug/mL


title: HN019_ISO_0_2


title: MB2003-2-Xylan


title: axo2.A4


title: Ananascomosus_I377-T01_good


title: MB2003-1-Pectin


title: Ananascomosus_I378-J04_good


title: axo2.A1


title: Bl-04_ISO_0_1


title: HN019_ISO_4_1


title: Ananascomosus_I378-J02_good

description: Green_merge.C_coverage.wig.gz  Green_merge.CG.wig.gz  Green_merge.CHG.wig.gz  Green_merge.CHH.wig.gz


title: U2932_E1

status: Public on Sep 26 2018

city: Shanghai

first: Juan

last: Yan

address: 555 Zuchongzhi Road

department: Antitumor Pharmacology

institute: Shanghai Institute of Materia Medica

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

organism: Homo sapiens

source_name: Diffuse large B-cell lymphoma

extract_protocol:
Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell strain


title: U2932_c3

value: DMSO


title: U2932_E3


title: U2932_c2


title: U2932_c1


title: U2932_E2


title: S7721_E2

source_name: Hepatocellular carcinoma


title: Bl-04_ISO_0_2


title: S7721_c2


title: MB2003-1-Xylan


title: S7721_c3


title: pfeif_E3

value: Pfeiffer


title: S7721_E1


title: pfeif_E1


title: pfeif_E2


title: pfeif_c3


title: pfeif_c2


title: WT_CMP_2

type: RNA

city: Sendai

first: Kazuhiko

last: Igarashi

state: Miyagi

address: Seiryo 2-1

country: Japan

institute: Tohoku University

description: Common myeloid progenitors sorted from bone marrow of WT

hyb_protocol: A sureprint G3 mouse GE microarray slide was used for hybridization according to the manufacturer's protocols (Agilent)

scan_protocol: After hybridization, a slide was washed adequately and scanned immediately by using an Agilent DNA Microarray Scanner with one color scan setting

data_processing: Obtained scan data were analysed by using GeneSpring software (Agilent)

organism: Mus musculus

source_name: Bone marrow, common myeloid progenitor, WT, replicate2

label_protocol: Amplified samples were labeled with indocarbocyanine by using a Cy3 post-labeling reactive dye pack (Amersham)

extract_protocol: Total RNA was extracted from sorted common myeloid progenitors by using Rneasy Plus Micro Kit (QIAGEN) and was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion)

value: bone marrow

tag: cell type

value: common myeloid progenitor

value: wildtype


title: DKO_CMP_2

description: Common myeloid progenitors sorted from bone marrow of DKO

source_name: Bone marrow, common myeloid progenitor, DKO, replicate2


title: DKO_CMP_3

source_name: Bone marrow, common myeloid progenitor, DKO, replicate3


title: WT_CMP_1

source_name: Bone marrow, common myeloid progenitor, WT, replicate1


title: DKO_CMP_1

source_name: Bone marrow, common myeloid progenitor, DKO, replicate1


title: WT_CMP_3

source_name: Bone marrow, common myeloid progenitor, WT, replicate3


title: S7721_E3


title: S7721_c1


title: pfeif_c1


title: Tonsil-ONO

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

institute: University of Leicester

hyb_protocol: Labelled cRNA was then hybridized over night at 65 ˚C onto the SurePrint G3 Human Gene Expression v3 8x60K Microarray (Agilent, Santa Clara, CA, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters

source_name: Tonsil-ONO

label_protocol: A total of 100 ng of total RNA was reverse transcribed, converted into complementary RNA (cRNA) and labelled with Cy3 using the LowInput QuickAmp Labeling Kit One-Color according to manufacturer’s protocol (Agilent, Santa Clara, CA, USA).

extract_protocol: RNA was extracted with Trizol/chloroform followed by purification using PureLink RNA Mini kit (12183018A, ThermoFisher scientific) and PureLink DNase/ carrier RNA (12185010, Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Purified CD4+ T-cells from human tonsil cells or patient cells with PTCL were pre-treated for 30 minutes with ITK inhibitors (ibrutinib or ONO0779500) (1 µM) or DMSO. The cells were then stimulated with 10 μg/ml plate-bound anti-CD3 and soluble anti-CD28 (2 µg/ml) with IL-12 (10 ng/mL) for 4 hours.

value: Control, CD4+ T-cells

tag: gender

value: Female

value: 72 years old


title: Tonsil-Ibrutinib

source_name: Tonsil-Ibrutinib


title: S. clavuligerus oppA2::acc_22.5h_rep2

type: mixed

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

country: Spain

institute: University of León

description: Biological replicate 2 of 2. oppA2::acc_22.5h-rep2

hyb_protocol: Cy3-cDNA (300 ng) and Cy5-labeled gDNA (2,5 pmol) were mixed, resuspended in 32 μl of hybridization solution (Agilent) and applied on the microarray surface. Hybridizations were carried out at 55°C and extended to 60 h to improve the quality of the results.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarrays data were processed with the Bioconductor package limma (Smyth and Speed 2003; Smyth 2004). Background corrected signals (the median background signal was substracted from the mean foreground signal) were log2-transformed and normalized with the global median procedure (within arrays), and with the cyclic loess procedure (between arrays). The Mg value is the normalized log2 of Cy3/Cy5 intensities, which is proportional to the abundance of the transcript for a particular gene.

organism: Streptomyces clavuligerus

source_name: oppA2::acc_22.5h _totalRNA

label_protocol: Labelling reactions were performed according to the recommendations described by BioPrime® Array CGH Genomic Labeling Systems (Life Technologies). Total RNA was labelled with Cy3-dCTP (Amersham) using random primers and SuperScript™ II reverse transcriptase (Invitrogen). gDNA was labelled with Cy5-dCTP (Amersham) from random primers extended with the Klenow fragment of DNA polymerase (Roche). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

growth_protocol: Culture conditions were optimized using SA medium (Starch-Asparagine, Aido et al., 1994) and the samples to extract RNA were collected at 22.5 h, 46.5 h and 60 h of the cultures.

extract_protocol: lisozime 30 mg/ml in TE was added to stabilized culture samples. After 10 min, 600 µl RLT-β-mercaptoethanol was added to samples, mixed with vortex and, samples within microtubes containing silica beads were processed in FastPrep equipment with the following program: 30 s 6.5 m/s, 1 min at 0 °C, 30 s 6.5 m/s, 1 min at 0 °C. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.

treatment_protocol: Samples from the Streptomyces cultures were stabilized with two volumes of RNA Protect Bacteria Reagent (Qiagen) for 5 min.

tag: time

source_name: ATCC 27064_ Stationary growth phase _genomicDNA [reference]

extract_protocol: Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995).

