title: m_TAC2W_1


title: WT_K27ac_S1

status: Public on Mar 13 2020

type: SRA

city: Philadelphia

first: Salina

last: Yuan

state: PA

address: 421 Curie Blvd

department: Medicine

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse (GRCm38, May 23 2014) and the Drosophila melanogaster (dm6, August 2014) reference genomes using STAR (v2.5.1) with default settings.
Duplicate and low-quality reads (PHRED score <30) were removed using SAMtools.
Peaks were called with MACS2 with default settings (H3K27ac and H3K4me1) and broad settings (H3K36me2 and H3K27me3). Blacklisted peaks (https://sites.google.com/site/anshulkundaje/projects/blacklists) were excluded in all subsequent analysis.
Genome_build: mm10 (GRCm38) + dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: ChIPRX-normalized bigwig files were generated from bam files using deepTools.

molecule: genomic DNA

organism: Mus musculus

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 10% glutamine, and 150 µg/mL gentamicin at 37°C, 5% CO2, 21% O2, and 100% humidity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Details in Methods section.
Libraries were prepared according to the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) protocol.

treatment_protocol: No treatment was applied.

tag: genotype/variation

value: wildtype

tag: cell type

value: Pancreatic cancer cells

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: spike-in genome

value: Drosophila melanogaster genomic DNA


title: MSI-H, likely Lynch due MLH1 germline sample 5 tumor tissue.

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1 aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal

extract_protocol:
Patient FFPE blocks were obtained from our tissue registry and after a pathologist review, samples with sufficient amounts of tissue were selected for RNA extraction from tumor and paired normal tissue.
Total RNA was quantitated using the Qubit RNA BR assay (Invitrogen) and quality was assessed using the DV200 value (the percentage of RNA fragments greater than 200 bases in length) as determined by the Agilent 2100 Bioanalyzer RNA Nano kit.  For samples with a DV200>30% the RNA input for RNA-seq analysis was 200 ng.  For samples with a DV200 score between 20-30% the amount of RNA used was increased to 400 ng to compensate for RNA degradation.  Samples with a DV200 score below 20% were not used in the study since previous studies in our lab have shown that these rarely provide acceptable results.

tag: phenotype (msi-h or mss)

value: MSI

tag: genetics of msi-h

tag: phenotype(normal/tumor)

value: tumor


title: MSI-H, MLH1 hypermethylation, sample 11 normal tissue.

value: normal


title: MSI-H, likely Lynch due MLH1 germline sample 4 tumor tissue.


title: m_TAC11W_2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description:
TAC heart tissue
mouse_TAC_bulk_CM_readCount.csv

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 or hg38 genome via STAR v2.5.2b
Then assigned by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm9
Genome_build: hg38
Supplementary_files_format_and_content: csv, read/UMI matrix
16W_20W_total_cell_umi.csv (column header format: SC(singlecell)_ChIP ID_rowID_colID)

molecule: polyA RNA

source_name: TAC11W CM

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL.
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

treatment_protocol: Tissues were cut into slices by using Vibrating-blade Microtome (Leica, VT1200S) and homogenized in low temperature and then the tissues were digested using XXIV protease (Sigma, P8038-250) and Collagenase II (Worthington LS004176) to enrich myocites; tissues were  homogenized and  digested using Cardiomyocyte Isolation Enzyme 1 (with papain) for Pierce Primary Cell Isolation Kits (Thermo 88288) to enrich non-cadiomyocites.

tag: gender

value: male

tag: tissue

value: TAC heart tissue


title: MSI-H, likely Lynch due MLH1 germline sample 3 tumor tissue.


title: m_sham_2

description:
normal heart tissue
mouse_TAC_bulk_CM_readCount.csv

source_name: TAC sham CM

value: normal heart tissue


title: Nsd2KO_K36me2_S1

value: H3K36me2 (Abcam, ab9049)


title: m_TAC11W_1


title: MSI-H, likely Lynch due MLH1 germline sample 2 tumor tissue.

source_name: Ovarian


title: MSI-H, MLH1 hypermethylation, sample 17 tumor tissue.


title: m_sham_1


title: MSI-H, likely Lynch due MLH1 germline sample 14 tumor tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 15 tumor tissue.


title: m_8W_1_CM

description:
normal heart CM
mouse_normal_CM_bulk_readCount.csv

source_name: normal heart CM

value: normal heart CM


title: MSI-H, likely Lynch due MLH1 germline sample 12 tumor tissue.


title: m_20W_2_CM


title: m_8W_2_CM


title: m_20W_1_CM


title: m_14W_2_CM


title: MSI-H, likely Lynch due MLH1 germline sample 8 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 10 tumor tissue.


title: m_17W_2_CM


title: MSI-H, likely Lynch due MLH1 germline sample 11 tumor tissue.

source_name: Endometrial


title: m_14W_1_CM


title: m_17W_1_CM


title: MSI-H, likely Lynch due MLH1 germline sample 7 normal tissue.


title: m_11W_1_CM


title: MSI-H, likely Lynch due MLH1 germline sample 6 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 3 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 4 normal tissue.


title: m_11W_2_CM


title: m_113547_16W20W_CM

description:
normal heart single cell
16W_20W_total_cell_umi.csv

source_name: normal heart single cell

value: normal heart single cell (Non-cardiomyocyte)

tag: age

value: 16W, 20W (mixed sample; non-demultiplexed)


title: m_113515_16W20W_NCM

value: normal heart single cell (cardiomyocyte)


title: MSI-H, likely Lynch due MLH1 germline sample 2 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 14 normal tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 13 tumor tissue.


title: MSI-H, likely Lynch due MLH1 germline sample 15 normal tissue.


title: Late progenitor mut (contain 3 rep)

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: HSCs (LSK+CD34-Flt3-CD48-CD150+), MPP2 (LSK+CD34+Flt3-CD48+CD150+), MPP3 (LSK+CD34+Flt3-CD48+CD150-), MPP4 LSK+CD34+Flt3+CD48+CD150-), CMP Lin-Sca-1-cKit+CD34+IL7r-CD16/32low) and MEP (Linegae-Sca-1-cKit+CD34-IL7r-CD16/32-)

data_processing:
Paired end reads were aligned to the transcriptome by bwa (version 0.6.2-r126)
The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M)
The right mate of each read pair was mapped to the ensemble of all gene groups and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left mate contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch and adjacent gene sequence. The left read was not used for quantification. For each cell barcode and gene locus, the number of UMIs was aggregated and, based on binomial statistics, converted into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include transcript count values for each Sample

source_name: Bone Marrow

extract_protocol:
Bone marrow progenitor cells were srted, flash frozen on liquid nitrogen, and RNA was harvested using Cel-Seq2 protocol. Cel-Seq2  was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Cel-seq2 protocols

value: Haematopoetic progenitor cells

tag: genotype

value: Mof -/+

tag: illumina index

tag: sequence depth

value: 25.00 million


title: MSI-H, likely Lynch due MLH1 germline sample 13 normal tissue.


title: MPPs mut (contain 3 rep)


title: MSI-H, likely Lynch due MLH1 germline sample 12 normal tissue.


title: Late progenitor wt (contain 3 rep)

value: wild type


title: MSI-H, likely Lynch due MLH1 germline sample 11 normal tissue.


title: MPPs wt (contain 3 rep)


title: Early progenitor wt (contain 3 rep)


title: Early progenitor mut (contain 3 rep)


title: MSI-H, likely Lynch due MLH1 germline sample 10 normal tissue.


title: ORA59_DAPseq_sample

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: DAPSeq_Sample 54

data_processing:
Library strategy: DAP-Seq
base-calling using RTA 2.7.7
alignment using Bowtie 2 v.2-2.0.5 with default parameters
The Genome wide Event finding and Motif discovery (GEM) tool was used to identify the target summits in DAP-seq data
Significant enrichments of histone modifications and histone variants were identified with the SICER software
gene ontology enrichment was assessed using clusterProfiler
Genome_build: TAIR10
Supplementary_files_format_and_content: GEM output as significant binding sites

organism: Arabidopsis thaliana

source_name: Three day old etiolated seedlings

extract_protocol:
DAP-seq assays were carried as previously described (O'malley et al., 2016) DOI: 10.1016/j.cell.2016.04.038
Conducted as previously described (O'malley et al., 2016) DOI: 10.1016/j.cell.2016.04.038

value: Three day old etiolated seedlings


title: SC-4

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Read counts are obtained using featureCounts from Subread v1.6.0 with –fracOverlap 1 option
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Monocyte-derived macrophages

growth_protocol: Normal human donor CD14+ monocytes were isolated from TRIMA leukoreduction filters following platelet apheresis  at the blood donor center at Roswell Park Comprehensive Cancer Center (RPCCC).

extract_protocol:
RNA was isolated from cells using TRIzol™ Reagent (Invitrogen, Carlsbad, CA)
RNA libraries were prepared using the Illumina TruSeq RNA Exome protocol.

treatment_protocol: Cells were cultured for 1 week at a density of 10^6/well in 6 well plates with 50 ng/ml recombinant human macrophage colony stimulating factor (M-CSF) (Life Technologies, Carlsbad, CA), 1x GlutaMAX-I (Life Technologies) and 1mM sodium pyruvate. (Mediatech,Manassas, VA) to generate M0 macrophages. For M1 or M2 macrophage polarization, M0 cells were treated for two days with 20 ng/ml recombinant human IFN-Ɣ (Life Technologies) and 50 ng/ml Escherichia coli LPS (SigmaAldrich, St. Louis, MO), or 20 ng/ml recombinant human IL4 (Life Technologies), respectively. For siRNA treatment, a day before induction of M1 polarization, M0 macrophages were transfected with 100 nM of negative control (Silencer negative control no. 1, product number AM4611, Life Technologies) or equimolar mix of two human APOBEC3A siRNAs (Silencer 45715 and 45810, respectively, with sense sequences 5’-GACCUACCUGUGCUACGAATT-3’ and 5’-GCAGUAUGCUCCCGAUCAATT-3’, Life Technologies) using Lipofectamine RNAiMAX (Life Technologies), following the manufacturer’s protocol. IFN-Ɣ and LPS were added with 2ml medium to each well, to induce M1 polarization, and cells were harvested at 48h.

