title: E110019_LB_0.5_BR2_2


title: E110019_LB_0.5_BR1_2

status: Public on May 10 2017

type: SRA

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

library_source: transcriptomic

data_processing:
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, B171, C581-05, E110019, 401140, 402290, 401588, 302053, 100329, 103385 TEPEC, 300059 TEPEC

molecule: total RNA

organism: Escherichia coli E110019

source_name: Escherichia coli cells

growth_protocol: The EPEC strains were grown overnight in Luria-Bertani (LB) media and were inoculated 1:100 into 250 ml of fresh LB or DMEM and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

extract_protocol:
RNA was isolated from cells grown in LB or DMEM using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: E110019_DMEM_0.5_BR1_2


title: C581_05_DMEM_0.5_BR2_2

organism: Escherichia coli C581_05


title: 402290_DMEM_0.5_BR2

organism: Escherichia coli 402290


title: C581_05_DMEM_0.5_BR1_2


title: C581_05_LB_0.5_BR2_2


title: C581_05_LB_0.5_BR1_2


title: 402290_DMEM_0.5_BR1


title: 402290_LB_0.5_BR2


title: NT2D1p39 POLR3G ChIP rep2

city: Turku

first: Riikka

last: Lund

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, University of Turku

library_source: genomic

data_processing:
SmallRNA reads were trimmed using trim_galore to remove primer sequences, low-quality bases from read ends, and to discard trimmed reads < 18bp. The reads were then mapped to hg19 reference transcriptome (with tRNAs) using tophat2 (v2.0.13) with default parameters. PolyA+ reads were mapped to hg19 transcriptome using tophat2 (v2.0.13) with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using the total exon length of the isoform with the longest total exon length and normalizing by this length and sequencing depth (according to the number of uniquely mapped reads obtained from htseq). For smallRNA-seq, genes with length > 250bp were excluded.
ChIP-seq data: reads with average quality below 20 were removed and reads with length 20-50 bp were retained with Trimmomatic 0.32, the reads were mapped to hg19 genome with Bowtie2 2.2.6 and non-unique reads were discarded, the ChIP peaks were called with MACS 1.0.1. with default parameters, except arbitrary shift size of 100 bp was used instead of shifting model and p-value cut off was 1.00E-04 for POL peak detection.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in RNA-seq data or RPM in smallRNA-seq data, in ChIP-seq data the bigwig files contain the enrichment intensities and bed files the peaks with p-value =<0.0001.

molecule: genomic DNA

organism: Homo sapiens

source_name: Embryonal carcinoma stem cells

growth_protocol: hESC (S1-13): mTeSR1+matrigel, NT2D1 (S14-16): DMEM+15%FCS

extract_protocol:
Qiagen all prep for smallRNA (S7-13) and mRNA (S1-6), ChIP-DNA (S14-18): Qiagen MinElute PCR Purification Kit
smallRNA-seq (S7-13): Illumina TruSeq smallRNA, mRNA-seq (S1-6): Illumina TruSeq mRNA, ChIP-seq (S14-18): Diagenode Microplex Library Preparation kit v2

tag: cell type

tag: passages

tag: genotype

value: 46 XY +complex

tag: chip antibody

value: anti-POLR3G (SZ3070, Prof. Nouria Hernandez)


title: NOMO-1 D10 Ctrl rep1

city: Cambridge

first: Carly

middle: T

last: Campbell

state: Massachusetts

address: 400 Technology Sq, 4th Fl

institute: Epizyme

data_processing:
After sequencing, basecall files were converted into FASTQ output files using Illumina CASAVA software and other tools developed at EA (available at https://github.com/ExpressionAnalysis/ ea-utils/). FASTQ data were demultiplexed, and sequencing adapters and other low quality bases were clipped to prepare reads for alignment using fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Filtered reads were used in alignments and quanitfcation against hg.fa using RSEMv1.2, rsem-calculate-expression, and bowtie v0.12.9 with parameters "rsem-calculate-expression --fragment-length-mean <SAMPLE_INSERT_MEAN> --fragment-length-sd <SAMPLE_INSERT_MEAN_STANDARD_DEV> --bowtie-path bowtie-0.12.9 --bowtie-chunkmbs 256 --bowtie-e 500 --bowtie-m 100 --keep-intermediate-files --paired-end -p 10 --output-genome-bam <FASTQ1> <FASTQ2> /<path_to_reference>/rsem3_hg19_eaGene3.fa <SAMPLEID>.rsem  > <SAMPLEID>.rsem.out 2>&1 #> <SAMPLEID>.rsem.genes.results"
Raw read counts were normalized across all samples using upper quartile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx file containing normalized rna-seq counts

source_name: AML cell line

growth_protocol: Pinometostat resistant cells were cultured in media supplemented with 4.5 μM of the inhibitor. Every 3-4 days cell number and viability was assessed by trypan blue exclusion staining (Vi-CELL, Beckman Coulter) and growth media and pinometostat replaced, splitting cells back to a density of 2x105 cells/mL.

extract_protocol:
Cells were pelleted, flash frozen, RNA extracted with AllPrep DNA/RNA Mini Kit. Total RNA samples were converted into cDNA libraries using the TruSeq Total Stranded RNA Library Prep Kit (Illumina)
Starting with 100 ng of total RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads. This mRNA was chemically fragmented and converted into single-stranded cDNA using reverse transcriptase and random hexamer primers, with the addition of Actinomycin D to suppress DNA-dependent synthesis of the second strand. Double-stranded cDNA was created by removing the RNA template and synthesizing the second strand in the presence of dUTP in place of dTTP. A single A base was added to the 3’ end to facilitate ligation of sequencing adapters, which contain a single T base overhang. Adapter-ligated cDNA was amplified by polymerase chain reaction to increase the amount of sequence-ready library. During this amplification the polymerase stalls when it encounters a U base, rendering the second strand a poor template. Accordingly, amplified material used the first strand as a template, thereby preserving the strand information. Final cDNA libraries were analyzed for size distribution and using an Agilent Bioanalyzer (DNA 1000 kit, Agilent # 5067-1504), quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824), then normalized to 2 nM in preparation for sequencing

treatment_protocol: Samples were collected after 28 days (KOPN-8) or 53 days (NOMO-1) of pinometostat dosing at 4.5 µM for whole transcriptome analysis through RNA-seq. In order to distinguish changes in gene expression due to DOT1L inhibition from acquired resistance, naïve cells were dosed with 4.5 μM pinometostat for 10 days and included in the RNA sequencing analysis as a reference for sensitivity to pinometostat. All samples were then evaluated relative to the vehicle control.

tag: cell line


title: NOMO-1 D10 Ctrl rep2


title: NOMO-1 D10 Ctrl rep3


title: Nomo D10 Treated rep1

description: NOMO1_+_4_5_uM_5676_Day_10_2_5e6_cells_L9_1


title: Nomo D10 Treated rep3

description: NOMO1_+_4_5_uM_5676_Day_10_2_5e6_cells_L21_1


title: Nomo D10 Treated rep2

description: NOMO1_+_4_5_uM_5676_Day_10_2_5e6_cells_L18_1


title: NOMO-1 Res rep1

description: NOMO-1_+_4_5_uM_5676_3e6_p3+_2014-9-17_LL_L13_1


title: NOMO Res Ctrl rep3


title: KOPN-8 D10 Ctrl rep2


title: KOPN-8 D10 Ctrl rep3


title: NOMO-1 Res rep2

description: NOMO-1_+_4_5_uM_5676_3e6_p3+_2014-9-17_LL_L14_1


title: NOMO-1 Res rep3

description: NOMO-1_+_4_5_uM_5676_3e6_p3+_2014-9-17_LL_L7_1


title: KOPN-8 D10 Treated rep3

description: KOPN8_+_4_5_uM_5676_Day_10_2_5e6_cells_L8_1


title: NOMO Res Ctrl rep2


title: KOPN-8 D10 Treated rep1

description: KOPN8_+_4_5_uM_5676_Day_10_2_5e6_cells_L3_1


title: KOPN-8 D10 Treated rep2

description: KOPN8_+_4_5_uM_5676_Day_10_2_5e6_cells_L3_1 (2)


title: KOPN-8 D28 Ctrl rep1


title: KOPN-8 D28 Ctrl rep3


title: KOPN-8 Resistant rep3

description: KOPN-8_+_4_5_uM_5676_3e6_p2_2014-9-9_WF_L9_1


title: KOPN-8 Resistant rep2

description: KOPN-8_+_4_5_uM_5676_3e6_p2_2014-9-9_WF_L20_1


title: KOPN-8 Resistant rep1

description: KOPN-8_+_4_5_uM_5676_3e6_p2_2014-9-9_WF_L12_1


title: 402290_LB_0.5_BR1


title: JIA47

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: JIA patient prior to MTX treatment

data_processing:
fastq seqences aligned to hg19 using Tophat
number of reads calculated for each Entrez gene
differential expression analysis performed using edgeR
log-2 transformed rpkm (reads per kilobase of transcript per million reads mapped) computed and adjusted for batch difference between cohorts using ComBat
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited log2rpkm, with genes in rows and samples in columns

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA extraction was performed using RNeasy columns (Qiagen) or mirVana miRNA Isolation (Ambion) protocols, respectively for samples stored in TRIzol (cohort 1) or RNAlater (cohort 2).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mtx response status

value: non-responder

tag: cohort

tag: condition

value: juvenile idiopathic arthritis (JIA)


title: JIA46

description: JIA patient prior to MTX treatment

value: responder


title: JIA45

description: JIA patient prior to MTX treatment


title: JIA44

description: JIA patient prior to MTX treatment


title: JIA43

description: JIA patient prior to MTX treatment


title: JIA41

description: JIA patient prior to MTX treatment


title: NOMO Res Ctrl rep1


title: JIA42

description: JIA patient prior to MTX treatment


title: JIA40

description: JIA patient prior to MTX treatment


title: KOPN-8 D10 Ctrl rep1


title: JIA38

description: JIA patient prior to MTX treatment


title: JIA39

description: JIA patient prior to MTX treatment


title: JIA37

description: JIA patient prior to MTX treatment


title: KOPN-8 D28 Ctrl rep2


title: JIA35

description: JIA patient prior to MTX treatment


title: JIA30

description: JIA patient prior to MTX treatment


title: JIA36

description: JIA patient prior to MTX treatment


title: JIA33

description: JIA patient prior to MTX treatment


title: JIA32

description: JIA patient prior to MTX treatment


title: JIA34

description: JIA patient prior to MTX treatment


title: JIA29

description: JIA patient prior to MTX treatment


title: JIA27

description: JIA patient prior to MTX treatment


title: JIA31

description: JIA patient prior to MTX treatment


title: JIA25

description: JIA patient prior to MTX treatment


title: 16C-25C 5 days A

city: Wageningen

first: Alice

last: Pajoro

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

data_processing:
Reads were mapped to the TAIR10 genome using TopHat
Reference based full length transcript isoform reconstruction was performed using Cufflinks
MISO package was used to estimate to quantify AS-events (PSI values)
Genome_build: TAIR10
Supplementary_files_format_and_content: excel file contains PSI values 16°C and 25°C day 1, day 3 and day 5 for differential splicing events.

