title: H2AK119UB ChipSeq from 2473 necrotic region

city: Cleveland

first: Briana

last: Prager

address: 9500 Euclid Ave.

institute: Cleveland Clinic

data_processing:
Adapters and low-quality reads were trimmed using Trim Galore
Sequences were aligned using Bowtie2
Duplicates were removed using Picard
Peaks were called using MACS2
Genome_build: HG19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: necrotic region of CW2473 glioblastoma specimen

value: CD15-positive glioma stem cells (GSCs)

value: H2AK119Ub (10 mg, Cell signaling, #8240S)


title: 197.WT_1mM-NAC_6G_6h

status: Public on Oct 01 2017

type: SRA

city: los angeles

first: Prabhat

middle: Kumar

last: Purbey

state: California

address: 675 Charles E. Young Drive South

department: MIMG

country: USA

institute: UCLA

description: samples1-5 are no treatment control for this set

library_source: transcriptomic

data_processing:
RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
All aligned reads were imported to SeqMonk. The mRNA expression was calculated by totaling all uniquely aligned exonic reads. The raw reads were converted to RPKM by dividing the reads by the cDNA length and the total number of uniquely mapped reads in the sample.
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

molecule: total RNA

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to stimulation.

extract_protocol:
total RNA was biochemically purified as previously described (Bhatt et al, Cell 2012). Cells were resuspended in TriReagent and RNAs were purified using Rneasy columns (Qiagen).
All mRNA libraries were generated using the Illumina Truseq v.2 kit with a few modifications: strand specific libraries were generated using the dUTP method. Briefly, the second strand cDNA was synthesized in the presence of dUTP. Prior to library amplification, the second strand was degraded with dUTPase. Few libraries were genearted using TruSeq Stranded mRNA Library Prep  Kit as per manufacturere's instructions.

tag: tissue

value: bone marrow

tag: cell type

value: macrophage

tag: strain

tag: genotype

value: wildtype

tag: stimulus

value: 1mM NAC + Ionizing Radiation

tag: time point (h)


title: 198.WT_100uM-NAC_6G_0.5h

value: 100uM NAC + Ionizing Radiation


title: H3K27Me3_ChipSeq from 2473 necrotic region

state: OH

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: chip antibody

value: H3K27Me3 (5 mg; Active Motif, 39155)


title: 200.WT_100uM-NAC_6G_2h


title: 195.WT_1mM-NAC_6G_1h


title: input DNA from 2473 necrotic region


title: 196.WT_1mM-NAC_6G_2h


title: 207.WT(p53)_rep1_24h

value: 6Gray Ionizing Radiation


title: 194.WT_1mM-NAC_6G_0.5h


title: 193.WT_1mM-NAC_cont

value: 1mM NAC + No-Radiation


title: H2AK119UB ChipSeq from 2473 enhancing region

value: enhancing region of CW2473 glioblastoma specimen


title: 189.ERKi&P38i-1h_rep2

value: Erki&p38i + No-Radiation


title: 192.ERKi&P38i_6G_2h_rep2

value: Erki&p38i+ Ionizing Radiation


title: input DNA from 2473 enhancing region


title: H3K27Me3_ChipSeq from 2473 enhancing region


title: 190.ERKi&P38i_6G_0.5h_rep2


title: 188.P38i_6G_2h_rep2

value: p38i + Ionizing Radiation


title: 187.P38i_6G_1h_rep2


title: H2AK119UB ChipSeq from 2451 necrotic region

value: necrotic region of CW2451 glioblastoma specimen


title: 186.P38i_6G_0.5h_rep2


title: H3K27Me3_ChipSeq from 2451 necrotic region


title: input DNA from 2451 necrotic region


title: 181.ERKi-1h_rep2

value: Erki + No-Radiation


title: 182.ERKi_6G_0.5h_rep2

value: Erki + Ionizing Radiation


title: H2AK119UB ChipSeq from 2451 enhancing region

value: enhancing region of CW2451 glioblastoma specimen

value: CD15-positive glioma stem cells (GSCs)


title: 180.DMSO_6G_2h_rep2

value: bone marrow

value: DMSO + Ionizing Radiation


title: 178.DMSO_6G_0.5h_rep2

value: macrophage

value: wildtype


title: 176.ERKi&P38i_6G_2h_rep1


title: input DNA from 2451 enhancing region


title: H3K27Me3_ChipSeq from 2451 enhancing region


title: 179.DMSO_6G_1h_rep2


title: 191.ERKi&P38i_6G_1h_rep2


title: 173.ERKi&P38i-1h_rep1


title: 177.DMSO-1h_rep2

value: DMSO + No-Radiation


title: 175.ERKi&P38i_6G_1h_rep1


title: AIMP2OE3

city: STANFORD

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford University

description:
Sample name: RHH1420
AIMP2 overexpression replicate 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.4.2a.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include the coverage, edited reads and editing level for each site.

source_name: HEK293, AIMP2 overexpression

extract_protocol:
Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA-seq libraries were prepared as described by Zhang et al. (doi:10.1038/nmeth.2736).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: genotype/variation

value: AIMP2 overexpression


title: 174.ERKi&P38i_6G_0.5h_rep1


title: WT5

description:
Sample name: RHH1413
Wild type replicate 5

source_name: HEK293, wild type

value: wild type


title: 170.P38i_6G_0.5h_rep1


title: 171.P38i_6G_1h_rep1


title: 185.P38i-1h_rep2

value: p38i + No-Radiation


title: 183.ERKi_6G_1h_rep2


title: 169.P38i-1h_rep1


title: 184.ERKi_6G_2h_rep2


title: 172.P38i_6G_2h_rep1


title: 168.ERKi_6G_2h_rep1


title: 166.ERKi_6G_0.5h_rep1


title: 165.ERKi-1h_rep1


title: 164.DMSO_6G_2h_rep1


title: 163.DMSO_6G_1h_rep1


title: AIMP2OE1

description:
Sample name: RHH1411
AIMP2 overexpression replicate 1


title: WT6

description:
Sample name: RHH1419
Wild type replicate 6


title: ADAR1OE4

description:
Sample name: RHH1399
ADAR1 overexpression replicate 4

source_name: HEK293, ADAR1 overexpression

value: ADAR1 overexpression


title: 162.DMSO_6G_0.5h_rep1


title: 161.DMSO-1h_rep1


title: ADAR2OE4

description:
Sample name: RHH1400
ADAR2 overexpression replicate 4

source_name: HEK293, ADAR2 overexpression

value: ADAR2 overexpression


title: ADAR2OE3

description:
Sample name: RHH1398
ADAR2 overexpression replicate 3


title: ADAR1OE3

description:
Sample name: RHH1397
ADAR1 overexpression replicate 3


title: AIMP2OE2

description:
Sample name: RHH1412
AIMP2 overexpression replicate 2


title: ADAR2OE2

description:
Sample name: RHH1396
ADAR2 overexpression replicate 2


title: SSUV16

city: New York

first: Hong

last: Sun

state: NY

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

data_processing:
Raw sequence data (Fastq) were loaded into Biomedical Genomics Workbench Version 3.5.3 (Qiagen) for data analysis.
The raw Fastq files were trimmed to remove any remaining adaptors and ambiguous nucleotides.
The trimmed sequence files were aligned to human genome (Hg38) allowing two mismatches.
Reads mapped to the exons of a gene were summed at the gene level. Gene expression levels were quantified as total read per million (TPM).
Differential gene expression was analyzed using Advance RNA-seq plug-in tool (Qiagen) by comparing each treated group versus corresponding control group. TMM (trimmed mean of M values) normalization was performed to adjust library sizes before differential expression analysis.
Genome_build: Hg38
Supplementary_files_format_and_content: TPM

source_name: HaCaT cells

growth_protocol: Human Keratinocyte HaCaT cells were culturedin DMEM medium (4.5 g/L glucose) containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37℃ and 5% CO2.

extract_protocol:
Total RNA was extracted from sham and ssUVR-exposed cells using the Trizol reagent (Life Technologies, Gaithersburg, MD).
RNA-Seq libraries were prepared using Illumina TruSeq RNA-sample preparation kit according to the manufacture’s instruction.

treatment_protocol: Cells were treated with various doses of solar simulated ultra violet

value: immortalized human keratinocytes

tag: treatment

value: ssUVR, 12 J/cm2

tag: ssuvr treatment

value: 5 repetitve, recovery


title: SSUV14

value: sham


title: SSUV15


title: ADAR1OE2

description:
Sample name: RHH1395
ADAR1 overexpression replicate 2


title: SSUV13


title: 154.WT(Irf1)_rep2_24h

value: 6Gray Ionizing Radiation


title: 157.IRF1_rep2_1h


title: 155.IRF1_rep2_0

value: No-radiation


title: 156.IRF1_rep2_0.5h


title: 158.IRF1_rep2_2h


title: 159.IRF1_rep2_6h


title: ADAR2OE1

description:
Sample name: RHH1394
ADAR2 overexpression replicate 1


title: 167.ERKi_6G_1h_rep1

value: Erki + Ionizing Radiation


title: 153.WT(Irf1)_rep2_6h

value: bone marrow


title: 152.WT(Irf1)_rep2_2h


title: 151.WT(Irf1)_rep2_1h


title: 160.IRF1_rep2_24h


title: ADAR1OE1

description:
Sample name: RHH1393
ADAR1 overexpression replicate 1


title: SSUV11

value: 5 repetitve


title: SSUV10

value: ssUVR, 6 J/cm2


title: 148.IRF1_rep1_24h

value: macrophage


title: 149.WT(Irf1)_rep2_0

value: wildtype


title: WT4

description:
Sample name: RHH1392
Wild type replicate 4


title: WT3

description:
Sample name: RHH1391
Wild type replicate 3


title: 150.WT(Irf1)_rep2_0.5h


title: 146.IRF1_rep1_2h


title: 147.IRF1_rep1_6h


title: SSUV9


title: WT1

description:
Sample name: RHH1389
Wild type replicate 1


title: WT2

description:
Sample name: RHH1390
Wild type replicate 2


title: SSUV6


title: SSUV8

value: ssUVR, 3 J/cm2


title: 144.IRF1_rep1_0.5h


title: 143.IRF1_rep1_0


title: 140.WT(Irf1)_rep1_2h


title: 142.WT(Irf1)_rep1_24h


title: 145.IRF1_rep1_1h


title: SSUV12


title: 139.WT(Irf1)_rep1_1h


title: SSUV7


title: 141.WT(Irf1)_rep1_6h


title: Input DNA

city: La Jolla

first: George

last: Sen

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

data_processing:
Bowtie was used to align the raw reads to hg19 and MACs was used for peak calling.
The peaks and their associated statistics were generated in Partek Genomics Suite.
Genome_build: hg19
Supplementary_files_format_and_content: xls file containing processed data. Data includes SMC1 peak regions and associated statistics

source_name: Human epidermal keratinocytes

growth_protocol: Primary human epidermal keratinocytes (neonatal) were grown two-dimensionally in subconfluent conditions in the absence of Calcium. Life technologies Keratinocyte SFM medium was used.