value: Peripheral blood-drived macrophages

tag: treatment

value: Interferon gamma and LPS

tag: sirna treatment

value: Scrambled (control) siRNA

tag: donor


title: SC-1-


title: SC-2


title: KD-4

value: APOBEC3A siRNA


title: TCP23_DAPseq_sample

description: DAPSeq_Sample 53


title: DREB2B_DAPseq_sample

description: DAPSeq_Sample 50


title: ZAT18_DAPseq_sample

description: DAPSeq_Sample 52


title: RVE2_DAPseq_sample

description: DAPSeq_Sample 51


title: KD-1


title: KD-2


title: WRKY51_DAPseq_sample

description: DAPSeq_Sample 49


title: M0-2nd

value: M-SCF


title: HY5_DAPseq_sample

description: DAPSeq_Sample 48


title: M0-3rd


title: ERF1_DAPseq_sample

description: DAPSeq_Sample 47


title: Non-transgenic_IgG_control_ChIPseq_sample4

description: ChIPSeq_Sample 46

data_processing:
base-calling using RTA 2.7.7
Reads were aligned by bowtie2 v2.0.5 using only the first 65 bases against the Arabidopsis thaliana TAIR10 reference genome.
Shiftsize was calculated using phantompeakqualtools and default parameters
Peaks called with MACS2 version 2.0.10 with parameters "callpeak -c --format=SAM --gsize=1.19e8 -p 99e-2 --nomodel --shiftsize=[from phantompeakqualtools] --down-sample --call-summits". A concatenated file of all non-transgenic control IP reads was used as the control in peak calling
ChIPPeakAnno was used for annotation. gene ontology enrichment was assessed using clusterProfiler
Genome_build: TAIR10
Supplementary_files_format_and_content: Summit region output created by MACS2 in bed format.

growth_protocol: Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.

extract_protocol:
Conducted as described in O'Malley et al. 2016 (doi: 10.1016/j.cell.2016.04.038) and Chang et al. 2013 (10.7554/eLife.00675). Harvested seedlings were crosslinked with 1% formaldehyde under vacuum for 20 minutes then snap-frozen in liquid nitrogen. Nuclei were extracted from frozen, ground seedlings according to Qiao et al. 2016 (10.1126/science.1225974) then sonicated according to Chang et al .2016 using a Diagenode bioruptor to yield an average DNA fragment size of approximately 150-300 bases. Transcription-factor DNA complexes were isolated by immunoprecipitation with polyclonal anti-GFP raised in goat from David Dreschel (Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany) or, for non-transgenic controls, IgG from goat. These complexes were then retrieved using Protein G Dynabeads (Life Technologies).
Conducted as described in Chang et al. 2013 (10.7554/eLife.00675) with one modification. Size selection was performed on SPRI beads, instead of on gels, with upper and lower cut-offs to yield a fragment size-range of 150-500 nucleotides. Sequencing was conducted on the Illumina HiSeq 2500 platform.

treatment_protocol: Air or JA treated for 2h

value: Air treatment for 2h

value: Goat IgG whole molecule (Jackson ImmunoResearch, 005-000-003)


title: M0-1st


title: Non-transgenic_IgG_control_ChIPseq_sample2

description: ChIPSeq_Sample 44


title: Non-transgenic_IgG_control_ChIPseq_sample1

description: ChIPSeq_Sample 43


title: ANAC055_JA_2hr_ChIPseq_rep3

description: ChIPSeq_Sample 42

value: Col-0 ANAC055::ANAC055-Ypet

value: JA treatment for 2h

value: Goat anti-GFP (from David Dreschel)


title: ATAF2_DAPseq_sample

description: DAPSeq_Sample 55


title: STZ_JA_2hr_ChIPseq_rep1

description: ChIPSeq_Sample 38

value: Col-0 STZ::STZ-Ypet


title: ANAC055_JA_2hr_ChIPseq_rep2

description: ChIPSeq_Sample 41


title: ANAC055_JA_2hr_ChIPseq_rep1

description: ChIPSeq_Sample 40


title: STZ_AIR_ChIPseq_rep1

description: ChIPSeq_Sample 35


title: STZ_AIR_ChIPseq_rep2

description: ChIPSeq_Sample 36


title: STZ_AIR_ChIPseq_rep3

description: ChIPSeq_Sample 37


title: MYC2_JA_2hr_ChIPseq_rep3

description: ChIPSeq_Sample 30

value: Col-0 MYC2::MYC2-Ypet


title: MYC3_JA_2hr_ChIPseq_rep1

description: ChIPSeq_Sample 32

value: Col-0 MYC3::MYC3-Ypet


title: MYC2_JA_2hr_ChIPseq_rep2

description: ChIPSeq_Sample 29


title: MYC2_JA_2hr_ChIPseq_rep1

description: ChIPSeq_Sample 28

data_processing:
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using TrimGalore 0.4.5, then aligned to the TAIR10 genome assembly using TopHat 2.1.1
Reads were counted using HTSeq. Differentially expressed genes were identified using edgeR 3.6.2
Quantification of transcripts was performed using Salmon v0.8.1
The TSIS R package was used to perform the isoform switch analysis
Genome_build: TAIR10 and AtRTD2-QUASI
Supplementary_files_format_and_content: csv files include readcount and TPM values for each Sample


title: MYC3_JA_2hr_ChIPseq_rep2

description: ChIPSeq_Sample 33


title: Col-0_JA_8hour_RNAseq_rep3

description:
toptags_JA_8_hr.csv
RNASeq_Sample 21

extract_protocol:
RNeasy Plant Mini Kit (74903, Qiagen)
cDNA library preparation and subsequent single read sequencing was carried as previously described (Song,L et al., 2016) DOI: 10.1126/science.aag1550

treatment_protocol: JA treatment in time series 0-24 h

value: JA treatment for 8h


title: Col-0_JA_12hour_RNAseq_rep1

description:
toptags_JA_12_hr.csv
RNASeq_Sample 22

value: JA treatment for 12h


title: Col-0_JA_8hour_RNAseq_rep1

description:
toptags_JA_8_hr.csv
RNASeq_Sample 19


title: Col-0_JA_12hour_RNAseq_rep3

description:
toptags_JA_12_hr.csv
RNASeq_Sample 24


title: Col-0_JA_24hour_RNAseq_rep3

description:
toptags_JA_24_hr.csv
RNASeq_Sample 27

value: JA treatment for 24h


title: Col-0_JA_12hour_RNAseq_rep2

description:
toptags_JA_12_hr.csv
RNASeq_Sample 23

value: Three day old etiolated seedlings


title: VLP DNA short read ddm1rdr6 Rep 2

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Library strategy: DNA-seq
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: bigWig
Supplementary_files_format_and_content: Long read VLP DNA-seq: bigWig, vcf (Structural variant calls produced by Sniffles on nanopore long-read alignments to the TAIR10 genome. The number of reads supporting each SV call is given in the RE tag.)

molecule: other

source_name: 4 week-old whole inflorescence stems

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium and seedlings were transplanted to soil 7 day after germination.

extract_protocol:
VLPs were isolated using sucrose buffer and ultracentrifugation. DNase I was treated to remove genomic DNA. After RNase A and proteinase K treatments, VLP DNA was extracted with phenol:chloroform.
NEBNext Ultra DNA Library Prep Kit

tag: ecotype

value: 4 week-old whole inflorescence stems

tag: fraction

value: VLP DNA


title: VLP DNA short read ddm1 Rep 1


title: Col-0_JA_2hour_RNAseq_rep3

description:
toptags_JA_2_hr.csv
RNASeq_Sample 15


title: Col-0_JA_2hour_RNAseq_rep1

description:
toptags_JA_2_hr.csv
RNASeq_Sample 13


title: VLP DNA short read ddm1rdr6 Rep 3


title: VLP DNA short read ddm1 Rep 2


title: Col-0_JA_8hour_RNAseq_rep2

description:
toptags_JA_8_hr.csv
RNASeq_Sample 20


title: Col-0_JA_4hour_RNAseq_rep2

description:
toptags_JA_4_hr.csv
RNASeq_Sample 17

value: JA treatment for 4h


title: Col-0_JA_24hour_RNAseq_rep1

description:
toptags_JA_24_hr.csv
RNASeq_Sample 25


title: Col-0_JA_4hour_RNAseq_rep3

description:
toptags_JA_4_hr.csv
RNASeq_Sample 18


title: Col-0_JA_24hour_RNAseq_rep2

description:
toptags_JA_24_hr.csv
RNASeq_Sample 26


title: Col-0_JA_2hour_RNAseq_rep2

description:
toptags_JA_2_hr.csv
RNASeq_Sample 14


title: Col-0_JA_4hour_RNAseq_rep1

description:
toptags_JA_4_hr.csv
RNASeq_Sample 16


title: VLP DNA short read wild-type Rep 3

value: wild-type


title: VLP DNA short read wild-type Rep 2


title: Col-0_JA_1hour_RNAseq_rep3

description:
toptags_JA_1_hr.csv
RNASeq_Sample 12

value: JA treatment for 1h


title: Col-0_JA_1hour_RNAseq_rep2

description:
toptags_JA_1_hr.csv
RNASeq_Sample 11


title: MYC3_JA_2hr_ChIPseq_rep3

description: ChIPSeq_Sample 34


title: STZ_JA_2hr_ChIPseq_rep2

description: ChIPSeq_Sample 39


title: VLP DNA short read ddm1rdr6 Rep 1


title: Col-0_JA_0_5hour_RNAseq_rep2

description:
toptags_JA_0_5hr.csv
RNASeq_Sample 8

value: JA treatment for 0.5h


title: Col-0_JA_0_5hour_RNAseq_rep1

description:
toptags_JA_0_5hr.csv
RNASeq_Sample 7


title: Microsome polysomal RNA ddm1 Rep 3

data_processing:
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: bigWig
Supplementary_files_format_and_content: Long read VLP DNA-seq: bigWig, vcf (Structural variant calls produced by Sniffles on nanopore long-read alignments to the TAIR10 genome. The number of reads supporting each SV call is given in the RE tag.)