value: Stationary growth phase


title: S. clavuligerus oppA2::acc_46.5h_rep1

description: Biological replicate 1 of 2. oppA2::acc_46.5h-rep1

source_name: oppA2::acc_46.5h _totalRNA


title: S. clavuligerus oppA2::acc_60.0 h_rep1

description: Biological replicate 1 of 2. oppA2::acc_60.0h-rep1

source_name: oppA2::acc_60.0h _totalRNA


title: Ca1a_A

city: shanghai

first: Wei

last: Jin

state: Shanghai

address: 688 Hongqu road

department: breast cancer surgery

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were then mapped to GRCh38.p5 genome using hisat2
Gene-level quantification and analysis of differentially expressed  genes (DEGs): FPKM value of each gene was calculated using cufflinks , and the read counts of each gene were obtained by htseq-count . DEGs were identified using the DESeq R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential  expression.
Genome_build: hg38 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell line

growth_protocol: Ca1a cells were culture in DMEM/F12 medium with 5% horse serum,10ug/ml Insulin, 20ng/ml EGF, 100ng/ml Cholera Toxin,0.5ug/ml hydrocortisone and MDA-MB-231 cultured in L15 with 10% FBS

extract_protocol:
total RNA was extracted using TRIzol reagent (Invitrogen Corporation) and QC by Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus transfection

value: breast cancer cell line

tag: passages

tag: treatment

value: TMEM126A overexpression


title: Ca1a_P

value: control vector


title: AL-157_L1

city: Providence

first: Jessica

last: Schuster

state: RI

address: 200 Chestnut St

department: Pediatrics

institute: Women and Infants Hospital

data_processing:
Reads were mapped to the NCBI Build UCSC Hg19 human genome using the Burrows-Wheeler Aligner (BWA v0.6.2)
The SAM files were converted to BAM files with SamTools (v0.1.18) and duplicate readswere removed using Picard Tools (v1.77)
Model-based Analysis for ChIP-Seq (MACS v1.4) was used to identify significantly enriched regions (peaks) using p < 1 x 10-5 as the significance threshold for each individual and technical replicate independently
DiffBind with consensus peak sets taken over technical replicates, overlap =3 and summarize overlaps (default=union) as counting method and DESeq2 were used to identify Differentially Methylated Regions (DMRs).
Genome_build: hg19
Supplementary_files_format_and_content: Tab deliminated text file with peak counts for each sample with header containing sample titles

source_name: Placenta

extract_protocol:
Samples of villous parenchyma were taken from four quadrants between the chorionic and basal plate.  Samples were placed immediately into RNAlaterTm (Ambion, Inc., #AM7021) and stored at -80°C.  Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue kit (Qiagen, # 69506) and quantified on a NanoDrop 1000. 5ug of DNA was digested to fragment size 200-300 base pairs using dsDNA Fragmentase enzyme at 370C for 30 minutes (New England Biolabs, #MO348L). Fragments were end-repaired, 3’-ends were adenylated, and appropriate adapter indexes were ligated using the Truseq protocol (Illumina). Between each reaction, fragments were cleaned using Agencourt AmPure magnetic beads (Beckman Coulter, # A63881). Fragments were then amplified by PCR at 980C/30 sec; 10 cycles of 980C/10sec, 600C/30sec, 720C/30sec; and 720C 5min with a hold at 100C. Enriched fragments were then cleaned using Agencourt AmPure magnetic beads and quantified before methylation-dependent immunoprecipitation.
Methylated-DNA immunoprecipitation was performed using the Methylated-DNA IP kit

tag: tissue

value: Placenta

value: villous parenchyma

tag: gestational age

tag: fetal sex


title: AL-157_L2


title: AL-183_L1

value: Male


title: PP015_L6


title: PP015_L2


title: AL-183_L6


title: 231_7G

value: TMEM126A knockdown


title: 231N


title: AL-157_L6


title: AL-183_L2


title: S. clavuligerus oppA2::acc_46.5h_rep2

description: Biological replicate 2 of 2. oppA2::acc_46.5h-rep2

tag: strain


title: CAB-Ibrutinib

source_name: CAB-Ibrutinib

value: Peripheral T-cell lymphoma

tag: age

value: 36 years old


title: S. clavuligerus oppA2::acc_60.0 h_rep2

description: Biological replicate 2 of 2. oppA2::acc_60.0h-rep2


title: CAB-Unstimulated

source_name: CAB-Unstimulated


title: Tonsil-DMSO

source_name: Tonsil-DMSO


title: CAB-DMSO

source_name: CAB-DMSO


title: S. clavuligerus oppA2::acc_22.5h_rep1

description: Biological replicate 1 of 2. oppA2::acc_22.5h-rep1


title: Tonsil-Unstimulated

source_name: Tonsil-Unstimulated


title: PP015_L1


title: CAB-ONO

source_name: CAB-ONO


title: PP014_L6


title: PP014_L2


title: PP014_L1


title: PP013_L6


title: PP013_L1


title: PP007_L6


title: PP013_L2


title: PP006_L6


title: PP007_L2


title: PP007_L1


title: PP004_L6


title: PP006_L1


title: Donor3_memory Tregs [S09]

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
ATAC-seq was performed according to published protocol with minor modification as described in PMC4874839. Paired-end libraries (50 cycles) were prepared according to ATAC-seq protocol with three biological replicates (i.e. cells from 3 different individuals) for each library. The sequencing was performed using Illumina 2000. To obtain the open chromatin regions, reads were aligned to hg19 using Bowtie v2.2.9 with parameters [--maxins 175 --no-discordant --no-mixed]. Properly paired and uniquely mapped alignments were extracted. The open chromatin regions were identified using Homer findPeaks tool with parameters [-region -size 500 -minDist 50 -tbp 0].  All the open chromatin peaks were merged using bedtools to obtain a set of all potential peaks. For each replicate, the differential set of open chromatin regions for each pair of samples (i.e. memory vs naïve, memory vs CD161, naïve v CD161) were extracted using homer getDifferentialPeaks with parameter ?F 2 and the set of all potential peaks. For each pair of samples, the common peaks among three replicates were extracted using bedtools multiinter. All the common differential open chromatin regions were merged using bedtools and displayed using seqMINER with three clusters. To identify motifs that are enriched in each cluster, we used homer findMotifsGenome on all known motifs.
Genome_build: hg19
Supplementary_files_format_and_content: peak files

source_name: Memory Tregs

extract_protocol:
Cells were captured for each sample and libraries were sequenced on the Illumina Hiseq 2500 instrument.
Paired-end libraries (50 cycles) were prepared according to the published ATAC-seq protocol in Shih et al., Cell 2016

treatment_protocol: Cells were isolated from freshly drawn blood

tag: subject status/id

value: Healthy Donor 3

value: peripheral blood

value: CD4+CD25+ cells

tag: sorted cell type


title: Donor3_naive Tregs [S08]

source_name: Naïve Tregs

value: CD4+CD25hiCD127loCD45RA+ (naïve) Tregs


title: Donor3_CD161+ Tregs [S10]

source_name: CD161+ Tregs

value: CD4+CD25hiCD127loCD45RA-CD161+ Tregs


title: PP003_L2


title: PP001_L2


title: PP003_L6


title: PP004_L1


title: Donor2_CD161+ Tregs [S07]

value: Healthy Donor 2


title: PP004_L2


title: Donor2_naive Tregs [S05]


title: PP003_L1


title: Donor1_naive Tregs [S02]

value: Healthy Donor 1


title: PP006_L2


title: Donor2_memory Tregs [S06]


title: Donor1_memory Tregs [S03]


title: PP001_L1


title: Donor1_CD161+ Tregs [S04]


title: SDOS2 [Ribo-seq]