extract_protocol:
DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
Library prep and sequencing was carried out by The Scripps Research Institute Next Generation Sequencing Core (https://scripps.edu/california/research/ngs/index.html)

treatment_protocol: 10 million cells were crosslinked with formaldehyde and used in the experiment. The ChIP experiment was done using the Myers Lab ChIP-seq protocol

value: Primary human epidermal keratinocytes

value: Neonatal foreskin


title: 138.WT(Irf1)_rep1_0.5h


title: SMC1A ChIP

value: Bethyl rabbit anti-SMC1 (A300-055A)


title: SSUV5


title: 137.WT(Irf1)_rep1_0


title: SSUV4

value: single


title: 135.IRF3_rep2_0

description: sample 83 is the WT_0_control for this exp


title: 131.WT(irf3)_rep1_0


title: DLD1-exosome-3

city: Nashville

first: Yongchao

last: Dou

state: Tennessee

address: 2525 west end

institute: vanderbilt medical center

data_processing:
Illumina software used for basecalling.
reads were mapped and annotaed by tophat2
edgeR was used to do the differential analysis
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and followings are reads counts

source_name: cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% bovine growth serum until 80% confluent.

extract_protocol:
Exosomes were isolated from conditioned medium of DKO-1, Dks-8, and DLD-1 cells as previously described, with slight modification(Higginbotham et al. 2011). Pooled media as descripted above was centrifuged for 10 min at 300 X g to remove cellular debris, and the resulting supernatant was then filtered through a 0.22-m polyethersulfone filter (Nalgene, Rochester, NY) to reduce microparticle contamination.  The filtrate was concentrated ~300-fold with a 100,000 molecular-weight cutoff centrifugal concentrator (Millipore).  The concentrate was then subjected to high-speed centrifugation at 150,000 X g for 2 hr.  The resulting exosome-enriched pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2) and washed by centrifuging again at 150,000 X g for 3 hr.  The wash steps were repeated a minimum of 3 times until no trace of phenol-red was detected.  The resulting pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2) and protein concentrations were determined with a MicroBCA kit (Pierce).  The number of exosomes per g of protein was determined by means of nanoparticle tracking analysis (NanoSight, Wiltshire, UK).  Analysis was performed on three independent preparations of exosomes.
Total RNA containing both long RNA as well as miRNA fractions was extracted from exosomes or cell lines using Trizol followed by miRNeasy Kit purification according to manufacturer's protocol. Final elution was made in 60µl RNase free sterile distilled water. The concentration and integrity of the extracted total RNA was estimated by Qubit® 2.0 Fluorometer (Invitrogen, Carlsbad, California), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively.  RNA samples with a RIN value of at least 7.0 or higher was used for further processing. Approximately five hundred ng of total RNA was required for proceeding to downstream RNA-seq applications. Briefly, Ribo-zero Magnetic Gold rRNA removal kit (Epicenter, IIlumina Inc.) was used to remove the ribosomal RNA from the total RNA. Next, the first strand synthesis was performed using NEBNext RNA first strand synthesis module (New England BioLabs Inc., Ipswich, MA, USA). Immediately, Directional second strand synthesis was done using NEBNExt Ultra Directional second strand synthesis kit using manufacturer's recommended protocol. Following this the cDNA was then taken into into a standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house genomics service lab (GSL) primers. Library quality was assessed by Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on these samples. Raw reads were de-multiplexed using a bcl2fastq conversion software v1.8.3 (Illumina, Inc.) with default settings.

treatment_protocol: To collect exosomes, these cells were then washed 3 times with PBS and cultured for 24 hr in serum-free medium. The medium was collected and replaced with ionomycin-containing media for 1 hr, after which ionomycin-containing media was collected and pooled with the previously collected serum-free medium.

tag: sample type

value: exosomes


title: DLD1-exosome-2


title: SSUV2

value: immortalized human keratinocytes


title: 136.IRF3_rep1_6G_24h

description: sample 88 is the WT_6G_24h  for this exp


title: SSUV3

value: ssUVR, 12 J/cm2


title: 134.IRF3_rep1_0


title: 129.SCID_rep2_6h

value: Scid


title: DLD1-exosome-1


title: DLD1-cell-2

value: cell


title: DLD1-cell-1


title: SSUV1

value: sham


title: Human_Epithelial_A549_IL1B_2

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Human sequencing data was aligned against human reference genome hg38 using Tophat2: tophat --library-type fr-firststrand <reference_genome.gtf> -1 <forward_strand.fa> -2 <reverse_strand.fa> -o <output.sam>. Mouse sequencing data was aligned against mm10 using Hisat2: hisat2 -q --dta --rna-strandness FR –x <reference_genone.gtf> -1 <forward_strand.fa> -2 <reverse-strand file.fa> –S <output.sam>.
Output SAM files were then sorted and converted to BAM files (samtools sort -@ 8 –o output.bam output.sam) and indexed (samtools index –b output.bam) in Samtools
Differential expression of protein coding genes and lncRNAs in human macrophages and epithelium (Gencode v23 - human macrophages and epithelium.txt) and mouse RAW cells (Gencode m12 - mouse macrophages.txt) was assessed with the geometric option (DESeq) in Cuffdiff v2.2.1.3 using a significance threshold of q <0.05: cuffdiff --FDR=0.05 --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled -u <reference_genome.gtf> <control_1.bam>,<control_x.bam> <activated_1.bam>,<activated_x.bam> -o <output_file_name>using Cuffdiff (V2.2.1.2)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values for each group and differential expression between groups

source_name: Human alveolar A549 epithelial cells

extract_protocol:
RNA was extracted from cells using the Rneasy kit which included on on-column Dnase treatment. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human alveolar A549 epithelial cells


title: DKS8-exosome-3


title: 127.SCID_rep2_1h

value: bone marrow

value: 6Gray Ionizing Radiation


title: 126.SCID_rep2_0.5h


title: 125.SCID_rep2_0

value: No-radiation


title: 124.WT(Scid)_rep2_24h

value: macrophage


title: 128.SCID_rep2_2h


title: DKS8-exosome-2


title: Human_Epithelial_A549_IL1B_1


title: 122.WT(Scid)_rep2_2h

value: wildtype


title: 121.WT(Scid)_rep2_1h


title: 123.WT(Scid)_rep2_6h


title: DKS8-exosome-1


title: 119.WT(Scid)_rep2_0


title: 118.SCID_rep1_24h

description: samples 13-18 are control wildtype for this set of exp


title: Human_Epithelial_A549_Control_2

value: media


title: DKS8-cell-2


title: 116.SCID_rep1_2h


title: Human_Epithelial_A549_Control_1


title: DKS8-cell-1


title: 120.WT(Scid)_rep2_0.5h


title: Human_Epithelial_A549_IL1B_3


title: 115.SCID_rep1_1h


title: DKO1-exosome-3


title: 114.SCID_rep1_0.5h


title: Human_Macrophage_LPS_4

source_name: Human monocyte-derived macrophage

value: Human monocyte-derived macrophage

value: LPS


title: 113.SCID_rep1_0


title: 106.STING_rep2_24h

value: Sting-/-


title: DKO1-exosome-2


title: DKO1-exosome-1


title: Human_Macrophage_LPS_3


title: DKO1-cell-2


title: Human_Macrophage_LPS_1


title: DKO1-cell-1


title: 103.STING_rep2_1h


title: 101.STING_rep2_0


title: Human_Epithelial_A549_Control_3


title: 117.SCID_rep1_6h


title: 99.WT(sting)_rep2_6h


title: Human_Macrophage_Control_3


title: 130.SCID_rep2_24h


title: 104.STING_rep2_2h


title: 105.STING_rep2_6h


title: 96.WT(sting)_rep2_0.5h


title: 97.WT(sting)_rep2_1h


title: Human_Macrophage_Control_2


title: 94.STING_rep1_24h


title: 95.WT(sting)_rep2_0


title: 102.STING_rep2_0.5h


title: Human_Macrophage_LPS_2


title: 92.STING_rep1_2h


title: 93.STING_rep1_6h


title: Human_Macrophage_Control_4


title: 91.STING_rep1_1h


title: Human_Macrophage_Control_1


title: 88.WT(sting)_rep1_24h


title: 90.STING_rep1_0.5h


title: 100.WT(sting)_rep2_24h


title: HCT116_Bortezomib_2

city: Shanghai

first: Chen-Ying

last: Liu

address: 1665 Kong Jiang Road

country: China

institute: Xinhua Hospital, Shanghai Jiao Tong University

data_processing:
Reads mapping by the STAR software
Differnetial expressed genes were analyzed by the Deseq2 software. P<0.05 was considered as statistically significant.
Genome_build: hg19
Supplementary_files_format_and_content: excel file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj

source_name: HCT116 Bortezomib treatedl cells

growth_protocol: Grown in the DMEM+10% FBS

extract_protocol:
following the RNA protocol of RNAiso Plus (Takara)
A total amount of  0.2 μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis  was  subsequently  performed  using  DNA  Polymerase  I  and  RNase  H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of  DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: RKO cells were treated with  JQ1 (1 μM) for 6 h. HCT116 cells were treated with DMSO, JQ1 (1 μM) , Bortezomib (5nM), JQ1 (1 μM)+Bortezomib (5nM) for 6h.


title: HCT116_JQ1+Bortezomib_2

source_name: HCT116 JQ1+Bortezomib treatedl cells


title: 98.WT(sting)_rep2_2h


title: HCT116_Bortezomib_1


title: 89.STING_rep1_0


title: HCT116_JQ1+Bortezomib_1


title: 84.WT(sting)_rep1_0.5h


title: HCT116_JQ1_2

source_name: HCT116 JQ1 treatedl cells


title: 87.WT(sting)_rep1_6h


title: 83.WT(sting)_rep1_0


title: 85.WT(sting)_rep1_1h


title: 81.ATM_rep2_6h

value: Atm-/-


title: 82.ATM_rep2_24h


title: 86.WT(sting)_rep1_2h


title: HCT116_JQ1_1


title: HCT116_DMSO_2

source_name: HCT116 control cells


title: MG1655_LB2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

description: processed data files: K12_LB.xlsx

data_processing:
We use Rockhopper for alignment and the complete analysis of data
Genome_build: NC_018220 and NC_000913
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2

organism: Escherichia coli

extract_protocol:
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 80.ATM_rep2_2h


title: HCT116_DMSO_1


title: 78.ATM_rep2_0.5h


title: MG1655_LB1

description: processed data files: K12_LB.xlsx


title: 77.ATM_rep2_0


title: 79.ATM_rep2_1h


title: AtCGA1_INPUT_Rep2

city: Toronto

first: Zhenhua

last: Xu

state: ON

address: 25 Willcocks St.