source_name: Inflorescence tissues

extract_protocol:
Microsomes were isolated using sucrose-gradient ultracentrifugation. Polysomal RNA was extracted by FLAG-RPL18 immunoprecipitation.
ScriptSeq v2 RNA-Seq Library Preparation Kit

tag: expressing

value: Inflorescence tissues

value: Microsome polysomal RNA


title: Col-0_JA_0_5hour_RNAseq_rep3

description:
toptags_JA_0_5hr.csv
RNASeq_Sample 9


title: Microsome polysomal RNA ddm1rdr6 Rep 1


title: Col-0_JA_0_25hour_RNAseq_rep3

description:
toptags_JA_0_25hr.csv
RNASeq_Sample 6

value: JA treatment for 0.25h


title: Col-0_JA_0_25hour_RNAseq_rep1

description:
toptags_JA_0_25hr.csv
RNASeq_Sample 4


title: Microsome polysomal RNA ddm1rdr6 Rep 2


title: Total polysomal RNA ddm1rdr6 Rep 3

extract_protocol:
Polysomes of FLAG-RPL18 were immunoprecipitated with anti-FLAG. Input RNA was set aside for total RNA. Eluted polysome-associated RNA was extracted using Direct-zol RNA miniprep kit.
ScriptSeq v2 RNA-Seq Library Preparation Kit

value: Total polysomal RNA


title: Col-0_JA_0_25hour_RNAseq_rep2

description:
toptags_JA_0_25hr.csv
RNASeq_Sample 5


title: MYC2_JA_2hr_ChIPseq_rep4

description: ChIPSeq_Sample 31

value: JA treatment for 2h

tag: chip antibody

value: Goat anti-GFP (from David Dreschel)


title: Microsome polysomal RNA ddm1 Rep 1


title: Total polysomal RNA ddm1 Rep 3


title: Col-0_JA_0hour_RNAseq_rep1

description: RNASeq_Sample 1

value: JA treatment for 0h


title: Total polysomal RNA ddm1rdr6 Rep 1


title: Total polysomal RNA ddm1rdr6 Rep 2


title: VLP DNA short read wild-type Rep 1


title: Total polysomal RNA ddm1 Rep 1


title: ChIP-seq_myc2_air_H2A.Z

description:
Sample 8
Wig file contains:
SICER comparison Sample 7 vs Sample 8

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600),  FDR (0.01)
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with SICER output

source_name: histone variant

growth_protocol: etiolated seedlings

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment or 4 hours of JA treatment

value: etiolated seedlings

tag: antibodies

value: H2A.Z (Active Motif, 39647)


title: ChIP-seq_myc2_4hJA_H2A.Z

description:
Sample 9
Wig file contains:
SICER comparison Sample 8 vs Sample 7


title: Col-0_JA_0hour_RNAseq_rep2

description: RNASeq_Sample 2


title: ChIP-seq_Col-0_4hJA_H2A.Z

description:
Sample 7
Wig file contains:
SICER comparison Sample 6 vs Sample 5


title: Total polysomal RNA ddm1 Rep 2


title: Total RNA ddm1rdr6 Rep 3

value: Total RNA


title: Col-0_JA_1hour_RNAseq_rep1

description:
toptags_JA_1_hr.csv
RNASeq_Sample 10

value: Three day old etiolated seedlings


title: ChIP-seq_Col-0_air_H2A.Z

description:
Sample 6
Wig file contains:
SICER comparison Sample 5 vs Sample 6


title: Microsome polysomal RNA ddm1rdr6 Rep 3


title: Microsome polysomal RNA ddm1 Rep 2


title: Col-0_JA_0hour_RNAseq_rep3

description: RNASeq_Sample 3


title: Total RNA ddm1 Rep 3


title: ChIP-seq_Col-0_4hJA_H3K4me3

description:
Sample 3
Wig file contains:
SICER comparison Sample 3 vs Sample 2

source_name: histone modification

value: H3K4me3 (EMD Millipore, 04-745)


title: Total RNA ddm1rdr6 Rep 1


title: Total RNA ddm1 Rep 2


title: ChIP-seq_Col-0_IgG

description: Sample 1

source_name: control

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: ChIP-seq_myc2_air_H3K4me3

description:
Sample 4
Wig file contains:
SICER comparison Sample 4 vs Sample 5


title: IMQ_lidocaine_1 [skin tissue]

city: Shanghai

first: Qianqian

last: YIN

address: Chongqing South Road

department: Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina bcl2fastq software was used for base-calling
STAR(2.5.3a) software was used for read alignment, parameter setting as follows:—twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated, and then normalized with TMM standard; DESeq2 software was used to filter differentially expressed genes, according to the standard that |log2(fold change)|>=1 and P value <=0.05
Genome_build: rno6
Supplementary_files_format_and_content: xls

organism: Rattus norvegicus

source_name: skin tissue

growth_protocol: SD rats of 250g body weight were kept in the SPF condition.

extract_protocol:
Rats were sacrificed and back skin were collected. Back skin tissues were freezed quickly in liquid nitroge and grind up in the tissue lyser. Total RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were divided into 3 groups: 1. WT group: WT rats without any treatment; 2. IMQ group:  rats treated with IMQ-induction on the back skin for consecutive 6 days; 3. IMQ+lidocaine group: rats treated with IMQ-induction for consecutive 6 days in addition to 4 days' epidural injection of 1% lidocaine from day 3 of IMQ induction.

tag: strain

value: Sprague Dawley

value: back skin

tag: weight

tag: phenotype

value: Wild type

value: imiquimod(IMQ)-induced psoraisis-like rat model with epidural injection of 1percent lidocaine


title: ChIP-seq_Col-0_air_H3K4me3

description:
Sample 2
Wig file contains:
SICER comparison Sample 2 vs Sample 2


title: IMQ_3 [skin tissue]

value: imiquimod(IMQ)-induced psoraisis-like rat model


title: IMQ_lidocaine_2 [skin tissue]


title: Total RNA ddm1 Rep 1

value: Inflorescence tissues


title: WT_3 [skin tissue]


title: WT_2 [skin tissue]


title: IMQ_lidocaine_3 [skin tissue]


title: IMQ_2 [skin tissue]


title: Ly10_SR3029_1uM_rep3

city: New York

first: Prabhjot

middle: Singh

last: Mundi

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

data_processing:
Alignment with STARv2.5.3
Gene-level raw counts summarization with STARTv2.5.3 quant-mode
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature generation with limma (R bioconductor package)
Genome_build: GRCh38v89
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification

source_name: OCI-Ly10 Diffuse Large B-cell Lymphoma Cell Line

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
RNAs were extracted with using Qiagen Rneasy mini kit
Strand specific sequencing libraries were generated from rRNA depleted total RNAs using the NEBNext® Ultra Directional RNA Library Prep Kit for Illumina
RNA Sequencing was performed on an Illumina NextSeq 500 sequencer.

treatment_protocol: All the samples were treated with indicated concentration of drugs for 3 hours.

tag: cell line


title: Ly10_SR3029_1uM_rep2

value: OCI-Ly10 Diffuse Large B-cell Lymphoma Cell Line


title: Ly10_SR3029_1uM_rep1


title: Total RNA ddm1rdr6 Rep 2

tag: tissue


title: ChIP-seq_myc2_4hJA_H3K4me3

description:
Sample 5
Wig file contains:
SICER comparison Sample 5 vs Sample 4


title: Ly10_CTRL_rep3

value: CTRL


title: GATA1_ChIP-seq_rep2

data_processing:
The library was completed and amplified through a PCR following the DeepSeq using the NEBNext® UltraTM DNA Library Prep Kit for Illumina default instructions (NEB #E7645). ChIP libraries were sequenced using an Illumina HiSeq 3000.
FASTA files were then transferred to Galaxy Platform (Afgan et al., 2016), where we conducted a) Genome alignment (mm10) by Bowtie2 version 2.3.0.1 (Langmead and Salzberg, 2012) using default parameters. B) Quality control was assessed by deeptools (Ramírez et al., 2016). And C) and calling Peaks by MACS2 software (Feng et al., 2012), in which bandwidth was set to 300, lower mfold bound to 5, upper mfold bound to 500. Peak detection was based on q-value (minimum FDR cutoff as 0.05). For build model we selected the shifting mode.
coverage files were generated using bamCoverage from deeptools2
Genome_build: mm10

growth_protocol: HPC7 cells were mainted in IMDM supplement with 10% fetal calf serum and 50 ng/mL stem-cell factor (SCF)