organism: Arabidopsis thaliana

source_name: 16C-25C 5 days

growth_protocol: Plants were grown in short day conditions (8h light/16h dark) at 16°C for 5 weeks.

extract_protocol:
For each sample, tissue from ~10 plants was collected. Using jeweler’s forceps, leaves were removed to obtain SAM enriched tissue. Total RNA was extract using the InviTrap Spin Plant RNA Mini Kit ( REF: 1064100300) from Invitek according to the manufacturer’s protocol. DNAse treatment was performed to remove genomic DNA. DNase I digestion was performed on total RNA using Turbo DNase I from Ambion. RNA integrity was checked on 1% (w/v) agarose gel after DNase I treatment.
Samples were prepared for sequencing using the TruSeq Stranded mRNA Sample Prep kit (REF 15032613) from Illumina according to the manufacturer’s protocol.

treatment_protocol: Temperature treatment: plants were moved to 25°C.

tag: ecotype

tag: time point

value: Day 5 after temperature change

tag: temperature

value: 25 °C

tag: tissue

value: SAM and early stages leaves


title: JIA26

description: JIA patient prior to MTX treatment


title: 16C-25C 5 days B


title: 16C-25C 5 days C


title: 16C-25C 3 days C

source_name: 16C-25C 3 days

value: Day 3 after temperature change


title: JIA23

description: JIA patient prior to MTX treatment


title: JIA24

description: JIA patient prior to MTX treatment


title: JIA22

description: JIA patient prior to MTX treatment


title: 16C-25C 3 days A


title: 16C-25C 3 days B


title: 16C-25C 1 day C

value: Day 1 after temperature change


title: JIA21

description: JIA patient prior to MTX treatment


title: 16C-25C 1 day B


title: JIA18

description: JIA patient prior to MTX treatment


title: JIA20

description: JIA patient prior to MTX treatment


title: JIA19

description: JIA patient prior to MTX treatment


title: JIA28

description: JIA patient prior to MTX treatment


title: 16C-16C 1 day C

value: 16 °C


title: 16C-25C 1 day A


title: JIA17

description: JIA patient prior to MTX treatment


title: 16C-16C 1 day B


title: 16C-16C 1 day A


title: sdg26-1 biological replicate C 25 °C

data_processing:
Reads were mapped to the TAIR10 genome using TopHat2
Reference based full length transcript isoform reconstruction was performed using Cufflinks
MISO package was used to estimate to quantify AS-events (PSI values)
Genome_build: TAIR10
Supplementary_files_format_and_content: excel file contains PSI values 16°C and 25°C day 1 for WT, sdg8-2 and sdg26-1. For signicantly different splicing events

tag: genotype/variation


title: JIA16

description: JIA patient prior to MTX treatment


title: R541Q SFVmac vector in HT1080 cells

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Paired-end reads were cropped to remove linker and virus LTR sequences.
Cropped paired reads were aligned to human genome hg38 using BWA MEM.
High-quality alignemnts were selected with samtools view -F 4 -F 256 -q 1.
The remaining alignements were parsed to select unique integration sites and extract coordinates of the central base pair step for each site.
Genome_build: hg38
Supplementary_files_format_and_content: bed

growth_protocol: cells were cultured at 37°C, in DMEM supplemented with 10% FBS in 5% CO2 atmosphere

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACTAGTACGGAGTCGC (with 3´ end blocked by an amino group modifier) and 5´-GCCATGGAATATGCAATCTGACGCGACTCCGTACTAG. SFVmac integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCCATGGAATATGCAATCTGAC and 5´- GTGGGTACTACACTTATCATAAGAGG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCCATGGAATATGCAATCTGAC and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXXGTTCCTAAGGATAATCAATACACAATATTC.

tag: infection protocol

value: HT1080 cells were infected with SFVmac vector produced by transfection of 293T cells with pcDWS001  (R541Q) and pcoPE (used at a ratio of 28:1).


title: JIA14

description: JIA patient prior to MTX treatment


title: sdg26-1 biological replicate B 25 °C


title: JIA15

description: JIA patient prior to MTX treatment


title: R540Q PFV vector in MRC5 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACGAGGCGTCTAATGC (with 3´ end blocked by an amino group modifier) and 5´-GCTATAGCAGCACATCAGTTAGGCATTAGACGCCTCG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCTATAGCAGCACATCAGTTAG and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCTATAGCAGCACATCAGTTAG and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: MRC5 cells were infected with PFV vector produced by transfection of 293T cells with pczDWP001 (R540Q) and pcoPE (used at a ratio of 28:1).


title: WT PFV vector in MRC5 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TAGTCCCTTAAGCGGAG (with 3´ end blocked by an amino group modifier) and 5´-GTAATACGACTCACTATAGGGCCTCCGCTTAAGGGAC. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTAATACGACTCACTATAGGGC and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTAATACGACTCACTATAGGGC and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: MRC5 (transformed)

value: MRC5 cells were infected with PFV vector produced by transfection of 293T cells with pczDWP001 (WT) and pcoPE (used at a ratio of 28:1).


title: JIA12

description: JIA patient prior to MTX treatment


title: sdg26-1 biological replicate A 25 °C


title: sdg8-2 biological replicate C 25 °C


title: sdg8-2 biological replicate B 25 °C


title: JIA11

description: JIA patient prior to MTX treatment


title: sdg8-2 biological replicate A 25 °C


title: JIA10

description: JIA patient prior to MTX treatment


title: WT PFV vector in HT1080 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TAGTCCCTTAAGCGGAG (with 3´ end blocked by an amino group modifier) and 5´-GTAATACGACTCACTATAGGGCCTCCGCTTAAGGGAC. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTAATACGACTCACTATAGGGC and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTAATACGACTCACTATAGGGC and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HT1080 cells were infected with PFV vector produced by transfection of 293T cells with pczDWP001 (WT) and pcoPE (used at a ratio of 28:1).


title: R540Q PFV (codon-optimized, 4-component) vector in HepG2 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACCGGTCAGCATAGTG (with 3´ end blocked by an amino group modifier, and 5´-phosphorylated) and 5´-GACTTGAACCGTAGCATCTAAGCACTATGCTGACCGG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGACTTGAACCGTAGCATCTAAG and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGACTTGAACCGTAGCATCTAAG and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HepG2 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (R540Q), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: Col-0 biological replicate C 25 °C

source_name: Wild type_25 °C

value: Wild type


title: JIA9

description: JIA patient prior to MTX treatment


title: WT SFVmac vector in HT1080 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACTGAGACGTCGATGC (with 3´ end blocked by an amino group modifier) and 5´-GATCATGCGAGATACATCTCAGGCATCGACGTCTCAG. SFVmac integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGATCATGCGAGATACATCTCAG and 5´- GTGGGTACTACACTTATCATAAGAGG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGATCATGCGAGATACATCTCAG and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXXGTTCCTAAGGATAATCAATACACAATATTC.

value: HT1080 cells were infected with SFVmac vector produced by transfection of 293T cells with pcDWS001  (WT) and pcoPE (used at a ratio of 28:1).


title: JIA8

description: JIA patient prior to MTX treatment

value: non-responder


title: Col-0 biological replicate A 25 °C


title: Col-0 biological replicate B 25 °C


title: JIA7

description: JIA patient prior to MTX treatment

value: juvenile idiopathic arthritis (JIA)


title: R540Q PFV (codon-optimized, 4-component) vector in HEK293T cells

extract_protocol:
DNA was extracted from infected cells five days post-infection using a Gentra Puregene kit (Qiagen).
Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACGATGCGGTAACTGC (with 3´ end blocked by an amino group modifier) and 5´-GTATCTCAACAAGCAGCTTGAGGCAGTTACCGCATCG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTATCTCAACAAGCAGCTTGAG3' and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGTATCTCAACAAGCAGCTTGAG and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HEK293T cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (R540Q), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: WT PFV (codon-optimized, 4-component) vector in HEK293T cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACTGAGACGTCGATGC (with 3´ end blocked by an amino group modifier) and 5´-GATCATGCGAGATACATCTCAGGCATCGACGTCTCAG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGATCATGCGAGATACATCTCAG and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGATCATGCGAGATACATCTCAG and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HEK293T cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (WT), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: JIA6

description: JIA patient prior to MTX treatment

value: responder


title: R540Q PFV (codon-optimized, 4-component) vector in MRC5 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACGGTGAGCGCATATC (with 3´ end blocked by an amino group modifier) and 5´-CAACTTGCGTGCAATTAACGAGGATATGCGCTCACCG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAACTTGCGTGCAATTAACGAG and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAACTTGCGTGCAATTAACGAG and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: MRC5 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (R540Q), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: JIA13

description: JIA patient prior to MTX treatment


title: sdg26-1 biological replicate A 16 °C

value: SAM and early stages leaves


title: WT PFV (codon-optimized, 4-component) vector in MRC5 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACTAGTACGGAGTCGC (with 3´ end blocked by an amino group modifier) and 5´-GCCATGGAATATGCAATCTGACGCGACTCCGTACTAG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCCATGGAATATGCAATCTGAC and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGCCATGGAATATGCAATCTGAC and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: MRC5 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (WT), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: JIA4

description: JIA patient prior to MTX treatment


title: JIA5

description: JIA patient prior to MTX treatment


title: R540Q PFV vector in HT1080 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TAGTAGTCACGAGCGTC (with 3´ end blocked by an amino group modifier) and 5´-CAGTTAGACTACACGTTAGACGGACGCTCGTGACTAC. PFV integration sites were amplified using primers 5´-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAGTTAGACTACACGTTAGACG and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAGTTAGACTACACGTTAGACG and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HT1080 cells were infected with PFV vector produced by transfection of 293T cells with pczDWP001 (R540Q) and pcoPE (used at a ratio of 28:1).


title: sdg26-1 biological replicate B 16 °C

value: 16 °C


title: JIA3

description: JIA patient prior to MTX treatment


title: R540Q PFV (codon-optimized, 4-component) vector in HT1080 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACTGATACCGGCGTAG (with 3´ end blocked by an amino group modifier, and 5´-phosphorylated) and 5´- GAGCCTACGTTACGCAATATAGCTACGCCGGTATCAG. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGAGCCTACGTTACGCAATATAG and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGAGCCTACGTTACGCAATATAG and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HT1080 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (R540Q), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: sdg8-2 biological replicate C 16 °C


title: PFV intasome in vitro control

source_name: deproteinized human genomic DNA reacted with recombinant PFV intasome

extract_protocol: Genomic DNA extracted non-infected HT1080 cells using a GenElute kit (Sigma-Aldrich) was incubated with PFV intasome assembled with recombinant integrase and synthetic U5 donor DNA. The reaction products were deproteinized and repaired with Phi29 DNA polymerase (New England Biolabs). To amplify integration sites, DNA was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TAGTCCCTTAAGCGGAG (with 3´ end blocked by an amino group modifier) and 5´-GTAATACGACTCACTATAGGGCCTCCGCTTAAGGGAC. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTG CTGAACCGCTCTTCCGATCTGTAATACGACTCACTATAGGGC and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTT CCGATCTGTAATACGACTCACTATAGGGC and 5´- AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).