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
Base-calling was perfomed by Clinical Genomics Center, Mount Sinai Hospital using a Hi-seq 2500 sequencer
ChIP-Seq reads were mapped to the Arabidopsis Tair10 genome using Bowtie2 (Version 2.2.6) under the default option except with -N 1 --no-unal, which means the mapping process allows 1 mismatch between each read and the genome and the final report does not include those reads which are not mapped to the genome.
Multiple loci mapping reads were removed using the grep command by filtering out the reads with the tab of XS:i:, which only presents when a read matches multiple locations on the genome.
Peak calling was performed using Model-based Analysis for ChIP-Seq package MACS (Version 1.4.2). Some default MACS options were adjusted: effective genome size was set as 1.2e+8, which is the proximate Arabidopsis genome size; band width was optimized to make sure a well-shaped peak shift model is generated and -w -S arguments were used to allow MACS program generating a single wiggle file including each chromosome for peak visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated by MACS program, they contains the tag counts for each peak across each chromosome. They can be imported into Intergretive Genomics Viewer (IGV) to visualize the peaks enrichment for the gene of interest.
Supplementary_files_format_and_content: bed files were also generated by MACS program, they contains the information of all peaks that are enriched in the IP samples compared to the INPUT sample. Each bed file contains the chromosome and start and end position of each peak on the genome. It also has the peak scores which represents -10*LOG10(p-value)

organism: Arabidopsis thaliana

source_name: Whole rosette leaves

growth_protocol: Arabidopsis plants were planted in Sunshine LA4 soil mix (Sun Gro Horticulture Ltd, Canada) and grown in growth chambers (22℃ day/18℃ night, 16hrs light/8hrs dark, 150 μmol · m-2 · s-1 light density, 60% humidity).

extract_protocol:
ChIPed DNA was prepared from the leaves of 3-week-old myc-tagged overexpression plants using the protocols described in (Gendrel et al., 2005). Briefly, freshly harvested leaves were cross-linked in 1% formaldehyde under vacuum. The chromatin was extracted, sonicated (10% sonicated chromatin was saved as INPUT sample without incubating with anti-myc antibody) and the DNA was immunoprecipitated by anti-myc antibody (Millipore) as the IP sample. Both IP and INPUT DNA were purified and over 15 ng of each DNA from two biological replicates of each genotype were used for library construction
Library construction was performed at Clinical Genomics Center, Mount Sinai Hospital, Toronto, Canada.

tag: ecotype

tag: age

tag: day length

value: Long day

value: Anti-myc antibody


title: AtCGA1_INPUT_Rep1


title: 76.WT(atm)_rep2_24h


title: 75.WT(atm)_rep2_6h


title: AtCGA1_IP_Rep2


title: AtCGA1_IP_Rep1


title: 74.WT(atm)_rep2_2h


title: RKO_DMSO_1

source_name: RKO control cells

value: RKO


title: 73.WT(atm)_rep2_1h


title: RKO_DMSO_2


title: RKO_JQ1_2

source_name: RKO JQ1 treated cells


title: 72.WT(atm)_rep2_0.5h

source_name: bone marrow-derived macrophages


title: AtGNC_INPUT_Rep1


title: AtGNC_IP_Rep2


title: AtGNC_IP_Rep1


title: 71.WT(atm)_rep2_0


title: HUVEC4_DMSO_0

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
The reads were aligned with STAR (version  2.4.0c), and genes annotated in Gencode v18 were quantified with  featureCounts (v1.4.3-p1). Normalization and differential expression was   done with the Bioconductor package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: DESEQ2 normalized counts for genes.

source_name: Blood Vessel-Vein

growth_protocol: Cells were grown in Endothelial Cell Medium (ECM, Sciencell) in 12 well plates to full confluency. Cells were used between P2 and P7.

extract_protocol:
Total RNA was harvested using Trizol (Thermo Fisher Scientific) DNAse treated (Qiagen) and cleaned with the RNeasy mini extraction kit (Qiagen) according to manufacturer's recommendations.
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500

treatment_protocol: Once confluency was reached, cells were serum starved with ECM base medium (Sciencell) for 4 hours, treated with inhibitors or vehicle for 60 min, followed by a 30 min 50ng/ml VEGF stimulation. FOXO1 inhibitor (AS1842856) at 0.5 µM and 0.1% DMSO as vehicle.

tag: individual

value: DONOR 2

value: DMSO

tag: time

value: 0 minutes

value: endothelial cell


title: AtGNC_INPUT_Rep2


title: 68.ATM_rep1_2h

description: samples 7-12 are control wildtype for this set of exp

tag: tissue

value: bone marrow


title: 67.ATM_rep1_1h

tag: cell type

value: 6Gray Ionizing Radiation


title: RKO_JQ1_1


title: HUVEC2_DMSO_30

value: DMSO + VEGF

value: 30 minutes


title: HUVEC1_DMSO_0

value: DONOR 1


title: HUVEC1_DMSO_30


title: WR_E_L38_3

city: Beijing

first: Jun

last: Wang

state: Beijing

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: De novo assembled reference transcriptome generated from the mixture of all samples
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xls table files.

organism: Vitis vinifera

source_name: grape berry

growth_protocol: The experiment was conducted in 2014 on seven-year-old grapevines grafted onto SO4 rootstock in southern China. The grape viticulture regime in this subtropical region was dominated by double cropping systems per year. The vines were planted in east-west rows under a rain-shelter treatment with an inter- and intra-row vine spacing of 3.5 m × 1.5 m and were managed in a closing Y-shaped training system with 2 × 4/5 shoots per meter and 1.0 m cordon above ground.

extract_protocol:
Three biological replicates for each sample were performed. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA).  RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The vines are pruned twice and the grapes are harvested twice per year. To produce the first crop, the vines were pruned and enforced with 2.5%-3.0% hydrogen cyanamide in mid-February when the temperature was maintained above 10 °C. The terminal bud was not sprayed to avoid apical dominance. Then, the grapevines were in full bloom around mid-April, while the veraison stage ranged from mid-June to early July, followed by the harvest stage (summer grape). This whole period was termed the summer cropping cycle. Then, the vines were pruned and forced again in August, leading to the second crop (winter grape) in early January of the following year. In detail, the grapevines were pruned on approximately 20th August, were manually defoliated and an average of 5-10 buds were left for each cane. Hydrogen cyanamide was smeared only at the terminal bud and in the vicinity of the pruning-wound surface. Then, the bud burst 5-8 days later and initiated the winter cropping cycle.

tag: cultivar

value: Riesling

tag: Stage

tag: crop

value: Winter


title: O11-MU_ChIPSeq

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

data_processing:
CASAVA1.8.2 (Illumina) were used for image analysis and base calling.
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L40 (Length).
Cleaned data were then mapped to the maize reference genome using Bowtie2 with default parameters and allowing unique reads only.
Peak detection was done using MACS v2.0.10 using the indicated criteria.
UCSC bedGraph files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Ensembl plants release-28 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include contains information about called peaks.
Supplementary_files_format_and_content: bed files include the peak summits locations for every peaks.

organism: Zea mays subsp. mays

source_name: kernal

extract_protocol:
Endosperm lysates were clarified from sonicated nuclei. O11-DNA complexes were isolated with O11-antibody. o11 mutant seeds were used as negtive control.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Catalog# IP-202-1012). ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. Barcode sequences of adapters correspond to the following: CTTGTA, 685-wt-1_combined; TTAGGC, 685-mu-1_combined. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Illumina Genome Analyzer (GA) sequencing was performed by the OSUCCC Nucleic Acid Shared Resource-Illumina GA II Core.

tag: genotype

value: mutant (o11/o11)

value: 15 days after pollination (DAP)

value: kernel


title: 66.ATM_rep1_0.5h

value: macrophage

tag: strain

value: Atm-/-

tag: stimulus

tag: time point (h)


title: 65.ATM_rep1_0

value: No-radiation


title: 70.ATM_rep1_24h


title: 64.IFNAR_rep2_6G_24h

value: Ifnar-/-


title: BFHK37_FOXINH_30

source_name: Urinary-Kidney

value: DONOR 37

tag: treatment

value: FOXO1 INHIBITOR + VEGF


title: WR_E_L38_2


title: 62.IFNAR_rep2_6G_2h


title: WR_E_L36_3


title: BFHK37_DMSO_30

value: endothelial cell


title: 69.ATM_rep1_6h

value: bone marrow


title: 63.IFNAR_rep2_6G_6h

value: 6Gray Ionizing Radiation


title: HUVEC3_DMSO_30

value: DMSO + VEGF


title: HUVEC3_DMSO_0

value: DMSO

value: 0 minutes


title: BFHK37_FOXINH_0

value: FOXO1 INHIBITOR


title: 61.IFNAR_rep2_6G_1h


title: WR_E_L36_2

value: Riesling

value: Winter


title: O11-WT_ChIPSeq

value: wildtype

value: 15 days after pollination (DAP)

