title: RNA-Seq, t=7.5 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv

data_processing:
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
genome build: hg19
processed data files format and content: tsv file with FPKM counts for each sample

extract_protocol:
For RNA-Seq, RNA was collected using TRIZOL reagent and purified using Zymo RNA Clean up kit and DNAse treated.
RNA-Seq libraries were prepared using Illumina TruSeq mRNA Library Prep Kit.


title: MAF1_macrophage1

status: Public on Aug 21 2017

type: SRA

city: Palo Alto

first: Kevin

last: Van Bortle

state: CA

address: 3165 Porter Dr

department: Genetics

country: USA

institute: Stanford University

description:
ChIP-seq macrophage biological replicate 1
Processed data file: MAF1_peak_edgeR.txt

library_source: genomic

data_processing:
Biological replicates and experimental conditions (-PMA; +PMA) were sequenced together on an Illumina HiSeq2000 (paired-end, 100) for each individual experiment type (RNA-seq, ChIP-seq, PRO-seq), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed ChIP and ATAC sequencing reads were mapped to the hg19 genome using Bowtie v 2.2.4, duplicate reads were removed by Picard tools v. 1.92 and mitochondrial reads filtered before peak-calling using MACS2 v. 2.1.0.
Alignment of sequencing reads to the current hg19 annotation of human tRNA genes (gtRNAdb; (Chan and Lowe 2009; Chan and Lowe 2016)) included the upstream and downstream 100 nt flanking genomic regions.
Genome_build: hg19
Supplementary_files_format_and_content: tDNA count files were generated by extracting reads over tRNA genes (100nt flanking) and non-tRNA genes and normalized counts determined by DESeq; ATAC and ChIP peaks were determined using MACS2 v. 2.1.0. Changes in chromatin accessibility and histone occupancy were determined by differential read count analyses (EdgeR) over merged peak lists for each factor

molecule: genomic DNA

organism: Homo sapiens

source_name: THP-1 cells, + PMA exposure, MAF1 ChIP

growth_protocol: THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 105 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65C overnight, followed by digestion of RNA (30 min RNase incubation at 37C) and digestion of protein (30 min proteinase K incubation at 45C). ChIP DNA was then purified on a minElute column (Qiagen)
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 10^5 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer.

tag: cell line

tag: pma exposure

value: 72 hr PMA exposure

tag: cell type

value: derived macrophages

tag: chip antibody

value: anti-MAF1 (Santa Cruz sc-365312 lot # G1411)


title: CTL_TNF_Batch4_425_13589

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from immortalized N/TERT-2G keratinocytes

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the human reference genome (NCBI build 37) using Bowtie and splice junctions were identified using TopHat with default settings.
Read counts were estimated for each gene using an in-house python script (see Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, et al. 2014. Transcriptome analysis of psoriasis in a large case-control Sample: RNA-Seq rovides insights into disease mechanisms. J Invest Dermatol 134:1828-1838)
Expression values were expressed as the number of reads per kilobase per million mapped reads (RPKM).
Genome_build: NCBI build 37
Supplementary_files_format_and_content: Processed data includes raw read counts and RPKM values for all human genes (NCBI build 37) and each sample (.txt files).

molecule: total RNA

source_name: keratinocyte

growth_protocol: N/TERT-TR-shTRAF3IP2 cells were generated by transfecting N/TERT-TR cells with a lentivirus expressing an shRNA (targeting sequence 5’-GCCAGATGCTTGTGTATCCTC-3’) mapping to the 3’ untranslated region of the TRAF3IP2 gene (NM_147686 and NM_001164281 encoding TRAF3IP2 isoforms 2 and 3, respectively). N/TERT-TR-shTRAF3IP2 cells were grown in complete keratinocyte serum-free medium (KSFM, Life Technologies, Carlsbad, CA) adjusted to 0.4 mM CaCl2, with feedings every two days. Cells were plated at 8,000 cells/cm2. Cells were then grown for seven days, at which point they were confluent.

extract_protocol:
Total RNA was isolated using the RNeasy plus isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.  An Agilent Bioanalzyer (Agilent Technologies, Santa Clara, CA) was used to assess RNA quality and quantity.
Polyadenylated RNA was purified and used to prepare complementary DNA libraries for high throughput sequencing using the Illumina mRNA-Seq kit according to the manufacturer’s protocol (Illumina, San Diego, CA). Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: TRAF3IP2 shRNA expression was induced by addition of Tet (1µg/ml) to the medium the day after seeding. Cells were stimulated with IL-17 and/or TNF. Recombinant human IL-17A and TNF were purchased from R&D Systems (Minneapolis, MN).

tag: batch id

tag: tetracycline

value: TET(-)

tag: treatment

value: TNF


title: TET_TNF_Batch4_425_13593

value: TET(+)


title: TET_CTL_Batch4_425_13591

value: control


title: CTL_IL17_Batch4_425_13588


title: RNA-Seq, t=7.5 h, IR 10Gy, rep1

city: Boston

first: Antonina

last: Hafner

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

description: RNASeqGEO.tsv

growth_protocol: MCF7 and MCF7 p53sh cells were grown in RPMI+10%FBS

treatment_protocol: Cells were either untreated (t=0h timepoints), treated with 10Gy gamma irradiation and collected at corresponding timepoints (t= xh); or treated with 10Gy gamma irradiation following 3 additions of Nutlin 3a (Sigma) according to the protocol described in Purvis et al. 2012 (PMID:23452846)

tag: passage

value: between 4-14 for all experiments


title: Pooled 8 weeks sample

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

description:
hBLT Mouse
P0

data_processing:
hisat2 -p ${CORES} -x genome -1 ${FQ1} -2 ${FQ2} -S ${FQ1/.fastq.gz/.sam}
featureCounts -T ${CORES} -t exon -g gene_name -s 1 -a ${GTF} -o Jon_mRNA.txt Ctrl.bam …
Genome_build: hg19
Supplementary_files_format_and_content: text table, DESeq2 normalized log2 expression level.

source_name: Human CD3+,CD45 + T-cells in humanized mice

extract_protocol:
Total RNA was extracted and quantified using the miRNeasy Kit (Qiagen) according to manufacturer's protocol.  mRNAs were purified and amplified to cDNA using the Ovation RNA-seq V2  System (NuGEN).
Libraries were prepared and indexed using NEBNext Ultra DNA Library Prep Kit for Illumina, and NEBNext Multiplex Oligos

treatment_protocol: Circulating T-cells were isolated from whole blood via Flow Cytometry. Cells were identified as T-cells using CD3+ and CD45+ double surface markers.

value: CD3+,CD45 + T-cells

tag: sample age

value: 8 weeks

tag: gender

value: Male


title: CTL_IL17TNF_Batch4_425_13590


title: RNA-Seq, t=5 h, IR 10Gy , rep3

description: RNASeqGEO.tsv


title: MAF1_monocyte1

description:
ChIP-seq monocyte biological replicate 1
Processed data file: MAF1_peak_edgeR.txt

source_name: THP-1 cells, - PMA exposure, MAF1 ChIP

value: ( - PMA )

value: monocytes


title: RNA-Seq, t=1 h, IR 10Gy , rep3

description: RNASeqGEO.tsv


title: TET_IL17TNF_Batch4_425_13594


title: RNA-Seq, t=0 h, rep3

description: RNASeqGEO.tsv


title: RNA-Seq, t=12 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: TET_IL17_Batch5_425_13600


title: 2_both_BRD4_KD_RNA

city: San Francisco

first: Melanie

last: Ott

address: 1650 Owens St.

institute: Gladstone Institutes

data_processing:
Adapter trimming and read quality control was performed using the fastq-mcf tool.
ChIP-/ATAC-seq reads were aligned using bowtie2
RNA-seq reads were aligned with tophat2
ChIP-/ATAC-seq peaks were called using thresholding methods, BCP, Homer, and MACS2
Genome_build: hg19
Supplementary_files_format_and_content: .wig files for ChIP-/ATAC-seq, excel file for RNA-seq

source_name: J-Lat A72

growth_protocol: J-Lat A72 cells were cultured in RPMI supplemented with 10% FBS, 1% glutamine, and 1% penicillin- streptomycin at 37°C, 5% CO2 at an optimal seeding density of 500,000 cells/mL.

extract_protocol:
Genomic DNA was extracted using the QIAquick PCR Purification Kit (Qiagen). RNA was isolated via RNeasy Plus Mini Kit (Qiagen).
ChIP libraries were generate using the Ovation Ultralow Library Systems V2 (NuGEN). ATAC libraries were generated using the Nextera DNA Sample Prep Kit (Illumina). RNA libraries were generated using the Ovation RNA-Seq System V2 (NuGEN).

treatment_protocol: All JQ1 treatments were at 625nM for ~18h. shRNA transductions were performed as in (Boehm et al. 2013a).

tag: genotype


title: TET_IL17_Batch3_336_11061


title: TET_IL17TNF_Batch3_336_11063


title: Pooled 16 weeks

description:
hBLT Mouse
P3

value: 16 weeks


title: RNA-Seq, t=4 h, IR 10Gy, rep3

description: RNASeqGEO.tsv


title: RNA-Seq, t=2.5 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: TET_IL17_Batch4_425_13592


title: MAF1_monocyte2

description:
ChIP-seq monocyte biological replicate 2
Processed data file: MAF1_peak_edgeR.txt


title: RNA-Seq, t=24 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: 2_short_BRD4_KD_RNA


title: Pooled 20 weeks

description:
hBLT Mouse
P4

value: 20 weeks


title: RNA-Seq, t=10 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: TET_TNF_Batch3_336_11062


title: 1_both_BRD4_KD_RNA


title: TET_CTL_Batch3_336_11060


title: 2_long_BRD4_KD_RNA


title: 2_scramble_RNA


title: Control Sample

description:
control human T-cells
Control

source_name: Human CD3+,CD45 + T-cells

value: Mature reference (adult human)


title: CTL_CTL_Batch4_425_13587


title: CTL_IL17TNF_Batch3_336_11059


title: CTL_TNF_Batch3_336_11058


title: 1_short_BRD4_KD_RNA


title: RNA-Seq, t=7 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=8 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: 1_long_BRD4_KD_RNA


title: RNA-Seq, t=5 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=11 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: CTL_IL17_Batch3_336_11057


title: RNA-Seq, t=9 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=3 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: TET_CTL_Batch2_336_11044


title: 2_DMSO_ATAC

description: transposed genomic DNA

value: DMSO


title: 1_scramble_RNA


title: RNA-Seq, t=6 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: 3_JQ1_input


title: CTL_IL17_Batch2_336_11041


title: 3_DMSO_input


title: CTL_CTL_Batch3_336_11056


title: CTL_CTL_Batch2_336_11040


title: TET_TNF_Batch2_336_11046


title: 2_JQ1_ATAC

description: transposed genomic DNA


title: TET_IL17TNF_Batch2_336_11047


title: WT4.IRX4_GATC_GTAC

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

data_processing:
Library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) genome using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, they contain smoothed data that can be directly uploaded to UCSC for visualization.