extract_protocol:
For the HPC7 cell line ChIP-seq, 500.000 cells were fixed either with 0.1% PFA (H4K16ac profile) or 1% (GATA-1 profile) for 10 minutes at room temperature and quenched with 0.125M glycine.
Lysates were transferred into 0.1 mL Bioruptor Microtube (Diagenode C30010015, Liège, Belgium) and the chromatin was sheared using an NGS Bioruptor Sonicator (Diagenode) at default intensity and cycles of 30'' ON/30'' OFF Sonication time was calibrated for the different cell types: 10 minutes for MEPs and 15 minutes for HSCs/HPC7. After sonication, samples were centrifuged at high speed for 15 minutes at 4oC to pellet precipitated SDS. Chromatin extracts were diluted 1 to 5 with Sonication Equilibration Buffer (10 mM TrisCl, 140 mM NaCl, 0.1 % Sodium Deoxycholate, 1% Tx-100, 1 mM EDTA, 1X Protease Inhibitors (Roche) (Lara-Astiaso et al., 2014) . Chromatin was pre- cleared before adding the antibodies by adding 50 μL of protein A/agarose DNA bead; samples were kept in constant rotation for 2 hours at 4oC. After that, chromatin samples were centrifuged at 3000 rpm for 5 minutes at 4oC, supernatants was transferred to fresh 1.5 mL micro centrifuge tubes and 2 μg of anti-MOF (#A300-992A, Bethyl), anti-GATA-1 (#181544, Abcam) or anti-H4K16ac (#07-329, Millipore) was added to the diluted chromatin extracts and incubated for 20 hours at 4oC. Samples centrifugation supernatant was collected and 20 μL of protein A-dynabeads (Thermo Fisher Scientific), previously blocked with 1% BSA, was added to the samples, samples were kept in constant rotation for 2 hours at 4oC. Then, we centrifuged the samples at 3000 rpm at room temperature and supernatants were kept. Samples were washed with high-salt buffer (50 mM HEPES pH 7.9, 500 mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate) twice, once with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% deoxycholate), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA) and then eluted in 10 μL of elution buffer (Qiagen). Eluate was treated with 2μl of RNaseA (Qiagen) for 30 minutes at 37oC, followed by 2.5 μl of Proteinase K (Thermo-fischer) treatment for two hours at 55oC. After that, temperature was increased to 65oC for 8 hours to revert formaldehyde crosslinking. Chromatin was quantified by Qubit Fluorometric Quantitation (Thermo Fisher Scientific) DNA high- sensitivity kit (#Q32854, Thermo Fisher Scientific) and quality was evaluated by fragment analyzer. The library was completed and amplified through a PCR following the DeepSeq using the NEBNext® UltraTM DNA Library Prep Kit for Illumina default instructions (NEB #E7645). ChIP libraries were sequenced using an Illumina HiSeq 3000. FASTA files were then transferred to Galaxy Platform (Afgan et al., 2016), where we conducted a) Genome alignment (mm10) by Bowtie2 version 2.3.0.1 (Langmead and Salzberg, 2012) using default parameters. B) Quality control was assessed by deeptools (Ramírez et al., 2016). And C) and calling Peaks by MACS2 software (Feng et al., 2012), in which bandwidth was set to 300, lower mfold bound to 5, upper mfold bound to 500. Peak detection was based on q-value (minimum FDR cutoff as 0.05). For build model we selected the shifting mode.

value: Hematopoietic precursor cell-7

tag: passage

tag: accession

tag: antibody

value: anti-GATA-1 (#181544, Abcam)


title: Input_DNA_MOF_GATA1_rep1


title: Input_DNA_K16_rep2


title: Ly10_CTRL_rep2


title: Input_DNA_K16_rep1


title: MOF_ChIP_seq_rep1

value: anti-MOF (#A300-992A, Bethyl)


title: GATA1_ChIP-seq_rep1


title: Ly10_CTRL_rep1


title: Input_DNA_MOF_GATA1_rep2


title: H4K16ac_ChIP-seq_rep2

value: anti-H4K16ac (#07-329, Millipore)


title: WT_1 [skin tissue]

tag: genotype


title: Z138_SR3029_3uM_rep1

source_name: Z-138 Mantle Cell Lymphoma Cell Line (Blastoid Variant)

tag: treatment


title: H4K16ac_ChIP-seq_rep1


title: Z138_SR3029_1uM_rep3

value: Z-138 Mantle Cell Lymphoma Cell Line (Blastoid Variant)


title: Z138_SR3029_1uM_rep2


title: Z138_SR3029_1uM_rep1


title: urothelial carcinoma, P17_S3b

type: RNA

city: Lund

first: Nour-al-dain

last: Marzouka

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturers specifications

data_processing:
Control probe filtering and background correction was performed within the BioArray Software Environment (BASE). Only the shared probes in the two platforms were used.
Matrix Non-normalized files: The raw intensity values subjected only to background correction.
Matrix Non-normalized_gene files: To produce matrix for genes, the median for the probes in the same gene was used.  No normalization applied.

label: biotin

source_name: fresh-frozen resection sample of urothelial carcinoma

extract_protocol: Two different extraction methods (RNeasy and AllPrep)

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.

tag: tumor stage

value: Ta

tag: tumor grade

tag: days from initial tumor

tag: molecular subtype by gex

value: Uro


title: urothelial carcinoma, P18_S1b

scan_protocol: According to the manufacturers specifications

value: PUNLMP


title: MSI-H, MLH1 hypermethylation, sample 2 tumor tissue.

tag: phenotype (msi-h or mss)

value: MSI

tag: genetics of msi-h

tag: phenotype(normal/tumor)

value: tumor


title: Z138_CTRL_rep2


title: Z138_CTRL_rep3


title: urothelial carcinoma, P17_S2a

label_protocol: According to the manufacturers specifications


title: urothelial carcinoma, P17_S2b


title: urothelial carcinoma, P17_S1


title: Z138_CTRL_rep1


title: h_NCM-8

description:
normal heart tissue
human_heart_tissue_readCount.csv

source_name: normal heart tissue

tag: gender

value: male

value: normal heart tissue


title: h_NCM-6


title: urothelial carcinoma, P17_S2c

description: Same tumor and same raw data as in GSE32894 (GSM814190)


title: h_NCM-7


title: Z138_SR3029_3uM_rep3


title: Z138_SR3029_3uM_rep2


title: MOF_ChIP_seq_rep2


title: urothelial carcinoma, P16_S2c

description: Same tumor and same raw data as in GSE32894 (GSM814167)


title: urothelial carcinoma, P16_S2a


title: h_NCM-5


title: urothelial carcinoma, P15_S1b

description: Same tumor and same raw data as in GSE32894 (GSM814237)


title: h_NCM-4


title: h_NCM-2


title: h_NCM-3


title: urothelial carcinoma, P18_S1a

description: Same tumor and same raw data as in GSE32894 (GSM814203)


title: urothelial carcinoma, P15_S1a


title: urothelial carcinoma, P14_S1b

value: GU

tag: same tumor, different assay


title: h_NCM-1


title: urothelial carcinoma, P17_S3a


title: IMQ_1 [skin tissue]

tag: strain

value: Sprague Dawley

value: back skin

tag: weight

tag: phenotype

value: Wild type

value: imiquimod(IMQ)-induced psoraisis-like rat model


title: urothelial carcinoma, P14_S1a

description: Same tumor and same raw data as in GSE32894 (GSM814209)


title: h_HF-7

description:
heart failure
human_heart_tissue_readCount.csv

source_name: heart failure

tag: tissue

value: heart failure tissue


title: human_fibroblast_PolyA_RNAseq_KdV_healthy_control4

description: KdV=Koolen-de-Vries

data_processing:
Reads were mapped to hg38 using STAR with default parameters,
transcripts were counted using featureCounts.
For differential expression analysis we used DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: featureCounts count table output

growth_protocol: Fibroblast cell lines were established from skin biopsies of confirmed Koolen de-Vries syndrome patients and healthy controls. Cells were maintained in in a humidified incubator at 37°C and 5% CO2 in DMEM (GlutaMAX supplement, Life Technologies), 100 U/ml penicillin, 100 μg/ml streptomycin and 10% foetal calf serum (FCS). All fibroblast lines tested negative for Hepatitis B, Hepatitis C, HIV and human Herpes virus 4 and 8. Fibroblasts were passaged at ~90% confluency.

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen)
TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: subject status

value: healthy control

tag: cell type

value: fibroblasts


title: human_fibroblast_PolyA_RNAseq_KdV_healthy_control2

description: KdV=Koolen-de-Vries


title: h_HF-6


title: urothelial carcinoma, P13_S1b


title: human_fibroblast_PolyA_RNAseq_KdV_healthy_control3

description: KdV=Koolen-de-Vries


title: human_fibroblast_PolyA_RNAseq_KdV_patient3

description: KdV=Koolen-de-Vries

value: Koolen de Vries patient


title: human_fibroblast_PolyA_RNAseq_KdV_healthy_control1

description: KdV=Koolen-de-Vries


title: urothelial carcinoma, P13_S1a

description: Same tumor and same raw data as in GSE32894 (GSM814074)


title: human_fibroblast_PolyA_RNAseq_KdV_patient2

description: KdV=Koolen-de-Vries


title: h_HF-5


title: h_HF-4


title: human_fibroblast_PolyA_RNAseq_KdV_patient1

description: KdV=Koolen-de-Vries


title: urothelial carcinoma, P16_S2b


title: urothelial carcinoma, P12_S2


title: h_HF-3


title: urothelial carcinoma, P12_S1

description: Same tumor and same raw data as in GSE32894 (GSM814058)


title: Dm_S2cell_Rpb3_ChIPseq_JQ1_1h_rep1_IP

description: dBRD4=fs(1)h , dBRD4-S indicating short isoform of dBRD4

data_processing:
Paired-end 75 bp reads were trimmed (TrimGalore, quality threshhold 20), then mapped using Bowtie2, BAM files of biological replicates were merged using SAM Tools
Coverage files were generated with deepTools3 (v3.0.1) bamCompare with a binsize of 1 (bin size of 10 for H3 profiles). The X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H4K16ac, H3, Rpb3; Input subtraction for Drosophila Biotin-dBRD4-S and dBRD4. For Rpb3 profiles SES scaling (signal extraction method) was applied
Genome_build: dm6
Supplementary_files_format_and_content: bigwig file format, Input normalized ChIP enrichments