tag: chip antibody


title: BFHK15_FOXINH_30

value: DONOR 15

value: 30 minutes


title: WR_E_L36_1


title: 60.IFNAR_rep2_6G_0.5h

value: macrophage


title: 59.IFNAR_rep2_0

value: Ifnar-/-

value: No-radiation


title: BFHK15_FOXINH_0


title: WR_E_L35_3


title: BFHK15_DMSO_30


title: HUVEC2_DMSO_0

value: DONOR 2


title: WR_E_L35_2


title: WR_E_L38_1


title: WR_E_L35_1


title: BFHK20_FOXINH_30

value: DONOR 20

value: FOXO1 INHIBITOR + VEGF

value: endothelial cell


title: 57.WT(ifnar)_rep2_6G_6h

value: bone marrow

value: 6Gray Ionizing Radiation


title: BFHK15_DMSO_0

value: DMSO

value: 0 minutes


title: 55.WT(ifnar)_rep2_6G_1h


title: SR_E_L38_3

value: Riesling

value: Summer


title: 56.WT(ifnar)_rep2_6G_2hl

value: wildtype


title: BFHK20_FOXINH_0

value: FOXO1 INHIBITOR


title: SR_E_L38_2


title: SR_E_L38_1


title: 54.WT(ifnar)_rep2_6G_0.5h


title: BFHK37_DMSO_0

value: DONOR 37


title: SR_E_L36_3


title: 53.WT(ifnar)_rep2_0


title: BFHK20_DMSO_0


title: BFHK20_DMSO_30

value: DMSO + VEGF

value: 30 minutes


title: SR_E_L36_2


title: BFHK21_FOXINH_30

value: DONOR 21


title: SR_E_L36_1


title: 58.WT(ifnar)_rep2_6G_24h

value: macrophage


title: 52.IFNAR_rep1_6G_24h

value: Ifnar-/-


title: 51.IFNAR_rep1_6G_6h


title: BFHK21_FOXINH_0


title: BFHK21_DMSO_30


title: 50.IFNAR_rep1_6G_2h


title: 49.IFNAR_rep1_6G_1h


title: SR_E_L35_3


title: 48.IFNAR_rep1_6G_0.5h


title: 47.IFNAR_rep1_0

value: No-radiation


title: SR_E_L35_1


title: SR_E_L35_2


title: 46.WT(ifnar)_rep1_6G_24h


title: U87 control 2

city: Amsterdam

first: Nora

last: Pencheva

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Brain tumor
Barcode used: GATCAGA

data_processing:
Base calling was performed using Illumina RTA 1.18.64.
Reads passing filter were converted to fastq reads using bcl2fastq (version 1.8.4).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Filtered reads were mapped using Tophat 2.0.12, using bowtie1, against the human build 38 (Ensembl) using a gene transfer file (GTF) version 77 (Ensembl). The parameters that were used by Tophat were: --prefilter-multihits, --no coverage-search, --transcriptome index and --library-type firststrand.
Raw read counts were generated using a custom script which is based on the same ideas as htseq-count. Reads that were uniquely mapped were used for determining the gene expressions for each sample.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *raw_count.txt: Tab-delimited text files include raw read counts.
Supplementary_files_format_and_content: *norm_count.txt: Tab-delimited text files include normalized read counts, which were obtained after normalizing the raw read count data using the DESeq2 package (www.bioconductor.org).

source_name: Malignant glioblastoma cells, poorly invasive control

growth_protocol: U87 cells were grown in standard DMEM media supplemented with 10% FBS, 1% L-Glutamine, and 1% Pen/Strep.

extract_protocol:
Briefly, 0.2x volumes of chloroform (Chloroform stab./Amylene, Biosolve) was added to the Trizol homogenate and the tube(s) (Falcon, 15mL) were shaken vigorously. The tube(s) were incubated for 2-3 minutes at room temperature and centrifuged (Hettich, rotanta 46 RS) for 1 hour at 4 °C . Approximately 70% of the upper aqueous phase was transferred to a clean 15 mL tube and 0.5x volume of isopropanol (33539, Sigma-Aldrich) was added. The tube(s) were incubated overnight at -20 °C and centrifuged for 30 minutes at 4 ° C. The supernatant was removed and the pellet was washed twice with 80% ethanol (32221-2.5L, Sigma-Aldrich). The total RNA pellet was air-dried for 8 minutes and dissolved in an appropriate volume of nuclease-free water (AM9937, Ambion Life Technologies) and quantified using NanoDrop UV-VIS Spectrophotometer. The total RNA was further purified using the MinElute Cleanup Kit (74204, Qiagen) according to the manufacturer's instructions. Quality and quantity of the total RNA were assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA). Total RNA samples having RIN>8 were subjected to library generation.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E). Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, part # 18064-014) with the addition of Actinomycin D. Second strand synthesis was performed using Polymerase I and RNaseH with replacement of dTTP for dUTP. The generated cDNA fragments were 3' end adenylated and ligated to Illumina Paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a 10nM multiplex sequencing pool and stored at -20 °C.
The libraries were sequenced with 65 base single reads on a HiSeq 2500 using V4 chemistry (Illumina Inc., San Diego).

treatment_protocol: U87 parental cells were allowed to invade organotypic brain slices for 1 week in the presence of neural stem cell media supplemented with FGF/EGF. After 1 week, invasive and non-invasive/control populations were isolated from the brain slice cultures, expanded in vitro for 3-5 days, and processed for RNA extraction and deep sequencing.

tag: cell line

value: malignant glioblastoma cell line

tag: gbm cell population

value: poorly invasive


title: U87 brain invasive clone 2

description:
Brain tumor
Barcode used: TAGCTTA

source_name: Malignant glioblastoma cells, highly invasive

value: highly invasive


title: 45.WT(ifnar)_rep1_6G_6h

value: bone marrow

value: 6Gray Ionizing Radiation


title: U87 brain invasive clone 1

description:
Brain tumor
Barcode used: ATGTCAG


title: WC_E_L38_1

value: Cabernet Sauvignon

value: Winter


title: 44.WT(ifnar)_rep1_6G_2hl


title: WC_E_L36_3


title: CW2012_5_bulk

data_processing:
For gene expression analysis, reads were aligned to the hg19 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et  al., 2009).
The distribution of alignments was analyzed using the CollectRnaSeqMetrics module of Picard v1.89 (http://picard.sourceforge.net/).
FPKM values for known genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option. FPKM values were Quantile Normalized.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM values from Cufflinks

source_name: Human cortical brain

extract_protocol:
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.

value: Primary GBM


title: 43.WT(ifnar)_rep1_6G_1h

value: wildtype


title: U87 control 1

description:
Brain tumor
Barcode used: AGTTCCG


title: CW2012_4_bulk.tumor


title: CW2012_1_bulk


title: WC_E_L36_2


title: 41.WT(ifnar)_rep1_0


title: CW1987_6_bulk


title: WC_E_L36_1


title: WC_E_L35_3


title: 42.WT(ifnar)_rep1_6G_0.5h


title: CW1987_4_bulk


title: WC_E_L38_3


title: 40.MT_rep2_6G_24h


title: CW1987_1_bulk.tumor


title: 39.MT_rep2_6G_6h


title: WC_E_L38_2


title: WC_E_L35_2


title: BFHK21_DMSO_0

value: DMSO

value: 0 minutes

value: endothelial cell


title: WC_E_L35_1


title: CW1987_5_bulk


title: 38.MT_rep2_6G_2h


title: SC_E_L38_3

value: Summer


title: 37.MT_rep2_6G_1h


title: RKI1xp1.CD133POS

source_name: Intracranial xenograft

growth_protocol: RKI1 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

extract_protocol:
Cells were dissociated from the tumor, depleted of mouse cells twice by Miltenyi mouse depletion kit and MACS magnetic sorting and then lysed in Trizol.
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.

value: RKI1 cells


title: SC_E_L38_2


title: CW789xp2.CD133POS

growth_protocol: CW789 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW789 cells


title: 36.MT_rep2_6G_0.5h

value: macrophage


title: 35.MT_rep2_0_cont

value: No-radiation


title: SC_E_L36_3


title: 34.WT(mt)_rep2_6G_24h


title: SC_E_L38_1


title: CW2025_3_CD133POSPOS

growth_protocol: CW2025_3 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW2025_3 cells


title: 33.WT(mt)_rep2_6G_6h


title: SC_E_L36_1


title: CW1924.CD133POS

growth_protocol: CW1924 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW1924 cells


title: CW2012_1_CD133POS

growth_protocol: CW2012_1 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW2012_1 cells


title: SC_E_L36_2


title: SC_E_L35_3


title: CW1919_CD133POS

growth_protocol: CW1919 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW1919 cells


title: SC_E_L35_2


title: CW1918_CD133POS

growth_protocol: CW1918 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW1918 cells


title: 31.WT(mt)_rep2_6G_1h

value: bone marrow

value: 6Gray Ionizing Radiation


title: SC_E_L35_1

value: Cabernet Sauvignon


title: 30.WT(mt)_rep2_6G_0.5h

value: wildtype


title: 29.WT(mt)_rep2_0_cont


title: eWAT rep3

city: Boston

first: Yi

last: Chen

state: Massachusetts

address: 450 Brookline Ave CLS 11116

institute: Dana-Farber Cancer Institute

description: ribosomal loaded RNA

data_processing:
Library strategy: TRAP-seq
Reads mapping and transcripts identification were performed by The Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA.
Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) using Tophat and assembled reads into transcripts using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited (txt) files include FPKM values of genes

source_name: epididymal white adipose tissue

extract_protocol:
Small pieces (50–100 mg) of frozen brown, inguinal white and epididymal white adipose tissues were Dounce homogenized in 4 mL homogenization buffer. After centrifugation at 13,000 rpm for 10 min, the lipid layer was removed and the supernatant was collected and incubated with anti-GFP antibody (5 mg/mL; Abcam, ab290) for 1 hr at 4 ˚C. Protein G dynabeads were washed twice in low-salt wash buffer, added to the homogenates with antibody, and subsequently incubated for 30 min. Dynabeads with immunoprecipitates were washed three times in high-salt wash buffer. Following the last wash, RLT buffer with b-mercaptoethanol was added to dynabeads, and RNA was extracted using a QIAGEN Micro RNeasy kit per the manufacturer’s instructions.
Extracted RNA (100 ng) was processed for rRNA removal using the Epicenter rRNA depletion kit per the manufacturer’s instructions. rRNA-depleted RNA was subsequently used to generate single-end sequencing libraries using the Illumina RNA TruSeq Library Kit per the manufacturer’s instructions.