organism: Mus musculus

source_name: E11.5 mouse embryonic heart

growth_protocol: Ctcf fl/+; Nkx2.5-Cre x Ctcf fl/fl crosses. Embryonic hearts (control and Ctcf KO) were taken at 11.5dpc, taking the day in which the plug was found as 0.5dpc.

extract_protocol:
Chromatin was extracted from single cells preparations from pulled hearts samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.  Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.
Primers with Illumina adaptors were used to amplify the library.

tag: developmental stage

tag: tissue

value: heart

value: wildtype


title: TET_IL17_Batch2_336_11045


title: 1_JQ1_ATAC

description: transposed genomic DNA


title: RNA-Seq, t=11 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=10 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: CTL_IL17TNF_Batch2_336_11043


title: WT3.NDUFS6_GATC_GTAC


title: 1_JQ1_input


title: RNA-Seq, t=4 h, IR 10Gy + Nutlin, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=8 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=0 h, rep2_2

description: RNASeqGEO.tsv


title: CTL_TNF_Batch2_336_11042


title: RNA-Seq, t=24 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=12 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=6 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: 3_JQ1_BRD4

value: Abcam ab128874


title: 2_JQ1_polII

value: Santa Cruz N-20, sc-899


title: RNA-Seq, t=5 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: 2_JQ1_input


title: 2_JQ1_BRG1

value: Abcam ab110641


title: 1_DMSO_ATAC

description: transposed genomic DNA


title: 2_DMSO_input


title: RNA-Seq, t=9 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=3 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: WT4.NDUFS6_GATC_GTAC


title: KO1.NDUFS6_GATC_GTAC

value: CTCF KO


title: 1_DMSO_input


title: 2_DMSO_BRG1


title: RNA-Seq, t=0 h, rep1_2

description: RNASeqGEO.tsv


title: WT2.NDUFS6_GATC_GTAC


title: RNA-Seq, t=7 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=9 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv

source_name: MCF7 p53sh


title: WT1.NDUFS6_GATC_GTAC


title: 2_DMSO_BRD4


title: 1_JQ1_polII


title: 3_DMSO_BRD4


title: KO2.NDUFS6_GATC_GTAC


title: RNA-Seq, t=4 h, IR 10Gy + Nutlin, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=5 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: WT2.IRX4_GATC_GTAC


title: KO2.IRX4_GATC_GTAC


title: 1_JQ1_BRD4


title: KO1.IRX4_GATC_GTAC


title: 2_JQ1_BRD4


title: WT2.5PCTCF_GATC_GTAC


title: WT3.IRX4_GATC_GTAC


title: 2_DMSO_polII


title: 1_DMSO_polII


title: RNA-Seq, t=10 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: RNA-Seq, t=2 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: KO4.IRX4_GATC_GTAC


title: KO3.NDUFS6_GATC_GTAC


title: RNA-Seq, t=0 h, rep2_p53sh

description: RNASeqGEO.tsv


title: 1_DMSO_BRD4


title: WT1.5PCTCF_GATC_GTAC


title: WT1.IRX4_GATC_GTAC


title: KO2.5PCTCF_GATC_GTAC


title: RNA-Seq, t=7 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: MOLM13-72-hrs-6-oxRRBS

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were quality and adapter trimmed using Trim Galore with RRBS option.
The trimmed reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using Bismark aligner.
Methylation calls were performed by Bismark.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: bismark coverage report (tab-delimited): <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: Myeloid leukemia cell

growth_protocol: Human cell lines were grown in RPMI media with 10-20% FBS, mouse progenitors were cultured in Optimem media supplemented with 10%FBS and SCF, IL3 and IL6 cytokines

extract_protocol:
DNA was isolated by proteinase K digestion, phenol chloroform extraction and ethanol precipitation
Bisulfite sequencing libraries were prepared using the TruMethyl-Seq Kit from CEGX following standard Illumina protocols

treatment_protocol: Human cell lines were treated with vitamin C in culture for 0, 12 and 72hrs. Mouse progenitors were treated with 1ug/ml Doxycycline to turn off Tet2 shRNA expression for 14 days

tag: cancer type

value: Leukemia

value: Human myeloid cell

tag: time


title: MOLM13-72-hrs-5-oxRRBS


title: KO1.5PCTCF_GATC_GTAC


title: PTH_3

city: ROCHESTER

first: Longze

last: Zhang

state: NY

address: 55 FAIRHILL DR.

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.36 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
REFERENCE - GRCm38.p5 + Gencode-M12 Annotation
READ COUNTING - subread-1.5.0p3, featurecounts, Unique   "-s 0 -t exon -g gene_name"
Multi-Mapping "-s 0 -M -t exon -g gene_name"
DIFFERENTIAL EXP. - DESeq2_1.12.4
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
Genome_build: mm9
Supplementary_files_format_and_content: deSeq2_counts txt: counts
Supplementary_files_format_and_content: deSeq2_NormCounts txt: Normal counts
Supplementary_files_format_and_content: deSeq2_PTH_vs_C txt: p value
Supplementary_files_format_and_content: deSeq2_rlog_NormCounts txtL log count

source_name: MC/9_rPTH treated

growth_protocol: MC/9 (ATCC® CRL-8306™), growth protocol from ATCC: https://www.atcc.org/Products/All/CRL-8306.aspx#culturemethod; 7F2 (ATCC® CRL-12557™): growth protocol from ATCC: https://www.atcc.org/Products/All/CRL-12557.aspx#culturemethod

extract_protocol:
mast cells were collected, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10nM rPTH treated for 24hours

value: mast cell line

tag: treated wth

value: 10nM rPTH for 24hours


title: RNA-Seq, t=24 h, IR 10Gy, rep2

description: RNASeqGEO.tsv

value: between 4-14 for all experiments


title: RNA-Seq, t=11 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=4 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: KO3.IRX4_GATC_GTAC


title: RNA-Seq, t=3 h, IR 10Gy, rep2_p53sh

description: RNASeqGEO.tsv


title: RNA-Seq, t=9 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: 1_JQ1_BRG1


title: C3

value: none (control)


title: RNA-Seq, t=12 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: 1_DMSO_BRG1


title: C1


title: MOLM13-0-hrs-3-oxRRBS


title: RNA-Seq, t=6 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: PTH_1


title: RNA-Seq, t=10 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: MOLM13-12-hrs-14-oxRRBS


title: PTH_2


title: RNA-Seq, t=5 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: MOLM13-12-hrs-15-oxRRBS


title: Zbtb18-ES rep3

city: Yangling

first: Haibo

address: 3rd, Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13. The clean reads were then aligned to mouse genome (version: mm10) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.We applied DEseq algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) Fold Change>2 or <0.5; ii) FDR<0.05.
Pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value and FDR.
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
We present Gene co-expression Networks to find the relations among genes. Gene co-expression Networks were built according to the normalized expression values of genes selected from genes in significant GO-terms. For each pair of genes, we calculate the Pearson Correlation and choose the significant correlation pairs (FDR<0.05) to constructed the network.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: J1 ES cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using IonProton,The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols.

value: embryonic stem cell

value: Zbtb18 stable expressed


title: Zbtb18-ES rep1


title: RNA-Seq, t=8 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=4 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=2 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: HL60-72-hrs-11-oxRRBS


title: MOLM13-12-hrs-13-oxRRBS


title: C2


title: HL60-72-hrs-10-oxRRBS


title: MOLM13-0-hrs-1-oxRRBS


title: MOLM13-0-hrs-2-oxRRBS


title: RNA-Seq, t=7 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: MOLM13-72-hrs-4-oxRRBS


title: HL60-72-hrs-12-oxRRBS


title: RNA-Seq, t=3 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: RNA-Seq, t=10 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv


title: RNA-Seq, t=1 h, IR 10Gy, rep2

description: RNASeqGEO.tsv


title: Foxj3-ES rep2

value: Foxj3 stable expressed


title: Foxj3-ES rep1


title: HL60-12-hrs-18-oxRRBS


title: HL60-0-hrs-9-oxRRBS


title: Zbtb18-ES rep2


title: HL60-12-hrs-16-oxRRBS


title: RNA-Seq, t=7 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv


title: HL60-0-hrs-8-oxRRBS


title: Foxj3-ES rep3


title: RNA-Seq, t=5 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv


title: RNA-Seq, t=0 h, rep2_1

description: RNASeqGEO.tsv


title: MM Stage 0 rep 2

city: Brno

first: Neha

last: Shukla

address: Kamenice 753

department: Plant Molecular Biology

country: Czech Republic

institute: CEITEC

data_processing:
Basecalling was performed using CASAVA version 1.8
Quality assessment was carried out using FastQC and quality filtering of raw reads was done for mean phred quality score of 20 and any contaminating adapter sequences were removed using PrinSeq and Cutadapt.
After filtering for the good quality reads, reads were aligned independently onto S. lycopersicum and M. Incognita genomes using TopHat v2.0.14 on default parameters.
After alignment, uniquely mapped reads were further quantified using HTSeq based on gene annotations.
Genome_build: S. lycopersicum genome build SL2.50; M. Incognita WB release 5 (http://parasite.wormbase.org/).  The gene annotations are publicly available at: http://parasite.wormbase.org/Meloidogyne_incognita_prjea28837/Info/Index/
Supplementary_files_format_and_content: bigWig files for each sample; tab-delimited text files include read count values for each Sample.

molecule: polyA RNA

organism:
Solanum lycopersicum
Meloidogyne incognita

source_name: Whole roots

growth_protocol: Tomato seeds were germinated in trays (36cm x 25cm x 7cm) in sterile soil:solrite (1:4) at 22±2ºC, 16h light/8h dark cycle in greenhouse chamber. Three week old seedlings were transferred to black potted trays (4cm in diameter) in soil:sand (1:1). Stocks of Meloidogyne incognita were maintained on susceptible tomato and brinjal plants in a greenhouse culture room. Infected roots were collected; egg masses were hand-dissected and kept in autoclaved double distilled water for hatching at room temperature.

extract_protocol:
RNA extraction protocol not provided.
Transcriptome libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina, USA) according to the manufacturer’s protocol.

treatment_protocol: Five-week old tomato seedlings were inoculated with 1500 freshly hatched J2s per plant and water (control) in black potted trays. Whole roots at different days post infection (dpi) were collected with two to five technical replicates.

tag: control or experimental sample

value: Control

value: roots

tag: tomato cultivar

value: MM

tag: days post rkn inoculation

value: 0 days post inoculation

tag: disease developmental stage

value: No disease


title: HL60-0-hrs-7-oxRRBS

tag: cell type


title: MM Stage 0 rep 1


title: RNA-Seq, t=4 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv

tag: cell line


title: RNA-Seq, t=3 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv


title: M36 Infected Stage 2 rep 2

value: Sample

value: M36:Transgenic MM line

tag: tomato susceptibility to root-knot nematode infection

value: resistant

value: 5,6,7 days post inoculation

value: Stage 2


title: HL60-72-hrs-3-input

data_processing:
Library strategy: hMeDIP-Seq
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The reads were aligned to the human genome (build hg19/GRCh37) using Bowtie2 aligner with local alignment.
Poorly mapped reads (mapping quality <30) were removed using samtools.
Duplicate reads were removed using Picard.
Peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: *bed: Bed files include peaks.