title: sdg8-2 biological replicate B 16 °C


title: JIA1

description: JIA patient prior to MTX treatment


title: JIA2

description: JIA patient prior to MTX treatment


title: WT PFV (codon-optimized, 4-component) vector in HepG2 cells

extract_protocol: Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TAACGTAGGTGCGCATC (with 3´ end blocked by an amino group modifier) and 5´-CAGGATGCGTAATACGAATCTCGATGCGCACCTACGT. PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAGGATGCGTAATACGAATCTC and 5´-GTGTGAA CTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTCAGGATGCGTAATACGAATCTC and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HepG2 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (WT), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: WT PFV (codon-optimized, 4-component) vector in HT1080 cells

extract_protocol:
Cellular genomic DNA isolated 5 days post-infection was digested with BfaI/BanII/CviQI and ligated to a linker made by annealing oligonucleotides 5´- TACCGGTCAGCATAGTG (with 3´ end blocked by an amino group modifier) and 5´-GACTTGAACCGTAGCATCTAAGCACTATGCTGACCGG.
PFV integration sites were amplified using primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGACTTGAACCGTAGCATCTAAG and 5´-GTGTGAACTACACTTATCTTAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGACTTGAACCGTAGCATCTAAG and 5´- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTXXXXXCTTAAATGATGTAACTCCTTAGGATAATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

value: HT1080 cells were infected with PFV vector produced by transfection of 293T cells with pcoPG4 (WT), pcoPPol, pcoPE, and pMD9 (used at a ratio of 4:2:1:28).


title: sdg8-2 biological replicate A 16 °C


title: Col-0 biological replicate C 16 °C

source_name: Wild type_16 °C


title: control14

description: control

extract_protocol:
RNA extraction was performed using RNeasy columns (Qiagen) or mirVana miRNA Isolation (Ambion) protocols, respectively for samples stored in TRIzol (cohort 1) or RNAlater (cohort 2).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: control

value: age-matched control


title: sdg26-1 biological replicate C 16 °C

extract_protocol:
For each sample, tissue from ~10 plants was collected. Using jeweler’s forceps, leaves were removed to obtain SAM enriched tissue. Total RNA was extract using the InviTrap Spin Plant RNA Mini Kit ( REF: 1064100300) from Invitek according to the manufacturer’s protocol. DNAse treatment was performed to remove genomic DNA. DNase I digestion was performed on total RNA using Turbo DNase I from Ambion. RNA integrity was checked on 1% (w/v) agarose gel after DNase I treatment.
Samples were prepared for sequencing using the TruSeq Stranded mRNA Sample Prep kit (REF 15032613) from Illumina according to the manufacturer’s protocol.


title: III_rep3

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

country: China

institute: Sichuan Agricultural University

data_processing:
Paired-ended sequencing raw reads (PE 50bp) generated from MeDIP-seq were used to remove the containing adaptors and low quality reads. The clean reads (remaining reads) were aligned to the maize genome (RefGen_v3) (Schnable et al., 2009) using Soap2 (Li et al., 2009), allowing up to 2 bp mismatches to the reference genome and only returning uniquely mapped reads. The analyses of MeDIP-seq data were analyzed using the R/Bioconductor package MEDIPS (Lienhard et al., 2014).  For each sample, the aligned reads were extended to a length of 300 bp in the sequencing direction. The genome was divided into adjacent 500 bp windows, and all additional calculations were applied to each window. Subsequently, methylation levels were quantified using MEDIPS to produce the relative methylation signal values (RMS) for further analysis. The mean relative methylation score (RPM) in each window across various regions of interest (e.g., promoters, 5'-UTR, 3'-UTR, exons, introns, CpG islands (CGIs)) was used to analyze the differentially methylated regions (DMRs).
Genome_build: maize genome (RefGen_v3)
Supplementary_files_format_and_content: wig files were generated and separated by each chromosome.

organism: Zea mays

source_name: embryonic callus (stage III)

growth_protocol: all inbred line 18-599R seedlings as described (Shen et al., 2012) were grown in the growth chamber at 27 ¡C with humidity of 70%. In brief, after 12 days (d) of self-pollination, immature ear of each plant was harvested.

extract_protocol:
Genomic DNA was extracted from the samples using TaKaRa Universal Genomic DNA Extraction Kit Ver. 3.0 (DV811A) (TaKaRa, Osaka, Japan) according to the manufacturer's instructions.
In total, 12 genomic DNA samples (three biological replicates at each of the four stages) were sonicated to produce DNA fragments ranging from 100 bp to 500 bp. After DNA end-repair and 3'dA-tailing using the Paired-end DNA Sample Prep Kit (Illumina, San Diego, CA, USA), the DNA samples were ligated to Illumina sequencing primer adaptors. Double-stranded DNA was denatured and immunoprecipitated using an anti-5-methycytosine monoclonal antibody (Zymo Research, Orange, CA, USA). For each biological replicate, the following procedures were performed as described (Li et al., 2010). After excising and purifying 220 bp to 320 bp bands from the gel, the products were quantified using an Agilent 2100 Analyzer (Agilent Technologies, Santa Clara, CA, USA) and qPCR qualification. Finally, ultra-high-throughput 50 bp paired-end sequencing was performed using the Illumina HiSeq 2000 (BGI, Shenzhen, China) according to the manufacturer's protocols.

treatment_protocol: The immature embryos (1.5mm - 1.8mm) were isolated and cultured with optimized N6 medium aseptically at 27C in darkness for 15 d. Samples were collected from three individuals each day and pooled for three biological replicates at each stage. Generally, after inoculating, the immature embryos were divided into three stages according to their morphological features(Shen et al., 2012) through 1-5 d (intumescent embryo, Stage I), 6-10 d (initial callus formation, Stage II), and 11-15 d (embryonic callus formation, Stage III), respectively. The embryos from immediately harvested ears without inoculation were collected with three biological replicates and used as a control group (0 d, CK) in this study.

tag: inbred line

value: embryonic callus (stage III)


title: III_rep2


title: Col-0 biological replicate B 16 °C

value: Wild type


title: control13

description: control


title: III_rep1


title: Col-0 biological replicate A 16 °C


title: II_rep2

source_name: initial callus (stage II)

value: initial callus (stage II)


title: H3-ChIP 25°C biological replicate C

data_processing:
Reads were aligned to the Arabidopsis thaliana genome TAIR10 using Bowtie2 (Langmead et al., 2009), using the default parameters.
H3K36me3 modified regions were identified the “Dpeak” function in DANPOS2 (Chen et al., 2013) with default parameters, except for the parameter – l (read extension length)  that was set to 150bp, the size of monocleosomal DNA. H3 ChIP-seq was used as control to normalize for nucleosme occupancy.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files contain H3K36me3 enriched regions for each condition 16°C and 25°C day1.

source_name: H3-ChIP 25°C

extract_protocol:
For each sample, 0.5 g of plant material were used for each biological replicate. Material was collected at from plant growing at 16 °C, as well as at 1 day after the plants were moved to 25°C (5-6 h after lights on). Using jeweler’s forceps, leaves were removed to obtain SAM enriched tissue. ChIP experiments were performed following a previously published protocol (Kaufmann et al., Nature Protocols 2010). After the preclearing step the sample was split, one aliquot was incubated with anti-H3K36me3 antibody (ab9050, abcam)and the other with anti-H3 antibody (ab1791, abcam).
Samples were prepared for Illumina sequencing using the ThruPLEX DNA-seq Kit (Cat. No: R400429) from Rubicon Genomics according to the manufacturer’s protocol.

value: 25 °C

value: anti-H3 antibody (ab1791, abcam)


title: control12

description: control


title: control11

description: control


title: H3-ChIP 25°C biological replicate B


title: control10

description: control


title: I_rep2

source_name: intumescent embryo (stage I)

value: intumescent embryo (stage I)


title: control8

description: control


title: I_rep3


title: II_rep1


title: H3K36me3-ChIP 25°C biological replicate D

source_name: H3K36me3-ChIP 25°C

value: anti-H3K36me3 antibody (ab9050, abcam)


title: H3-ChIP 25°C biological replicate A


title: control6

description: control


title: I_rep1


title: control7

description: control


title: H3K36me3-ChIP 25°C biological replicate A


title: H3K36me3-ChIP 25°C biological replicate C


title: H3K36me3-ChIP 25°C biological replicate B


title: CK_rep3

source_name: immature embryos without inoculation (CK)


title: II_rep3


title: H3-ChIP 16°C biological replicate C

source_name: H3-ChIP 16°C


title: control5

description: control


title: CK_rep2

value: immature embryos without inoculation (CK)


title: CK_rep1


title: H3-ChIP 16°C biological replicate B

value: SAM and early stages leaves


title: control4

description: control


title: control3

description: control


title: 300059_TEPEC_DMEM_0.5_BR2

organism: Escherichia coli 300059

extract_protocol:
RNA was isolated from cells grown in LB or DMEM using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: H3-ChIP 16°C biological replicate A


title: 300059_TEPEC_DMEM_0.5_BR1


title: H3K36me3-ChIP 16°C biological replicate D

source_name: H3K36me3-ChIP 16°C


title: control9

description: control


title: H3K36me3-ChIP 16°C biological replicate C


title: 100329_DMEM_0.5_BR1

organism: Escherichia coli 100329

source_name: Escherichia coli cells


title: H3K36me3-ChIP 16°C biological replicate B


title: 100329_DMEM_0.5_BR2


title: 100329_LB_0.5_BR2


title: 100329_LB_0.5_BR1


title: new shoot tip repeat 1

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

data_processing:
The RNA-seq reads were aligned to the bamboo genome (P_heterocycla.1) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: P_heterocycla.1
Supplementary_files_format_and_content: bigWig

organism: Phyllostachys edulis

source_name: new shoot tip

growth_protocol: Bamboo materials from leptomorph rhizome tip, new shoot tip and  bud  were harvested from the field of Fujian Agriculture and Forestry University in 2015.