value: epididymal white adipose tissue

tag: age

value: 8 weeks

value: wild type


title: CW738xp2.CD133POS

growth_protocol: CW738 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CW738 cells


title: eWAT rep2

description: ribosomal loaded RNA


title: CCF_3145_xp1POSPOS

growth_protocol: CCF_3145 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF_3145 cells


title: 28.MT_rep1_6G_6h

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to stimulation.


title: 27.MT_rep1_6G_2h


title: CCF3136xp1.CD133POS_JR15

growth_protocol: CCF3136 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3136 cells


title: eWAT rep1

description: ribosomal loaded RNA


title: 26.MT_rep1_6G_1h

value: macrophage


title: iWAT rep3

description: ribosomal loaded RNA

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue


title: CCF3094_xp1_CD133POS

growth_protocol: CCF3094 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3094 cells


title: iWAt rep2

description: ribosomal loaded RNA


title: 32.WT(mt)_rep2_6G_2h


title: CCF3029xp1.CD133POS

growth_protocol: CCF3029 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3029 cells


title: iWAT rep1

description: ribosomal loaded RNA


title: 24.MT_rep1_0_cont

value: No-radiation


title: CCF3028xp2.CD133POS_JR21

growth_protocol: CCF3028 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3028 cells


title: BAT rep3

description: ribosomal loaded RNA

source_name: brown adipose tissue


title: CCF2997xp1.CD133POS

growth_protocol: CCF2997 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF2997 cells


title: 22.WT_mt__rep1_6G_2h

value: bone marrow


title: CCF3128xp1.CD133POS_JR27

growth_protocol: CCF3128 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3128 cells


title: BAT rep2

description: ribosomal loaded RNA

value: brown adipose tissue


title: BAT rep1

description: ribosomal loaded RNA


title: CCF1914_2_Flank_x_p1_CD133POS

source_name: Subcutaneous xenograft

growth_protocol: CCF1914_2 cells from a primary patient derived GBM tumor model were injected subcutaneously into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF1914_2 cells


title: 21.WT_mt__rep1_6G_1h

value: wildtype

value: 6Gray Ionizing Radiation


title: 20.WT_mt__rep1_6G_0.5h


title: 2907xp1.CD133POS

growth_protocol: 2907 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: 2907 cells


title: CCF3038xp2.CD133POS

growth_protocol: CCF3038 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: CCF3038 cells


title: LysM RICTOR KO moMAC1

city: Baltimore

first: Maureen

middle: R.

last: Horton

state: MD

address: 1830 E. Monument Street, 5th floor

department: Department of Medicine

institute: Johns Hopkins University School of Medicine

description: group D

data_processing:
NextSeq 500/550 V2 Systems suite version 2.1.2, bcl2fastq2 version 2.17.1.14. Data processing Illumina NextSeq 500/550 V2 reads were trimmed and clipped for quality control based on sliding windows considering quality and length thresholds to determine the quality at which it is sufficiently low to trim the 3′-end of reads and also determines the quality at which it is sufficiently high enough to trim the 5′-end of reads. This approach finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads. Quality Threshold < 30
the pre-processing operations included a quality check (FastQC), removal of adapter content (used during sequencing), quality thresholding (remove any bad quality reads)
FastQC v0.10.1.
High-quality reads were then imported into a fast splice junction mapper for RNA-Seq reads and this aligns RNA-Seq reads to genomes using the ultra high-throughput short read aligner. The mapping results were then analyzed to identify splice junctions between exons, for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline by the Transcriptomic Analysis Pipeline (proprietary pipeline designed in-house).
Reads were mapped to the reference genome. This aligns RNA-Seq reads to the genome using a short read aligner and discovers the splice sites.The resulting alignment files were used to generate a transcriptome assembly. TopHat (v 2.1.1) used
The major stages of analysis included read mapping to the latest reference genome (GRCM38), assembly of the mapped reads to identify expressed transcripts and genes, followed by quantification and comparison of the assembled transcriptomes between cells.
Gene and transcript expression between the comparing RNASeq samples were quantified and reported as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) units
Genome_build: GRCM38
Supplementary_files_format_and_content: genes.fpkm_tracking

source_name: sorted peritoneal monocytic macrophages (CD11b+F4/80loTIM4-)

growth_protocol: IL-4c (recombinant IL-4 (5µg) and anti-IL-4 ab (12.5µg) IP injection on days 0 and 2 and sorted on day 4

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Extracted RNA were sent to Admera Health to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.

treatment_protocol: Sorting with FACSAria II

value: LysM Cre + RICTOR KO


title: LysM RICTOR KO moMAC2

description: group D

value: IL-4c (recombinant IL-4 (5µg) and anti-IL-4 ab (12.5µg) IP injection on days 0 and 2 and sorted on day 4


title: ES.Cell_Derived_Normal_neural_progentor

source_name: Cell line

growth_protocol: NPCs derived from ES cells were grown in serum-free culture conditions.

value: NPCs derived from ES cells


title: 25.MT_rep1_6G_0.5h

extract_protocol:
total RNA was biochemically purified as previously described (Bhatt et al, Cell 2012). Cells were resuspended in TriReagent and RNAs were purified using Rneasy columns (Qiagen).
All mRNA libraries were generated using the Illumina Truseq v.2 kit with a few modifications: strand specific libraries were generated using the dUTP method. Briefly, the second strand cDNA was synthesized in the presence of dUTP. Prior to library amplification, the second strand was degraded with dUTPase. Few libraries were genearted using TruSeq Stranded mRNA Library Prep  Kit as per manufacturere's instructions.

value: macrophage


title: 18.WT_rep3_6G_24h


title: LysM WT moMAC1

description: group C

value: LysM Cre+


title: LysM WT moMAC2

description: group C


title: LysM RICTOR KO ResMAC 3

description: group B

source_name: sorted peritoneal tissue resident macrophages (CD11b+F4/80hiTIM4+)


title: 16.WT_rep3_6G_2h


title: 23.WT_mt__rep1_6G_6h


title: 17.WT_rep3_6G_6h


title: 15.WT_rep3_6G_1h


title: LysM RICTOR KO ResMAC 2

description: group B


title: 14.WT_rep3_6G_0.5h


title: LysM RICTOR KO ResMAC 1

description: group B


title: 13.WT_rep3_0_Cont


title: LysM WT ResMAC 1

description: group A


title: 11.WT_rep2_6G_6h


title: LysM WT ResMAC 3

description: group A


title: 19.WT_mt__rep1_0_cont


title: 1987_5_CD133POS

growth_protocol: 1987_5 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.


title: LysM WT ResMAC 2

description: group A


title: 10.WT_rep2_6G_2h


title: G123

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
RNA-seq: the cDNA library with a fragment length range of 250 bp (±25 bp) was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500)
Filtering: the trimming adapter sequences were removed and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the software
Aligning: The reads of each accession were aligned into the referenced transcriptome.
Gene expression analysis: Gene expression levels were measured in the RNA-Seq analysis as expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM). The DEseq software was used to identify differentially expressed genes. DESeq analysis was performed by fitting normalized count data with a generalized linear model (GLM) estimating a negative binomial distribution to the calculated mean values of the two biologically independent samples. For each gene, fold changes and P values (pval) as well as P values adjusted (padj) for multiple testing with the Benjamini-Hochberg procedure, were used to control false discovery rate (FDR). The Sequence with a padj of less than 0.05 was deemed to be significantly differentially expressed genes (DEGs)

organism: Allium sativum

source_name: Bulbs

growth_protocol: Field experiments were carried out following a randomized complete block design with two replicates. Fifty garlic cloves for each accession were planted into a five-row plot, with a distance of 10 cm between plants within a row and 20 cm between rows, in Sept 15, 2014,

extract_protocol:
Total RNA of each sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, USA) according to the manufacturer’s protocol.  The RNA was stored at -80° for cDNA library preparation
RNA of each sample was separately used to construct the cDNA library with a fragment length range of 250 bp

treatment_protocol: The bulbs of five individuals for each accession were collected, when the bulbs is expanding.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use.

value: bulbs

value: bulb expanding


title: G127


title: 07.WT_rep2_0_Cont

data_processing:
RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
All aligned reads were imported to SeqMonk. The mRNA expression was calculated by totaling all uniquely aligned exonic reads. The raw reads were converted to RPKM by dividing the reads by the cDNA length and the total number of uniquely mapped reads in the sample.
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

source_name: bone marrow-derived macrophages

value: No-radiation


title: G121


title: 09.WT_rep2_6G_1h


title: 08.WT_rep2_6G_0.5h


title: G120


title: 06.WT_rep1_6G_24h


title: HUVEC4_DMSO_30

source_name: Blood Vessel-Vein

growth_protocol: Cells were grown in Endothelial Cell Medium (ECM, Sciencell) in 12 well plates to full confluency. Cells were used between P2 and P7.

value: DONOR 2

value: DMSO + VEGF

value: 30 minutes

value: endothelial cell


title: G118


title: 02.WT_rep1_6G_0.5h

value: bone marrow


title: 03.WT_rep1_6G_1h

value: wildtype


title: G112


title: G122


title: G119


title: 01.WT_rep1_0_Cont


title: Neurite_RNAseq_koAX24_1

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 80) using STAR_2.4.2a.
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM 1.2.21 with default parameters.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TPM value) of each gene in each cells in CSV format

molecule: polyA RNA

source_name: injured Cpeb1 knockout neurites

growth_protocol: Timed pregnancies were set up from wild-type (C57BL/6) or Cpeb1 flox/flox (background strain C57BL/6) transgenic mice. Cortical neurons were isolated from E16.5 embryos and plated on transwell chambers with PET membranes and 3um pores (Millipore). At 7 dpi, injured samples had their neurites cut by scraping the under side of the membrane with a cotton swab. At 8 dpi and 24 hours after injury, neurites were lysed for RNA. Mice were bred in house at the DKFZ Center for Preclinical Research facility.  All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Cell bodies of neurons cultured in transwell chambers were removed by scraping the upper side of the membrane with a DNAse- and RNAse-free cotton swap. The membranes were cut out with a scapel, rinsed briefly in PBS, then put into lysis buffer from the RNAqueous-Micro kit (Ambion) and RNA was isolated following the manufacturer’s instructions.
RNA-sequencing libraries were prepared using the Smart-seq2 protocol as published in (Picelli et al., 2014). Briefly, 1ng of DNAse-treated RNA from neuronal processes were used as input material. Reverse transcription was performed using SuperScript II reverse transcriptase, an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide. cDNA was amplified by PCR with KAPA HiFi DNA polymerase for 14 cycles. The resulting cDNA libraries were purified using AMPure XP beads, and 500pg of purified cDNA was taken for tagmentation and 11 cycles of amplification using the Nextera XT DNA sample preparation kit (Illumina), followed by a further cleanup step using AMPure XP beads.