source_name: Myeloid leukemia cells, vitamin C, 72h, input

growth_protocol: Human cell lines were grown in RPMI media with 10-20% FBS.

extract_protocol:
DNA was isolated by proteinase K digestion, phenol chloroform extraction and ethanol precipitation.
Libraries were prepared according to Illumina standard protocols. 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.

treatment_protocol: Human cell lines were treated with vitamin C in culture for 0 and 72hrs.

value: Human myeloid cells

value: Leukemia

tag: treatment

value: Vitamin C

tag: antibody

tag: sample type

value: genomic background


title: M36 Infected Stage 2 rep 1

description:
M36_I_567
The corresponding uninfected sample was not paired-end sequenced for any replicate. Thus, sample was downsampled for further analysis.


title: RNA-Seq, t=2 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv

tag: passage

value: between 4-14 for all experiments


title: HL60-72-hrs-2-input


title: M36 Uninfected Stage 2 rep 2


title: RNA-Seq, t=0 h, rep1_p53sh

description: RNASeqGEO.tsv


title: HL60-12-hrs-17-oxRRBS

value: Human myeloid cell


title: RNA-Seq, t=9 h, IR 10Gy, rep1_p53sh

description: RNASeqGEO.tsv


title: M36 Uninfected Stage 2 rep 1


title: HL60-72-hrs-1-input


title: M36 Infected Stage 1 rep 2

value: 1,2,3 days post inoculation

value: Stage 1


title: RNA-Seq, t=12 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=11 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: M36 Infected Stage 1 rep 1

description:
M36_I_123
The corresponding uninfected sample was not paired-end sequenced for any replicate. Thus, sample was downsampled for further analysis.

value: roots


title: RNA-Seq, t=10 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: HL60-0-hrs-3-input

source_name: Myeloid leukemia cells, vitamin C, 0h, input


title: M36 Uninfected Stage 1 rep 2

value: Control


title: HL60-0-hrs-3-hMeDIP

source_name: Myeloid leukemia cells, vitamin C, 0h, hMeDIP

value: hMeDIP enrichment


title: HL60-72-hrs-1-hMeDIP

source_name: Myeloid leukemia cells, vitamin C, 72h, hMeDIP


title: RNA-Seq, t=8 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: M36 Uninfected Stage 1 rep 1

value: No disease


title: RNA-Seq, t=7 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: HL60-0-hrs-2-hMeDIP


title: M36 Stage 0 rep 1

value: 0 days post inoculation


title: HL60-72-hrs-3-hMeDIP


title: PR Infected Stage 5 rep 2

value: Sample

value: Pusa Ruby

value: susceptible

value: 26,27,28 days post inoculation

value: Stage 5


title: HL60-72-hrs-2-hMeDIP

value: Human myeloid cells

value: Leukemia


title: RNA-Seq, t=6 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: PR Infected Stage 5 rep 1


title: RNA-Seq, t=5 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: M36 Stage 0 rep 2

value: M36:Transgenic MM line

value: resistant


title: MOLM13-72-hrs-27

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

extract_protocol:
RNA was isolated from cells according to the RNeasy Qiagen Kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human myeloid cell

tag: dox


title: RNA-Seq, t=24 h, IR 10Gy, rep1

description: RNASeqGEO.tsv

value: between 4-14 for all experiments


title: PR Uninfected Stage 5 rep 2


title: HL60-0-hrs-1-hMeDIP

value: Vitamin C


title: MOLM13-72-hrs-25


title: HL60-0-hrs-1-input

value: genomic background


title: RNA-Seq, t=4 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: MOLM13-72-hrs-23


title: PR Uninfected Stage 5 rep 1

value: Control

value: roots


title: HL60-0-hrs-2-input


title: RNA-Seq, t=9 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: RNA-Seq, t=2 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: MOLM13-12-hrs-22


title: RNA-Seq, t=1 h, IR 10Gy, rep1

description: RNASeqGEO.tsv


title: PR Infected Stage 4 rep 1

value: 18,19,20 days post inoculation

value: Stage 4


title: MOLM13-12-hrs-21


title: RNA-Seq, t=0 h, rep1_1

description: RNASeqGEO.tsv


title: MOLM13-12-hrs-20


title: PR Uninfected Stage 4 rep 1

value: No disease


title: PR Infected Stage 4 rep 2

value: Sample

value: Pusa Ruby


title: PR Uninfected Stage 4 rep 2

value: susceptible


title: RNA-seq of Arabidopsis thaliana: Dark Grown [Dark-RNA4]

city: Cardiff

first: Daniel

middle: Antony

last: Pass

state: South Glamorgan

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description:
Dark-RNA4
processed data column: ES08

data_processing:
Alignment: bowtie allowing 3 base missmatches against TAIR10 genome from paired-end input
Total coverage: Joined paired reads with bamToBed -bedpe
Feature alignments: danpos.py to manual specification
RNAseq: tophat2 with Araport11.gtf annotation and TAIR10.fasta reference genome
Isoform Analysis: cufflinks with Araport11.gtf  and TAIR10.fasta
Quantification and Differential Expression analysis: HTseq and edgeR (Anders, S. et. al., Bioinformatics, 2015)(Robinson et al., Bioinformatics, 2009)
Genome_build: Athal Col0 TAIR10
Supplementary_files_format_and_content: Wig.gz: Fixed width genomic traces of MNase digested samples at midpoints or total coverage at size separation; *csv: Rawcounts and edgeR output

organism: Arabidopsis thaliana

source_name: RNA-seq_Dark Grown

growth_protocol: Arabidopsis cell line (Columbia ecotype, Col-0) was maintained in 250 mL Erlenmeyer flasks, filled with 50 mL of cell culture medium (Gamborg’s B5 basal medium with minor organic (Sigma G5893) in 1.1 mg/L 2,4-D, 3 mM MES and 3% sucrose)(described in Lee et al., 2010 and Tanurdzic et al., 2008). Cells were grown on a rotary shaker 160 rpm at 23°C (LS-X (Lab Shaker), Kuhner Shaker X). Constant light was used whereas dark grown cells were incubated under the same shaking and temperature condition but the flask were covered of aluminum foil. Cell line was subcultured every 7 days with a 2:50 (inoculum: fresh medium) dilution ratio. Cultures were carried out in duplicates.

extract_protocol:
Chromatin Digestion
Pelleted cell culture was ground in a liquid nitrogen-cooled pestle and mortar to generate a cell powder. 1mL of the powder was suspended in a 0.5mL modified spheroplast digestion buffer & Nonidet P40 (SDBN: 1M sorbitol, 10mM NaCl, 50 mM TrisŸHCl pH7.5, 5mM MgCl2, 1 mM CaCl2, 1 mM 2-mercaptoethanol, 0.5 mM spermidine, 0.075% Nonidet P40). 300 µl of cells were transferred into 1.5mL microcentrifuge tube containing 30 or 120 units of MNase (Affimetrix). Cells were digested with MNase at 37°C for 3 min. The MNase digestion reactions were stopped by addition of and thorough mixing 30 µl of STOP solution containing 5% SDS and 250 µl EDTA. DNA was extracted by addition of an equal volume of 2X CTAB supplemented with PVP (200 mM Tris-HCl, 40 mM EDTA, pH 8.0; 2.8 M NaCl, 4% w/v CTAB, 2% PVP-40 cas number 9003-39-8) was added to the digestion reaction and incubated at 45°C for 15 mins. DNA was separated from protein by two phenol:chloroform (300:300) steps. DNA was precipitated with sodium acetate and propan-2-ol then washed in 80% ethanol and dried. Samples were incubated with 10X RNase A at 37°C for 1h with 100U unmodified T4 polynucleotide kinase (NEB) for further 30 min at 37°C.
MNase digested DNA was separated on 1.5% agarose gel, stained with ethidium bromide for 10 min at 80V, DNA fragments ranging from 20 bp to 1 kb were cut out and gel pieces containing DNA were placed in a Costar Spin-X 0.45 µm cellulose acetate centrifuge tube filter (Sigma CLS8136). Two series of freeze-thaws (-80C for 10 mins/RT for 10 mins) were performed to macerate the gel. Filter tubes were centrifuged twice (14kg; 5 min; RT) with a 180 degree rotation of the tubes between the two spins. DNA in the aqueous phase was then extracted with phenol:chloroform (200:200), and precipitated at -80°C for 30 mins with sodium acetate to propan-2-ol and finally washed with 80% ethanol before being resuspended in  ultrapure milliQ water.
RNA isolation
Total RNA was extracted using the RNeasy Plant mini Kit (Qiagen, http://www.qiagen.com).
Nucleic acid quantification and quality check
DNA samples were quantified on QubitTM 2.0 Fluorometer with dsDNA BR assay according to manufacturer’s instructions.
RNA was quantified using QubitTM 2.0 fluorometer with Qubit RNA BR assay according to manufacturer’s instructions. RNA quality was checked on 1.5% agarose gel.
Exeter Sequencing Service and Computational core facilities at the University of Exeter performed the Genomic and RNA library preparation, quantification and 50bp paired end sequencing on HiSeq 2500.

treatment_protocol: Light grown cells were sampled 5 days or 16 hours after subculture. Dark grown cells were adapted to dark conditions for 2 weeks with a 7-day subculture. Dark grown cells were sampled 16-hour after the 2nd subculture. Cells were sampled by harvesting 30mL of cell culture and washed with autoclaved ultrapure water. Cells were frozen in liquid nitrogen and ground into a fine powder. The cell powder was either stored at -80°C or used directly for MNase digestion and RNA isolation.