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
Strand-specific RNA-Seq libraries generated from samples above were constructed using SMART method and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

value: new shoot tip


title: new shoot tip repeat 3

institute: Fujian Agriculture and Forestry University


title: e9.5 AVC Hand2 null-mutant (2)

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Reads were aligned to the mm9 reference genome and to the Mus Musculus transcriptome (iGenome refGene) using TopHat v2.0.13 (PMID: 23618408). The option --no-coverage-search was specified, while all the other parameters were left to default.
Gene-wise counts were calculated using htseq-count (PMID: 25260700) setting -s to no and considering the same reference transcriptome. Only those reads with a unique match to the genome were considered (samtools view -q1).
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63.
Supplementary_files_format_and_content: *.counts.txt list the raw counts per gene as inferred by htseq-count.

organism: Mus musculus

source_name: e9.5 AVC Hand2 null-mutant

growth_protocol: The Hand2 d/d (null-Mutant) allele was generated by Cre-mediated deletion of the entire Hand2 coding regions in the germline (PMID: 20386744). Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from toe biopsies and yolk sacs, respectively.

extract_protocol:
Atrioventricular canals were hand-dissected from isolated hearts using Tungsten needles, flash-frozen individually in Qiagen RTL buffer and stored at -80 °C until genotyped. For each genotype, four replicates of four pooled AVCs with the same distribution of somite stages and sex ratios were prepared and RNA was extracted using Qiagen RNeasy Micro kit according to the manufacturer's protocol."
The quality of total RNA (30-60ng) from the four wild-type and Hand2-deficient samples was analyzed using the RNA 6000 Pico kit in combination with the Agilent 2100 Bioanalyzer. Seven of the eight samples had RIN values >=8.5, while the RNA extracted from one wild-type sample was of suboptimal quality. Therefore, only three wild-type and all four Hand2-deficient samples were processed for sequencing. Ribosomal RNA was depleted using the Ribo-Zero Magnetic Gold Kit (Epicentre). RNA-Seq libraries were prepared using the Clontech SMARTer Low Input RNA kit (Clontech). The resulting cDNA was subjected to eight cycles of PCR amplification and sequenced on a Illumina HiSeq 3000 instrument with a SR50 protocol.

tag: stain background

value: Outbred NMRI mice

value: Hand2 d/d (null-mutant)

tag: developmental stage

value: gestational day e9.0-e9.25

value: embryonic heart

value: Atrioventricular canal tissue

tag: library type

value: Unstranded


title: e9.5 AVC Hand2 wt (3)

source_name: e9.5 AVC Hand2 wt

value: wild type


title: e9.5 AVC Hand2 null-mutant (1)


title: bud repeat 2

source_name: bud

value: bud


title: e9.5 AVC Hand2 null-mutant (4)


title: e9.5 AVC Hand2 null-mutant (3)


title: control1

description: control

source_name: Peripheral blood mononuclear cells

value: control

value: age-matched control


title: e9.5 AVC Hand2 wt (2)


title: control2

description: control


title: new shoot tip repeat 2


title: 300059_TEPEC_LB_0.5_BR2

tag: strain


title: bud repeat 1


title: leptomorph rhizome tip repeat 3

source_name: leptomorph rhizome tip

value: leptomorph rhizome tip


title: leptomorph rhizome tip repeat 2


title: leptomorph rhizome tip repeat 1


title: 300059_TEPEC_LB_0.5_BR1


title: H3K36me3-ChIP 16°C biological replicate A

value: 16 °C


title: LS174T CDX2-/- 2XindCDX2 (4 ng/ml Dox) clone 6D6

status: Public on May 09 2017

city: Copenhagen

first: Lars

last: Hansen

address: 3B Blegdamsvej

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
RNA-seq
average read length: 116 bp

data_processing:
Ion Proton software was used for basecalling
Sequencing reads were mapped to hg19 and bioinformatics analysis was conducted using CLCs Genomic Workbench (CLC bio/Qiagen, DK), STARBowtie2 followed by Cufflinks for expression analyses
genome build: hg19
processed data files format and content: text files with RPKM, gene name and ID for RNA-seq

molecule: polyA RNA

source_name: column goblet cells

growth_protocol: LS174T human intestinal cell line was maintained in Ham’s nutrient mixture F12/Dulbecco’s modified Eagle’s medium (1:1) supplemented with 10% fetal bovine serum and 1% Glutamine

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen, GE) as recommended by the manufacturer. Polyadenylated RNA was isolated from total RNA using standard protocols (Dynabeads mRNA Direct Micro Kit, Ambion/Life Technologies, USA) starting with 5 μg total RNA.
Library preparation for NGS using Ion Torrent technology (Life Technologies, USA) was carried out according to the manufacturers recommendations (Ion Total RNA-Seq Kit v2, Ion torrent/Life Technologies, USA), and sequenced using an Ion Proton system (Life Technologies, USA). Quality control, quantification of RNA and libraries was carried out using using Agilent RNA 6000 Nano Kit or Agilent High Sensitivity DNA kit and Agilent Bioanalyzer (Agilent Technologies, USA). In brief, approximately 50 ng polyA RNA was fragmented down to 100-300 base fragments using RNaseIII for 1-3 min followed by adapter ligation, amplification for 9-14 cycles and barcoding using Ion Express RNA-Seq Barcode kit (Ion Torrent/Life Technologies, USA). The final library fragment size and concentration was determined by Agilent Bioanalyzer analysis followed by template preparation using Ion PI Template OT2 200 Kit v3 (Life Technologies, USA) and Ion One Touch System followed by NGS on an Ion Proton system using Ion PI™ Chip Kit v2. In general two transcriptome libraries were barcoded and analyzed on one Ion PI v2 chip. Sequencing depth for the RNA-Seq data sets ranged from 34.5 to 44.6 mill reads/sample with 95.4-97.7% mappable reads to the hg19 reference data base. Mean read length for transcriptome RNA-Seq data ranged from 116 bp to 136 bp.

treatment_protocol: The Tet-On3G system was induced with Dox (Sigma-Aldrich, USA) in a range between 0.004-4 μg/mL for CDX2 knock-in (KI) clones and 0.001-5 μg/mL for T2EYFP KI clones. Dox was added to the medium every 24 h for one or two days, and medium was exchanged every 48 h after Dox removal. Controls where Dox was not added to the medium were used (0 μg/mL of Dox).

tag: cell type

value: column goblet cells

tag: clone name

tag: cdx2 -/- or cdx2+/- tet3g ko

value: LS174T_CDX2-/- Tet3G KO

tag: dox induction

value: 4 ng/ml

tag: antibody


title: LS174T CDX2-/- 2XindCDX2 (0 ng/ml Dox) clone 6D6

description:
RNA-seq
average read length: 120 bp

tag: cell line

value: 0 ng/ml


title: LS174T CDX2 -/- clone 3D6

description:
RNA-seq
average read length: 116 bp


title: LS174T CDX2-/- 1XindCDX2 (4 ng/ml Dox) clone 7D9

description:
RNA-seq
average read length: 117 bp


title: e9.5 AVC Hand2 wt (4)


title: LS174T CDX2 ChIP-seq2

description:
CDX2-immunoprecipitated DNA
average read length: 129 bp

data_processing:
Ion Proton software was used for basecalling
The detection of CDX2 ChIP seq peaks and the location of the closest gene was performed using CisGenome ver. 2 (Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, and W.H. and Wong (2008) An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol, 26, 1293–1300).
genome build: hg19
processed data files format and content: peak coordinates and nearest gene for ChIP-seq data

extract_protocol:
LS174T cells grown for five days in a 30x30 cm culture dish were cross-linking and sonicated as described previously to generate fragments of ~0.2 to 1.2 kb. Hereafter, the ChIP-protocol was performed as previously reported (Coskun,M., Troelsen,J.T. and Nielsen,O.H. (2011) The role of CDX2 in intestinal homeostasis and inflammation. Biochim. Biophys. Acta, 1812, 283–9). Briefly, immunoprecipitation was done in four replicates and performed overnight at 4ºC using specific antibodies to human CDX2 (CDX2-88, Biogenex, USA) and the influenza hemagglutinin (HA) epitope (rabbit polyclonal α-HA; Santa Cruz Biotechnology Inc, Heidelberg, Germany), used as a negative control. Immunocomplexes were recovered with 50 μl protein A/G beads (Invitrogen/ThermoFisher Scientific, USA). Verification of the enrichment in the CDX2-immunoprecipitated DNA samples was done by qPCR analyzing the DNA level from known CDX2-targets in the CDX2-immunoprecipitated samples and comparison it to level in the negative control (HA-immunoprecipitated DNA).
Library preparation for NGS was carried out with the Ion Xpress Plus gDNA Fragment Library Kit according to User Bulletin 4473623: Ion ChIP-seq Library Preparation on the Ion Proton System (Life Technologies, USA), starting with 10ng DNA. Quality control of the libraries was carried out using using Experion DNA 1K analysis kit and the Experion System (Bio-Rad Laboratories, USA). In brief, 10ng DNA was end-repaired and ligated to barcode adaptors from the Ion Xpress Barcode Adapters 1-16 Kit (Life Technologies, USA), followed by nick repair and amplification for 18 cycles. The amplified libraries were subjected to two rounds of bead capture with the Agencourt AMPure XP Kit (Beckman Coulter, USA) to size-select fragments approximately 160-340 bp in length. The final library concentration was determined by Qubit analysis (ThermoFisher Scientific, USA). The barcoded ChIP- and IP control- DNA-libraries were handled similarly to the RNA-Seq library and analyzed on a single Ion PI™ Chip v2. For the ChIP- and IP control- DNAlibraries a total of 54.5 mill reads (21.8 and 32.7 mill respectively) were obtained and 98.5% were mappable to the reference hg19 data base with a mean read length of 130bp.

value: wt

value: Anti-CDX-2, Clone CDX2-88; cat.no. AM392-10M; Biogenex


title: bud repeat 3


title: LS174T ChIP-seq control DNA

description:
control-immunoprecipitated DNA
average read length: 130 bp

value: HA-probe Antibody (Y-11); cat.no. sc-805; Santa Cruz Biotechnology


title: LS174T wt

description:
RNA-seq
average read length: 112 bp


title: LS174T CDX2-/- 2XindCDX2 (40 ng/ml Dox) clone 6D6

description:
RNA-seq
average read length: 123 bp

value: 40 ng/ml


title: Healthy control 2 Untreated

city: Boston

first: Janet

last: Chou

state: MA

address: 1 Blackfan Circle, Karp 10007D

department: Immunology

institute: Boston Children's Hospital

description:
Cuff_Gene_Counts
Cuff_Gene_Counts.filtered
Cuff_Isoform_Counts

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg19 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1
Differential expression testing was performed by DESeq2 (v1.10.1) as part of the VIPER analysis pipeline (https://bitbucket.org/cfce/viper/)
Genome_build: hg19
Supplementary_files_format_and_content: Excel files for combined analysis of all samples and Bam files for raw data on each sample

source_name: Cultured dermal fibroblasts

growth_protocol: Skin biopsies to generate fibroblast cell lines were collected from patients. Fibroblasts were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 50,000 U penicillin, 50,000 μg streptomycin, 10 μM HEPES, and 2 mM Glutamine. Cells were routinely cultured every three days by seeding 200,000 cells in 10 cm cell culture plates.