treatment_protocol: All neurons were infected with AAV2 expressing Cre under the ubiquitous CAG promoter at the time of plating

tag: background strain

value: Neurites from cultured neurons

value: 8 days in vitro

tag: genotype/variation

value: Cpeb1 flox/flox


title: G117


title: G110


title: 12.WT_rep2_6G_24h

first: Prabhat

address: 675 Charles E. Young Drive South

institute: UCLA

value: 6Gray Ionizing Radiation


title: 05.WT_rep1_6G_6h


title: G109


title: Neurite_RNAseq_koAX24_2


title: G100


title: G102


title: 04.WT_rep1_6G_2h


title: Neurite_RNAseq_koAX_2

source_name: naïve Cpeb1 knockout neurites


title: Neurite_RNAseq_wtAX24_1

source_name: injured wild-type neurites

value: wild-type


title: Neurite_RNAseq_wtAX24_2


title: Neurite_RNAseq_wtAX24_3


title: Neurite_RNAseq_wtAX_1

source_name: naïve wild-type neurites


title: G98


title: Neurite_RNAseq_wtAX_2


title: G99


title: G94


title: G108


title: G91


title: Neurite_RNAseq_koAX_1


title: Neurite_RNAseq_wtAX_3


title: G90


title: G97


title: G89


title: G87


title: G92


title: G86


title: Brain Adar1 E861A/E861A MDA5-/- [JBL279]

first: Jin

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR v2.4.2a.
Editing level was calculated by dividing the number of G reads by the sum of A and G reads for each site.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the coverage, edited reads and editing level for each site.

source_name: Brain

extract_protocol:
Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent. mmPCR-seq libraries were prepared as decirbed by Zhang et al (doi:10.1038/nmeth.2736).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: Embryonic day 12.43


title: Brain R2 Adar1 E861A/+ MDA5-/- [JBL287]

value: Embryonic day 12.46


title: Brain R2 Adar1 E861A/+ MDA5-/- [JBL286]

value: Embryonic day 12.45


title: Heart Adar1 E861A/E861A MDA5-/- [JBL278]

source_name: Heart

value: Heart

value: Embryonic day 12.42


title: BM Adar1 E861A/E861A MDA5-/- [JBL280]

source_name: Bone marrow

value: Bone marrow

value: Embryonic day 12.44


title: G85

value: bulbs

value: bulb expanding


title: Brain R2 Adar1 +/+ MDA5-/- [JBL288]

value: Embryonic day 12.47


title: G84


title: Spleen Adar1 E861A/E861A MDA5-/- [JBL277]

source_name: Spleen

value: Spleen

value: Embryonic day 12.41


title: Thymus Adar1 E861A/E861A MDA5-/- [JBL276]

source_name: Thymus

value: Thymus

value: Embryonic day 12.40


title: G83


title: Kidney Adar1 E861A/E861A MDA5-/- [JBL275]

source_name: Kidney

value: Kidney

value: Embryonic day 12.39


title: G82


title: Liver Adar1 E861A/E861A MDA5-/- [JBL274]

source_name: Liver

value: Liver

value: Embryonic day 12.38


title: BM Adar1 E861A/E861A MDA5-/- [JBL272]

value: Embryonic day 12.36


title: G81


title: Brain Adar1 E861A/E861A MDA5-/- [JBL271]

value: Brain

value: Embryonic day 12.35


title: Ovary Adar1 E861A/E861A MDA5-/- [JBL273]

source_name: Ovary

value: Ovary

value: Embryonic day 12.37


title: Heart Adar1 E861A/E861A MDA5-/- [JBL270]

value: Heart

value: Embryonic day 12.34


title: G77

value: bulbs

value: bulb expanding


title: G79


title: G78


title: Spleen Adar1 E861A/E861A MDA5-/- [JBL269]

value: Spleen

value: Embryonic day 12.33


title: G76


title: Kidney Adar1 E861A/E861A MDA5-/- [JBL267]

value: Embryonic day 12.31


title: G75


title: Liver Adar1 E861A/E861A MDA5-/- [JBL266]

value: Embryonic day 12.30


title: G74


title: G71


title: G72


title: G73


title: G68


title: G80


title: Brain R1Adar1 E861A/+ MDA5-/- [JBL263]

value: Embryonic day 12.27


title: BM Adar1 E861A/+ MDA5-/- [JBL264]

value: Bone marrow

value: Embryonic day 12.28


title: Spleen Adar1 E861A/+ MDA5-/- [JBL261]

value: Embryonic day 12.25


title: G66


title: G65


title: G64


title: 24h_2

city: Yokohama

first: Momoko

last: Ikeuchi

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

data_processing:
Reads were mapped on TAIR10 Arabidopsis genome using CLC genomics workbench.
Supplementary_files_format_and_content: excel, RPKM

source_name: wounded hypocotyls

growth_protocol: Plants were grown in the dark on MS-0 plates.

extract_protocol:
RNAeasy plant mini kit (Qiagen)
Truseq stranded mRNA sequencing kit (illumina)

treatment_protocol: Etiolated hypocotyls were sharply cut and incubated in the dark on MS-0 plates.

value: hypocotyls

tag: time point


title: G63

tag: tissue


title: 24h_1


title: 12h_3


title: Thymus Adar1 E861A/E861A MDA5-/- [JBL268]

value: Thymus

value: Embryonic day 12.32


title: G62


title: Ovary Adar1 E861A/+ MDA5-/- [JBL257]

value: Ovary

value: Embryonic day 12.21


title: 12h_2


title: G61


title: Ovary Adar1 E861A/E861A MDA5-/- [JBL265]

value: Embryonic day 12.29


title: Heart Adar1 E861A/+ MDA5-/- [JBL262]

value: Heart

value: Embryonic day 12.26


title: BM Adar1 E861A/+ MDA5-/- [JBL256]

value: Embryonic day 12.20


title: 12h_1


title: Brain R1 Adar1 E861A/+ MDA5-/- [JBL255]

value: Brain

value: Embryonic day 12.19


title: Heart Adar1 E861A/+ MDA5-/- [JBL254]

value: Embryonic day 12.18


title: 6h_2


title: G59

value: bulbs

value: bulb expanding


title: G58


title: Thymus Adar1 E861A/+ MDA5-/- [JBL260]

value: Embryonic day 12.24


title: G57


title: Kidney Adar1 E861A/+ MDA5-/- [JBL259]

value: Kidney

value: Embryonic day 12.23


title: 6h_3

value: hypocotyls


title: Thymus Adar1 E861A/+ MDA5-/- [JBL252]

value: Thymus

value: Embryonic day 12.16


title: 3h_3


title: G60


title: Spleen Adar1 E861A/+ MDA5-/- [JBL253]

value: Spleen

value: Embryonic day 12.17


title: Kidney Adar1 E861A/+ MDA5-/- [JBL251]

value: Embryonic day 12.15


title: 6h_1


title: Liver Adar1 E861A/+ MDA5-/- [JBL258]

value: Liver

value: Embryonic day 12.22


title: Liver Adar1 E861A/+ MDA5-/- [JBL250]

value: Embryonic day 12.14


title: G53


title: Ovary Adar1 E861A/+ MDA5-/- [JBL249]

value: Ovary

value: Embryonic day 12.13


title: 3h_2


title: G55


title: G56


title: 1h_3


title: BM Adar1 +/+ MDA5-/- [JBL248]

value: Bone marrow

value: Embryonic day 12.12


title: G51

value: bulbs

value: bulb expanding


title: 3h_1


title: 1h_2


title: G50


title: 1h_1


title: Heart Adar1 +/+ MDA5-/- [JBL246]

value: Heart

value: Embryonic day 12.10


title: 0h_3

value: hypocotyls


title: Spleen Adar1 +/+ MDA5-/- [JBL245]

value: Embryonic day 12.9


title: G48


title: 0h_2


title: G49


title: G46


title: 0h_1


title: Thymus Adar1 +/+ MDA5-/- [JBL244]

value: Thymus

value: Embryonic day 12.8


title: Liver Adar1 +/+ MDA5-/- [JBL242]

value: Embryonic day 12.6


title: Kidney Adar1 +/+ MDA5-/- [JBL243]

value: Kidney

value: Embryonic day 12.7


title: Ovary Adar1 +/+ MDA5-/- [JBL241]

value: Embryonic day 12.5


title: ileum Apc+/- replicate 3

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description:
Heterozygous mice Apc+/- and non-floxed cdx 2 allel
il3apc

data_processing:
Base call with CASAVA v1,7
Mapping with tophat 2.0.11 using the options --b2-sensitive -a 5 -p 5 --library-type fr-unstranded -r 180 --mate-std-dev 80 and the exon-exon reference from ensembl v75
Quantification of reads to genes with HTSeq version 0.5.3p3
Genome_build: GRCm38
Supplementary_files_format_and_content: Non-normalized read count at the gene levels (ensembl gene identifier from release 75) from HTSeq version 0.5.3p3

source_name: ileum Apc+/-

growth_protocol: Not applicable

extract_protocol:
total RNA extracted from mouse tissue in Trizol (Life Technologies)
TruSeq mRNA version 2

treatment_protocol: + Tamoxifen + bnaphthoflavone when indicated

value: Ileum


title: ileum Apc+/- replicate 2

description:
Heterozygous mice Apc+/-
il2apc


title: G43

source_name: Bulbs


title: ileum Apc+/- replicate 1

description:
Heterozygous mice Apc+/- and non-floxed cdx 2 allel
il1apc


title: G44


title: ileum conditional cdx2-/- ; Apc+/- replicate 3

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
il3tt

source_name: ileum conditional cdx2-/- ; Apc+/-

value: + Tamoxifen + bnaphthoflavone


title: G42


title: ileum conditional cdx2-/- ; Apc+/- replicate 2

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
il2tt


title: Brain R1 Adar1 +/+ MDA5-/- [JBL247]

city: STANFORD

last: Li

value: Brain

value: Embryonic day 12.11


title: G40


title: EL4 shCTCF RNA-seq r2

city: Bethesda

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: RNA-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified peak of ChIP-Seq using MACS and calculated the RPKM of each gene in RNA-seq
Using our 3e Hi-C data, the topological domain were identified based on the the approach in Dixon et al., 2012.
Genome_build: mm9
Supplementary_files_format_and_content: Bed3: plan text file. The three columns are chrom, start position, end position.
Supplementary_files_format_and_content: BedGraph: plan text file. The four columns are chrom, start position, end position, data value.