tag: ecotype background

value: 16h post-stratification cell culture

tag: growth condition

value: Dark


title: MOLM13-0-hrs-19

tag: cancer type

value: Leukemia


title: MOLM13-0-hrs-18

tag: time


title: PR Infected Stage 3 rep 1

tag: tissue

value: 13,14,15 days post inoculation

value: Stage 3


title: RNA-seq of Arabidopsis thaliana: Dark Grown [Dark-RNA2]

description:
Dark-RNA2
processed data column: ES04


title: MOLM13-0-hrs-16

value: Human myeloid cell


title: RNA-seq of Arabidopsis thaliana: Dark Grown [Dark-RNA3]

description:
Dark-RNA3
processed data column: ES06


title: HL60-72-hrs-15


title: PR Uninfected Stage 3 rep 2

tag: control or experimental sample


title: RNA-Seq, t=3 h, IR 10Gy, rep1

description: RNASeqGEO.tsv

value: between 4-14 for all experiments


title: RNA-seq of Arabidopsis thaliana: Dark Grown [Dark-RNA1]

description:
Dark-RNA1
processed data column: ES02


title: PR Infected Stage 2 rep 2

tag: tomato cultivar

value: 5,6,7 days post inoculation

value: Stage 2


title: HL60-72-hrs-14


title: RNA-seq of Arabidopsis thaliana: Light Grown [Light-RNA4]

description:
Light-RNA4
processed data column: ES07

source_name: RNA-seq_Light Grown

value: Light


title: HL60-12-hrs-7


title: RNA-seq of Arabidopsis thaliana: Light Grown [Light-RNA3]

description:
Light-RNA3
processed data column: ES05


title: PR Infected Stage 2 rep 1

value: roots

tag: days post rkn inoculation


title: RNA-seq of Arabidopsis thaliana: Light Grown [Light-RNA2]

description:
Light-RNA2
processed data column: ES03


title: PR Uninfected Stage 2 rep 2

value: Control

tag: disease developmental stage


title: HL60-12-hrs-5

tag: cell type


title: PR Uninfected Stage 2 rep 1


title: Mnase-seq of Arabidopsis thaliana: Dark Grown High digest [Dark-H2]

source_name: Mnase-seq_Dark Grown High digest

tag: mnase digestion

value: High


title: RNA-seq of Arabidopsis thaliana: Light Grown [Light-RNA1]

description:
Light-RNA1
processed data column: ES01


title: HL60-12-hrs-12


title: PR Infected Stage 3 rep 2

tag: tomato susceptibility to root-knot nematode infection


title: PR Infected Stage 1 rep 2

value: 1,2,3 days post inoculation

value: Stage 1


title: Mnase-seq of Arabidopsis thaliana: Dark Grown High digest [Dark-H1]


title: PR Infected Stage 1 rep 1

value: Sample

value: Pusa Ruby


title: PR Uninfected Stage 3 rep 1

value: susceptible

value: No disease


title: HL60-0-hrs-2

value: Leukemia


title: Mnase-seq of Arabidopsis thaliana: Dark Grown Low digest [Dark-L2]

source_name: Mnase-seq_Dark Grown Low digest

value: 16h post-stratification cell culture

value: Dark

value: Low


title: PR Uninfected Stage 1 rep 1


title: PR Uninfected Stage 1 rep 2


title: HL60-72-hrs-13

value: Human myeloid cell


title: HL60-0-hrs-1


title: PR Stage 0 rep 2

value: 0 days post inoculation


title: Mnase-seq of Arabidopsis thaliana: Light Grown High digest [Light-H1]

source_name: Mnase-seq_Light Grown High digest


title: PR Stage 0 rep 1


title: Mnase-seq of Arabidopsis thaliana: Dark Grown Low digest [Dark-L1]


title: Mnase-seq of Arabidopsis thaliana: Light Grown High digest [Light-H2]


title: Mnase-seq of Arabidopsis thaliana: Light Grown Low digest [Light-L2]

source_name: Mnase-seq_Light Grown Low digest


title: Mnase-seq of Arabidopsis thaliana: Light Grown Low digest [Light-L1]


title: JGI

city: Pune

first: Narendra

last: Kadoo

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

department: Biochemical Sciences

country: India

institute: CSIR-National Chemical Laboratory

data_processing:
Library strategy: Long SAGE
Ditag extraction using in-house developed Perl Scripts
Mapping using seqmap tool
Generation of normalized values using trimmed mean of M-values normalization method (TMM) available in edgeR package
Differential expression analysis using Audic and Claverie test (ACT test) and Chi-square test (Chi)
Supplementary_files_format_and_content: tab delimited text files containing tag sequences and their counts

organism: Cicer arietinum

source_name: chickpea seedling

growth_protocol: Chickpea seedlings of both susceptible and resistant cultivars were raised in greenhouse

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA isolation kit (Sigma-Aldrich, USA)
Long SAGE protocol as per the manual

treatment_protocol: Control libaries (JGC ans DVC) were mock-inoculated while Inoculated libraries (JGI snd DVI) were challenged with Foc race 1, 2 and 4

value: Both root and shoot

tag: phenotype

value: Susceptible to Foc

tag: inoculant

value: Fusarium oxysporum f. sp. ciceri (Foc)


title: JGC

value: Sterile de-ionized water


title: mrna-seq OO c

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

description: OO c

data_processing:
The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).
Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA).
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by LC Sciences before subsequent
For homology annotation, non-redundant sequences were annotated based on the following databases: Swiss-Prot (a manually annotated and reviewed protein sequence database); Nr (NCBI non-redundant protein sequences); Pfam (protein family); KEGG (KEGG Ortholog database); and KOG (euKaryotic Ortholog Groups).
Supplementary_files_format_and_content: The expression level of each transcript was measured as the number of clean reads mapped to its sequence. The mapped clean read number was normalized to RPKM (reads per kilo of per million mapped reads) with RSEM 1.2.3. We used DESeq to determine the FDR threshold. FDR < 0.05 and fold change > 2 were considered to indicate significant expression abundance.

organism: Odontobutis potamophilus

source_name: gonad

growth_protocol: A total of 18 one-year-old dark sleepers (Odontobutis potamophila),9 male and 9 female, all under the same culturing conditions, were obtained from Nanjing Fisheries Research Institute, Jiangsu Province, China.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analyzed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
For six cDNA library constructions, approximately 5μg of total RNA per sample was used for the RNA sample preparations. The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA). After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software

treatment_protocol: Testes and ovaries from 9 male and 9 female dark sleepers were collected for RNA extraction. Samplings of testes (OT a, OT b, and OT c) and ovaries (OO a, OO b, and OO c) had three biological replicates, each made up of three different individual gonad tissues.

tag: age

value: ovary


title: mrna-seq OO b

description: OO b


title: Erthyrocytic stages (3/3)

city: Parkville

first: Lee

middle: Ming

last: Yeoh

state: VIC

address: Bio21 Institute, 30 Flemington Rd

country: Australia

institute: The University of Melbourne

data_processing:
Build genome index with bowtie 2.2.9: bowtie2-build PlasmoDB-28_PbergheiANKA_Genome.fa <bowtie_ref>
Map reads with tophat 2.1.1, bowtie 2.2.9, samtools 1.3.1, boost 1.60.0: tophat -p 8 --library-type fr-firststrand --max-intron-length 3000 --min-intron-length 4 --output-dir <output_directory> <bowtie_ref> <1.fastq> <2.fastq>
Analyse for differential expression with limma 3.28.14, voom (edgeR 3.4.0), Rsubread 1.22.2, R 3.3.1:        fa_targets <- readTargets(file=fa_bam_list)        fa_celltype <- factor(fa_targets$CellType)        fa_design <- model.matrix(~fa_celltype)        fa_fcounts <- featureCounts(files=fa_targets$BamFile,annot.ext=gff_file,isGTFAnnotationFile=TRUE,nthreads=8,isPairedEnd=TRUE,strandSpecific=2)        fa_isexpr <- rowSums(cpm(fa_fcounts$counts) > 3) >= 3        fa_x <- fa_fcounts$counts[fa_isexpr,]        fa_y <- voom(fa_x,fa_design,plot=TRUE)        plotMDS(fa_y,xlim=c(-5,5))        fa_fit <- eBayes(lmFit(fa_y,fa_design))        write.csv(topTable(fa_fit,coef=2,number=Inf,p.value=0.05),file="limma_out_fa")        write.csv(topTable(fa_fit,coef=2,number=Inf,p.value=1),file="limma_out_fa_full")
Quantify RPKM counts with limma 3.28.14, Rsubread 1.22.2, R 3.3.1:        all_targets <- readTargets(file=all_bam_list)        all_celltype <- factor(all_targets$CellType)        all_design <- model.matrix(~all_celltype)        all_fcounts <- featureCounts(files=all_targets$BamFile,annot.ext=gff_file,isGTFAnnotationFile=TRUE,nthreads=8,isPairedEnd=TRUE,strandSpecific=2)        x <- DGEList(counts=all_fcounts$counts, genes=all_fcounts$annotation[,c("GeneID","Length")])        x_rpkm <- rpkm(x,x$genes$Length)        write.csv(x_rpkm,file="all_rpkm")
Genome_build: PlasmoDB v28
Supplementary_files_format_and_content: A tab-delimited file that contains differential expression data for female gametocytes vs. asexual erythrocytic stages
Supplementary_files_format_and_content: A tab-delimited file that contains differential expression data for male gametocytes vs. asexual erythrocytic stages
Supplementary_files_format_and_content: A tab-delimited file that contains RPKM values for all samples.

organism: Plasmodium berghei ANKA

source_name: Erthyrocytic stages

extract_protocol:
Depleted of host cells
PolyA enrichment

tag: Stage

value: Asexual erythrocytic

tag: isolated from

value: mouse blood


title: Erthyrocytic stages (2/3)


title: mrna-seq OO a

description: OO a


title: mrna-seq OT c

description: OT c

value: testis


title: HL60-0-hrs-4

source_name: Myeloid leukemia cell

tag: dox


title: mrna-seq OT b

description: OT b


title: Erthyrocytic stages (1/3)


title: mirna-seq OO c

description: OO c

data_processing:
The libraries were sequenced by Illumina Hiseq2500 50SE (single end) at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
Briefly, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, TX, USA), to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Subsequently, unique sequences 18-26 nt in length were mapped to specific species precursors in miRBase 21.0 by Bowtie search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
Supplementary_files_format_and_content: miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Student t test based on the experimental design.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analyzed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 2.5 ug of total RNA were used to prepare small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).


title: Male gametocytes (3/3)

source_name: Male gametocytes

extract_protocol:
Purified by flow cytometry
PolyA enrichment

value: Male gametocyte


title: Male gametocytes (2/3)


title: mirna-seq OO b

description: OO b


title: Male gametocytes (1/3)


title: mrna-seq OT a

description: OT a


title: mirna-seq OT c

description: OT c


title: Female gametocytes (3/3)

source_name: Female gametocytes

value: Female gametocyte


title: mirna-seq OO a

description: OO a


title: DVI

value: Resistant to Foc


title: Female gametocytes (2/3)


title: mirna-seq OT a

description: OT a


title: mirna-seq OT b

description: OT b


title: Female gametocytes (1/3)


title: 1h_35psu_22gen_Amill

status: Public on Aug 20 2017

city: Townsville

first: Catalina

last: Aguilar

state: Queensland

address: 1 James Cook Dr.

department: Collegue of Public Health, Medical and Veterinary Sciences

institute: James Cook University

description: processed data file column: A1

data_processing:
Reads were mapped onto the Acropora millepora genome using TopHat2  --read-mismatches 5  --read-gap-length 4   --read-edit-dist 6  --read-realign-edit-dist 5  --min-intron-length 30  --min-segment-intron 30  --library-type fr-firststrand  --GTF  --b2-very-sensitive
Counts were generated using htseq-count
Differentially gene expression analysis was done using DESeq2
gene annotations for the processed data files are located at: http://dna.anu.edu.au/~huaying/amil_v1.0/

organism: Acropora millepora

source_name: adult coral

extract_protocol:
Total RNA was extracted using 3ml TRIzol Reagent for the coral adults and using RNAaqueous-Micro total RNA isolation kit (AMBION) for the juveniles.
Libraries were constructed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturers recommended protocol.