extract_protocol:
RNA was prepared using RNAeasy Mini kit (Qiagen) as per kit protocol and with DNase treatment (Qiagen). Quality control was performed at the Dana Farber Cancer Institute’s Molecular Biology core. Technical duplicates with a minimum RIN score of 7 were processed. cDNA was synthesized using Clontech SmartSeq v4 reagents from 1 ng of RNA and fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator.
Illumina standard mRNA libraries were prepared from cDNA using Rubicon Genomics Thruplex DNAseq reagents according to manufacturer’s protocol

treatment_protocol: Fibroblasts were treated with (20 ng/ml) of TNF-a in fibroblst culture media for 24 hours or left untreated (culture medium alone).

tag: genotype

value: Wild type (RelA+/+)

value: Skin

tag: passage


title: Healthy control 1 Untreated


title: Light 24+2hr

city: Taipei

first: Mai-Yi

last: Fan

address: No1, Sec. 1, Jen - Ai Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: skin tissue

growth_protocol: Animals were fed ad lib and housed in animal facilities with 12-hour light: 12-hour dark cycles.

extract_protocol:
Totoal RNA was extracted using Qiagen RNeasy kit(Cat No./ID: 74104)  according to the manufacturer's protocol
Total 1~2 g RNA was purified by using poly-T oligo-attached magnetic beads.The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Paired-end 150 nucleotide reads from each mRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).

treatment_protocol: The temperature within the light box was not elevated during light irradiation. The dorsal skin of 7-week old female mice whose dorsal hair cycle was in the second telogen phase was carefully shaved first with an electric clipper and then with a razor without damaging the skin. The mice were shielded by aluminum foil from their neck to the tail to avoid light irradiation and only the heads were exposed. The mice were in a prone position with eyes facing up toward the light emitting diodes. The mice were exposed to daily blue (4mW/cm2) irradiation at 2 J/cm2 at ZT1 (zeitgeber time) for days.

tag: treatment

value: light


title: Healthy control 3 Untreated

tag: tissue


title: Patient 2 24 hrs TNFa  (replica 1)

description:
TNF treated samples_Allpatient_v_Allcontrol.deseq.annot
Cuff_Gene_Counts
Cuff_Gene_Counts.filtered
Cuff_Isoform_Counts

value: RelA+/-


title: Patient 2 24 hrs TNFa (replica 2)


title: Control


title: E11.5-Face-2

city: Farmington

first: Justin

last: Cotney

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

description: Circularized chromatin conformation capture folllowed by sequening (4C-seq)

data_processing:
Library strategy: 4C-seq
Data processing included in supplementary file.
Genome_build: mm9
Supplementary_files_format_and_content: bigBed file of significant (p<=0.05) interactions between viewpoint and locations on same chromosome

source_name: Embryonic Craniofacial Tissue

growth_protocol: Timed matings and harvest of tissue according to approved University of Connecticut Health Center IACUC protocols

extract_protocol:
van de Werken, H.J.G., de Vree, P.J.P., Splinter, E., Holwerda, S.J.B., Klous, P., de Wit, E., and de Laat, W. (2012). 4C Technology: Protocols and Data Analysis (Elsevier Inc.).
van de Werken, H.J.G., de Vree, P.J.P., Splinter, E., Holwerda, S.J.B., Klous, P., de Wit, E., and de Laat, W. (2012). 4C Technology: Protocols and Data Analysis (Elsevier Inc.).
Amplification with viewpoint-specific primers (viewpoint 1: ACACTCTTTCCCTACACGACGCTCTTCCGATCTAATGATTGCATTAAGCCATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACACCCATAAACGTGACACT; viewpoint 2: ACACTCTTTCCCTACACGACGCTCTTCCGATCTCACAGAGTTCTAGGTGCATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGAACTGTAGCCTGTAGCCA; viewpoint 3: ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCAATCACAACAAGTCATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCTATCAAAGCCTTGGTTATT; viewpoint 4: ACACTCTTTCCCTACACGACGCTCTTCCGATCTGGGTTCTGAAACCATCCATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACCTCAACCTAGCCCTCTT; viewpoint 5: ACACTCTTTCCCTACACGACGCTCTTCCGATCTCCACATAAATCAAGGCCATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTATGGCAGTTTTGGTTAGAAA; viewpoint 6: ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGGAGGGAACCGAGTACATG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTGAGGTTACAGCCCATTAT followed by amplification with illumina barcode-containing primers: Truseq_HT_D501 AATGATACGGCGACCACCGAGATCTACACTATAGCCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;  Truseq_HT_D502 AATGATACGGCGACCACCGAGATCTACACATAGAGGCACACTCTTTCCCTACACGACGCTCTTCCGATCT;  Truseq_HT_D503 AATGATACGGCGACCACCGAGATCTACACCCTATCCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;  Truseq_HT_D504 AATGATACGGCGACCACCGAGATCTACACGGCTCTGAACACTCTTTCCCTACACGACGCTCTTCCGATCT;  TruSeq_HT_D701 CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT;  TruSeq_HT_D702 CAAGCAGAAGACGGCATACGAGATTCTCCGGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT;  TruSeq_HT_D703 CAAGCAGAAGACGGCATACGAGATAATGAGCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT;  TruSeq_HT_D704 CAAGCAGAAGACGGCATACGAGATGGAATCTCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

treatment_protocol: Crosslinking and nucelar isolation- see accompanying manuscript

value: pharyngeal arches


title: E11.5-Face-1


title: Patient 2 Untreated (replica 2)


title: Healthy control 2 24 hrs TNFa


title: Healthy control 1 24 hrs TNFa


title: Patient 1 Untreated  (replica 1)


title: LS174T CDX2 +/- clone 5B5

description:
RNA-seq
average read length: 136 bp

value: LS174T_CDX2+/- Tet3G KO


title: Patient 2 Untreated  (replica 1)


title: Patient 1 24 hrs TNFa  (replica 1)


title: Healthy control 3 24 hrs TNFa


title: WT_RA_4C_HoxA1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
The 4Cseqpipe tool was used to map and analyze the 4C-seq experiments. Using the 4cseqpipe.pl script, fastq files were converted to “raw” format, valid 4C-seq products were mapped to restriction fragments in the genome, aligned data were normalized, and near-cis domainograms were generated. Default options were utlized, and a trend resolution of 10000 was implemented for the domainograms. Output bedgraph files give normalized coverage values across relevant loci corresponding to the published figures.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate. The bedgraph files (for 4C-seq samples) give normalized coverage values across relevant loci corresponding to the published figures.

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF).

extract_protocol:
RNA was extracted using Trizol reagent (Life technologies). RNAse free DNaseI (Sigma) was used to eliminate DNA contamination and the treated RNA was purified with RNeasy mini kit (Qiagen).
For ChIP, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). 100 µg sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-croslinking and submitted for library preparation.
4C-seq was performed following the protocol published in (van de Werken et al. 2012). In brief, cross-linked chromatin was digested with DpnII, ligated under diluted conditions. Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol:
For RA-induced differentiation, ESCs were grown in plain N2B27 media with 1 µM all trans retinoic acid without addition of 2i or LIF.
For shRNA knockdown, ESCs were infected with lentivial shRNA in the presense of 10ug/ml polybrene for 12 hours and then seleted with 2 ug/ml puromycin for 48h before harvest for ChIP-seq or RNA-seq experiments.

value: embryonic stem cell

tag: genotype/variation

value: Wildtype/WT


title: Patient 1 Untreated (replica 2)


title: WT_4C_HoxA1


title: WT_RA_4C_E1


title: DKO_RA_4C_HoxA1

value: Double enhancer KO/DKO


title: DKO_4C_HoxA1


title: WT_4C_E1


title: nonTsh_RA_ChIP_H3K4me2

tag: shRNA

value: nonTsh

tag: chip antibody

value: H3K4me2 (Homemade, #27)


title: nonTsh_RA_RNA_2


title: WT_nonTsh_RA_RNA_Rep2


title: nonTsh_RA_RNA_1


title: Patient 1 24 hrs TNFa (replica 2)


title: WT_nonTsh_RA_ChIP_H3K4me3_Rep2

value: H3K4me3 (Homemade, #28)


title: WT_nonTsh_RA_ChIP_H3K27Ac_Rep1


title: WT_nonTsh_ChIP_input


title: WT_nonTsh_ChIP_H3K4me3_Rep2


title: WT_nonTsh_RA_ChIP_H3K4me1

value: H3K4me1 (Homemade, #24)


title: WT_nonTsh_RA_RNA_Rep1


title: WT_nonTsh_RA_ChIP_H3K4me3_Rep1


title: WT_nonTsh_RA_ChIP_H3K27Ac_Rep2


title: WT_nonTsh_ChIP_H3K27Ac_Rep2


title: WT_nonTsh_ChIP_H3K27Ac_Rep1


title: nonTsh_ChIP_H3K4me2


title: WT_SET1Ash_RA_ChIP_H3K4me3_Rep1


title: WT_SET1Ash_RA_RNA_Rep1


title: WT_SET1Ash_RA_ChIP_H3K4me3_Rep2


title: WT_SET1Ash_RA_RNA_Rep2


title: WT_nonTsh_ChIP_H3K4me1


title: WT_nonTsh_ChIP_H3K4me3_Rep1


title: WT_SET1Ash_RA_ChIP_H3K27Ac_Rep2


title: WT_SET1Ash_RA_ChIP_H3K4me1


title: WT_SET1Ash_RA_ChIP_H3K27Ac_Rep1


title: WT_SET1Ash_ChIP_input


title: WT_SET1Ash_ChIP_H3K27Ac_Rep2


title: WT_SET1Ash_ChIP_H3K4me1


title: WT_SET1Ash_ChIP_H3K4me3_Rep1


title: WT_RNA_Rep3


title: WT_SET1Ash_ChIP_H3K27Ac_Rep1


title: WT_RNA_Rep4


title: WT_RNA_Rep2


title: WT_RNA_Rep1


title: WT_RA_RNA


title: WT_SET1Ash_ChIP_H3K4me3_Rep2


title: WT_RA_ChIP_SET1A

value: SET1A (Homemade, #919)


title: WT_RA_ChIP_H3K4me2


title: WT_RA_ChIP_MLL2

value: MLL2 (Homemade, #9173)


title: WT_RA_ChIP_MLL4

value: MLL4 (Homemade, #825)


title: WT_RA_ChIP_H3K4me1_Rep1


title: WT_RA_ChIP_H3K4me1_Rep2


title: WT_RA_ChIP_H3K4me1_Rep3


title: WT_RA24h_RNA_Rep4


title: WT_RA_ChIP_H3K27Ac_Rep1


title: WT_RA_ChIP_H3K27Ac_Rep2


title: WT_RA24h_RNA_Rep3


title: WT_RA24h_RNA_Rep1


title: WT_RA_ChIP_H3K4me3


title: WT_RA12h_RNA_Rep4


title: WT_RA12h_RNA_Rep3


title: WT_RA24h_RNA_Rep2


title: WT_RA12h_RNA_Rep2


title: WT_RA12h_RNA_Rep1


title: 83H1_061213

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

data_processing:
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
The read files from one male (83H1_061213) and one female (8SK7_071413) animal were concatenated into a single fastq file for assembly in Trinity v2.0.4 using a minimum K-mer coverage of 3, a minimum overlap value of 25 and a minimum contig length of 400 nucleotides on the CyVerse Atmosphere cloud computing platform.
Annotation of the de novo assembly was obtained by BLASTx searches of the human subset of the uniprot_swissprot database augmented with conserved domian mapping and gene ontology assignment using Blast2GO.
Reads were mapped to the de novo Trinity assembly, using RSEM v 1.2.21 with bowtie2 as the alignment engine and read counts were generated as TPM (transcripts per million) at the gene level on the CyVerse Atmosphere cloud computing platform.
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Accession Number" contains the accession number of the top hit from BLASTx searches of the human subset of the UniProt-SwissProt database.  The third column "Entrez Gene ID" contains the Entrez Gene ID, if assigned, following BLASTx searches and Blast2GO annotation. The remaining columns contain the TPM values for each sample as generated by RSEM.  A TPM > 0 in at least half the samples and an average TPM ≥ 1 across all samples was required for all further data analysis.  Only genes meeting these requirements are included in the processed data table.