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples “Federico II”

data_processing:
Library strategy: Ribo-seq
Adapter trim: 3’ adapter was trimmed from the reads by cutadapt and only reads with good sequencing qualities (ASCII quality score > 33) and longer than 25 nt were kept
Bowtie2 alignment: reads were aligned to rRNA and tRNA sequences with Bowtie 2 and only the non-rRNA/tRNA reads were kept for further analysis
TopHat2 alignment: reads were aligned to the human genome (hg38) using TopHat 2 and those uniquely aligned were kept
HTseq and DESeq2 analysis: we then employed HTseq to get the "exon" count of each read and we use these outputs to run DESeq2 to look for differentially translated transcripts between conditions
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are CSV files quantifying the number of reads in each transcript.

source_name: HeLa cells

growth_protocol: HeLa cells were grown on 15-cm dishes until were approximately 85% confluent

extract_protocol:
Following 15 min incubation with 100 μg/ml cycloheximide (Sigma-Aldrich; C4859) at 37°C, cells were washed with ice cold PBS and 1 mL of lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton-X100) was added. Cells were then collected and incubated on ice; glass beads (Sigma-Aldrich; G8772) were added to the lysate and cells were broken by vortexing at medium speed for 3 pulses of 10 s. After 10 min of incubation on ice, lysates were centrifuged for 10 min at 10000 rpm at 4°C, and the supernatant was recovered.
RNA was partially digested with 3.5 μl of RNase I (100 U/μl, Invitrogen AM2294) per 800 μl of lysate. After 15 min of incubation at 24°C, lysates were placed on ice and supplemented with 10 μl of SUPERaseIn (20 U/μl, Invitrogen AM2694). Lysates were then loaded on a 34% sucrose cushion (34% sucrose in 20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT and 100 μg/ml cycloheximide) and monosomes were pelleted by centrifugation for 1 hr at 70000 rpm using a Beckman TLA 100.3 rotor. RNA was extracted from the pellet and ribosome protected footprints (RPFs) of 30 nucleotides were purified on a 15% TBE-Urea polyacrylamide gel (Invitrogen). RPFs were depleted of ribosomal RNA with the Ribo-Zero rRNA removal kit (Epicentre MRZH116) according to manufacturer’s indications. cDNA libraries were generated as described in Ingolia, NT et al Nat Protoc 7, 1534–1550 (2012), and sequenced by Solexa using a HiSeq 2000, Single Read, 50 nt.

treatment_protocol: Cells were treated with doxycycline (1 ug/mL) for 24 hrs to induce the expression of GFP-fusion proteins

value: T-REx-HeLa Cell Line

tag: genotype

value: SDOS-eGFP under Tet repressor

tag: rna type

value: Ribosome protected fragments


title: SDOS1 [Ribo-seq]


title: PP001_L6


title: SDOS3 [Ribo-seq]


title: GFP3 [Ribo-seq]

value: eGFP under Tet repressor


title: GFP2 [Ribo-seq]


title: GFP1 [Ribo-seq]


title: D149_NSC

city: Bangalore

first: Odity

last: Mukherjee

state: Karnataka

address: GKVK

department: ADBS

country: India

institute: Institute of Stem Cells and Regenerative Medicine (InStem)

description: 2x100 paired-end sequence reads

data_processing:
The reads were aligned to the reference genome using tophat v2.0.13
Transcript assembly and quantification was performed using cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: neural stem cells

growth_protocol: NSC were generated from on-feeder iPSCs by Dual SMAD inhibition using SB431542 and LDN193189. Rosettes were routinely purified to get pure Neural Stem Cells further maintained in DMEM/F12 supplemented in B27 supplement, N2 supplement, 8ng bFGF, 1x Glutamax, 1x NEAA, 1x Penstrep, Heparin.

extract_protocol:
Total RNA extracted using Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human pluripotent stems derived neural stem cells

tag: passage number


title: NIH5_NSC

description: 2x100 paired-end sequence reads


title: D161_NSC

description: 2x100 paired-end sequence reads


title: D149_iPSC

description: 2x100 paired-end sequence reads

source_name: human induced pluripotent stem cells

growth_protocol: iPSCs were generated by electroporation of Yamanaka  factors in Lymphoblastoid cell lines and were maintained in standard ES medium( 20% KOSR in K/O DMEM supplemented with 20ng bFGF ,  Beta-mercaptoethanol,  1X Glutamax, 1x NEAA, 1x PenStrep)

value: LCL derived human pluripotent stem cells


title: D161_iPSC

description: 2x100 paired-end sequence reads


title: Ananascomosus_I378-J01_good

source_name: green tip of leaf

value: "D" leaf


title: Lox KO AA E17.5 rep2

city: St. Louis

last: Wagenseil

state: Missouri

address: One Brookings Dr., CB 1185

institute: Washington University

hyb_protocol: 5ng of cDNA were fragmented and hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 2.0 ST Array.  Affymetrix Gene 2.0 microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip 7G 3000 scanner.

data_processing: The gene array data was analyzed with the Affymetrix GeneChip Command Console and raw .CEL files generated were analyzed using Expression Console software with Affymetrix default RMA Gene

label: biotin

source_name: Lox knockout ascending aorta embryonic day 17.5

label_protocol: Targets were labeled using Nugen Encore Biotin kit according to the standard NuGenOvationPico WTA System Amplification from 5ng of total RNA

growth_protocol: mice sacrified at specified developmental stages, tissue snap frozen in liquid nitrogen, mice genotype, like tissues pooled in groups of 8

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (Qiagen)