value: adult coral

tag: treatment

value: Control (35 PSU)


title: 1h_35psu_26gen_Amill

description: processed data file column: A3


title: 1h_35psu_33gen_Amill

description: processed data file column: A4


title: 1h_25psu_34gen_Amill

description: processed data file column: B5

value: 25 PSU


title: 1h_25psu_23gen_Amill

description: processed data file column: B2


title: 1h_25psu_26gen_Amill

description: processed data file column: B3


title: 1h_35psu_34gen_Amill

description: processed data file column: A5


title: 1h_25psu_33gen_Amill

description: processed data file column: B4


title: 1h_35psu_23gen_Amill

description: processed data file column: A2


title: 1h_25psu_22gen_Amill

description: processed data file column: B1


title: 1h_35psu_22gen_Amill rep 2

data_processing:
Reads were mapped onto the Acropora millepora genome using TopHat2  --read-mismatches 5  --read-gap-length 4   --read-edit-dist 6  --read-realign-edit-dist 5  --min-intron-length 30  --min-segment-intron 30  --library-type fr-firststrand  --GTF  --b2-very-sensitive
Counts were generated using htseq-count
Differentially gene expression analysis was done using DESeq2


title: 48h_28psu_245_Amill

description: processed data file column: D6

source_name: juveniles coral

value: Juvenile

value: 28 PSU


title: 1h_25psu_22gen_Amill rep 2


title: 24h_25psu_23gen_Amill rep 2


title: 48h_28psu_244_Amill

description: processed data file column: D5


title: 48h_28psu_239_Amill

description: processed data file column: D4


title: RNA-seq_h3.1kd-1_rep2

city: Beijing

first: Danhua

last: Jiang

address: No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology

data_processing:
Reads were aligned to the Arabidopsis genome (TAIR10) using TopHat.
Reads per gene were counted by HTSeq.
Reads per gene were normalized and compared with DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read counts.

source_name: Seedlings, h3.1kd-1

extract_protocol:
Total RNA was extracted using an RNeasy plus mini kit (Qiagen).
RNA-seq libraries were generated from total RNA with a TruSeq RNA library prep kit (Illumina) following the manufacturer’s instructions.

tag: genotype/variation

value: seedlings


title: RNA-seq_h3.1kd-2_rep2

source_name: Seedlings, h3.1kd-2


title: 48h_28psu_233_Amill

description: processed data file column: D2

tag: time


title: RNA-seq_Col_rep2

source_name: Seedlings, WT

tag: ecotype

value: Col

value: wildtype

tag: tissue


title: RNA-seq_Col_rep1


title: RNA-seq_h3.1kd-1_rep1


title: 24h_35psu_22gen_Amill rep 2


title: 48h_35psu_222_Amill

description: processed data file column: C4


title: 48h_28psu_222_Amill

description: processed data file column: D1


title: 24h_28psu_209_Amill

description: processed data file column: B6


title: 48h_35psu_215_Amill

description: processed data file column: C2


title: 48h_35psu_220_Amill

description: processed data file column: C3


title: 24h_28psu_208_Amill

description: processed data file column: B5


title: 48h_28psu_238_Amill

description: processed data file column: D3


title: 24h_28psu_203_Amill

description: processed data file column: B4


title: cryab Homo 573 (cryab-R120G homo1)

city: St. Louis

first: Usha

last: Andley

state: MO

address: 660 S. Euclid Avenue

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine

data_processing:
Basecalls performed with Casava v1.8
Reads were aligned to Ensembl GRCm38.76 with STAR v2.0.4b
Gene counts were produced with Subread:featureCounts v1.4.5 and transcript/isoform counts were estimated with Sailfish v0.6.3

Genome_build: GRCm38.76
Supplementary_files_format_and_content: gene count text file

source_name: Lens

extract_protocol: Library preparation was performed using a Clontech poly-A kit according to the manufacturer’s protocol. The resulting cDNA was then blunt ended, an A base was added to the 3’ ends, and Illumina sequencing adapters were ligated to the ends. The ligated fragments were then amplified for 12 cycles using primers that incorporated unique index tags and the resulting fragments were sequenced on an Illumina HiSeq 2500 sequencing system using single reads extending 50 bases and targeting 30M reads per sample.

tag: strain

tag: postnatal age

value: cryaa-R49C homozygous mutant knock-in


title: cryab Het 549 (cryab-R120G Het 3)

value: cryaa-R49C heterozygous mutant


title: cryab Het 566 (cryab-R120G het 2)


title: 24h_28psu_197_Amill

description: processed data file column: B2


title: cryab Homo 565 (cryab-R120G homo2)


title: 48h_35psu_214_Amill

description: processed data file column: C1


title: 48h_35psu_226_Amill

description: processed data file column: C5


title: DVC

value: Both root and shoot

value: Sterile de-ionized water


title: CHT-HSPC rep2

first: Yuanyuan

last: Xue

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology，Chinese Academy of Sciences

description: CHT-HSPC rep2

data_processing:
Reads were aligned to the GRCz10 genome assembly using TopHat2 for RNA-seq
For each sample, reads counts of all genes were computed using HTSeq 0.6.1
Identifieded differentially expressed genes with R package DEGseq
Genome_build: z10
Supplementary_files_format_and_content: Reads count for each gene

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol: The CD41:GFP positive cells and kdrl:mCherry positive cells were sorted from the tail region of 52 hpf zebrafish embryos by FACS and the total RNA was isolated by QIAGEN RNeasy Mini Kit  (Cat. No. 74104). The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. Counts were normalized for mRNA abundance and differential expression analysis was performed using DEGseq R package.

value: embryos

value: hematopoietic stem and progenitor cells

value: 52 hpf

value: CHT


title: wt 575 (cryab-R120G wt3)

value: wild-type


title: RNA-seq_h3.1kd-2_rep1


title: wt 572 (cryab-R120G wt 2)


title: cryab Homo 548 (cryab-R120G homo3)


title: CHT-EC rep2

description: CHT-EC rep2

value: endothelial cells


title: wt 569 (cryab-R120G wt1)


title: 24h_35psu_193_Amill

description: processed data file column: A6

value: Control (35 PSU)


title: homo2 (cryaa-R49C Homo2)


title: homo3 (cryaa-R49C Homo3)


title: 24h_28psu_202_Amill

description: processed data file column: B3


title: het2 (cryaa-R49C Het2)


title: 24h_35psu_187_Amill

description: processed data file column: A4


title: 24h_35psu_192_Amill

description: processed data file column: A5


title: cryab Het 574 (cryab-R120G het1)


title: homo1 (cryaa-R49C Homo1)


title: het3 (cryaa-R49C Het3)


title: 24h_35psu_186_Amill

description: processed data file column: A3


title: CHT-EC rep1

description: CHT-EC rep1


title: het1 (cryaa-R49C Het1)


title: wt3 (cryaa-R49C WT3)


title: 24h_35psu_181_Amill

description: processed data file column: A2


title: wt2 (cryaa-R49C WT2)


title: CHT-HSPC rep1

description: CHT-HSPC rep1


title: 24h_35psu_34gen_Amill

description: processed data file column: C5

value: adult coral


title: 24h_28psu_196_Amill

description: processed data file column: B1

value: Juvenile


title: ChIP-seq_H3K27me3_h3.1kd-2_rep1

description: Human DNA was used to calculate the reference derived normalization factor.

data_processing:
Reads were mapped to the Arabidopsis genome (TAIR10) or human genome (hg38/GRCh38) using Bowtie2.
The number of H3K27me3 reads aligned to human genome were first normalized based on the number of input reads, and then was used to calculate reference derived normalization factor.
BedGraph files were created using the deepTools utility bamCoverage with a bin size of 10bp.
The number of reads in each bin in the bedGraphs were then scaled by the reference derived normalization factor to generate reference-adjusted reads per million (RRPM).
H3K27me3 enriched regions were identified using MACS2.
Genome_build: TAIR10 (Arabidopsis), hg38/GRCh38 (human)
Supplementary_files_format_and_content: *bigwig: Normalized coverage of H3K27me3.

organism:
Arabidopsis thaliana
Homo sapiens

source_name: Seedlings, h3.1kd-2, H3K27me3 ChIP

extract_protocol:
Mononucleosomes from 10-day-old Arabidopsis seedlings and human HEK293 cells generated by micrococcal nuclease (MNase) digestion were subjected to ChIP. To generate Arabidopsis mononucleosomes, nuclei were extracted from 10-day-old seedlings, and were subsequently subjected to MNase digestion in N buffer (15mM Tris pH7.5, 250mM sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 1mM CaCl2, 1mM DTT, 10mM ß-mercaptoethanol, protease inhibitor cocktail). EDTA and EGTA were added to a final concentration of 10mM each to stop the MNase digestion. Nuclei were lysed by adding NaCl to a final concentration of 500mM, and soluble materials containing mononucleosomes were recovered after centrifugation. To generate mononucleosomes from human HEK293 cells, nuclei were extracted by hypotonic lysis and treated with MNase in N buffer. DNA was extracted from a portion of mononucleosomes to determine the concentration of mononucleosomes. Same amount of mononucleosomes from different Arabidopsis samples were mixed with a constant amount of human mononucleosomes before immunoprecipitation with anti-H3K27me3 antibody.
Sequencing libraries were prepared using a TruSeq DNA sample prep kit (Illumina).

value: 10 days

tag: human cell line

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: wt1 (cryaa-R49C WT1)


title: ChIP-seq_H3K27me3_h3.1kd-1_rep1

source_name: Seedlings, h3.1kd-1, H3K27me3 ChIP

value: seedlings


title: H4

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
The sequencing data were aligned using an RefSeq hg19 reference with STAR software (version 2.3.0.1)
The Cufflinks software suite (version 2.1.1) was used for differential expression analysis, with standard parameters and RefSeq hg19 reference annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with FPKM and associated p-values, q-values for RefSeq annotated transcripts

growth_protocol: cell lines were maintained in Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 4.5g/L D-Glucose, 1X L-glutamine, 10% Fetal Bovine Serum and 1X Penicillin/Streptomycin and cultured in an 37°C humidified 5% CO2 atmosphere

extract_protocol:
RNA was isolated from cells using the Trizol reagent (ThermoFisher), and purified according to the manufacturer’s protocol. All purified RNA was subsequently treated with DNaseI digestion to remove possible DNA contaminants (Qiagen). The quality of RNA used for cDNA library preparation was verified using the RNA nano 6000 analysis chip on a BioAnalyzer 2000 series instrument (Agilent Technologies) to ensure an RNA integrity value greater than or equal to 9.
The cDNA libraries for sequencing were prepared from poly(A)+-selected mRNA, according to Illumina’s TruSeq Stranded mRNA sequencing preparation kit. Briefly, 1µg RNA was purified for mRNA. Then mRNA material was fragmented and denatured, in preparation for first and second strand cDNA synthesis steps. Finally, the 3’ ends were adenylated to ligate strand-specific adapter sequences to cDNA material and amplified using PCR.  Purity and size of cDNA library products were confirmed using a BioAnalyzer instrument. Library concentrations were determined via RT-qPCR using the Library Quantification Kit (KapaBiosystems). The samples were then prepared and sequenced on an Illumina HiSeq Series instrument, with one sample per sequencing lane to achieve > 2 x 108 reads per sample.
stranded RNAseq

treatment_protocol: cells were incubated in 37°C humidified 5% CO2 conditions with 0.5% oxygen for 16h in an INVIVO2 400 chamber (Baker BioScience Solutions).