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells (Invitrogen) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80

extract_protocol:
cells were fixed for 10min in 1.8% of formaldehyde at 23 °C, nuclei were isolated, chromatin was fragmented by sonication (Covaris), The lysate was clarified by centrifugation before immunoprecipitation, and eluted by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using AMPure XP Beads (Beckman Coulter); for Rpb3 ChIP experiments Drosophila Virilis chromatin was added prior to IP as spike control. For Biotin ChIP experiments exogenous Biotin-labeled DNA fragments were added prior to IP as spike control.
NEB Next Ultra II

treatment_protocol: for RNAi: dsRNA was added to the cell culture medium, 10µg dsRNA per 1mio cells, cells were harvested after 4 days of RNAi, for dBRD4 inhibitor treatments: DMSO or inhibitor was added to the cell culture medium

tag: cell line background

value: S2 cells

tag: genotype/variation

value: wild type

tag: knockdown or inhibitor treatment

value: 1h JQ1 treatment, 5µM (Cayman Chemicals, 1187)

tag: chip antibody

value: Rpb3 antibody (Akhtar lab)


title: urothelial carcinoma, P10_S2

tag: tumor stage

tag: tumor grade

tag: days from initial tumor

value: Uro


title: het_15.coutt

data_processing:
For single cell library preparation the CEL-Seq2 protocol (Hashimshony et al., 2016) was used with a nanoliter pipetting robot (mosquito® HTS, TTP Labtech) and the original volumes were reduced by 5-fold. 384-well plates (Corning, PCR-384-RGD-C) were prepared with 240 nl lysis buffer in every well. Lysis buffer consisted of the following reagents with final ratio in parentheses: 20 nl of 10 mM dNTP (1/12), 40 nl of 1:100000 ERCC mix 1 or 2 (2/12), 140 nl of water with 0.35% Triton® X-100 (7/12) and 40 nl of 25 ng/μl of 1 out of 192 uniquely barcoded polydT primers with UMI (2/12) (Table S4). Following the dispense of 240 nl of lysis buffer, 1.2 μl of hydrophobic encapsulation barrier (Vapor-Lock, Qiagen, 981611) were added to every well.
For transcript quantification we followed Herman et. al. (Herman et. al. 2018) pipeline. Briefly, paired end reads were aligned to the transcriptome by bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus and gene loci were merged to larger gene groups, if loci overlapped by >75%. This procedure resulted in 34,111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene groups and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left mate contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch and adjacent gene sequence. The left read was not used for quantification. For each cell barcode and gene locus, the number of UMIs was aggregated and, based on binomial statistics, converted into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Bone marrow

extract_protocol:
FACS sorting from Bone Marrow
CEL-seq2
single-cell RNA-seq

tag: genotype

value: mof +/-


title: Dm_S2cell_Rpb3_ChIPseq_dBET6_1h_rep1_IP

value: 1h dBEt6 treatment, 100nM (Bradner, Gray lab)


title: h_HF-1

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL.
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

value: male


title: h_HF-2


title: Dm_S2cell_Rpb3_ChIPseq_DMSO_1h_rep1_IP

value: 1h DMSO treatment


title: het_14.coutt


title: het_13.coutt


title: h_HCM-8

description:
hypertrophic cardiomyopathy
human_heart_tissue_readCount.csv

source_name: hypertrophic cardiomyopathy

value: hypertrophic cardiomyopathy tissue


title: urothelial carcinoma, P10_S1

description: Same tumor and same raw data as in GSE32894 (GSM814128)

tag: molecular subtype by gex


title: urothelial carcinoma, P9_S1

description: Same tumor and same raw data as in GSE32894 (GSM814088)

value: GU (GU by IHC)


title: Dm_S2cell_Rpb3_ChIPseq_JQ1_1h_rep2_IP


title: het_12.coutt


title: het_11.coutt


title: h_HCM-6

tag: gender


title: urothelial carcinoma, P8_S1

value: Ta


title: h_HCM-7


title: Dm_S2cell_Rpb3_ChIPseq_DMSO_1h_rep2_IP


title: Dm_S2cell_Rpb3_ChIPseq_dBET6_1h_rep2_IP


title: Dm_S2cell_ChIPseq_JQ1_1h_rep2_Input


title: urothelial carcinoma, P8_S2

description: Same tumor and same raw data as in GSE32894 (GSM814221)


title: urothelial carcinoma, P7_S2


title: het_10.coutt


title: het_16.coutt


title: het_9.coutt


title: h_HCM-5


title: h_HCM-4


title: h_HCM-3


title: Dm_S2cell_ChIPseq_DMSO_1h_rep2_Input


title: het_7.coutt


title: h_HCM-2


title: Dm_S2cell_ChIPseq_JQ1_1h_rep1_Input


title: urothelial carcinoma, P6_S1

description: Same tumor and same raw data as in GSE32894 (GSM814253)


title: het_6.coutt


title: h_HCM-1


title: Dm_S2cell_ChIPseq_dBET6_1h_rep1_Input


title: urothelial carcinoma, P5_S3

description: Same tumor and same raw data as in GSE32894 (GSM814159)

tag: same tumor, different assay


title: Dm_S2cell_ChIPseq_DMSO_1h_rep1_Input


title: het_5.coutt


title: het_4.coutt


title: urothelial carcinoma, P7_S1

description: Same tumor and same raw data as in GSE32894 (GSM814114)


title: het_3.coutt


title: urothelial carcinoma, P4_S2

description: Same tumor and same raw data as in GSE32894 (GSM814252)


title: het_2.coutt


title: Dm_S2cell_ChIPseq_dBET6_1h_rep2_Input


title: urothelial carcinoma, P6_S2


title: urothelial carcinoma, P3_S2


title: het_8.coutt


title: Kit-B6-AOM+CA Sample 3

city: Ribeirao Preto

first: Juliana

middle: Yumi

last: Sakita

state: Sao Paulo

address: Av. do Café, s/ nº

department: Genetics

country: Brazil

institute: Ribeirao Preto Medical School - University of Sao Paulo

data_processing:
Checking of the Fastq read data quality, alignment of reads to the mouse genome (NCBI37.p3/mm9) and read counts were carried out using the Qiagen software GeneGlobe Data Analysis Center. Data normalization, gene identification, differentially expressed genes (p < 0.05) between Kit-B6 and Kit-W/SH mouse groups were done using the R package DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is a tab-delimited file containing unnormalized gene counts

source_name: Colon Preneoplastic Lesion

extract_protocol:
Following tumorsharvesting and freezing steps, RNA extraction was performed with Qiagen RNeasy (#74106) and Qiagen RNase-free DNase kits (#79254).
QIAseq Targeted RNAseq Mouse Immuno-Oncology panel (#333005) and QIAseq Targeted RNA 96-Index I (#333117) were used to generate cDNA libraries.

treatment_protocol: In order to induce sporadic collorectal cancer in mice, animals were intraperitoneally injected with six azoxymethane carcinogen (AOM - 10mg/kg/week) and tumors were collected after 18 weeks of the last injection. Preneoplastic lesions were detected in mice that underwent 3 intraperitoneal injections of azoxymethane (AOM) throughout 3 weeks and were euthanatized (CO2 chamber) following other 3 weeks. To evaluate mast cells role in the development of preneoplastic lesions, mice received farmacological interventions that consisted in: 1) cromolyn (CA) injection together with azoxymethane carcinogen (AOM+CA) for 3 weeks followed by euthanasia after other 3 weeks; 2) azoxymethane carcinogen injection for 3 weeks  followed by cromolyn injection throughout 3 weeks and euthanasia (AOM-CA)

tag: strain

value: Colon

tag: age

value: 14th week postnatal

tag: treatment

value: Mice were submitted to cromolyn (CA) injection together with azoxymethane carcinogen (AOM+CA) for 3 weeks followed by euthanasia after other 3 weeks


title: Kit-B6-AOM-CA Sample 2

tag: tissue

value: Mice were submitted to azoxymethane carcinogen (AOM) injection for 3 weeks followed by cromolyn (CA) injection throughout 3 weeks and euthanasia (AOM-CA)


title: Kit-B6-AOM-CA Sample 1


title: het_1.coutt


title: urothelial carcinoma, P4_S1


title: Kit-B6-AOM+CA Sample 2


title: urothelial carcinoma, P3_S1

description: Same tumor and same raw data as in GSE32894 (GSM814129)


title: mouse_AdultOmentum_3 (For supplementing the Mouse Cell Atlas data)

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: Microwell-seq analysis

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: developmental stage

value: Adult

tag: Sex

value: Female

value: Omentum


title: mouse_AdultOmentum_4 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: mouse_AdultOmentum_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: control_16.coutt

value: wild type


title: urothelial carcinoma, P5_S4


title: Kit-B6-AOM+CA Sample 1


title: mouse_AdultStomach_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis

value: Stomach


title: Kit-B6-AOM-CA Sample 3


title: control_15.coutt


title: urothelial carcinoma, P1_S2

description: Same tumor and same raw data as in GSE32894 (GSM814147)

value: Uro


title: mouse_FetalStomach_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis

value: Fetal


title: Kit-B6-AOM Sample 3

value: Preneoplastic lesions (PN) were generated by 3 intraperitoneal injections of azoxymethane (AOM) throughout 3 weeks and were euthanatized following other 3 weeks


title: urothelial carcinoma, P1_S1


title: mouse_FetalStomach_1 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: Kit-B6-AOM Sample 2


title: control_14.coutt


title: control_13.coutt


title: Kit-B6-AOM Sample 1


title: mouse_FetalPancreas_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis

value: Pancreas


title: control_12.coutt


title: mouse_AdultOmentum_1 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: mouse_FetalPancreas_1 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: Kit-W/sh-PN Sample 2

value: C57BL/6 (cKitw-sh)

value: Kit "sash" mutation


title: Kit-W/sh-PN Sample 3


title: control_11.coutt


title: urothelial carcinoma, P2_S1

description: Same tumor and same raw data as in GSE32894 (GSM814127)

value: Basal


title: control_10.coutt


title: mouse_AdultPleura_1 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis

value: Pleura


title: control_9.coutt


title: Kit-B6-PN Sample 3

value: Colon


title: Kit-W/sh-PN Sample 1

value: 14th week postnatal


title: mouse_AdultArenalGland_3 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis

value: ArenalGland


title: mouse_AdultPleura_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: control_8.coutt


title: mouse_AdultArenalGland_2 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: Kit-B6-PN Sample 2


title: mouse_AdultArenalGland_1 (For supplementing the Mouse Cell Atlas data)

description: Microwell-seq analysis


title: Kit-B6-PN Sample 1


title: Tat101C22G_3 (gene)