value: ascending aorta

tag: gene

value: Lox

value: KO

tag: devlopmental stage

value: B6 albino


title: Lox WT DA P1 rep2

source_name: Lox wildtype descending aorta postnatal day 1

value: descending aorta

value: WT


title: LoxWT AA P1 rep2

source_name: Lox wildtype ascending aorta postnatal day 1


title: Efemp2 KO DA E17.5 rep2

source_name: Efemp2 knockout descending aorta embryonic day 17.5


title: Lox WT AA E17.5 rep2

source_name: Lox wildtype ascending aorta embryonic day 17.5


title: Efemp2 KO AA E17.5 rep2

source_name: Efemp2 knockout ascending aorta embryonic day 17.5


title: Lox KO DA P1 rep1

source_name: Lox knockout descending aorta postnatal day 1


title: Lox WT DA E17.5 rep2

source_name: Lox wildtype descending aorta embryonic day 17.5


title: Lox KO AA E17.5 rep1


title: Lox KO AA P1 rep1

source_name: Lox knockout ascending aorta postnatal day 1


title: Lox WT AA P1 rep1


title: Lox WT DA P1 rep1


title: Efemp2 KO AA P1 rep1

source_name: Efemp2 knockout ascending aorta postnatal day 1


title: Lox KO AA P1 rep2


title: Lox WT AA E17.5 rep1


title: Lox KO DA E17.5 rep1

source_name: Lox knockout descending aorta embryonic day 17.5


title: Lox KO DA E17.5 rep2


title: Lox WT DA E17.5 rep1


title: Lox KO DA P1 rep2


title: NIH5_iPSC

description: 2x100 paired-end sequence reads

tag: cell type


title: Efemp2 KO AA P1 rep2


title: Efemp2 WT AA P1 rep1

source_name: Efemp2 wildtype ascending aorta postnatal day 1


title: Efemp2 KO DA P1 rep1

source_name: Efemp2 knockout descending aorta postnatal day 1


title: Efemp2 WT DA P1 rep2

source_name: Efemp2 wildtype descending aorta postnatal day 1


title: Efemp2 KO DA E17.5 rep1


title: Efemp2 KO AA E17.5 rep1


title: Efemp2 KO DA P1 rep2


title: Efemp2 WT DA E17.5 rep2

source_name: Efemp2 wildtype descending aorta embryonic day 17.5


title: Efemp2 WT DA P1 rep1


title: Efemp2 WT AA E17.5 rep1

source_name: Efemp2 wildtype ascending aorta embryonic day 17.5


title: Efemp2 WT DA E17.5 rep1


title: Eln KO DA P1 rep2

source_name: Eln knockout descending aorta postnatal day 1

value: Eln


title: Eln WT AA P1 rep1

source_name: Eln wildtype ascending aorta postnatal day 1


title: Eln WT DA E17.5 rep2

source_name: Eln wildtype descending aorta embryonic day 17.5


title: Eln KO AA E17.5 rep1

source_name: Eln knockout ascending aorta embryonic day 17.5


title: Efemp2 WT AA E17.5 rep2


title: Eln WT DA E17.5 rep1


title: Eln KO AA E17.5 rep2


title: Eln KO AA P1 rep1

source_name: Eln knockout ascending aorta postnatal day 1


title: Efemp2 WT AA P1 rep2


title: Eln KO DA E17.5 rep1

source_name: Eln knockout descending aorta embryonic day 17.5


title: Eln KO DA P1 rep1


title: Eln WT AA E17.5 rep1

source_name: Eln wildtype ascending aorta embryonic day 17.5


title: Eln WT AA P1 rep2


title: 2WND

city: Toronto

first: Li

last: Guo

address: 101 College Street

country: Canada

institute: University Health Network

description: Isolated AEC-II cells were cultured without doxcycline for 2 weeks

hyb_protocol: GeneChip® Fluidics Script FS450_0002

scan_protocol: Scanned on Affymetrix GeneChip Scanner 3000

data_processing: Mouse Gene 2.0 ST experiment and analysis were performed using the standard workflow (Expression Console) by Microarray Facility, The Centre for Applied Genomics, The Hospital for Sick Children

label_protocol: RNA was prepared using the Ambion WT Pico kit

growth_protocol: Cells were cultured at 5% CO2, 37°C

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen)

treatment_protocol: AEC-II cells were cultured for 2 weeks without Dox (2WND) prior to Dox-treatment (+D), and doxycycline was removed after 2 weeks.

value: Lung

tag: developmental stage

value: Adult


title: Eln WT DA P1 rep1

source_name: Eln wildtype descending aorta postnatal day 1


title: Eln WT AA E17.5 rep2


title: Eln KO DA E17.5 rep2


title: Eln KO AA P1 rep2


title: 2WND+2W+D+2W-D

description: Induced cells with subsequent 2-week culture in Dox-free media

source_name: cells were cultured for 2 weeks without Dox (2WND), followed by 2-week dox treatment (2WND+2W+D, AEC-II-iPL cells), AEC-II-iPL cells with subsequent 2-week culture in Dox-free media (2WND+2W+D+2w-D)


title: Day0

source_name: Day0 freshly isolated AEC-II cells


title: 2WND+2W+D

description: Cultured cells exposed to dox for 2 weeks

source_name: cells were cultured for 2 weeks without Dox (2WND), followed by 2-week dox treatment (2WND+2W+D, AEC-II-iPL cells)


title: iPS

source_name: iPS


title: Eln WT DA P1 rep2


title: SPT16HA6 rep1 tp0 Sonicated Input_reused

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

institute: UBC

description: sample is identical to GSM2985383

data_processing:
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 1000 bp were selected for using AWK
Coverage per million fragments was calculated and converted to wig file format
Genome_build: saccer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

source_name: Yeast

growth_protocol:
Yeast strains were arrested in G1 with alpha factor, treated with 400 μg/mL 1,10-phenanthroline monohydrate for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

extract_protocol:
Sonication ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in lysis buffer and sonicated to produce an average fragment size of 250 bp (30 seconds on / 30 seconds off for 15 mintues total sonication time in Diagenode Biorupter). Sonicated lysates were clarified by centrifugation at 9000g for 10 minutes, and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Sequencing libraries were prepared as described previously (Maltby et al. 2012; Martin et al. 2017). Briefly, 2 ng of ChIP or input material was end-repaired, A-tailed, and adapters ligated, before PCR amplification with indexed primers. We performed 10 and 11 rounds of PCR amplification for MNase and sonication ChIP-seq experiments, respectively. All DNA purification steps used SPRI (Solid Phase Reversible Immobilization) magnetic beads. Samples were pooled, gel-purified (50 bp - 600 bp region) and sequenced on an Illumina HiSeq 2500.

treatment_protocol: 1% formaldehyde crosslinking

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 SPT16-HA6::HIS3

tag: chip antibody

tag: growth stage


title: SPT16HA6 rep2 tp0 Sonicated Input_reused

description: sample is identical to GSM2985384


title: SPT16HA6 rep2 tp pt15 Sonicated Input_reused

description: sample is identical to GSM2985386


title: SPT16HA6 rep1 tp pt15 Sonicated Input_reused

description: sample is identical to GSM2985385


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep9

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Gene expression data from mouse colon with or without AOM+DSS induced colitis. Conducted in wildtype mice or in mice with conditional inactivation (directed by villin-CRE) of the insuin receptor gene (INSR) in the intestinal epithelium.

hyb_protocol: The labeled samples were hybridized to the Mouse Gene 2.0 ST GeneChip array according to the manufacture's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol. Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA, USA).

data_processing: The RMA algorithm was used for the gereration of quantile normalized expression measures

label: Biotin

source_name: Distal colon

label_protocol: RNA was amplified and labeled using the WT Plus Expression Kit (Affymetrix) according to manufactures instructions. 250 ng total RNA was used as input

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Ambion/Life Technologies, USA) following the manufacturer’s protocol.

treatment_protocol: Female  villin-CRE-INSR-/-mice and INSRfl/fl littermates were injected i.p. with 7.4 mg/kg AOM, followed by one cycle of 3% DSS on week 2 for 7 days. All mice were euthanized by cervical dislocation in week 5,  3 weeks after the end of the first DSS cycle.

value: Adult (18-24 weeks)

value: villin-CRE-INSR-/-

tag: treatment

value: AOM+DSS


title: SPT16HA6_pt15_rep1_Sonicated_Spt16_IP

description: Associated input is GSM3030628, a re-use of GSM2985385


title: Mouse colon untreated INSRfl/fl biological rep10

value: INSRfl/fl

value: Untreated


title: SPT16HA6_pt15_rep2_100u_Mnase_Input

extract_protocol:
MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with 100u microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Sequencing libraries were prepared as described previously (Maltby et al. 2012; Martin et al. 2017). Briefly, 2 ng of ChIP or input material was end-repaired, A-tailed, and adapters ligated, before PCR amplification with indexed primers. We performed 10 and 11 rounds of PCR amplification for MNase and sonication ChIP-seq experiments, respectively. All DNA purification steps used SPRI (Solid Phase Reversible Immobilization) magnetic beads. Samples were pooled, gel-purified (50 bp - 600 bp region) and sequenced on an Illumina HiSeq 2500.