tag: cell line

tag: cancer

value: head and neck squamous cell carcinoma


title: ChIP-seq_H3K27me3_h3.1kd-2_rep2


title: 24h_35psu_26gen_Amill

description: processed data file column: C3


title: H2


title: 24h_35psu_23gen_Amill

description: processed data file column: C2


title: H1


title: ChIP-seq_H3K27me3_h3.1kd-1_rep2


title: 24h_35psu_22gen_Amill

description: processed data file column: C1


title: ChIP-seq_Input_h3.1kd-2_rep1

source_name: Seedlings, h3.1kd-2, input


title: ChIP-seq_Input_h3.1kd-2_rep2


title: H3


title: N3

source_name: normoxia


title: 24h_35psu_180_Amill

description: processed data file column: A1


title: N4


title: Day7 mock

city: Xuzhou

first: Yanhong

last: Wang

address: shanghai road number101

institute: Jiangsu Normal 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 rnor_5.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: mammary gland

extract_protocol:
mammary glands were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: mammary gland

value: lactating day 7

tag: genotype

value: wild type


title: ChIP-seq_Input_h3.1kd-1_rep2

source_name: Seedlings, h3.1kd-1, input


title: Day7 Rnase R


title: 24h_25psu_34gen_Amill

description: processed data file column: D5

value: 25 PSU


title: N2


title: ChIP-seq_Input_h3.1kd-1_rep1


title: Day1 mock

value: lactating day 1


title: N1


title: 24h_25psu_33gen_Amill

description: processed data file column: D4


title: 24h_35psu_33gen_Amill

description: processed data file column: C4


title: 24h_25psu_23gen_Amill

description: processed data file column: D2


title: 5d MI Foxp3DTR_Rep 2

status: Public on Aug 19 2017

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

data_processing:
Basecalls performed using CASAVA version 1.4
Adapter removal with cutadapt v1.1
quality trimming with erne-filter v1.4.6
alignment with STAR v2.5
read count with StringTie v 1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: splenic monocyte cells

extract_protocol:
Spleens were removed, single cell suspensions were made by mashing the spleens through a 40-μm filter, MACS depletion of T- and B-cells, FACS sorting of Ly6Chi splenic monocytes. RNA was extracted using RNeasy Micro (Qiagen) according to the manufacturer´s instructions. Ovation SoLo RNA-Seq Mouse System (NuGEN) was used with 20-50pg of RNA for library preparation.
RNA libraries were processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer´s instructions

treatment_protocol: Myocardial infarction was provoked by permanent ligation of the left anterior descending coronary artery. For sham surgery, thoracotomy was conducted without ligating the vessel.  All mice undergoing surgeries were injected with buprenophine (0.1 mg/kg i.p.) for analgesia. For Treg cell ablation, 500 ng diphtheria toxin per mouse were injected intraperitoneally on day 2 and day 1 before surgery. To prevent Treg cell rebound, 250 ng DTX per mouse were additionally injected on day 2 after MI or sham operation.

value: spleen

tag: operation

value: MI


title: 5d MI Foxp3DTR_Rep 4


title: 5d MI Foxp3DTR_Rep 3


title: 5d MI WT_Rep 4


title: 5d MI WT_Rep 3


title: 5d MI WT_Rep 2


title: 5d sham WT_Rep 1

value: sham


title: 5d sham WT_Rep 2


title: D_d2_ZT17-rep2

city: Hanover

first: Kathleen

last: Greenham

state: NH

address: 78 College St.

department: Biological Sciences

institute: Dartmouth College

description:
D11_rep2
R500_D_FPKM.txt

data_processing:
Illumina Casava was used for base-calling.
Reads were trimmed and filtered using trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic) with default settings and the following parameters: ILLUMINACLIP:../TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 HEADCROP:14 MINLEN:50
Reads were aligned to a modified version of the B. rapa Chiifu reference genome Brapa_sequence_v1.1.fa. GATK (https://www.broadinstitute.org/gatk/) was used to call SNPs in R500 with default settings. The vcf file generated by GATK was filtered to remove any SNPs with a quality score below 30, coverage below 10 and all heterozygous SNPs. The SNPs passing this filter were used to replace the Chiifu reference genome using the vcf-concensus tool in the VCFtools package (http://vcftools.sourceforge.net/perl_module.html). Tophat2 was used to align the RNA-seq read data to the modified Chiifu genome file  using default settings and firststrand library-type. Transcripts were assembled using cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) with the Chiifu reference Brassica_rapa.IVFCAASv1.19.gtf annotation file. Ran cuffdiff to generate FPKM values using the options: --library-type fr-firststrand  -no-diff  --no-js-tests.
Genome_build: B. rapa Chiifu v1.1, annotation: Brassica_rapa.IVFCAASv1.19.gtf
Supplementary_files_format_and_content: tab-delimited text files containing the FPKM values for both replicates at each time point. Files are separated based on well-watered and drought samples.

organism: Brassica rapa

source_name: Mature leaf tissue

growth_protocol: Plants were grown in growth chambers under 14h 22°C day/10h 1°8C night. PAR of growth 200 +/- 20, PAR of measurement 300 +/- 5, Relative daytime humidity 25%, Relative nighttime humidity 45%.

extract_protocol:
Leaf tissue was homogenized and resuspended in LBB buffer (100mM Tris-Cl pH7.5, 500mM LiCl, 10mM EDTA, 1% LiDs, 5mM DTT, 2-BME). mRNA was extracted directly from tissue lysate using Life Technologies Dynabeads oligo (dT)25 (cat. no. 61002), and DNase treated using ThermoFisher TURBO DNase (cat. no. AM2238) in the presence of EDTA. The concentration of mRNA was assessed using a Qubit (Invitrogen, ThermoFisher) and 55ng was used for the cDNA library preparation. The quality of the mRNA was assessed using the Agilent Technologies 2100 Bioanalyzer (Agilent), all RIN values were below 3.
The cDNA libraries were made according to the protocol in Wang et al. 2011 (PLoS One 6(10): e26426, doi:10.1371/journal.pone.0026426). The quality and size of the cDNA libraries were assessed using the Agilent Technologies 2100 Bioanalyzer (Agilent) and run on a gel. All library sizes were ~250bp resulting in insert sizes ~150bp with PE100 sequencing. Libraries were multiplexed 12-samples in a lane - well-watered rep1 timepoints 1-12, well-watered rep2 timepoints 1-12, drought rep1 timepoints 1-12, drought rep2 timepoints 1-12.

treatment_protocol: We exposed half the plants to a very mild drought treatment. Water was withheld 48h prior to the start of sampling. Drought treated plants displayed soil water potential values starting at -0.5 MPa on day 1 and -1.5 MPa at the end of the sampling.

value: Drought

tag: time point

value: ZT17 - 3h after lights off

tag: age

value: 19 DAS


title: Hrp48_HyperTRIBE_200AA_flexible_linker_rep2

city: Waltham

first: Weijin

last: Xu

address: 415 South st.

institute: Brandeis University

data_processing:
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016), with minor modifications.
Scripts available on GitHub (https://github.com/rosbashlab/TRIBE).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed.
PCR duplicate is removed with Picard v2.8.2
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format, (Chromosome, co-ordinate, co-ordinate, edit %, edit%_number of total reads)

organism: Drosophila melanogaster

source_name: S2 Cell

extract_protocol:
RNA from FACS-sorting cells are extracted by TRIZOL, RNA from manual sorted neurons are prepared using the method described in Abruzzi et al, 2015.
s2 cell mRNA libraries were prepared using Illumina Truseq kits according to manufacturers protocol.  Neuronal cell sorting libraries were prepared according to Abruzzi et al, 2015.

treatment_protocol: S2 cells were treated with CuSO4 to induce protein expression, neuron expression was induced by RU486

tag: selection method

value: Transient tranfection-FACS sorting

tag: tribe expression

value: induced


title: D_d2_ZT21-rep1

description:
D12_rep1
R500_D_FPKM.txt

tag: treatment

value: ZT21 - 3h before lights on


title: Hrp48_HyperTRIBE_200AA_flexible_linker_rep1


title: Hrp48_HyperTRIBE_100AA_flexible_linker_rep2


title: Hrp48_HyperTRIBE_100AA_flexible_linker_rep1


title: Hrp48_HyperTRIBE_50AA_flexible_linker_rep1


title: D_d2_ZT21-rep2

description:
D12_rep2
R500_D_FPKM.txt


title: D_d2_ZT17-rep1

description:
D11_rep1
R500_D_FPKM.txt


title: 5d MI Foxp3DTR_Rep 1


title: D_d2_ZT13-rep2

description:
D10_rep2
R500_D_FPKM.txt

value: ZT13 - 1h before lights off


title: Hrp48_HyperTRIBE_50AA_flexible_linker_rep2


title: Hrp48_HyperTRIBE_15AA_flexible_linker_rep2


title: D_d2_ZT9-rep2

description:
D9_rep2
R500_D_FPKM.txt

value: ZT9 - 9h after lights on


title: D_d2_ZT9-rep1

description:
D9_rep1
R500_D_FPKM.txt


title: D_d2_ZT13-rep1

description:
D10_rep1
R500_D_FPKM.txt


title: D_d2_ZT5_rep1

description:
D8_rep1
R500_D_FPKM.txt

value: ZT5 - 5h after lights on


title: D_d2_ZT1-rep2

description:
D7_rep2
R500_D_FPKM.txt

value: ZT1-1h after lights on


title: Hrp48_HyperTRIBE_162AA_rigid_linker_rep2


title: D_d2_ZT5_rep2

description:
D8_rep2
R500_D_FPKM.txt


title: Hrp48_HyperTRIBE_162AA_rigid_linker_rep1


title: 5d sham WT_Rep 3


title: Hrp48_HyperTRIBE_15AA_flexible_linker_rep1


title: D_d1_ZT21-rep2

description:
D6_rep2
R500_D_FPKM.txt

value: 18 DAS


title: Day1 Rnase R

value: Sprague-Dawley

value: mammary gland

value: wild type


title: Hrp48_HyperTRIBE_81AA_rigid_linker_rep2


title: D_d1_ZT21-rep1

description:
D6_rep1
R500_D_FPKM.txt


title: Hrp48_HyperTRIBE_81AA_rigid_linker_rep1


title: D_d2_ZT1-rep1

description:
D7_rep1
R500_D_FPKM.txt


title: D_d1_ZT17-rep1

description:
D5_rep1
R500_D_FPKM.txt


title: DL5535

first: Erin

middle: K

last: Flaherty

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine

description: Un-affected control NGN2-induced neurons.

data_processing:
Alignment using STAR followed by subread.
Differential expression called by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw counts for each gene generated by subread.