growth_protocol: The R1 murine ES cells were cultured on feeder coated dishes in ES-qualified DMEM supplemented with various growth factors as described previously (Hu et al., 2013a). For generation of Th2 cells, naïve CD4+ T cells were isolated from the lymph nodes of C57BL/6 mice from the Jackson Laboratory (JAX) by staining with Pacific Blue-anti-CD62L, APC-anti-CD4, APC-Cy7- anti-CD44 and PE-anti-CD25 and sorting for CD4+CD25-CD62LhiCD44low population by FACSAria (BD Biosciences) as described before (Hu et al., 2013b). For Th2 condition induction, the cytokine and antibody cocktail containing IL-4 (5000U/ml), IL-2 (100U/ml), anti-IFNγ (10μg/ml) and anti-IL-12 (10μg/ml) was added to the cell culture and two rounds of polarization were performed (Hu et al., 2013b). EL4 cells were cultured in DMEM (Gibco Invitrogen) supplemented with 50 IU/mL penicillin and 50μg/mL streptomycin (Gibco Invitrogen) and 10% heat inactivated calf serum (Sigma, USA). Cultures was maintained by replacement of fresh medium every 3 days, and carefully kept cell density between 1 X 105 and 1 X 106 cells/ml.

extract_protocol:
For generating ChIP-Seq libraries, chromatin extracts were prepared by sonication of cells following crosslinking with 1% formaldehyde for 10min at room temperature. The ChIP was performed with 1 ug specific antibodies as described (Barski et al., 2007) and ChIP-Seq libraries were prepared using indexing primers as described (Hu et al., 2013a). RNA-Seq libraries using polyA RNA isolated from both the WT and KO cells were prepared as described (Chepelev et al., 2009).
Murine R1 ES cells and in vitro inducted Th2 cells were cross-linked with 1% formaldehyde for 10min at room temperature. 10 X106 cells were lysed by resuspending in 10ml lysis buffer (10mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP40; 10μl protease inhibitors (Sigma)) and incubation at 4°C with rotation for one hour. The cells were then treated with 400 μl 1xNEB cutsmart buffer + 0.1% SDS at 65°C for 10 minutes, followed by addition of 44μl 10% Triton X-100 to quench SDS. Chromatin was subsequently digested with 20 Units CviQ I (NEB), and 20 Units CviA II (NEB) at 25°C for 20 minutes, then 20 Units Bfa I (NEB) at 37°C for 20 minutes. The reaction was stopped by washing the cells twice with 600 ul wash buffer (10mM NaCl, 1mM EDTA, 0.1% triton-100). Then the samples were processed as the Hi-C protocol (Lieberman-Aiden et al., 2009) with modifications briefly described below. The DNA ends were blunted and labeled with biotin by Klenow enzyme in the presence of dCTP, dGTP, dTTP, biotin-14-dATP, followed by 3C ligation using T4 DNA ligase. After reverse crosslinking, the DNA was fragmented to 300-500 bp by sonication with a Bioruptor sonicator (Diagenode UCD-200). The samples were treated with T4 DNA polymerase to remove biotin labels at the DNA ends. The remaining biotinylated DNA fragments were then captured using Dynabeads MyOne Streptavin C1 Beads (Invitrogen) by incubating for 30 minutes at RT with rotation. The DNA on beads was end-repaired, followed by A-addition and ligation to the Illumina Paired End Adaptors as described previously. Following PCR-amplification of the libraries, DNA fragments from 300 to 600 bp were purified from 2% agarose gel and sequenced on HiSeq2000.

treatment_protocol: Genome Editing was carried out by CRISPR/Cas9 system (Cong et al., 2013). The CRISPR/Cas9 plasmid pairs were nucleofected by using Nucleofector Kit V according to the manufacturer’s instructions (Lonza). One plasmid expressing pGreenpuro was also co-transfected. After 24 hours, the cells were selected in fresh medium with 6mg/ml puromycin (Sigma). After 72 hours, limiting dilution was performed and selection was continued for 8–12 days. Individual clones were picked and genomic DNA was extracted by following the manufacturer’s instructions (Redextract-N-AMP tissue kit, SIGMA). Genotyping was done by using locus-specific PCR primers under the following PCR conditions: 98°C for 30 s; 35 cycle (98°C for 10 s, 60°C for 30 s, 72°C for 35 s); 72°C for 5 min; hold at 4°C. PCR products were run on 2% agarose gel. Positive clones were expanded for further experiments.


title: EL4 shluc RNA-seq r2

description: RNA-seq


title: EL4 shCTCF RNA-seq  r1

description: RNA-seq


title: ileum conditional cdx2-/- ; Apc+/- replicate 1

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
il1tt


title: G45


title: EL4 shluc RNA-seq r1

description: RNA-seq


title: G38


title: cecum conditional cdx2-/- replicate 5

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
L2dt

source_name: cecum conditional cdx2-/-

value: Cecum


title: EL4 RNA-seq

description: RNA-seq


title: G37

value: bulbs


title: Th2 Cohesin ChIP-Seq

description: ChIP-seq

tag: cell type


title: cecum conditional cdx2-/- replicate 4

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
L1dt


title: G36

value: bulb expanding


title: cecum conditional cdx2-/- ; Apc+/- replicate 3

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
C3tt

source_name: cecum conditional cdx2-/- ; Apc+/-


title: Th2 H3K9me3 ChIP-Seq

description: ChIP-seq


title: G41


title: Th2 H3K27ac ChIP-Seq

description: ChIP-seq


title: cecum conditional cdx2-/- ; Apc+/- replicate 1

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
C1tt


title: G35


title: cecum conditional cdx2-/- ; Apc+/- replicate 2

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
C2tt


title: G33


title: Cecum cdx2 +/- replicate 3

description:
Heterozygous mice cdx2+/-
het_3

source_name: Cecum cdx2 +/-


title: G32


title: ES 3e Hi-C 1

description: Super-C

source_name: Embryonic stem cells

value: Embryonic stem cells


title: cecum conditional cdx2-/- replicate 6

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
L3dt


title: Cecum cdx2 +/- replicate 2

description:
Heterozygous mice cdx2+/-
het_2


title: G30


title: G39


title: Th2 3e Hi-C 2

description: Super-C


title: G29


title: stomach WT replicate 2

description:
Wild type mouse
Stc_2

source_name: stomach WT

value: WT

value: Stomach


title: stomach WT replicate 3

description:
Wild type mouse
Stc_3


title: Th2 3e Hi-C 1

description: Super-C


title: Th2 CTCF ChIP-Seq

description: ChIP-seq


title: G27


title: gRNA 9-1 REP2

first: Timothy

middle: K

last: Lu

address: 77 Mass. Avenue

institute: Massachusetts Institute of Technology

description: gRNA 9-1_2

data_processing:
Reads were processed using the MIT BMC/BCC 1.2 pipeline (http://openwetware.org/wiki/BioMicroCenter:Software#BMC-BCC_Pipeline)
Sequenced reads were trimmed for adaptor sequence, demultiplexed, and mapped to Saccharomyces cerevisiae whole genome (SacCer3) using ArrayStar v11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using ArrayStar v11. Values were capped to an autocalculated minimum value based on the default settings
Genome_build: SacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; Mean RPKM and P-values (student t-test, FDR correction)

organism: Saccharomyces cerevisiae

source_name: ITox2C_dCas9-VP64_gRNA 9-1

growth_protocol: Cultures were grown overnight in Synthetic complete medium - Uracil + Glucose (2%) + Doxycycline (1 µg/mL). These cultures were diluted into the same fresh media to OD600  = 0.1 and were incubated at 30°C, 300 RPM. Samples were collected in mid-logarithmic phase (OD600 = 0.8) and flash-frozen in liquid nitrogen. Samples were kept in -80°C until further processing.

extract_protocol:
RNA was extracted using MasterPure Yeast RNA Purification kit (Epicentre) following the manufacturer’s protocol. mRNA libraries were prepared using the Illumina TruSeq library preparation kit, barcoded, multiplexed and sequenced by Illumina HiSeq.
RNA libraries were prepared for sequencing using standard TruSeq Illumina protocols. Multiplexing barcodes: Ref_1: TAGGCT, Ref_2: ATTCGG, gRNA 9-1_1: GACGAT, gRNA 9-1_2: TTGCCG

tag: growth stage

value: Mid-logaritmic

value: gRNA


title: G34

tag: Stage


title: G28


title: cecum WT replicate 3

description:
Wild type mouse
Cec_3

source_name: cecum WT


title: ES 3e Hi-C 2

description: Super-C


title: gRNA 9-1 REP1

description: gRNA 9-1_1


title: no gRNA REP2

source_name: ITox2C_dCas9-VP64_no gRNA

value: control


title: stomach WT replicate 1

description:
Wild type mouse
Stc_1


title: G26


title: G25


title: cecum WT replicate 2

description:
Wild type mouse
Cec_2


title: no gRNA REP1


title: G24


title: G23


title: cecum WT replicate 1

description:
Wild type mouse
Cec_1


title: Cecum cdx2 +/- replicate 1

description:
Heterozygous mice cdx2+/-
het_1


title: cecum conditional cdx2-/- replicate 3

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
T21_3


title: G22


title: G21


title: cecum conditional cdx2-/- replicate 2

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
T21_2


title: cecum conditional cdx2-/- replicate 1

description:
Conditional cdx2 mutant induced by tamoxifen and bnaphthoflavone, CreERT uder the control of CYP1A1 (Ah) Promoter
T21_1