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101C22G vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator with the change C22G)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Jurkat-TetOff were maintained in RPMI with 300 ug/ml geneticin and both Jurkat-Tat72 and Jurkat-Tat101 cell lines were maintained in RPMI with 300 ug/ml geneticin 300 ug/ml hygromycin B and (BD Biosciences and Clontech, respectively)

extract_protocol: Extracted with Qiagen RNeasy mini columns (Qiagen)

tag: cell type

value: Jurkat


title: Tat101wt_3 (gene)

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101 vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator)


title: control_6.coutt


title: Kit-W/sh-T Sample 4

source_name: Colon Tumor

value: 32th week postnatal

value: Intraperitoneal injection of six doses of azoxymethane carcinogen (AOM). Tumors were collected after 18 weeks of the last injection


title: Tat101C22G_1 (gene)


title: Kit-W/sh-T Sample 3


title: Tumor-infiltrating B (TIB) cells of mice treated by PBS

city: Guangzhou

first: Jian-You

last: Liao

state: Guangdong

address: 107# Yanjiang West Road

department: Sun Yat-Sen Memorial Hospital

institute: Sun Yat-Sen University

data_processing:
ScRNA-Seq data was processed using 10× Genomics CellRanger V3.0.2 pipeline. The resulting fastq files were passed to CellRanger’s count, which aligned all reads against mouse mm10 genomes using the STAR aligner. The data from libraries were pooled by running through CellRanger aggr to obtain unique molecular identifiers (UMIs) matrices. The UMI count matrix were processed using the R package Seurat (version 2.2.1). Both mkfastq and count were run with default parameters.
For each sample, the gene - barcode matrix was passed to the R (v. 3.5.3) software package Seurat (https://satijalab.org/seurat) (v2.2.1) for all downstream analyses. To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in terms of number of genes, number of UMIs, and percentage of mitochondrial genes using Seurat. Consequently, 7,528 single cells (2,420 from pre-treatment samples and 5,108 from post-treatment samples) were used for the following analyses. The cells were clustered using Seurat's FindClusters. T-distributed stochastic neighbor embedding (t-SNE) and modularity heatmap were created for graph-based cluster identification and subsequent dimensionality reduction. Marker genes for the individual clusters were identified using Seurat’s FindAllMarkers and only significantly upregulated markers (minimum log.FC ≥0 and FDR ≤ 1 × 10-75) were represented.
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: Tumor-infiltrating B cells

extract_protocol:
Cells were isolated from inoculated tumor tissues of C57/BL6 mice treated by PBS/Dox using flow cytometry.
ScRNA-seq libraries were constructed using Chromium Single Cell 3’ Reagent Kits v3 (10× GENOMICS) according to the manufacturer’s protocol.

treatment_protocol: Sample derived from inoculated tumor of C57/BL6 mice treated by PBS/Dox.

value: PBS

value: Inoculated tumor tissues

value: B cells


title: Tat101wt_2 (gene)


title: Tat101C22G_2 (gene)


title: Kit-W/sh-T Sample 5


title: Tumor-infiltrating B (TIB) cells of mice treated by Dox

value: Dox


title: Tat101wt_1 (gene)


title: NAA + BAP replicate 3

city: Amiens

first: Jerome

last: Duclercq

address: 33 rue St Leu

institute: UPJV

hyb_protocol: Arabidopsis Tiling 1.0R arrays (Affymetrix) were hybridized at the VIB Nucleomics Core (www.nucleomics.be) according to the manufacturer’s instructions.

data_processing: Data were normalized from CEL files using the robust multiarray average (RMA) algorithm (Irizarry et al., 2003). The probe annotation was obtained from athtiling1.0rcdf (Naouar et al., 2009). Differential expression analysis was determined using the eBayes function from the limma package in R (Smyth, 2004). P values were calculated and then transformed into false-discovery rates (FDR), or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue.

source_name: hormanl treatment, Protoplasting, FACS

growth_protocol: J0121 seeds were sterilized with chloral gas, sown in Petri dishes on 0.8 % agar with 1 % sucrose-containing 0.5 Murashige and Skoog (MS) medium, stored for 2 days at 4°C, and grown on vertically oriented plates in growth chambers under a 16-h-light/8-h-dark photoperiod at 18°C.

extract_protocol: RNA was extracted from pericycle cell sorted using the RNeasy Plant Mini Kit (Qiagen). A DNase treatment with the RNase-free DNase Set (Qiagen) was carried out for 15 min at 25°C. Total RNA concentration was determined using a Nanodrop ND-1000 spectrophotometer. All RNA samples were rejected if they did not reach a minimum concentration of 100 ng μl−1, a 260 nm/280 nm ratio between 1.8 and 2.0 and a RNA integrity number superior to 7.5, measured with an Agilent 2100 Bioanalyzer (Agilent, USA).

treatment_protocol: 5 days-old seedling were transfered on MS plate containing or not NAA or BAP or NAA + BAP during 3h. After treatment roots were cut off about 1 cm from their tip. Dissected roots were placed in protoplasting solution containing 0.1% pectolyase (Sigma-Aldrich P-5936) and 1.5% cellulysin (Calbiochem 219466) in buffer A (600 mM mannitol, 2 mM MgCl2, 0.1 % BSA, 2 mM CaCl2, 2 mM MES and 10 mM KCl, pH 5.5) inside 70 μm cell strainers placed in small Petri dishes and incubated for one hour at room temperature with agitation. Protoplasted cells were collected from Petri dishes and concentrated by spinning down (at approximately 800 RCF). The supernatant was aspirated and the cell pellet was resuspended in 1.5 ml of buffer A. The cell suspension was then filtered through a 40 μm cell strainer. GFP expressing cells were isolated on a fluorescence activated cell sorter (either a Cytomation MoFlo or a Becton Dickinson FACSVantage) fit with a 100 μm nozzle at a rate of 2,000 to 5,000 events per second. We mainly used a fluid pressure of 30 psi. Protoplasts from non-GFP expressing Columbia wild-type plants were used as a negative control for establishing sorting criteria based on the following cell properties: A) a cluster of live protoplasts with intact membranes was selected based on a high forward to side scatter ratio. B) GFP positive cells were selected by their emission intensity in the green channel (~530 nm) above negative controls. Cells were sorted directly into lysis buffer (Qiagen RLT buffer), mixed and immediately frozen at -80°C for later RNA extraction. An autofluorescence filter was established by eliminating cells that fluoresced at equal intensity in the green and orange (~575 nm) channels.

value: NAA + BAP

value: roots

value: pericycle cells


title: Kit-W/sh-T Sample 2

value: C57BL/6 (cKitw-sh)


title: control_5.coutt

value: wild type


title: control_3.coutt


title: Tat72_3 (gene)

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat72 vectors (Tat72 is the first exon of HIV-1 Tat protein regulator)


title: control_4.coutt


title: control_7.coutt


title: NAA + BAP replicate 1

scan_protocol: Arabidopsis Tiling 1.0R arrays (Affymetrix) were hybridized at the VIB Nucleomics Core (www.nucleomics.be) according to the manufacturer’s instructions.


title: Kit-W/sh-T Sample 1

value: Kit "sash" mutation


title: NAA + BAP replicate 2

label_protocol: Arabidopsis Tiling 1.0R arrays (Affymetrix) were hybridized at the VIB Nucleomics Core (www.nucleomics.be) according to the manufacturer’s instructions.


title: Kit-B6-T Sample 5


title: Tat72_1 (gene)


title: Tat72_2 (gene)


title: NAA replicate 3

value: NAA 1µM


title: control_1.coutt


title: HPC7 GATA1 IP

data_processing:
Genome alignment (mm10) by Bowtie2 version 2.3.0.1 (Langmead and Salzberg, 2012) using default parameters
Quality control was assessed by deeptools
Calling Peaks by MACS2 software (Feng et al., 2012), in which we settled bandwidth was settled for 300, lower mfold bound as 5, upper mfold bound as 500. Peak detection was based on q-value (minimum FDR cutoff as 0.05). For build model we selected the shifting mode.
For normalization based on log 2 fold changes IP/Input deeptool Bamcompare (Galaxy Version 2.5.1.0.0) was used
Coverage files were generate with bamCoverage module (Galaxy version 2.5.1.0.0) normalized coverage to 1x and effective geno size for mm10
Genome_build: mm10
Supplementary_files_format_and_content: Score represent the log2/fold change, wig we generated with bamCoverage module from deeptools software, Heatmap was generated eith the plotHeatmap module from deeptools and summary plots were generated with plotProflie module from deeptoools

source_name: Cell culture passage 3

growth_protocol: Mouse bone marrow (BM) cells were isolated from pooled femora, tibiae, ilia and vertebrae by fluxing and crushing in cold PBS 2%FCS using a mortar and pistil. Lysis of erythrocytes was performed using ACK Lysing Buffer (Thermo Fisher Scientific). To deplete lineage-positive cells we used the MojoSort™ Mouse Hematopoietic Progenitor Cell Isolation Kit (Biolegend#48003). Total BM was incubated with biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads. Magnetically labeled fraction was retained using a magnetic separator and untouched hematopoietic stem/progenitor cells (HSPC) were collected by decanting the liquid in a clean tube. 15000 HSCs (LSK+CD34-Flt3-) and 30.000 MEPs (Linegae-Sca-1-cKit+CD34-IL7r-CD16/32-)were sorted by a FACS Fusion II (Becton Dickinson). HPC7 were cultured in Iscove Modified Medium supplemented with 10% FCS and 10 ng/mL of SCF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The library was completed and amplified through a PCR following the DeepSeq using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina default instructions (NEB #E7645). ChIP libraries were sequenced using an Illumina HiSeq 3000.