source_name: Ngn2-induced neurons

growth_protocol: Neural progenitor cells were induced into neurons by overexpression of the pro-neural transcription factor NGN2 and grown for 21 days before RNA harvest.

extract_protocol:
Trizol was added to cells while in the plate, then phenol-chloroform extraction was performed.
KAPA Total 350bp kit using standard Illumina protocols.

tag: individual

value: mother

tag: genotype/variation

tag: disease status

value: Control


title: DL8735

description: Un-affected CNTNAP2 del NGN2-induced neurons.

value: father

value: CNTNAP2 del


title: D_d1_ZT13-rep2

description:
D4_rep2
R500_D_FPKM.txt

value: Drought


title: D_d1_ZT9-rep2

description:
D3_rep2
R500_D_FPKM.txt


title: D_d1_ZT9-rep1

description:
D3_rep1
R500_D_FPKM.txt


title: Hrp48_HyperTRIBE_50AA_rigid_linker_rep2


title: FMRP_HyperTRIBE_s2_rep2


title: DL7078

description: Affected CNTNAP2 del NGN2-induced neurons.

value: proband

value: Schizoaffective (SA) Disorder Diagnosis


title: FMRP_TRIBE_s2_rep1

value: Transient tranfection-FACS sorting

value: induced


title: D_d1_ZT5_rep2

description:
D2_rep2
R500_D_FPKM.txt


title: 12UBic MB r3

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

institute: King's College London

data_processing:
Raw reads were trimmed using trim-galore, utilising cutadapt14 (v0.4.0) to remove the Illumina Sequencing Adapter (AGATCGGAAGAGC) at the 3' end. Additionally, 12 bases were also trimmed from the 5' end of the reads since they showed a biased distribution. Reads were mapped to the human transcriptome using the human genome sequence GRCh38 and v82 gene annotations downloaded from Ensembl. Mapping was performed using tophat 15 (v2.1.0) and bowtie 16 (v1.1.0), enabling the fr-firststrand option of tophat to restrict mapping to the sense strand of the transcript. Reads were assigned to genes using the featureCounts program 17 (v1.5.0), counting fragments and ignoring multi-mapping reads, and restricted to the sense strand.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count files for each batch

source_name: Immortalised Human Myoblasts

growth_protocol: Myoblasts were plated at 312,000 cells per well in 12 well plates and cultured for 48 hours in cultured in Skeletal Muscle Cell Growth Medium (Promocel) supplemented with 20% foetal bovine serum, 50ug/ml Fetuin (bovine), 10ng/ml Epidermal Growth Factor (recombinant human), 1ng/ml Basic Fibroblast Growth Factor (recombinant human), 10ug/ml Insulin (recombinant human), 0.4ug/ml Dexamethasone and 50 ug/ml Gentamycin, at 37oC under 5% CO2.

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen, Manchester, UK) including DNase digestion from each cell line in triplicate. RNA quality/concentration were checked by LabChip Bioanalyzer (RIN>8.0) and Nanodrop.
RNA-seq libraries were prepared using the Agilent sureselect stranded RNAseq protocol, which allows polyA selection but was modified to work with ribodepletion. Libraries were sequenced on an Illumina HiSeq2500.

tag: pathology

tag: gender

value: Female

tag: batch


title: Hrp48_HyperTRIBE_15AA_rigid_linker_rep2


title: Hrp48_HyperTRIBE_50AA_rigid_linker_rep1


title: FMRP_HyperTRIBE_s2_rep1


title: D_d1_ZT1-rep1

description:
D1_rep1
R500_D_FPKM.txt


title: 12UBic MB r1


title: 12UBic MB r2


title: D_d1_ZT1-rep2

description:
D1_rep2
R500_D_FPKM.txt


title: E488Q_ADARcd_elav_rep2

source_name: Neuron

value: elav-geneswitch-gal4 expression-Manual cell sorting


title: Hrp48_HyperTRIBE_15AA_rigid_linker_rep1


title: D_d1_ZT5_rep1

description:
D2_rep1
R500_D_FPKM.txt

value: ZT5 - 5h after lights on


title: 12ABic MB r2

value: FSHD


title: 12ABic MB r3


title: Hrp48_HyperTRIBE_elav_rep1


title: E488Q_ADARcd_elav_rep1


title: D_d1_ZT17-rep2

description:
D5_rep2
R500_D_FPKM.txt

value: ZT17 - 3h after lights off

value: 18 DAS


title: WW_d2_ZT21-rep2

description:
W12_rep2
R500_WW_FPKM.txt

value: Well watered

value: ZT21 - 3h before lights on

value: 19 DAS


title: WW_d2_ZT21-rep1

description:
W12_rep1
R500_WW_FPKM.txt


title: Hrp48_HyperTRIBE_elav_rep2


title: WW_d2_ZT17-rep2

description:
W11_rep2
R500_WW_FPKM.txt


title: Hrp48_TRIBE_elav_rep2


title: WW_d2_ZT17-rep1

description:
W11_rep1
R500_WW_FPKM.txt


title: Hrp48_TRIBE_elav_rep1


title: WW_d2_ZT13-rep2

description:
W10_rep2
R500_WW_FPKM.txt

value: ZT13 - 1h before lights off


title: E488Q_ADARcd_s2_rep2


title: 16UBic MB r3

value: Control


title: Hrp48_HyperTRIBE_s2_rep2


title: 12ABic MB r1


title: WW_d2_ZT9-rep1

description:
W9_rep1
R500_WW_FPKM.txt

value: ZT9 - 9h after lights on


title: Hrp48_HyperTRIBE_s2_rep1


title: WW_d2_ZT5_rep2

description:
W8_rep2
R500_WW_FPKM.txt


title: WW_d2_ZT9-rep2

description:
W9_rep2
R500_WW_FPKM.txt


title: Hrp48_TRIBE_s2_rep2


title: 16UBic MB r1


title: 16UBic MB r2


title: 16ABic MB r3

value: Male


title: 54-12 MB r3


title: Hrp48_TRIBE_s2_rep1


title: WW_d2_ZT5_rep1

description:
W8_rep1
R500_WW_FPKM.txt


title: 54-12 MB r2


title: WW_d2_ZT13-rep1

description:
W10_rep1
R500_WW_FPKM.txt


title: WW_d1_ZT21-rep2

description:
W6_rep2
R500_WW_FPKM.txt


title: 54-12 MB r1


title: 54-A5 MB r3


title: 16ABic MB r2


title: WW_d1_ZT17-rep2

description:
W5_rep2
R500_WW_FPKM.txt


title: WW_d1_ZT21-rep1

description:
W6_rep1
R500_WW_FPKM.txt


title: 54-2 MB r3


title: 54-A5 MB r1


title: 54-A5 MB r2


title: humanCD3eTg

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Base call performed using OLB (version 1.9.4).
RNA-seq reads were aligned on mouse genome using TopHat (version 2.0.8) with Bowtie (version 2.1.0).
Processed data were generated using Cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: Plain text containing FPKM value for each gene

source_name: TEC of fetal thymus

extract_protocol:
CD45-EpCAM+PDGFRa- cells were sorted and lysed in TRIzol regent.  Illumina TruSeq RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: presence of thymocytes

tag: strain

value: C57BL/6J x CBA/J

tag: tissue

value: Fetal thymus

value: 15 dpc (Days post coitum)


title: 54-2 MB r1


title: B6J

value: absence of thymocytes


title: WW_d1_ZT17-rep1

description:
W5_rep1
R500_WW_FPKM.txt


title: 54-2 MB r2


title: WW_d1_ZT13-rep1

description:
W4_rep1
R500_WW_FPKM.txt


title: E488Q_ADARcd_s2_rep1

value: Transient tranfection-FACS sorting

value: induced


title: WW_d1_ZT9-rep1

description:
W3_rep1
R500_WW_FPKM.txt


title: WW_d1_ZT9-rep2

description:
W3_rep2
R500_WW_FPKM.txt


title: 16ABic MB r1

value: FSHD


title: WW_d1_ZT13-rep2

description:
W4_rep2
R500_WW_FPKM.txt


title: 54-A10 MB r3


title: D_d1_ZT13-rep1

description:
D4_rep1
R500_D_FPKM.txt

value: Drought


title: WW_d2_ZT1-rep2

description:
W7_rep2
R500_WW_FPKM.txt

value: ZT1-1h after lights on


title: WW_d2_ZT1-rep1

description:
W7_rep1
R500_WW_FPKM.txt

value: Well watered


title: 54-A10 MB r1


title: 54-6 MB r3


title: WW_d1_ZT1-rep1

description:
W1_rep1
R500_WW_FPKM.txt

value: 18 DAS


title: WW_d1_ZT5_rep1

description:
W2_rep1
R500_WW_FPKM.txt

value: ZT5 - 5h after lights on


title: WW_d1_ZT1-rep2

description:
W1_rep2
R500_WW_FPKM.txt


title: 54-6 MB r1


title: M82 rep1 MethylC-seq

status: Public on Aug 18 2017

city: Heidelberg

first: Quentin

last: Gouil

address: Studley Road

institute: Olivia Newton-John Cancer Research Institute

data_processing:
Reads were trimmed and filtered with Trim Galore! v0.4.2 (default parameters)
then mapped on Heinz genome SL2.50 using Bismark v0.17.0 \cite{Krueger2011} (first in paired-end mode with options `--score-min L,0,-0.2 -p 4 --reorder --ignore\_quals --no-mixed --no-discordant --unmapped', then unmapped read1 was mapped in single-end mode with the same quality parameter `-N 1')
Reads were deduplicated with `bismark\_deduplicate' and methylation calls were extracted using Bismark `methylation\_extractor' (with options `-r2 2' for paired-end reads).
Based on Bismark's cytosine report, methylated and unmethylated counts for cytosines of both strands were pooled into 300-bp bins sliding by 200 bp and separated by context (CG, CHG, and CHH). Bins with fewer than 10 counts or with coverage exceeding the $99^{th}$ percentile in one or more libraries were excluded from the analysis. We also excluded the introgressed regions: ch01 1 -- 86 Mb, ch02 44 -- 54 Mb and ch08 61 Mb -- 65866657 bp (end of chromosome).
Each introgression line was then compared to M82 by fitting a logistic regression on the methylated and unmethylated counts (R glm with `family = binomial'). The p-values were subjected to a Benjamini-Hochberg correction to control the false discovery rate at 5\%. Differentially methylated bins were further filtered by imposing thresholds on the absolute difference in methylation (average of replicates) between M82 and the introgression line: a difference of 25\% in the CG context, 20\% in CHG and 10\% in CHH. DMRs were constructed by merging overlapping differentially methylated bins.
Genome_build: Solanum lycopersicum Heinz SL2.50
Supplementary_files_format_and_content: Bismark cytosine reports: tab-separated values, with columns corresponding to chromosome, cytosine position, strand, methylated counts, unmethylated counts, context, trinucleotide context