organism: Tursiops truncatus

source_name: blood

extract_protocol:
Whole blood RNA was extracted using a PAXgene Blood RNA kit (Qiagen).
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

tag: date

tag: Sex

value: Male

tag: age

tag: location

value: Dophin Quest, Waikoloa, Hawaii

value: blood


title: WT_ChIP_input1

tag: cell type


title: WT_ChIP_MLL4


title: WT_ChIP_input2


title: 1FP3_062413

value: Female


title: WT_ChIP_MLL2


title: WT_ChIP_H3K4me2


title: WT_ChIP_H3K4me1_Rep2


title: WT_ChIP_H3K4me1_Rep3


title: WT_ChIP_H3K4me1_Rep1


title: WT_ChIP_H3K27Ac_Rep2


title: 1FP3_041813


title: 8SK7_071413


title: WT_ChIP_H3K27Ac_Rep1


title: 8SK7_092913


title: SET1Ash_RA_ChIP_H3K4me2


title: Smc1Ash_RA_RNA


title: MLL4dSET_nonTsh_ChIP_input

value: MLL4 SET deletion/MLL4dSET


title: SET1Ash_ChIP_H3K4me2


title: WT_ChIP_SET1A


title: MLL4dSET_nonTsh_ChIP_H3K4me1


title: MLL4dSET_nonTsh_RA_ChIP_H3K4me1


title: MLL4dSET_RA_RNA


title: MLL4dSET_nonTsh_RA_RNA_Rep1


title: WT_ChIP_H3K4me3


title: MLL4dSET_nonTsh_RA_RNA_Rep2


title: MLL4dSET_RA_ChIP_H3K4me1


title: MLL4dSET_RA_ChIP_H3K4me2


title: MLL4dSET_ChIP_H3K4me2


title: MLL4dSET_ChIP_H3K4me1


title: MLL4dSET_MLL3sh_RA_RNA_Rep1


title: MLL4dSET_MLL3sh_ChIP_input


title: MLL4dSET_MLL3sh_RA_ChIP_H3K4me1


title: MLL4dSET_MLL3sh_ChIP_H3K4me1


title: MLL4dSET_MLL3sh_RA_RNA_Rep2


title: MLL3KO_RA_RNA

value: MLL3 KO/MLL3KO


title: MLL4dSET_ChIP_input


title: MLL3KO_RA_ChIP_H3K4me1


title: MLL3KO_ChIP_H3K4me1


title: MLL3KO_RA_ChIP_H3K4me2


title: MLL2KO_RA_ChIP_H3K4me2

value: MLL2 KO/MLL2KO


title: MLL3KO_ChIP_input

value: embryonic stem cell


title: MLL3KO_ChIP_H3K4me2


title: MLL2KO_input


title: MLL1KO_input

value: MLL1 KO/MLL1KO


title: MLL2KO_RA_ChIP_H3K4me1


title: MLL2KO_ChIP_H3K4me2


title: MLL1KO_RA_ChIP_H3K4me1


title: MLL1KO_RA_ChIP_H3K4me2


title: MLL1KO_RA_RNA


title: MLL1KO_ChIP_H3K4me1


title: MLL1KO_ChIP_H3K4me2


title: MLL2KO_ChIP_H3K4me1


title: E2KO_RNA_Rep4

value: Enhancer 2 KO/E2KO


title: Halr1sh_RA_RNA

value: Wildtype/WT


title: E2KO_RNA_Rep3


title: E2KO_RNA_Rep2


title: E2KO_RA_ChIP_H3K4me1


title: E2KO_RA_ChIP_H3K27Ac


title: E2KO_RA24h_RNA_Rep4


title: E2KO_RNA_Rep1


title: E2KO_RA24h_RNA_Rep2


title: E2KO_RA12h_RNA_Rep4


title: E2KO_RA24h_RNA_Rep1


title: E2KO_RA24h_RNA_Rep3


title: E2KO_RA12h_RNA_Rep2


title: MLL2KO_RA_RNA


title: E2KO_ChIP_input


title: E2KO_RA12h_RNA_Rep3


title: E2KO_RA12h_RNA_Rep1


title: E2KO_ChIP_H3K27Ac


title: E2KO_ChIP_H3K4me1


title: E1KO_RNA_Rep3

value: Enhancer 1 KO/E1KO


title: E1KO_RNA_Rep4


title: E1KO_RA_ChIP_H3K4me1


title: E1KO_RA24h_RNA_Rep1


title: E1KO_RA24h_RNA_Rep3


title: E1KO_RA12h_RNA_Rep3


title: E1KO_RA12h_RNA_Rep4


title: E1KO_RA_ChIP_H3K27Ac


title: E1KO_RA12h_RNA_Rep1


title: E1KO_RA12h_RNA_Rep2


title: E1KO_ChIP_H3K4me1


title: E1KO_ChIP_H3K27Ac


title: DKO_nonTsh_RA_RNA_Rep2

value: Double enhancer KO/DKO

value: nonTsh


title: DKO_nonTsh_RA_ChIP_H3K4me3_Rep1

value: H3K4me3 (Homemade, #28)


title: DKO_nonTsh_RA_ChIP_H3K27Ac_Rep2


title: DKO_nonTsh_RA_ChIP_H3K4me3_Rep2


title: DKO_nonTsh_RA_RNA_Rep1


title: DKO_nonTsh_ChIP_input


title: E1KO_ChIP_input


title: DKO_nonTsh_ChIP_H3K4me3_Rep2


title: DKO_nonTsh_ChIP_H3K4me3_Rep1


title: DKO_nonTsh_ChIP_H3K27Ac_Rep2


title: DKO_nonTsh_ChIP_H3K4me1

value: H3K4me1 (Homemade, #24)


title: DKO_nonTsh_RA_ChIP_H3K27Ac_Rep1


title: DKO_SET1Ash_RA_RNA_Rep2


title: E1KO_RNA_Rep2


title: DKO_nonTsh_RA_ChIP_H3K4me1


title: E1KO_RA24h_RNA_Rep4


title: DKO_nonTsh_ChIP_H3K27Ac_Rep1


title: E1KO_RNA_Rep1


title: DKO_SET1Ash_RA_ChIP_H3K4me3_Rep1


title: DKO_SET1Ash_RA_ChIP_H3K4me3_Rep2


title: DKO_SET1Ash_RA_ChIP_H3K27Ac_Rep1


title: DKO_SET1Ash_RA_ChIP_H3K27Ac_Rep2


title: DKO_SET1Ash_RA_ChIP_H3K4me1


title: DKO_SET1Ash_ChIP_input


title: DKO_SET1Ash_ChIP_H3K4me3_Rep2


title: DKO_SET1Ash_ChIP_H3K4me3_Rep1


title: DKO_SET1Ash_ChIP_H3K4me1


title: DKO_SET1Ash_ChIP_H3K27Ac_Rep1


title: DKO_RNA_Rep3


title: DKO_SET1Ash_ChIP_H3K27Ac_Rep2


title: DKO_RNA_Rep2


title: DKO_RA_ChIP_H3K4me2

value: H3K4me2 (Homemade, #27)


title: DKO_RA_ChIP_H3K4me1_Rep2


title: DKO_RNA_Rep4


title: DKO_RA_ChIP_H3K4me1_Rep1


title: DKO_RNA_Rep1


title: DKO_RA_ChIP_H3K27Ac_Rep2


title: DKO_SET1Ash_RA_RNA_Rep1


title: DKO_RA24h_RNA_Rep4


title: DKO_RA12h_RNA_Rep4


title: DKO_RA24h_RNA_Rep3


title: DKO_RA24h_RNA_Rep2


title: DKO_RA24h_RNA_Rep1


title: DKO_RA12h_RNA_Rep2


title: DKO_RA12h_RNA_Rep1


title: DKO_RA12h_RNA_Rep3


title: DKO_ChIP_input2


title: DKO_ChIP_H3K4me2


title: DKO_ChIP_input1


title: DKO_ChIP_H3K4me1_Rep1


title: DKO_ChIP_H3K4me1_Rep2


title: ERC38 mixed embryo rep2 RNA-seq

city: New York

first: Sarah

middle: Elizabeth

last: Albritton

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.0.1 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.2 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.2 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.0.12 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.2. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.2, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.2 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: strain

tag: developmental stage

value: mixed embryo


title: N2 mixed embryo rep1 RNA-seq


title: N2 mixed embryo rep3 RNA-seq


title: DKO_ChIP_H3K27Ac_Rep2


title: DKO_RA_ChIP_H3K27Ac_Rep1


title: N2 mixed embryo rep2 RNA-seq


title: DKO_ChIP_H3K27Ac_Rep1


title: ERC38 mixed embryo rep1 RNA-seq


title: ERC09 input Paired End rep1

description: The PE DNAseq reads were used to analyze bombardment insertions using discordant read pairs.


title: ERC08 input Paired End rep1


title: N2 input Paired End rep1

description: The 'ERC08 input' and 'ERC09 input' PE DNAseq reads were used to analyze bombardment insertions using discordant read pairs. The 'N2 input' PE DNAseq reads were used as a negative control in these analyses.


title: Gli3+/- Rep1

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

institute: UCL

data_processing:
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.