title: SPT16HA6_tp0_rep1_Sonicated_Spt16_IP

description: Associated input is GSM3030626, a re-use of GSM2985383

growth_protocol:
Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD


title: SPT16HA6_pt15_rep1_100u_Mnase_Input


title: SPT16HA6_tp0_rep2_Sonicated_Spt16_IP

description: Associated input is GSM3030627, a re-use of GSM2985384


title: SPT16HA6_tp0_rep1_100u_Mnase_Input


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep9


title: SPT16HA6_tp0_rep2_100u_Mnase_Input


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep10


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep10


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep8


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep8


title: Mouse colon untreated villin-CRE-INSR-/- biological rep10


title: Mouse colon untreated INSRfl/fl biological rep9


title: Mouse colon untreated villin-CRE-INSR-/- biological rep8


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep8


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep7


title: Mouse colon untreated villin-CRE-INSR-/- biological rep9


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep8


title: Mouse colon untreated INSRfl/fl biological rep8


title: SPT16HA6_pt15_rep2_Sonicated_Spt16_IP

description: Associated input is GSM3030629, a re-use of GSM2985386


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep9


title: SPT16HA6_pt15_rep2_100u_Mnase_Spt16_IP


title: SPT16HA6_tp0_rep2_100u_Mnase_Spt16_IP


title: SPT16HA6_tp0_rep1_100u_Mnase_Spt16_IP


title: SPT16HA6 rep2 tp pt15 Sonicated Rpb3 IP

source_name: SPT16HA6 tp pt15 Sonicated Rpb3 IP

extract_protocol:
Sonication ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in lysis buffer and sonicated to produce an average fragment size of 250 bp (30 seconds on / 30 seconds off for 15 mintues total sonication time in Diagenode Biorupter). Sonicated lysates were clarified by centrifugation at 9000g for 10 minutes, and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Sequencing libraries were prepared as described previously (Maltby et al. 2012; Martin et al. 2017). Briefly, 2 ng of ChIP or input material was end-repaired, A-tailed, and adapters ligated, before 11 rounds of PCR amplification with indexed primers. All DNA purification steps used SPRI (Solid Phase Reversible Immobilization) magnetic beads. Samples were pooled, gel-purified (50 bp - 600 bp region) and sequenced on an Illumina HiSeq 2500.

value: Rpb3 (Biolegend 665004, clone EP1002Y)


title: SPT16HA6 rep2 tp0 Sonicated Input

source_name: SPT16HA6 tp0 Sonicated Input


title: SPT16HA6 rep1 tp0 Sonicated Input


title: SPT16HA6 rep1 tp pt15 Sonicated Input

source_name: SPT16HA6 tp pt15 Sonicated Input


title: SPT16HA6 rep2 tp pt15 Sonicated Input


title: SPT16HA6_pt15_rep1_100u_Mnase_Spt16_IP


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep7


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep7


title: Mouse colon untreated INSRfl/fl biological rep7


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep7


title: SPT16HA6 rep2 tp0 Sonicated Rpb3 IP

source_name: SPT16HA6 tp0 Sonicated Rpb3 IP


title: SPT16HA6 rep1 tp0 Sonicated Rpb3 IP


title: SPT16HA6 rep1 tp pt15 Sonicated Rpb3 IP


title: cbe1 rep2

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

data_processing:
Sequencing data was mapped with TopHat and genes with significantly altered expression were identified with CuffDiff
Genome_build: TAIR10
Supplementary_files_format_and_content: Normalized expression and differentially expressed genes between Col0 and cbe1 mutant (CuffDiff)

molecule: polyA RNA

source_name: seedling

growth_protocol: Seedlings were germinated and grown on 1% sucrose MS plates under long day (16 hour light, 8 hour night) conditions for 7 days, then harvested, flash frozen with liquid nitrogen, and homogenized

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen), then treated with DNAse I recombinant RNase-free (Roche) and purified using the RNeasy Mini Kit (Qiagen); poly(A) purification and library preparation performed by the Genome Sequencing and Analysis Facility at The University of Texas at Austin
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: seedling

value: cbe1 mutant

value: 7-day old


title: Col0 rep3


title: Mouse colon untreated villin-CRE-INSR-/- biological rep7


title: cbe1 rep3


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep6


title: cbe1 rep1


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep5


title: Mouse colon untreated INSRfl/fl biological rep6


title: Mouse colon untreated villin-CRE-INSR-/- biological rep6


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep6


title: Col0 rep2


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep6


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep5


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep6


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep5


title: Mouse colon untreated villin-CRE-INSR-/- biological rep5


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep4


title: Mouse colon untreated INSRfl/fl biological rep5


title: Col0 rep1


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep4


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep5


title: Mouse colon untreated villin-CRE-INSR-/- biological rep4


title: siGiver-48h+AngII-3h_2

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description:
siGiver_AngII_2
Gene expression data from rat vascular smooth muscle cells transfected with Giver siRNA and treated with AngII.

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.6.

organism: Rattus norvegicus

source_name: Rat vascular smooth muscle cells transfected with Giver siRNA and treated with AngII

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol.

growth_protocol: Rat vascular smooth muscle cells (RVSMCs) were isolated from thoracic aortas of male Sprague-Dawley rats by enzymatic digestion and cultured in M199 medium supplemented with 10% FBS and antibiotics.

extract_protocol: Total RNAs were isolated using RNeasy reagent (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were transfected with either non-targeting control siRNA (siNTC) or rat Giver siRNA for 48 hours, and then treated with either 100 nM of Angiotensin II or equivalent volume of 1x PBS for 3 hours.

tag: strain/background

value: Sprague-Dawley

tag: gender

value: male

value: vascular smooth muscle cell

tag: sirna

value: Giver

value: Angiotensin II


title: siGiver-48h+PBS-3h_1

description:
siGiver_PBS_1
Gene expression data from rat vascular smooth muscle cells transfected with Giver siRNA and treated with PBS.

source_name: Rat vascular smooth muscle cells transfected with Giver siRNA and treated with PBS

value: PBS


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep4

tag: strain

tag: age


title: siNTC-48h+PBS-3h_1

description:
siNTC_PBS_1
Gene expression data from rat vascular smooth muscle cells transfected with control siRNA and treated with PBS.

source_name: Rat vascular smooth muscle cells transfected with control siRNA and treated with PBS

value: non-targeting control


title: Mouse colon untreated INSRfl/fl biological rep4


title: siGiver-48h+AngII-3h_1

description:
siGiver_AngII_1
Gene expression data from rat vascular smooth muscle cells transfected with Giver siRNA and treated with AngII.


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep3


title: siNTC-48h+PBS-3h_2

description:
siNTC_PBS_2
Gene expression data from rat vascular smooth muscle cells transfected with control siRNA and treated with PBS.


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep3


title: siNTC-48h+AngII-3h_2

description:
siNTC_AngII_2
Gene expression data from rat vascular smooth muscle cells transfected with control siRNA and treated with AngII.

source_name: Rat vascular smooth muscle cells transfected with control siRNA and treated with AngII


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep4


title: siGiver-48h+PBS-3h_2

description:
siGiver_PBS_2
Gene expression data from rat vascular smooth muscle cells transfected with Giver siRNA and treated with PBS.