title: S4 Corn Stover 1

city: Santa Barbara

first: John

last: Henske

address: Engineering II Building

department: Department of Chemical Engineering

institute: University of California, Santa Barbara

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
CS1

data_processing:
Aligned reads from all conditions to transcriptomes using Trinity utility align_and_estimate_abundance.pl with RSEM estimation method
Genome_build: de novo
Supplementary_files_format_and_content: tab delimited text files containing estimated abundances of each transcript

organism: Anaeromyces robustus

source_name: Whole organism

growth_protocol: Cultures grown in ~ 10 ml Medium C (Davies et. al, J Gen Microbiol. 1993 Jun;139 Pt 6:1395-400.) at 39°C to mid-log phase (P≥5 psi)

extract_protocol:
Qiagen RNEasy Mini Kit (Plant/Fungi Protocol)
Illumina TruSeq Stranded mRNA library standard protocol

treatment_protocol: See characteristics for energy source treatments

tag: energy substrate

value: Corn Stover

tag: growth phase harvested from

value: Exponential growth


title: S4 Corn Stover 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
CS2


title: G20


title: S4 Switchgrass 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
SG3

value: Switchgrass


title: G19


title: WT 2

first: Abbe

middle: Rose

last: Clark

address: 4 Blackfan Circle, HIM 534

institute: Harvard, Brigham and Women's Hospital

description:
processed data column header: YZ_6_3806
genes.results.txt
Differential_expression_analysis_AT1RTgvWT.txt

data_processing:
Illumina software was used for basecalling.
Sequenced reads were mapped to Rnor_5.0 whole genome using STAR (Version 2.5.2b) with parameters -runThreadN 5 --twopassMode Basic -outSAMtype BAM SortedByCoordinate -outSAMstrandField intronMotif -limitBAMsortRAM 30000000000 -quantMode TranscriptomeSAM
Gene expression levels were estimated using RSEM (Version 1.3.0) with parameters -p 8 -bam -alignments -paired-end
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: tab-delimited text files include gene counts for all samples and differential expression analysis results

organism: Rattus norvegicus

source_name: Glomerulus

extract_protocol:
Glomeruli were isolated and RNA was harvested using Trizol reagent. An automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague Dawley

value: Glomerulus

value: 21.9 weeks

tag: genotype

value: wild type

value: Vehicle


title: G93

last: Liu


title: S4 Switchgrass 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
SG2


title: AT1R Tg Veh 2

description:
processed data column header: YZ_5_3805
genes.results.txt
Differential_expression_analysis_AC1903vVeh.txt
Differential_expression_analysis_AT1RTgvWT.txt

value: 17.4 weeks

value: AT1R Tg


title: S4 Switchgrass 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
SG1


title: WT 1

description:
processed data column header: YZ_4_3798
genes.results.txt
Differential_expression_analysis_AT1RTgvWT.txt

value: 20.4 weeks


title: G18

value: bulbs

value: bulb expanding


title: S4 Reed Canary Grass 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
RCG3

value: Reed Canary Grass


title: G16


title: G17


title: S4 Reed Canary Grass 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
RCG2


title: S4 Reed Canary Grass 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
RCG1


title: AT1R Tg AC1903 rep1

description:
processed data column header: YZ_1_3787
genes.results.txt
Differential_expression_analysis_AC1903vVeh.txt

value: 23.0 weeks


title: G15


title: S4 Avicel 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
A2

value: Avicel


title: G14


title: G11


title: AT1R Tg AC1903 rep2

description:
processed data column header: YZ_2_3796
genes.results.txt
Differential_expression_analysis_AC1903vVeh.txt


title: S4 Cellobiose 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
CB3

value: Cellobiose


title: S4 Avicel 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
A1


title: G10


title: S4 Cellobiose 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
CB2


title: G9


title: WT control

city: Tucson

first: Kerry

middle: Kevin

last: Cooper

state: AZ

address: 1117 E. Lowell St.

department: School of Animal and Comparative Biomedical Sciences

institute: University of Arizona

description:
Two replicates were merged:
WT rep1 (AC1)
WT rep2 (BC1)

data_processing:
The MiSeq Reporter software (v2.3) demultiplexed the samples based on the barcodes for each sample, then the barcodes and adaptors were removed and a FASTQ file for each sample was generated and used for further analysis
There is no reference genome available for P. elongata, therefore the Trinity software (v2.0.6) generated a de novo transcriptome utilizing the Illumina reads from all the samples pooled together.
The original de novo Trinity transcriptome assembly resulted in 84,136 contigs, these contigs were then examined for potential contamination by BLASTing all of the contigs against the NCBI non-redundant (nr) protein database using the blastx command in the DIAMOND (v0.71) program, and then the output matches were screened for non-plant matches using the MEGAN6 program. In total 44 contigs were identified as contamination (10 bacterial matches, 34 fungal matches), and were removed from the transcriptome prior to analysis.
The transcriptome was employed as a reference for further analysis (Kim et al. 2013). Next, the Tuxedo software suite, Bowtie 2 software (v2.1.0), TopHat2 software (v2.0.9), Cufflinks software (v2.1.1), and Cuffdiff software (v2.2.1) determined sequences with differential expression levels in response to salt stress in comparison to the controls (Trapnell et al. 2012). The Tuxedo suite mapped, quantified and determined the expression differences between these conditions from the generated reads. Sequences with a q-value (<0.05) were considered statistically significantly expressed.

A de novo transcriptome has also been deposited in the TSA project under accession number: GFBN00000000

The data was also analyzed using the RSEM program (v1.3.0) to further determine the differentially expressed genes when the P. elongata was salt stressed compared to the controls. Contigs with a p-value (<0.004), which is equal to the q-value (<0.05) used for the Tuxedo software suite, were considered statistically significant.
Genome_build: There is no reference genome available for P. elongata, therefore the Trinity software (v2.0.6) generated a de novo transcriptome utilizing the Illumina reads from all the samples pooled together.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample; normalized abundance measurements output from Cuffdiff, also output from RSEM

organism: Paulownia elongata

source_name: Control plants

growth_protocol: Three-year-old P. elongata pots were grown in a greenhouse under 25-30°C, 75% relative humidity and 13 hours of natural sunlight for the experiment.

extract_protocol:
Total RNA was extracted from Paulownia leaves using Quick-RNA MiniPrep Kit (Zymo Research, USA) following the manufacturer’s protocol. Paulownia RNA was treated with DNase I (Life Technologies, USA) and the RNA Clean-Up kit (Zymo Research, USA) eliminated genomic DNA contamination.
Barcoded cDNA libraries were synthesized from 1 µg of total RNA using the TruSeq RNA Sample Prep Kit (v2; Illumina, USA) following the manufacturer’s Low Sample Protocol.

treatment_protocol: Plants were irrigated with 1.5 L of 125 mM NaCl every 24 hours for 10 days in Pro-Mix HP Mycorrhizae potting soil (ingredients: Canadian Sphagnum peat moss (65%-70%), perlite and limestone (Premier Tech Horticulture, Canada). Salt water drained completely through the soil and out of the pots. Control plants were irrigated under the same conditions with 1.5 L of water.

value: leaves

value: 3-year old pots

value: control


title: G8


title: S4 Cellobiose 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
CB1

value: Exponential growth


title: NH4_2

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

institute: CBGP-Universidad Politecnica de Madrid

data_processing:
The resulting reads were trimmed to remove adaptor sequences and low quality base-calls, and were aligned to the Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1) using Torrent Mapper version 3.0.1 with the parameters -n 4 -v stage1 map1 map2 map3.
Abundance measurement was calculated using the HTSeq Python script HTSeq-count v.0.6.0 (Anders et al., 2014) with the parameters -m intersection-strict -s n0 -i locus-tag -t gene
Genome_build: Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1)
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each Sample

organism: Synechocystis sp. PCC 6803

source_name: cells

extract_protocol:
RNA from Synechocystis cultures grown in ammonium and switched for 4 hours to nitrogen depleted conditions were extracted using PGTX 95 RNA extraction protocol described in (Pinto et al., 2009). Samples for RNA-seq were obtained simultaneously from same cultures used for chromatin immunoprecipitation experiments. The quantity and quality of total RNA were evaluated using RNA electropherograms (Agilent 2100 Bioanalyzer, Agilent Technologies)
RNA libraries were prepared for sequencing using standard Ion Torrent PGM Machine protocols.

value: growth in BG11C containing NH4


title: AT1R Tg Veh 1

description:
processed data column header: YZ_3_3797
genes.results.txt
Differential_expression_analysis_AC1903vVeh.txt
Differential_expression_analysis_AT1RTgvWT.txt

value: Sprague Dawley

value: Glomerulus


title: N2_2

value: 4 hours nitrogen starvation


title: N2_1


title: S4 Maltose 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
M2

value: Maltose


title: S4 Maltose 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
M1


title: S4 Maltose 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
M3


title: S4 Avicel 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
A3


title: G3


title: G5


title: G7


title: S4 Glucose 3

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
G3

value: Glucose


title: G13


title: G6


title: S4 Glucose 2

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
G2


title: G1 Alfalfa Stems 3

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
AS3

organism: Neocallimastix californiae

value: Alfalfa Stems


title: N2

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Illumina sequencing data were pre-processed with the standard Illumina pipeline version 1.6 and only 20% of sequences were then aligned to the Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1) using Bowtie2 version 2.2.4 with the parameters -p 4
bam files were normalized unsing bamcoverage from DeepTools version 2.0.1
peaks were called using MACS version 1.4.1 with the following setting: band width (300), p-value cutoff= (1.00e-05), and Bayespeak version 1.22.0 with the paramters: method ="lowerbound"
Genome_build: Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1)
Supplementary_files_format_and_content: bigWig files were generated using bamcoverage from DeepTools version 2.0.1.

extract_protocol:
DNA was purified using phenol:chloroform extraction followed by ethanol precipitation with ammonium acetate and glycogen. DNA was dissolved in DNAse-free purified water.
Libraries were prepared according to Dianogenode`s instructions accompanying the Dianogenode Microplex Library preparation Kit for Illumina sequencing platform.

value: anti-NtcA (in-house; generated in Rabbit by injecting Synechocystis´s NtcA previously purified)


title: G1 Alfalfa Stems 2

description:
G1_substrate_raw_tpm.txt
G1_substrate_raw_expectedcounts.txt
AS2


title: NH4


title: G2

value: bulbs

value: bulb expanding


title: NH4_1


title: S4 Glucose 1

description:
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
G1


title: N2input