source_name: Gli3+/-_fetal liver CD19+B220+

extract_protocol:
Fetal Livers were dissected from E17.5 embryos for each genotype and stained for surface markers CD19 and B220. The cells positive for both CD19 and B220 were sorted and RNA was extracted from these cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: HET; Gli3+/-

value: Embryonic day 17.5 (E17.5)

value: liver

value: CD19+B220+ cells


title: Gli3-/- Rep1

source_name: Gli3-/-_fetal liver CD19+B220+

value: KO; Gli3-/-


title: Gli3-/- Rep2


title: Gli3+/- Rep2


title: N2 mixed embryo rep4 RNA-seq


title: CJ19 input N2 MxEmb ChIP-seq

tag: antibody target

value: INPUT

tag: antibody (vendor, catalog#, lot#)

value: none (input)


title: SE176 input N2 MxEmb ChIP-seq


title: WildType Rep1

source_name: WT_fetal liver CD19+B220+

value: WT; Wildtype


title: CJ43 input N2 MxEmb ChIP-seq


title: SEA197 input ERC51 MxEmb ChIP-seq


title: SEA164 input ERC51 MxEmb ChIP-seq


title: SEA214 input ERC64 MxEmb ChIP-seq


title: SE210 input N2 MxEmb ChIP-seq


title: SEA167 input ERC54 MxEmb ChIP-seq


title: SEA166 input ERC54 MxEmb ChIP-seq


title: SE389 input ERC38 MxEmb ChIP-seq


title: SE391 input ERC38 MxEmb ChIP-seq


title: ERC08 input Paired End rep2


title: SE365 input ERC38 MxEmb ChIP-seq


title: LW78 input N2 MxEmb ChIP-seq


title: LW44 input TY1072 MxEmb ChIP-seq


title: SE344 input TY2205 MxEmb ChIP-seq


title: LW43 input TY1072 MxEmb ChIP-seq


title: E1KO_RA24h_RNA_Rep2

tag: cell line

value: embryonic stem cell


title: LW53 input N2 MxEmb ChIP-seq


title: SE243 input TY1072 MxEmb ChIP-seq


title: WildType Rep2


title: DPY27 ERC64 MxEmb rep1 ChIP-seq

description:
DPY27_ERC64_MxEmb_MACS141_e5_average.bw
DPY27_ERC64_MxEmb_MACS141_e10_peaks.bed

value: Covance, Jason Lieb JL00001

tag: antibody antigen

tag: antibody (host, clone)

value: Rabbit, polyclonal

tag: matching input

value: SEA214 input ERC64 MxEmb ChIP-seq


title: DPY27 ERC64 MxEmb rep2 ChIP-seq


title: DPY27 ERC51 MxEmb rep1 ChIP-seq

description:
DPY27_ERC51_MxEmb_MACS141_e5_average.bw
DPY27_ERC51_MxEmb_MACS141_e10_peaks.bed

value: SEA164 input ERC51 MxEmb ChIP-seq


title: DPY27 ERC51 MxEmb rep2 ChIP-seq

value: SEA196 input ERC51 MxEmb ChIP-seq


title: DPY27 ERC64 MxEmb rep3 ChIP-seq


title: SEA196 input ERC51 MxEmb ChIP-seq


title: DPY27 ERC54 MxEmb rep2 ChIP-seq

description:
DPY27_ERC54_MxEmb_MACS141_e5_average.bw
DPY27_ERC54_MxEmb_MACS141_e10_peaks.bed

value: SEA166 input ERC54 MxEmb ChIP-seq


title: DPY27 ERC54 MxEmb rep1 ChIP-seq

value: SEA167 input ERC54 MxEmb ChIP-seq


title: SDC3 ERC38 MxEmb rep4 ChIP-seq

description:
SDC3_ERC38_MxEmb_MACS141_e5_average.bw
SDC3_ERC38_MxEmb_MACS141_e10_peaks.bed

value: mixed embryo

value: Covance, Jason Lieb JL00002

value: SE391 input ERC38 MxEmb ChIP-seq


title: SDC3 ERC38 MxEmb rep3 ChIP-seq

value: SE389 input ERC38 MxEmb ChIP-seq


title: SDC3 ERC38 MxEmb rep1 ChIP-seq

value: SE365 input ERC38 MxEmb ChIP-seq


title: DPY27 ERC51 MxEmb rep3 ChIP-seq

value: SEA197 input ERC51 MxEmb ChIP-seq


title: SDC3 ERC38 MxEmb rep2 ChIP-seq


title: DPY27 ERC38 MxEmb rep3 ChIP-seq

description:
DPY27_ERC38_MxEmb_MACS141_e5_average.bw
DPY27_ERC38_MxEmb_MACS141_e10_peaks.bed


title: SDC2 TY1072 MxEmb rep2 ChIP-seq

description:
SDC2_TY1072_MxEmb_MACS141_e5_average.bw
SDC2_TY1072_MxEmb_MACS141_e10_peaks.bed

value: Covance, Jason Lieb JL00005

value: SE243 input TY1072 MxEmb ChIP-seq


title: H3 TY1072 MxEmb rep1 ChIP-seq

description:
H3_TY1072_MxEmb_MACS141_e5_average.bw
H3_TY1072_MxEmb_MACS141_e10_peaks.bed

value: Abcam, ab1791


title: SDC2 TY1072 MxEmb rep3 ChIP-seq

value: LW44 input TY1072 MxEmb ChIP-seq


title: DPY27 ERC38 MxEmb rep1 ChIP-seq

value: Covance, Jason Lieb JL00001


title: H3 TY1072 MxEmb rep2 ChIP-seq

value: Rabbit, polyclonal

value: LW43 input TY1072 MxEmb ChIP-seq


title: SDC2 TY2205 MxEmb rep2 ChIP-seq

description:
SDC2_TY2205_MxEmb_MACS141_e5_average.bw
SDC2_TY2205_MxEmb_MACS141_e10_peaks.bed

value: SE344 input TY2205 MxEmb ChIP-seq


title: DPY27 ERC38 MxEmb rep2 ChIP-seq


title: SDC2 TY1072 MxEmb rep1 ChIP-seq


title: DPY27 N2 MxEmb rep3 ChIP-seq

description:
DPY27_N2_MxEmb_MACS141_e5_average.bw
DPY27_N2_MxEmb_MACS141_e10_peaks.bed

value: CJ19 input N2 MxEmb ChIP-seq


title: DPY27 N2 MxEmb rep2 ChIP-seq

value: CJ43 input N2 MxEmb ChIP-seq


title: DPY27 N2 MxEmb rep4 ChIP-seq

value: SDI, SDQ3995

value: SE176 input N2 MxEmb ChIP-seq


title: DPY30 N2 MxEmb rep4 ChIP-seq

description:
DPY30_N2_MxEmb_MACS141_e5_average.bw
DPY30_N2_MxEmb_MACS141_e10_peaks.bed

value: mixed embryo

value: Covance, Jason Lieb JL00015

value: LW78 input N2 MxEmb ChIP-seq


title: H3K4me3 N2 MxEmb rep3 ChIP-seq

description:
H3K4me3_N2_MxEmb_MACS141_e5_average.bw
H3K4me3_N2_MxEmb_MACS141_e10_peaks.bed

value: Mouse, monoclonal


title: SDC3 N2 MxEmb rep4 ChIP-seq

description:
SDC3_N2_MxEmb_MACS141_e5_average.bw
SDC3_N2_MxEmb_MACS141_e10_peaks.bed

value: SDI, SDQ4047

value: SE210 input N2 MxEmb ChIP-seq


title: SDC3 N2 MxEmb rep5 ChIP-seq

value: Covance, Jason Lieb JL00002

value: LW53 input N2 MxEmb ChIP-seq


title: H3 N2 MxEmb rep1 ChIP-seq

description:
H3_N2_MxEmb_MACS141_e5_average.bw
H3_N2_MxEmb_MACS141_e10_peaks.bed

value: Abcam, ab1791


title: DPY30 N2 MxEmb rep5 ChIP-seq


title: SDC3 N2 MxEmb rep3 ChIP-seq


title: SDC3 N2 MxEmb rep2 ChIP-seq


title: hCAR-TG_Day60_CITCO_rep3

city: Seattle

first: lihua

last: cheng

state: WA

address: 4225 Roosevelt

department: DEOHS

institute: universtiy of washington

data_processing:
HiSeq control software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISA2 with parameters -q --pen-noncansplice1000000 -p 15 -x
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from cufflink. 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
Liver were removed, flash frozen in the liquid nitrogen, and RNA was extracted using RNA Bee reagent.TruSeq Stranded mRNA kit (Illumina, San Diego, CA)  was used with 1.25 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

value: post natal day 60

tag: genotype

value: hCAR-TG


title: SDC2 N2 MxEmb rep4 ChIP-seq

description:
SDC2_N2_MxEmb_MACS141_e5_average.bw
SDC2_N2_MxEmb_MACS141_e10_peaks.bed

value: Rabbit, polyclonal


title: hCAR-TG_Day60_CITCO_rep1


title: hCAR-TG_Day60_CITCO_rep2


title: hCAR-TG_Day60_CornOil_rep3


title: hCAR-TG_Day60_CornOil_rep1


title: hCAR-TG_Day60_CornOil_rep2


title: rnaseq.wt.rep2

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
cutadapt v1.2.1 was used with parameters "-a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -q 28 -O 5 -m 50" to filter for sequencing quality and remove the adapter (Illumina TrueSeq Adapter, Index 7, version from August 3, 2011), resulting in the initial sequencing read libraries.
Reads mapping to rRNA were filtered from the initial sequencing libraries using bowtie2 with option -un
For all ChIP-seq libraries (Cuff, control, Pol2 wt, Pol2 cuff), the remaining reads were aligned to the genome using bowtie2 v2.0.0-beta7 with default parameters
The aligned reads were further filtered using samtools v0.0.19 with parameters "view -F 4 -q 10", resulting in a collection of reads mapping uniquely to the genome
Cuff peaks were found using the IDR protocol (https://sites.google.com/site/anshulkundaje/projects/idr) (7) with MACS2 v2.0.10.20130501 applied to two replicates of Cuff ChIP-seq separately and three replicates for the control ChIP-seq merged.
For analysis of RNA-seq libraries, a dataset of known transcripts dmel-transcripts.gff was prepared by taking all records from dmel-all-no-analysis-r5.41.gff from FlyBase with one of "exon", "exon_junction", "mRNA", "rRNA", "tRNA" in column 3.
For each RNA-seq library (wt and cuff, 3 replicates each), tophat2 v2.0.8 was applied with parameters "--read-realign-edit-dist 0 -I 50000 -x 1 -n 3 -g 1 -M --microexon-search --max-segment-intron 50000 -G dmel-transcripts.gff --b2-sensitive", with the aim of having only reads mapping uniquely to the genome.
For each gene, the number of reads mapping sense to it was counted in each replicate, using bedtools genomecov v2.17.0.
For analysis of differential expression of protein-coding genes, DESeq v1.16.0 was used, with parameters method=pooled-CR, sharingMode=fit-only, fitType=parametric.
The p-values resulting from DESeq analysis were corrected for multiple testing with Benjamini-Hochberg procedure.
Genome_build: dm3
Supplementary_files_format_and_content: BED file with Cuff peaks. TXT files with results of differential read count analysis in protein coding genes for Pol2 ChIP-seq and RNA-seq cuff vs. wt.