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep3


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep3


title: siNTC-48h+AngII-3h_1

description:
siNTC_AngII_1
Gene expression data from rat vascular smooth muscle cells transfected with control siRNA and treated with AngII.


title: Donor3_naive Tregs_activated

hyb_protocol: Samples were run on GeneChip® Human Gene 1.0 ST Array (Affymetrix Ltd).

scan_protocol: standard Affymetrix protocol

data_processing: Data processing of Affymetrix arrays was carried out using Partek Genome Studio. The data were RMA normalized (including background correction, quantile normalization, Log2 transformation and median polish probeset summarization).

source_name: naive Tregs_activated

label_protocol: Fragmentation and labelling was performed using the Encore Biotin Module (NuGEN Technologies); all kits were employed following manufacturer’s instructions.

extract_protocol: RNA was isolated using RNeasy mini kit (QIAGEN) and Ovation PicoSL WTA System V2 (NuGEN Technologies) was used for reverse transcription and cDNA amplification steps.

treatment_protocol: 200,000 naïve, memory and CD161+ Tregs were either sorted from fresh blood directly into Trizol LS (Ambion) for baseline genetic profile or cells were polyclonally activated post-sorting for 4h with Dynabeads Human T-Activator CD3/CD28 (ratio 1:1) and then lyzed in Trizol LS.

tag: subject status/id

value: Healthy Donor 3

tag: sorted cell type

value: Naïve Tregs

value: Activated


title: Donor2_CD161+ Tregs_activated

source_name: CD161+ Tregs_activated

value: Healthy Donor 2

value: CD161+ Tregs


title: Donor2_memory Tregs_activated

source_name: memory Tregs_activated

value: Memory Tregs


title: Donor2_naive Tregs_activated


title: Donor1_memory Tregs_activated

value: Healthy Donor 1


title: Donor3_memory Tregs_activated


title: Donor3_CD161+ Tregs_activated


title: Donor1_naive Tregs_activated


title: Donor3_CD161+ Tregs_fresh

source_name: CD161+ Tregs_fresh

value: none; fresh


title: Donor1_CD161+ Tregs_activated


title: Mouse colon untreated INSRfl/fl biological rep3

value: Adult (18-24 weeks)

tag: genotype

value: INSRfl/fl

value: Untreated


title: Donor3_memory Tregs_fresh

source_name: memory Tregs_fresh


title: Donor2_CD161+ Tregs_fresh


title: Donor2_memory Tregs_fresh


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep2

value: villin-CRE-INSR-/-

value: AOM+DSS


title: Donor3_naive Tregs_fresh

source_name: naive Tregs_fresh


title: Donor1_naive Tregs_fresh


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep2


title: Donor1_memory Tregs_fresh


title: Donor1_CD161+ Tregs_fresh


title: immV2WT#3

city: Worcester

first: Joonsoo

last: Kang

state: MA

address: 368 Plantation St.

department: Pathology

institute: University of Massachusetts Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Thymus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 2 Weeks Old

tag: exclusion markers

value: CD4- CD8-

tag: phenotype markers

value: TCRd+ Vg2+ HSAhi

tag: separation method

value: FACSAria

tag: Sex

value: Mixed


title: immV2Sox4cKO#4


title: Donor2_naive Tregs_fresh

value: Naïve Tregs


title: DP.WT#5

value: CD4+ CD8+


title: immV2Sox4cKO#3


title: DP.Sox4cKO#5


title: Mouse colon untreated villin-CRE-INSR-/- biological rep3

source_name: Distal colon


title: Mouse colon untreated INSRfl/fl biological rep2


title: immV2WT#5


title: DP.Sox4cKO#4


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep2


title: DP.Sox4cKO#3


title: Mouse colon Tumor DSS AOM colitis villin-CRE-INSR-/- biological rep1


title: Mouse colon Tumor DSS AOM colitis INSRfl/fl biological rep1


title: Mouse colon DSS AOM colitis INSRfl/fl biological rep1


title: V2imm.KO#5


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep2


title: V2imm.WT#5


title: DP.WT#3


title: V2imm.KO#4


title: V2imm.WT#4


title: Mouse colon DSS AOM colitis villin-CRE-INSR-/- biological rep1


title: pooled_SMMC-7721_Input DNA

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human/mouse genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1e-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: Hepatocellular carcinoma

growth_protocol: U2932 and SMMC-7721 cells were grown in RPMI 1640 + 10%FBS at 37°C and 5% CO2. Pfeiffer cells were cultured in RPMI 1640 + 15%FBS at 37°C and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: U2932, Pfeiffer and SMMC-7721 were treated with 1 μM EPZ-6438 or DMSO for 6 days.

tag: cell strain


title: Mouse colon untreated villin-CRE-INSR-/- biological rep1


title: Mouse colon untreated INSRfl/fl biological rep1


title: EphB6_male KO Cc 3

city: Montreal

last: Shi

state: Quebec

address: 1855 Boulevard René-Lévesque O, 303

institute: University of Montreal

description: gene expression in adrenal gland

hyb_protocol: The labeled cRNA was normalized at 1,500 ng and hybridized on MouseWG-6_V2 array according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide. The BeadChips were incubated in an Illumina Hybridization oven at 58°C for 16 hours at a standard rocking speed of 5 according to the oven speedometer.

scan_protocol: Beadchips were washed according to Illumina’s protocol mentioned previously and scanned on an Illumina iScan Reader.

data_processing: The data were normalised using cubic spline normalisation with Illumina GenomeStudio

source_name: Adrenal gland

label_protocol: Biotinylated cRNA were prepared with Illumina® TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted using RNeasy Mini Kit from adrenal glands of male, female and castrated male Ephb6 KO mice and their WT counterparts. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: EphB6 KO

value: 2 months

value: Adrenal gland


title: EphB6_female WT Cc 3

description: gene expression in adrenal gland

value: EphB6 WT


title: EphB6_male WT Cc 3

description: gene expression in adrenal gland


title: EphB6_female KO Cc 3

description: gene expression in adrenal gland


title: Mouse colon untreated villin-CRE-INSR-/- biological rep2


title: EphB6_male WT Cc 1

description: gene expression in adrenal gland


title: EphB6_female KO Cc 2

description: gene expression in adrenal gland


title: EphB6_castrated WT Cc 3

description: gene expression in adrenal gland

value: EphB6_castrated WT


title: #66 bone marrow macrophage_RFP_positive

description: Gene expression RFP positive bone marrow macropahge from WT mouse

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: #66 bone marrow macrophage_RFP_positive

label_protocol: Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).

extract_protocol: RNA  was isolated with an RNeasy micro kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: bone marrow cells was collected from mouse and RFP-positive or negative macropahges were sorted by fow cytometer.

value: male


title: EphB6_male KO Cc 2

description: gene expression in adrenal gland


title: EphB6_female KO Cc 1

description: gene expression in adrenal gland


title: pooled_Pfeiffer_Input DNA

city: Shanghai

last: Yan

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

source_name: Diffuse large B-cell lymphoma

value: Pfeiffer

tag: chip antibody


title: EphB6_male KO Cc 1

description: gene expression in adrenal gland


title: PolII ChIP-seq

city: Houston

first: Kelvin

last: Yeung

state: TX

address: One Baylor Plaza, Room S242

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were mapped to the Drosophila reference genome dm3 using Burrows-Wheeler Aligner (BWA-MEM) in Unipro UGENE (v1.29.0) software using default parameters.
The aligned reads were then used for peak-calling by Model-based Analysis of ChIP-seq with default settings (MACS v1.4.2).
Genome_build: Drosophila reference genome dm3 (Release 5)
Supplementary_files_format_and_content: *.wig

organism: Drosophila melanogaster

source_name: L3 eye antennal discs

growth_protocol: Flies were raised at 25°C and late L3 larvae were collected for dissection.