value: haematopoeitic progenitor cell line (HPC7)

value: Wild type


title: TetOff_2 (gene)

source_name: CD4+ T cell line stably transfected with TetOff vector


title: TetOff_3 (gene)


title: NAA replicate 2


title: HPC7 H4K16ac IP


title: control_2.coutt


title: Kit-B6-T Sample 4

value: Colon


title: Kit-B6-T Sample 3


title: NAA replicate 1


title: HPC7 Input rep2


title: Kit-B6-T Sample 2


title: MS replicate 3

value: MS


title: HPC7 Input rep1


title: TetOff_1 (gene)

value: Jurkat


title: MS replicate 2


title: Kit-B6-T Sample 1

value: 32th week postnatal

value: Intraperitoneal injection of six doses of azoxymethane carcinogen (AOM). Tumors were collected after 18 weeks of the last injection


title: MS replicate 1


title: Pl_E12_5_CBb_2

city: Vienna, Austria

first: Daniel

last: Andergassen

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM Research Center for  Molecular Medicine of the  Austrian Academy of Sciences

description:
Balbc_validation_imprinted_ratio_fwd_strand_genes.txt
Balbc_validation_imprinted_ratio_rev_strand_genes.txt

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.3.1z12). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
STAR alignment of ChIP-seq data was conducted with different parameters to disable spliced reads, i.e. a maximum intron size of 1, and prevent soft clipping by enforcing end-to-end alignment (--alignEndsType EndToEnd). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1).
Based on the alignment efficiency for each sample we took the number of reads from the unaligned FASTQ file required to obtain 15 million aligned reads for RNA-seq and 20Mio for H3K27ac, then realigned these reads and performed all subsequent analysis on this data. The first reads were used from the unaligned FASTQ files. (see Supplemental table).
The Single Nucleotide Polymorphism (SNP) annotation file was created from a VCF file containing SNP variant data of 18 mouse strains, downloaded from the Sanger institute. SNP information for the strains CAST/EiJ and FVB/NJ were extracted and converted to the required browser extensible data (BED) format using a custom script that is available together with Allelome.PRO. Note that the name field in this file contains SNP information. Only homozygous high quality SNPs were used.
To define allelic expression using the Allelome.PRO pipeline, we downloaded the RefSeq annotation from the UCSC genome browser (mm10) on July 15th 2015 and removed transcripts with gene body length less than 100bp. To annotate the regions not covered by RefSeq we merged the reads from the 4 replicates (2x FVBxCAST and 2x CASTxFVB) for each tissue using SAMtools (version 1.2) and used Cufflinks (version 2.2.1) to perform a reference based assembly for each tissue (version 2.2.1). Next we used Cuffmerge to merge the assemblies from each tissue together with the RefSeq annotation (-g RefSeq.gtf). Next we discarded transcripts overlapping RefSeq in sense orientation and single exon transcripts. The final annotation consists of 23521 RefSeq genes (20743 protein-coding (NM) and 2778 NR non-coding) and 6290 assembled genes (XLOC) outside of the RefSeq annotation. Sliding windows were used to define allelic ChIP-seq (4Kb sliding windows for H3K27ac and H3K4me3 and 20kb sliding window for H3K27me3).
Defining allelic RNA-seq and ChIP-seq: Allele-specific expression and histone modification enrichment was detected from RNA-seq and ChIP-seq data as previously described using the Allelome.PRO program (Andergassen et al. 2015). Allelome.PRO settings for RNA-seq and H3K4me3: FDR 1%, allelic-ratio cut off 0.7, minread 2, annotation as described above. Allelome.PRO settings for H3K27ac & H3K27me3: FDR 1%, allelic-ratio cut off 0.7, minread 1, annotation as described above.
Defining XCI escapers: Allelome.PRO was run using a false discovery rate (FDR) of 1%, an allelic-ratio cut off of 0.6 and the minread parameter was set to 2. To increase the stringency in defining escapers, genes categorized as BAE in tissues with skewed or imprinted XCI (strain biased for CAST or maternal expression), but have as strain/imprinted score towards the CAST/MAT allele in all 4 replicates and an allelic-ratio above the ratio cutoff (0.6) were excluded from the analysis. Such cases can happen for lowly expressed genes, which are just below the FDR cutoff in one or more replicates.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the Allelom.PRO output for RNA-seq and Chip-seq

source_name: Placenta

growth_protocol: After reciprocal mating (CASTxFVB and FVBxCAST), 22 mouse tissues (x4 replicates) from individual females (XX), males (XY) or pooled litters (XY/XX)) were microdissected from pluripotent (1), embryonic (4), extra-embryonic (5), neo natal (2), adult (8) or from lactating females (2) (E3.5: embryonic stem cells (ESCs) (XY); E9.5: Visceral yolk sac endoderm (VE) (XY/XX); E12.5: liver (XY/XX), VE (XY/XX), Placenta (XX); E16.5: Brain, liver, heart, VE, Placenta (XX); 3 days postnatal: Brain, tongue (XX); adult: Brain, liver, heart, lung, spleen, thymus, leg muscle, virgin mammary glands (XX); lactating female: Brain, mammary glands (XX)). Male ESCs were isolated according to Bryja et al. 2006 and adapted to 2i media (Ying et al. 2003 and Ying et al. 2008). VE was isolated from visceral yolk sac according to Hudson et al. 2011. Mammary gland isolation was performed according to Joshi et al. 2010

extract_protocol:
Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
RNA-seq: DNaseI treated (DNA-FreeTM Ambion) total RNA (1-3 µg) was depleted for Ribosomal RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre) or enriched for polyA containing mRNA (Illumina). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described in Sultan et al. 2012 for strand-specific sequencing. ChIP-seq: Native ChIP was conducted as described in Regha et al. 2007. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina).

value: Placenta

value: CAST/EiJxBALBc


title: Mof-/+ MEP MOF IP

source_name: Bone Marrow

value: MEPs

value: Mof -/+


title: WT HSC MOF IP

value: HSCs


title: WT MEP MOF IP


title: Pl_E12_5_BbC_2

value: BALBcxCAST/EiJ


title: Pl_E12_5_CBb_1


title: BAP replicate 3

value: BAP 10µM

value: roots

value: pericycle cells


title: BAP replicate 1


title: Tamoxifen #30629623

city: ROCHESTER

first: Swaathi

last: Jayaraman

state: Minnesota

address: 200 1st St SW

department: Oncology

hyb_protocol: The IVT products were then bead-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 hours.

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA).

data_processing: The perfect match gene expression probes were normalized and summarized using Tukey’s median polish to obtain one value per probe-set for each sample. Differential expression between pair-wise treatment groups were tested using Student’s t-test. Genes were determined to be significantly regulated if their differential P-value was < 0.05. Fold changes were calculated by log 2 scale difference between the treatment and untreated groups.

source_name: MCF7 AC1

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

growth_protocol: MCF7AC1 breast cancer cells were cultured in phenol-red free IMEM medium supplemented with 10% fetal bovine serum (FBS) and 600 μg/ml geneticin (G418). Letrozole-resistant MCF7LR cells, were cultured in phenol-red free IMEM medium supplemented with 10% charcoal stripped FBS (Hyclone), 1% antibiotic-antimycotic (AA), 1 μM letrozole and 1 nM androstenedione.

extract_protocol: Total RNA from tissue samples were extracted using RNeasy Plus Mini Kit (Qiagen) and cDNA was generated using the ISCRIPT cDNA synthesis kit (Bio-Rad) using manufacturer’s instructions.

treatment_protocol: MCF7AC1 cells at 2.5 x 10^6 cells per 100 μl of 1:1 phosphate-buffered saline (PBS):Matrigel mixture were injected subcutaneously into the right and left flanks of 4-6 week old ovariectomized BALB/c athymic female nude mice (Harlan Laboratories). Upon development of palpable tumors (tumor volume: ~300 mm^3), the mice were randomized into treatment groups (n=30 mice/group) and were administered control (no drug), tamoxifen (500 µg/day) or letrozole (10μg/day) (all prepared as suspensions in 0.3% hydroxypropyl cellulose) subcutaneously or Z-endoxifen (25 mg/kg or 75 mg/kg) (prepared as suspensions in PEG400: Ascorbic Acid 50:50) by oral gavage. All animals were supplemented with 1.4 mg 90-day-release estrogen pellets (Innovative Research) and the drugs were administered once daily. In the mice treated with prolonged letrozole, administration of the drug was continued until resistance development. As an exploratory extension of this experiment, n = 9 tumors that had developed letrozole resistance were randzomized to Z-endoxifen (50 mg/kg) (n=5) or tamoxifen (n=4) for four weeks and tumors harvested for microarray and immunohistochemistry (IHC) analysis.

value: Tamoxifen

tag: cell line

value: MCF7 AC1


title: Tamoxifen #13619525


title: BAP replicate 2


title: Endoxifen #17628844

value: Endoxifen


title: Mof-/+ HSC MOF IP


title: Endoxifen #30787853


title: Pl_E12_5_CFF_W_2

description:
Embryo_transfer_validation_allelic_ratio_fwd_strand_genes.txt
Embryo_transfer_validation_allelic_ratio_rev_strand_genes.txt

value: CAST/EiJxFVB/NJ > embryo transfer to FVB/NJ


title: Endoxifen #20618802


title: Tamoxifen #32626845


title: Mof-/+ MEP Input


title: Pl_E12_5_CFF_W_1


title: 3077_c4_E_negative

city: Philadelphia

first: Salina

last: Yuan

address: 421 Curie Blvd

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapters were trimmed with cutadapt.
Reads were aligned to the mouse reference genome (GRCm38, May 23 2014) by Bowtie2.
Picard was used to identify and discard reads that aligned to the mitochondrial genome, as well as reads mapping to multiple genomic loci.
MACS2 with ‘-p 1e-7–nolambda–nomodel’ was applied on each ATAC-seq replicate separately to identify accessible chromatin.
Peaks were subsequently merged using BEDTools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: biWig files

source_name: pancreatic cancer cells

extract_protocol:
50,000 cells were sorted by APC-Ecadherin on FACSAria II sorter.
Libraries were prepared according to published protocols. Briefly, nuclei were isolated from sorted cells using a solution of 10 mM Tris-HC pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630. Immediately following nuclei isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 45 min. at 37oC. Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded with primers based on Illumina TruSeq indices (Table S5), and PCR amplified for 11 cycles using NEBNext High Fidelity 2x PCR master mix (New England Biolabs). Libraries were purified by extraction from a 6% TBE gel, followed by column purification with the Qiagen PCR Cleanup kit.