organism: Solanum lycopersicum

growth_protocol: plants were raised from seeds in compost (Levington M3) and maintained in a growth room at 23 $^{o}$C with 16/8 h light/dark periods with 60\% relative humidity, at a light intensity of 150 $\mu$mol photons m$^{-2}$.s$^{-1}$

extract_protocol:
DNA from leaf (2-week-old seedlings), mature flowers or pollen was extracted with the Puregene kit (QIAgen) following manufacturer's instructions.
Bisulfite library preparation was performed with a custom protocol similar to Urich et al. (2015). 1.2 µg DNA was sonicated on a Covaris E220 to a target size of 400bp and purified on XP beads (Ampure, ratio 1.8). DNA was end-repaired and A-tailed using T4 DNA polymerase and Klenow Fragment (NEB) and purified again using XP beads (ratio 1.8×). Methylated Illumina Y-shaped adapters for paired-end sequencing were ligated using Quick-Stick Ligase (Bioline). 450ng of purified (ratio 1.8×), adapter-ligated DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions. DNA was barcoded using 12 cycles of PCR amplification with KAPA HiFi HotStart Uracil+Ready Mix (Kapa Biosystems) with PE1.0 and custom index primers (courtesy of the Sanger Institute)

tag: cultivar

value: leaf

value: 2 weeks


title: 47055-17.5SMG

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

description:
17.5 dpc SMG
RNA-seq library reads.
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx

data_processing:
Illumina HiSeq Control Software used for basecalling.
Sequences were mapped to mm10 mouse genome using TopHat v2.0.11 (by use of Bowtie v2.2.2.0) with allowed segment-mismatches 3.
Sequences per gene were counted using Samtools (v0.1.19.0) /HTSeq (v0.6.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Normalized reads-per-million (RPM) for each gene in tab-delimited text files.
Supplementary_files_format_and_content: AdultParotidEmbryonicSMG_HTseqSummary.xlsx: Excel file with all normalized HTSeq results in single table.

source_name: Embryonic submandibular glands 17.5 dpc

growth_protocol: Adult male C57BL/6J from UTSW mouse breeding core. Embryonic mice from timed matings of ICR females. Noon of day of sperm plug is E0.5.

extract_protocol:
Parotid gland RNA preparation: Parotid glands were dissected and homogenized in 4 ml of Trizol (Invitrogen) with a Tekmar Tissuemizer, and RNA isolated per manufacturer's protocol.
Submandibular gland RNA preparation: Submandibular glands of embryonic mice were dissected in phosphate-buffered saline and kept on ice prior to homogenization. E13.5 d glands had the majority of their mesenchyme removed following treatment with 1.5 units/ml dispase (Invitrogen). Glands were homogenized in 0.5 ml Trizol (Invitrogen) with a plastic pestle and vortexing, and RNA isolated per manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols.

treatment_protocol: No treatment of mice.

tag: strain/background

value: ICR

value: pooled male and female

tag: age at sacrifice (days)

value: submandibular gland

tag: animal id


title: mRNAs from Burkholderia gladioli BSR3 wild type after 24h LB liquid culture

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
The reads were processed using BWA and SAMtools program.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization.
Genome_build: Burkholderia gladioli BSR3 ASM19474v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Burkholderia gladioli

source_name: Bacteria culture, BSR3, 24h

growth_protocol: Each bacteria strain was grown in LB liquid for either 10h or 24h.

extract_protocol:
All bacteria strains were grown in 2 ml of LB broth at 28°C with continuous shaking until reach mid-expotential phase (OD600 = 0.5), and subcultured for 10h or 24h in identical condition. Total RNA was extracted from 4 ml of each bacterial cultures using RNeasy Midi Kit (Qiagen, Valencia, CA) and residual genomic DNA contamination was subsequently removed using an RNase-Free DNase set (Qiagen, Valencia, CA) according to the manufacturer’s protocols. After DNase I treatment, a MICROBExpressTM bacterial mRNA enrichment kit (Ambion, Carlsbad, CA) was used to remove bacterial rRNA from the total RNA sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: wild type

tag: culture time


title: 58111-4

description:
Adult Parotid 4
RNA-seq library reads.
RIN: 9.1
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx

source_name: Adult parotid

value: Male

value: parotid gland


title: 58111-5

description:
Adult Parotid 5
RNA-seq library reads.
RIN: 8.6
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx


title: 47055-15.5SMG

description:
15.5 dpc SMG
RNA-seq library reads.
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx

source_name: Embryonic submandibular glands 15.5 dpc


title: 58111-1

description:
Adult Parotid 1
RNA-seq library reads.
RIN: 8.3
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx


title: 58111-3

description:
Adult Parotid 3
RNA-seq library reads.
RIN: 8.2
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx


title: mRNAs from Burkholderia gladioli COK94 (BSR3 bglu_2g11050::lacZ) mutant after 24h LB liquid culture

source_name: Bacteria culture, COK94, 24h

value: BSR3 bglu_2g11050::lacZ mutant


title: 48055-13.5SMG

description:
13.5 dpc SMG
RNA-seq library reads.
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx

source_name: Embryonic submandibular glands 13.5 dpc


title: PBS.4

city: New York

first: Gregory

last: Putzel

address: 430 East 29th Street

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: ILC2s sorted from small intestine

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

value: ID2 GFP reporter

value: PBS

value: small intestine

tag: cell type


title: mRNAs from Burkholderia gladioli COK94 (BSR3 bglu_2g11050::lacZ) mutant after 10h LB liquid culture

source_name: Bacteria culture, COK94, 10h


title: 54-A10 MB r2

value: Control


title: 58111-2

description:
Adult Parotid 2
RNA-seq library reads.
RIN: 8.7
Processed data file: AdultParotidEmbryonicSMG_HTseqSummary.xlsx


title: mRNAs from Burkholderia gladioli BSR3 wild type after 10h LB liquid culture

source_name: Bacteria culture, BSR3, 10h


title: NMU.3

value: NMU


title: PBS.2


title: NMU.1


title: WW_d1_ZT5_rep2

description:
W2_rep2
R500_WW_FPKM.txt

value: Well watered

tag: time point

tag: age


title: NMU.2

tag: treatment


title: 54-6 MB r2


title: ILC3_SI_SPF2

source_name: ILC3s sorted from small intestine


title: ILC3_SI_SPF3


title: ILC2_SI_SPF1


title: ILC2_SI_SPF3


title: ILC3_SI_SPF1


title: ILC2_SI_SPF2


title: Kidney Control Ig SAM24307744

city: South San Francisco

first: Jonathan

last: Sitrin

state: CA

address: 1 DNA Way

department: OMNI Human Genetics

institute: Genentech, Inc.

data_processing:
Alignment, HTSeqGenie and GSNAP
Filtering, HTSeqGenie. Only reads with  unique genomic alignments were analysed
Feature counting, HTSeqGenie. Gene models based on RefSeq
Normalization,  to obtain normalized reads per kilobase gene model per million total reads (nRPKM) values
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated text file, normalized RPKM (nRPKM) for each sample and gene

source_name: Kidney sorted live CD45+CD19-CD3+CD4+ T cells

growth_protocol: Female NZB x NZW F1 mice (NZB/W F1) were bred and crossed at the Jackson Laboratory then maintained at Genentech under specific pathogen-free conditions.

extract_protocol:
After in vitro culture, cells were lysed with RLT buffer supplemented with 2-mercaptoethanol (Sigma-Aldrich).  RNA was extracted using the RNEasy Mini or Micro Kit, depending on input (Qiagen #74104 and #74004).  For kidney samples, RNEasy cleanup kit (Qiagen #74204) was performed.  For all RNASeq experiments, Nanodrop 8,000 (Thermo Scientific) was used to quantify RNA and integrity was measured using the Bioanalyzer RNA 6,000 Pico Kit (Agilent).
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (Illumina) with 100-500ng input and amplified using ten cycles of PCR.

treatment_protocol: For anti-Ox40 agonist antibody treatments, cohorts were selected for age and proteinuria status at 12-13 weeks old (0mg/dL proteinuria), or 21-27weeks old (30-100mg/dL proteinuria), randomized by weight into treatment groups, and serum was collected prior to treatment for all experiments.  Mice were treated with anti-Ox40 (IgG1) or an isotype control IgG1 subcutaneously at a dose of 10mg/kg 3-times-per-week for 1-1.5wks

value: Control Ig

value: NZB/W F1 Female Mice


title: Kidney anti-Ox40 SAM24307743


title: PBS.3


title: PBS.1


title: Kidney anti-Ox40 SAM24306589


title: Kidney Control Ig SAM24306592


title: Kidney Control Ig SAM24306591


title: Kidney Control Ig SAM24306590


title: Kidney anti-Ox40 SAM24306587


title: Kidney anti-Ox40 SAM24306586


title: Spleen Control Ig SAM24306585

source_name: Splenic sorted live CD45+CD19-CD3+CD4+ T cells


title: Spleen Control Ig SAM24306583


title: Spleen Control Ig SAM24306582


title: Spleen Control Ig SAM24306584


title: Spleen anti-Ox40 SAM24306579


title: Spleen anti-Ox40 SAM24306581


title: Spleen anti-Ox40 SAM24306578


title: Spleen anti-Ox40 High TCR SAM24301812

source_name: Splenic enriched CD4+ T Cells

treatment_protocol: Splenic CD4 T cells were isolated from 21-27 week old (30-100mg/dL proteinuria) NZB/W F1 mice with the Mouse CD4+ T cell Isolation Kit (StemCell #19852) per manufacturer’s instructions and cultured in a sterile round-bottom 96-well culture dish (Costar #3799) at 2.5x105 cells/well with 10U/mL of IL-2 (Corning #354043).  Cells were treated with anti-Ox40 (IgG1) or an isotype control IgG1 (25ug/ml) along with 0, 1:10 or 1:1 ratio of T Cell Activator (anti-CD3/CD28) Dynabeads (ThermoFisher #11452).  After 48hours, cellular RNA was collected for RNASeq.

tag: treatment 1

value: 1:1 anti-CD3/CD28 Beads:Cell

tag: treatment 2


title: Spleen Control Ig High TCR SAM24301807


title: Spleen anti-Ox40 High TCR SAM24301811


title: Spleen anti-Ox40 High TCR SAM24301810


title: Spleen anti-Ox40 Low TCR SAM24301805

value: 0.1:1 anti-CD3/CD28 Beads:Cell


title: Spleen Control Ig Low TCR SAM24301803


title: Spleen Control Ig High TCR SAM24301808


title: Spleen anti-Ox40 Low TCR SAM24301804


title: Spleen anti-Ox40 Low TCR SAM24301806


title: Kidney anti-Ox40 SAM24306588


title: Kidney Control Ig SAM24306593


title: Spleen Control Ig Low TCR SAM24301801


title: Spleen anti-Ox40 no TCR SAM24301800

value: No anti-CD3/CD28 Beads


title: Spleen anti-Ox40 SAM24306580


title: Spleen anti-Ox40 no TCR SAM24301799


title: Spleen anti-Ox40 no TCR SAM24301798


title: Spleen Control Ig no TCR SAM24301795


title: Spleen Control Ig no TCR SAM24301796