extract_protocol:
400 Canton S third instar larval eye-antenna discs were dissected and crosslinked with 1% formaldehyde for 15 min and quenched by 125 mM Glycine for 5 min at room temperature. After washing with PBS, discs were lysed in lysis buffer (50 mM K-Hepes pH 7.8, 140 mM NaCl, 1 mM EGTA, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors) and sonicated with a Branson sonifier to shear chromatin to ~200 - 400 bp.  The chromatin lysate was precleared with protein A sepharose (GE healthcare, #17-5280-01) and incubated with antibody at 4°C overnight. Protein A sepharose was added to the lysate for 3 hours to capture chromatin complexes. After three washes with lysis buffer, once with high salt wash buffer (50 mM K-Hepes pH 7.8, 500 mM NaCl, 1 mM EGTA, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors) and once with TE (10 mM Tris pH8.0, 1 mm EDTA), chromatin complexes were eluted with 1% SDS, 10 mM Tris pH 8.0, and 1 mM EDTA at 65°C for 10 min, followed by reverse-crosslinking at 65°C overnight.
ChIP samples were purified using Qiagen PCR purification kit and sequenced based on the manufacturer’s instructions (Illumina, San Diego, CA).

tag: developmental stage

value: Late L3

value: eye antennal discs

value: Canton S

tag: antibody

value: anti-PolII antibody


title: #58 bone marrow macrophage_RFP_positive

city: Sendai

last: Igarashi

address: Seiryo 2-1

institute: Tohoku University

source_name: #58 bone marrow macrophage_RFP_positive


title: H3K27Ac ChIP-seq

tag: tissue

value: anti-H3K27Ac antibody


title: pooled_U2932_Input DNA


title: EphB6_male WT Cc 2

description: gene expression in adrenal gland


title: EphB6_female WT Cc 2

description: gene expression in adrenal gland


title: #63 bone marrow macrophage_RFP_positive

source_name: #63 bone marrow macrophage_RFP_positive

tag: gender


title: H3K18Ac ChIP-seq

value: anti-H3K18Ac antibody


title: SMMC-7721_H3K27ac_ChIPSeq_EPZ-6438


title: EphB6_castrated WT Cc 1

description: gene expression in adrenal gland


title: SMMC-7721_H3K27ac_ChIPSeq_DMSO


title: EphB6_female WT Cc 1

description: gene expression in adrenal gland


title: EphB6_castrated KO Cc 3

description: gene expression in adrenal gland

value: EphB6_castrated KO


title: EphB6_castrated WT Cc 2

description: gene expression in adrenal gland


title: #66 bone marrow macrophage_RFP_negative

description: Gene expression RFP negative bone marrow macropahge from WT mouse

source_name: #66 bone marrow macrophage_RFP_negative


title: EphB6_castrated KO Cc 1

description: gene expression in adrenal gland


title: #58 bone marrow macrophage_RFP_negative

source_name: #58 bone marrow macrophage_RFP_negative


title: Pfeiffer_H3K27ac_ChIPSeq_EPZ-6438


title: H3K4me1 ChIP-seq

value: anti-H3K4me1 antibody


title: U2932_H3K27ac_ChIPSeq_EPZ-6438


title: U2932_H3K27ac_ChIPSeq_DMSO


title: EphB6_castrated KO Cc 2

description: gene expression in adrenal gland


title: #63 bone marrow macrophage_RFP_negative

source_name: #63 bone marrow macrophage_RFP_negative


title: GFP2 [iCLIP-seq]

data_processing:
iCLIP data was processed following the iCount pipeline (Curk et al., 2016; https://github.com/tomazc/iCount). Briefly, 'iCount demultiplex' was used to separate and trim off molecular and sample barcodes as well as adapter sequences. The reads were then mapped to the human genome (GRCh38) using the STAR aligner (Dobin et al., 2013) (Curk et al., 2016). 'iCount xlsites' was used to determine the number of unique crosslinked sites (unique cDNA molecules) for any given position.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab separated text file. Contains peak coordinates.

source_name: HeLa cells

extract_protocol:
SDOS-eGFP cells were photoactivable ribonucleoside-cross-linked on ice at and 0.30 J cm−2 with UV light at 365 nM. eGFP cells were cross-linked on ice at 0.15 J cm−2 with UV light at 254 nM. Immediately after irradiation, cells were lysed in 1 mL of lysis buffer (NaCl 100mM, MgCl2 5mM, Tris pH 7.5 10mM, NP40 0.5%, SDS 0.1%, Na deoxycholate 0.5%, DTT 1mM (fresh), 1x AEBSF (fresh). The cell lysate was passed 3 times through 27 1/2G needle and sonicated using a bioruptor (Digenode) for 3 cycles of 10 seconds (pause 15 seconds), level M at 4ºC, then it was cleared by centrifugation at 17900g for 10 min at 4°C.
RNA was then partially digested by adding 10 μl of 1:100 dilution of RNase I (Ambion, AM2295), as well as 2 μl of Turbo DNase (Ambion, AM 2238). After 3 min of incubation at 37°C under shaking at 1100 rpm 11 μl of Ribolock (Invitrogen) were added to each lysate. The lysates were precleared by incubation with 50 µL of equilibrated control agarose beads (Thermo Scientific) for 30 min at 4°C under gentle rotation. eGFP-fusion proteins were then captured from precleared lysates by incubation with 40 µL of GFP-Trap agarose beads (GFP-Trap_A, Chromotek) per mL of lysate for 2 h, 4°C, gentle rotation. Beads were collected by centrifugation and washed twice with High salt buffer (NaCl 500mM, Tris HCL pH7.5 20mM, MgCl2 1mM, NP40 0.05%, SDS 0.10%, 1x AEBSF (fresh)); twice with Medium salt buffer (NaCl 250mM, Tris HCl pH7.5 20mM, MgCl2 1mM, NP40 0.05%, 1x AEBSF (fresh)) and twice with Low salt buffer (NaCl 150mM, Tris HCl pH7.5 20mM, MgCl2 1mM, NP40 0.01%, 1x AEBSF (fresh)). The RNA was then dephosphorylated, and 3’-linker ligated as described in [16]. The protein/RNA complexes were isolated as described in [17]. Samples were processed for subsequent steps as described in Huppertz et al 2014. cDNA libraries obtained after PCR amplification with universal Solexa primers (25 cycles) were multiplexed and sequenced using an Illumina Next-generation sequencing platform.

treatment_protocol: Cells were treated with doxycycline (1 ug/mL) for 16 hrs to induce the expression of GFP-fusion proteins. HeLa SDOS-eGFP cells were treated with 100 μM 4-thiouridine for 16 hrs before the lysis.