treatment_protocol: No treatment was used.

value: Pancreatic cancer cells

tag: ecad status

value: Negative

tag: antibody used to sort

value: anti-E-cadherin (Takara Bio, M108)


title: WT HSC Input

value: Wild type


title: Pl_E12_5_BbC_1

value: Placenta


title: Mof-/+ HSC Input


title: 3077_c4_E_positive

value: Positive


title: WT MEP Input

value: MEPs


title: H3 ddm1rdr6 Rep 2

data_processing:
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Supplementary_files_format_and_content: Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Supplementary_files_format_and_content: ChIP-seq: Adapter trimming was performed using Trimmomatic, and read quality was assessed with FastQC. Reads were aligned to the TAIR10 reference genome using BWA-MEM with default parameters. Only primary alignments were retained, and optical and PCR duplicates were removed using Samtools. Bedgraph files were generated using Bedtools (genomeCoverageBed –bg).

source_name: 10 day-old seedlings

extract_protocol:
Chromatin immunoprecipitation was performed using H3 antibody (Abcam; ab1791). After washing, DNA was eluted and reverse-crosslinked and purified with ChIP DNA clean and concentrator kit (Zymo Research).
NEBNext Ultra II DNA Library Prep Kit

tag: genetic background


title: 483_c6_E_negative


title: Second_myc2_JA_4hour_RNAseq_rep2

description: RNASeq_Sample 86

data_processing:
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using TrimGalore 0.4.5, then aligned to the TAIR10 genome assembly using TopHat 2.1.1
Reads were counted using HTSeq. Differentially expressed genes were identified using edgeR 3.6.2
Quantification of transcripts was performed using Salmon v0.8.1
The TSIS R package was used to perform the isoform switch analysis
Genome_build: TAIR10 and AtRTD2-QUASI
Supplementary_files_format_and_content: txt file with HTseq read count output

source_name: Three day old etiolated seedlings

extract_protocol:
RNeasy Plant Mini Kit (74903, Qiagen)
cDNA library preparation and subsequent single read sequencing was carried as previously described (Song,L et al., 2016) DOI: 10.1126/science.aag1550

value: Three day old etiolated seedlings

value: myc2 T-DNA mutant

value: JA treatment for 4h


title: 483_c6_E_positive


title: Second_myc2_JA_1hour_RNAseq_rep3

description: RNASeq_Sample 84

value: JA treatment for 1h


title: Second_myc2_JA_4hour_RNAseq_rep1

description: RNASeq_Sample 85


title: Letrozoleresistant #2

value: Letrozole Resistant


title: Second_myc2_JA_4hour_RNAseq_rep3

description: RNASeq_Sample 87


title: H3 ddm1 Rep 2


title: Endoxifen #6611810


title: Letrozoleresistant #3


title: Letrozoleresistant #1


title: H3 ddm1rdr6 Rep 1


title: 3077_c8_E_negative


title: Endoxifen #6632884


title: Second_myc2_JA_1hour_RNAseq_rep1

description: RNASeq_Sample 82


title: Second_myc2_JA_1hour_RNAseq_rep2

description: RNASeq_Sample 83


title: H3 ddm1 Rep 1


title: Lib_16_plate2_mof

data_processing:
Paired end reads were aligned to the transcriptome by bwa (version 0.6.2-r126)
The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M)
The right mate of each read pair was mapped to the ensemble of all gene groups and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left mate contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch and adjacent gene sequence. The left read was not used for quantification. For each cell barcode and gene locus, the number of UMIs was aggregated and, based on binomial statistics, converted into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include transcript count values for each Sample

extract_protocol:
Bone marrow progenitor cells were srted, flash frozen on liquid nitrogen, and RNA was harvested using Cel-Seq2 protocol. Cel-Seq2  was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Cel-seq2 protocols

value: Haematopoetic progenitor cells

value: Mof -/+

tag: illumina index

value: ACTTGA


title: H3 rdr6 Rep 2


title: Second_myc2_JA_0.5hour_RNAseq_rep3

description: RNASeq_Sample 81

value: JA treatment for 0.5h


title: Lib_15_plate2_mof

value: CAGATC


title: H3 rdr6 Rep 1


title: 3077_c8_E_positive

value: Pancreatic cancer cells


title: Second_myc2_JA_0.5hour_RNAseq_rep2

description: RNASeq_Sample 80


title: Second_myc2_JA_0.5hour_RNAseq_rep1

description: RNASeq_Sample 79


title: Second_myc2_JA_0hour_RNAseq_rep3

description: RNASeq_Sample 78

value: JA treatment for 0h


title: Lib_14_plate2_wt

value: wild type

value: GCCAAT


title: CLL_A_del17p_untreated_15

type: genomic

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital Ulm

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader with standard recommended settings

data_processing: The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 704), as well as probes giving unreliable measurements (884 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 759 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 251), probes binding to sequences on sex chromosomes (9 917) and probes with low standard deviation (69 867) were filtered out. The data obtained by the remaining 351 724 probes were used in downstream analyses.

label: Cy3 and Cy5

source_name: CLL, group A (del(17p) and/or TP53mut, untreated)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions

value: female

tag: treated

value: no

tag: response to therapy

value: not applicable

value: unmutated

value: yes

value: missense


title: H3 WT Rep 2

tag: genotype

value: wild-type


title: H3 WT Rep 1


title: H3K9me2 ddm1rdr6 Rep 2

extract_protocol:
Chromatin immunoprecipitation was performed using H3K9me2 antibody (Abcam; ab1220). After washing, DNA was eluted and reverse-crosslinked and purified with ChIP DNA clean and concentrator kit (Zymo Research).
NEBNext Ultra II DNA Library Prep Kit


title: het_HSC2

value: TGACCA


title: het_HSC1

value: Haematopoetic progenitor cells

value: TTAGGC


title: CLL_D_nodel17p_chemosensitive_19

source_name: CLL, group D (no del(17p) or TP53mut, chemosensitive)

value: male

value: none detected


title: Second_myc2_JA_0hour_RNAseq_rep1

description: RNASeq_Sample 76

value: Three day old etiolated seedlings

value: myc2 T-DNA mutant


title: CLL_C_del17p_refractory_11

source_name: CLL, group C (del(17p) and/or TP53mut, refractory)

value: refractory

value: frameshift


title: CLL_D_nodel17p_chemosensitive_20


title: wt_HSC2

value: wild type

value: CGATGT


title: Second_myc2_JA_0hour_RNAseq_rep2

description: RNASeq_Sample 77

value: JA treatment for 0h


title: H3K9me2 ddm1 Rep 2


title: Lib13_plate2_wt

value: ACAGTG


title: Second_Col-0_JA_4hour_RNAseq_rep3

description: RNASeq_Sample 75

value: JA treatment for 4h


title: CLL_E_nodel17p_refractory_15

source_name: CLL, group E (no del(17p) or TP53mut, refractory)

value: yes

value: unmutated

value: no

value: not applicable


title: Second_Col-0_JA_4hour_RNAseq_rep2

description: RNASeq_Sample 74


title: Second_Col-0_JA_4hour_RNAseq_rep1

description: RNASeq_Sample 73


title: wt_HSC1

value: Haematopoetic progenitor cells

value: ATCACG


title: H3K9me2 ddm1 Rep 1


title: H3K9me2 rdr6 Rep 2


title: H3K9me2 ddm1rdr6 Rep 1


title: CLL_E_nodel17p_refractory_14

value: male


title: CLL_D_nodel17p_chemosensitive_13_timepoint2

value: responded

value: none detected


title: CLL_C_del17p_refractory_10

value: unknown

value: female

value: splice site


title: H3K9me2 rdr6 Rep 1


title: CLL_B_del17p_relapsed_9

source_name: CLL, group B (del(17p) and/or TP53mut, relapsed)

value: relapsed

value: missence; splice site; missense


title: Second_Col-0_JA_1hour_RNAseq_rep3

description: RNASeq_Sample 72

value: Three day old etiolated seedlings

value: JA treatment for 1h


title: Second_Col-0_JA_1hour_RNAseq_rep2

description: RNASeq_Sample 71


title: H3K9me2 WT Rep 1

value: wild-type


title: H3K9me2 WT Rep 2


title: CLL_B_del17p_relapsed_10

value: yes


title: Second_Col-0_JA_1hour_RNAseq_rep1

description: RNASeq_Sample 70


title: Small RNA ddm1 pollen

data_processing:
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: bigWig
Supplementary_files_format_and_content: Long read VLP DNA-seq: bigWig, vcf (Structural variant calls produced by Sniffles on nanopore long-read alignments to the TAIR10 genome. The number of reads supporting each SV call is given in the RE tag.)

source_name: Pollen

extract_protocol:
Pollens were isolated using FACS based on SSC/FSC scatter plots. Total RNA was isolated from pollen with Trizol LS reagent by vortexing with glass beads for 5 minutes, and concentrated with Direct-zol columns (Zymo Research). 18 to 30-nt small RNA was size-selected using 15% polyacrylamide gel.
TruSeq small RNA sample preparation kit (Illumina)

tag: ecotype

value: Pollen

tag: fraction

value: Small RNA


title: Second_Col-0_JA_0.5hour_RNAseq_rep3

description: RNASeq_Sample 69

value: JA treatment for 0.5h