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
RNA-seq and ChIP-seq assays were performed in triplicate and for each biological replicate we dissected ovaries from approximately 30 female flies (2-4 days old). Total RNA was extracted using Trizol reagents (Life Technologies) and treated with turbo DNAse-free kit (Ambion) to eliminate traces. of genomic DNA. DNA-free total RNA was subjected to two rounds of rRNA depletion using the Ribo-Zero rRNA removal kit (Epicentre) as per the manufacturer's instructions. The same ChIP protocol was employed for the ChIP-seq assays as previously described (Pane et al. 2011; Blythe et al. 2009). The Cuff-EGFP expressing transgenic line, GFP antibodies and the conditions used for the Cuff ChIP-seq experiment were previously described (Pane et al. 2011; Blythe et al. 2009).
The RNA-seq library preparation was obtained with the ScriptSeq v2 kit (Epicentre) and the libraries were sequenced on the Illumina platforms. Chromatin fragments were used to generate DNA libraries with the ChIP-seq DNA Sample Prep kit (Illumina).

value: ovary

value: wt

value: 2-4 days


title: H3 N2 MxEmb rep2 ChIP-seq

value: SE176 input N2 MxEmb ChIP-seq


title: hCAR-TG_Day5_CITCO_rep2

value: post natal day 5


title: rnaseq.wt.rep1


title: rnaseq.wt.rep3


title: rnaseq.cuffmut.rep3

value: cuff


title: SDC2 N2 MxEmb rep5 ChIP-seq

value: mixed embryo


title: rnaseq.cuffmut.rep1


title: hCAR-TG_Day5_CornOil_rep1


title: WT_Day60_TCPOBOP_rep2

value: wild type


title: SDC2 N2 MxEmb rep3 ChIP-seq

value: Covance, Jason Lieb JL00005


title: hCAR-TG_Day5_CornOil_rep2


title: WT_Day60_TCPOBOP_rep3


title: rnaseq.cuffmut.rep2


title: WT_Day60_CornOil_rep2


title: WT_Day60_CornOil_rep1


title: WT_Day5_TCPOBOP_rep3


title: pol2chipseq.wt.rep1

tag: target


title: WT_Day5_TCPOBOP_rep1


title: WT_Day5_TCPOBOP_rep2


title: pol2chipseq.cuffmut.rep3


title: hCAR-TG_Day5_CITCO_rep3


title: pol2chipseq.cuffmut.rep2


title: hCAR-TG_Day5_CITCO_rep1


title: hCAR-TG_Day5_CornOil_rep3


title: WT_Day5_CornOil_rep2


title: WT_Day5_CornOil_rep1


title: pol2chipseq.cuffmut.rep1


title: pol2chipseq.wt.rep3


title: chipseq.cuff.rep1

value: Cuff


title: chipseq.cuff.rep2


title: EE8 input N2 MxEmb ChIP-seq

value: INPUT

value: none (input)


title: EE14 input N2 MxEmb ChIP-seq


title: WT_Day60_TCPOBOP_rep1


title: WT_Day60_CornOil_rep3


title: pol2chipseq.wt.rep2


title: EE13 input N2 MxEmb ChIP-seq


title: chipseq.contr.rep1


title: chipseq.contr.rep2


title: EE6 input N2 MxEmb ChIP-seq


title: siRNA_cid14Δ + pREP1-Rdp1_3

city: Munich

last: Halic

department: Biochemistry - Gene Center

country: Germany

institute: Ludwig-Maximilians-Universität

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million for siRNA and ChIP seq, normalization to reads mapping to protein coding genes for RNAseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

source_name: cid14Δ + pREP1-Rdp1_3

growth_protocol: cells were grown in liquid, rich YES medium or EMM -Leucine

extract_protocol:
Endogenous 3xFLAG-tagged Ago1-bound siRNA were purified by protein affinity purification and subsequent size selection on an 18% acrylamide gel. 2 pmol of a preadenylated 3' adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, 5'-App CTG TAG GCA CCA TCA AT/ddC/-3') were ligated in a 10 µl reaction with 5 U T4 RNA ligase (TaKaRa), ligation buffer without ATP and 5 U RNasin (Promega) at 20°C for 2 hours. The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor ligation was performed in a 10 µl reaction with 2 pmol 5' adaptor oligonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), 5 U RNasin (Promega), 0.06 µg BSA, 5 U T4 RNA ligase (Thermo Scientific) and 1x ligation buffer with ATP (Thermo Scientific) for 2 h at 20°C. The ligated products were gel purified and reverse transcribed with 10 pmol primer (RT primer: 5'- GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC GAT TGA TGG TGC CTA CAG-3') and the SuperScript III First Strand Synthesis System (Thermo Scientific). The cDNA was PCR-amplified with Q5 High-Fidelity 2x Master Mix (NEB) for 14-20 cycles using the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') and the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3').
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.

tag: genotype/variation

value: cid14{delta} + pREP1-Rdp1_3

tag: antibody for ip

value: anti-FLAG (Sigma-Aldrich, catalog#A2220, lot# SLBQ4019V)

tag: strain number

tag: target molecule

value: siRNA


title: EE9 input N2 MxEmb ChIP-seq


title: SE35 input TT2205 MxEmb ChIP-seq


title: siRNA_cid14Δ + pREP1-Rdp1_2

source_name: cid14Δ + pREP1-Rdp1_2

value: cid14{delta} + pREP1-Rdp1_2


title: EE4 input N2 MxEmb ChIP-seq


title: female flower-3

city: Hefei

first: Lifang

last: Wu

state: Anhui

address: 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China

institute: Hefei Institutes of Physical Science, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBI/UniProt using blastx
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using DEGseq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

organism: Vernicia fordii

source_name: female flower

extract_protocol:
Total RNA was isolated using RNAiso plus (Takara, Japan). RNA sequencing was performed using Illumina Hiseq 2500
RNA libraries were prepared for sequencing using standard Illumina protocols

value: flower

tag: Sex

value: female

value: stage 7

tag: age

value: 4-year old


title: SDC2 TY2205 MxEmb rep1 ChIP-seq

tag: strain

tag: developmental stage

value: Rabbit, polyclonal

value: SE35 input TT2205 MxEmb ChIP-seq


title: female flower-2


title: WT_Day5_CornOil_rep3

value: liver

value: post natal day 5


title: siRNA_dis3l2Δ

first: Mario


title: siRNA_cid16Δcid11Δ


title: H3K4me3 N2 MxEmb rep2 ChIP-seq

value: mixed embryo

tag: antibody target

value: Mouse, monoclonal

value: EE8 input N2 MxEmb ChIP-seq


title: female flower-1


title: siRNA_cid16Δcid1Δ


title: H3K4me3 N2 MxEmb rep1 ChIP-seq

tag: antibody (vendor, catalog#, lot#)

value: EE6 input N2 MxEmb ChIP-seq


title: male flower-3

source_name: male flower

value: male


title: chipseq.contr.rep3

value: ovary

value: wt

value: 2-4 days

value: none (input)


title: siRNA_cid16Δcid13Δ

value: anti-FLAG (Sigma-Aldrich, catalog#A2220, lot# SLBQ4019V)

value: siRNA


title: male flower-2

value: flower

value: stage 7


title: DPY30 N2 MxEmb rep3 ChIP-seq

value: Rabbit, polyclonal


title: male flower-1

value: 4-year old


title: DPY27 N2 MxEmb rep1 ChIP-seq

value: Covance, Jason Lieb JL00001


title: DPY30 N2 MxEmb rep2 ChIP-seq

value: EE14 input N2 MxEmb ChIP-seq


title: siRNA_cid14Δcid12Δ


title: DPY30 N2 MxEmb rep1 ChIP-seq

value: mixed embryo

value: EE9 input N2 MxEmb ChIP-seq


title: siRNA_cid14Δcid13Δ


title: SDC3 N2 MxEmb rep1 ChIP-seq

value: Covance, Jason Lieb JL00002

value: EE4 input N2 MxEmb ChIP-seq


title: siRNA_cid14Δcid11Δ


title: timepoint72 RNA-Seq.fastq

city: Carbondale

first: Bryan

middle: Manyasi

last: Musungu

address: 1125 Lincoln Dr.

department: Plant Biology

institute: Southern Illinois University Carbondale

description: Sample 22

data_processing:
Illumina Casava1.7 software used for basecalling.
Default CLC mapping settings, trimming and fastqc quality control of the reads, for both Z. mays and A. flavus, were done with CLC workbench 4.9 (Qiagen, Hilden, Germany).
RPKM and count values were then generated from CLC.
Genome_build: (AGPv3, INSDC Assembly GCA_000005005.5, Apr 2013) and A. flavus (JCVI-afl1-v2.0, INSDC Assembly GCA_000006275.1, Jan 2009).
Supplementary_files_format_and_content: RPKM/Count values for each Sample.

organism:
Zea mays
Aspergillus flavus

source_name: Zea mays kernel_72 hpi

growth_protocol: Maize B73 was grown in Clayton, NC during the years 2011 and 2013.  Seeds were planted on April 16.  Ears were hand pollinated from July 5-8 and covered with a paper bag.

extract_protocol:
Eight kernels per ear were ground and used for RNA isolation. Approximately one hundred milligrams of ground tissue was homogenized in a Virtis homogenizer (Virtis, Gardiner, NY) in Saturated Phenol, pH 6.6 for 2 min. Samples were then dissolved in Tris EDTA buffer, pH 8.0 (ACROS Organics, New Jersey, US), purified with 5:1 Acid Phenol: Chloroform, pH 4.5, and precipitated with ice-cold 100% ethanol overnight. Total RNA was purified again with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of RNA was analyzed using an RNA Pico chip on an Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A  time course study was performed by pin bar inoculating one ear (per time point) of maize B73 with A. flavus NR3357 and harvesting at 0, 6, 12, 18, 24, 30, 36, 42, 48 and 72 hours post inoculation.

tag: maize development stage

value: Milk

tag: maize cultivar

tag: aspergillus strain

tag: time point

value: 72 hrs post inoculation (hpi)

value: kernel


title: 57_Rep1_3357_3dpi_ear3_2011.fastq

description: Sample 21

tag: tissue


title: siRNA_cid14Δcid16Δ_b


title: SDC2 N2 MxEmb rep2 ChIP-seq

tag: antibody antigen

tag: antibody (host, clone)

tag: matching input

value: EE13 input N2 MxEmb ChIP-seq


title: 55_Rep1_3357_3dpi_ear1_2011.fastq

description: Sample 19


title: siRNA_cid14Δcid16Δ

tag: genotype/variation

tag: antibody for ip


title: timepoint48 RNA-seq.fastq

description: Sample 18

source_name: Zea mays kernel_48 hpi

value: 48 hrs post inoculation (hpi)


title: SDC2 N2 MxEmb rep1 ChIP-seq

value: EE6 input N2 MxEmb ChIP-seq


title: siRNA_cid14Δcid1Δ

value: anti-FLAG (Sigma-Aldrich, catalog#A2220, lot# SLBQ4019V)

tag: strain number

tag: target molecule

value: siRNA