tag: cell type

value: T-REx-HeLa Cell Line

value: eGFP under Tet repressor


title: SDOS2 [iCLIP-seq]

value: SDOS-eGFP under Tet repressor


title: SDOS3 [iCLIP-seq]


title: SDOS1 [iCLIP-seq]


title: GFP1 [iCLIP-seq]


title: iper TRAP rep2

description: replicate 2

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol using HiScan system

data_processing: The data were normalised using neqc() quantile normalisation with limma in R

label_protocol: Standard Illumina label protocol

growth_protocol: HeLa cells were grown on 10-cm dishes until were approximately 85% confluent

extract_protocol: Total RNA from HeLa cells was extracted using a standard acid guanidinium thiocyanate-phenol-chloroform extraction protocol

tag: protocol

value: iperTRAP

tag: cell line

value: T-REx™-HeLa Cell Line


title: sh TRAP rep3

description: replicate 3

value: shTRAP


title: iper SDOS rep2

description: replicate 2

value: iperSDOS


title: iper SDOS rep3

description: replicate 3


title: sh TRAP rep1

description: replicate 1


title: O

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

data_processing:
Fastq files were mapped using kallisto 0.43.1. kallisto quant -i ../transcripts.idx -o output --bias LD3047-name_L006_R1_001.fastq.gz LD3047-name_L006_R2_001.fastq.gz
Gene counts were tabulated using tximport.
Deconvolution was performed using Xcell v1.1 (xcell.ucsf.edu) or Cibersort using LM22 gene signature and 100 permutations (cibersort.stanford.edu).
Genome_build: GRCh38
Supplementary_files_format_and_content: "h5" is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length (can be read in by sleuth); "tsv" is a plaintext file of the abundance estimates without bootstrap estimates; "json" is a json file containing information about the run.

source_name: Bone marrow

growth_protocol: Human bone marrow aspirate

extract_protocol:
QIAGEN AllPrep Kit
Illumina TruSeq Stranded Total RNA Kit

treatment_protocol: Ficoll density gradient separation

value: Bone marrow

tag: age

value: mononuclear cells


title: U


title: T


title: iper SDOS rep1

description: replicate 1


title: sh SDOS rep1

description: replicate 1

value: shSDOS


title: sh SDOS rep3

description: replicate 3


title: iper GFP rep3

description: replicate 3

value: iperGFP


title: C


title: iper GFP rep1

description: replicate 1


title: J


title: H


title: sh SDOS rep2

description: replicate 2


title: C11: control

city: Norman

first: Carol

last: Webb

state: Oklahoma

address: Stephenson Parkway

department: Department of Medicine

institute: OUHSC

data_processing:
Created Bowtie index using the GrCh37 assembly of the human genome
Estimated abundances with RSEM using default parameters

source_name: PBMCs

extract_protocol:
MagMax Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Control

value: neutrophil

tag: sledai


title: C10: control


title: sh TRAP rep2

description: replicate 2


title: iper GFP rep2

description: replicate 2


title: C7: control


title: Pfeiffer_H3K27ac_ChIPSeq_DMSO

first: Juan

value: Pfeiffer


title: iper TRAP rep3

description: replicate 3


title: sh GFP rep2

description: replicate 2

value: shGFP


title: C6: control


title: C3: control

value: pDCs


title: B


title: iper TRAP rep1

description: replicate 1


title: SLE9: ARID3aHigh

value: System lupus erythematosus (SLE)


title: sh GFP rep1

description: replicate 1


title: A


title: sh GFP rep3

description: replicate 3


title: SLE25: ARID3aHigh


title: Healthy donor 3 [BA_3]

data_processing:
10x genomics cell ranger was used for initial analysis
Surat was used for data clustering and expression analysis

source_name: healthy donor_CD4+CD25+ T cells

extract_protocol:
Cells were captured for each sample and libraries were sequenced on the Illumina Hiseq 3000 instrument.
The experiment was performed using the 10X Genomics’ Chromium Single Cell 3’ gene expression V2 kit following the manufacturer’s instruction.  I1: Index, R1: 16 bp cell barcode + 10 bp UMI,  R2: Transcript

tag: subject status

value: Healthy Donor

value: blood

value: CD4+CD25+ T cells


title: Healthy donor 1 [BA_1]


title: Healthy donor 2 [BA_2]


title: SLE24: ARID3aHigh


title: SLE22: ARID3aHigh


title: SLE20: ARID3aNormal


title: SLE18: ARID3aNormal


title: SLE12: ARID3aNormal


title: C9: control


title: SLE17: ARID3aNormal


title: SLE11: ARID3aHigh


title: SLE10: ARID3aNormal


title: SLE6: ARID3aHigh


title: SLE5: ARID3aHigh


title: SLE4: ARID3aNormal


title: SLE7: ARID3aHigh


title: SLE3: ARID3aNormal


title: SLE1: ARID3aHigh


title: SLE23: ARID3aHigh


title: SLE14: ARID3aNormal


title: d10-m4533-plate13

city: New York

first: Efthymia

last: Papalexi

state: NY

address: 101 avenue of americas

institute: New York Genome Center

description:
RNA1_counts.csv
modified Smart seq2 library

data_processing:
Modified Smart Seq 2 data were processed using Drop-seq tools v1.12 (Macosko et al., 2015)
R1 reads: cell barcode, UMI read
R2 reads: cDNA read
Genome_build: Mus_musculus.GRCm38.84
Supplementary_files_format_and_content: comma separated values files for modified Smart-Seq 2 data
Supplementary_files_format_and_content: RNA1_counts.csv: raw counts for samples 1-9
Supplementary_files_format_and_content: RNA2_counts.csv: raw counts for samples 10-14

source_name: Lin- Tom+ mouse cells

extract_protocol:
We used a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript. Detailed protocol can be found here: dx.doi.org/10.17504/protocols.io.nkgdctw
Lin-  Tom+ single cells were sorted into 96well plates and a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript was used. Protocol can be found here dx.doi.org/10.17504/protocols.io.nkgdctw

value: Lin- Tom+  cells


title: d17_m606-plate4

description:
RNA2_counts.csv
modified Smart seq2 library


title: d17-m4528-plate8


title: d10-m4533-plate15


title: d17_m606-plate5


title: d17-m4528-plate7


title: d10-m4533-plate14


title: d17-m605-plate2


title: d17-m4528-plate9


title: d17-m605-606-plate3


title: d17-m605-plate1


title: d17-m4528-plate6


title: Non-lesional_Skin substitute_M49

city: Québec

first: Roxane

last: Pouliot

state: Québec

address: 1401, 18ème rue, aile R

institute: Centre de recherche en organogenese expérimentale de l'Université Laval/LOEX

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Psoriatic skin substitute

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50-200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Fibroblasts were cultured in Dulbecco-Vogt modification of Eagle's medium (DMEM) supplemented with 10% bovine growth serum, 100UI/mL penicillin and 25μg/mL gentamicin. Keratinocytes were cultured in a combination of DMEM with Ham's F12 (3:1), supplemented with 5% Fetal Clone II serum, 5μg/mL insulin, 0.4μg/mL hydrocortisone, 1e-10M cholera toxin, 10ng/mL human epidermal growth factors, 100UI/mL penicillin and 25 μg/mL gentamicin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104).

treatment_protocol: Biopsies of skin substitute were taken after 21 days of culture at the air-liquid interface.

tag: condition

value: Non-lesional

value: Male


title: Lesional_Skin substitute_F47

value: Lesional

value: Female


title: Non-lesional_Skin substitute_F47


title: Healthy_Skin substitute_F23

source_name: Healthy skin substitute

value: Healthy


title: Lesional_Skin substitute_M49