title: G118-M14_PolyA+_Intact male liver pool 2

description:
Sample name: G118_M14
poly-A selected RNA, strand-specific library


title: DR 26m PE Rep2 BS-seq

status: Public on Feb 24 2017

type: SRA

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Sciences, LLC

description: Dietary restricted

library_source: genomic

data_processing:
RNA-seq: Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7,  parameters: --paired --length 25).  A modified mouse reference genome (build GRCm38), with all known SNPs replaced by ‘N’ was set up to account for the hybrid genome of the C3H-C56BL/6 mice. Trimmed sequences were aligned using Tophat2 (v2.0.14, parameters: --no-mixed  --library-type=fr-firststrand -g 2 -p 15 -r 500 --mate-std-dev 525), supplying GENCODE annotation (release M9, main annotation) for improved mapping. Multi-mapped reads were filtered using samtools (v1.2, parameters: view -F 0x100 -b –h).  Data visualization and analysis was performed using SeqMonk, ClueGO {Bindea:2009hh} custom RStudio and the following Bioconductor packages: Deseq2, topGO and org.Mm.eg.db.
BS-seq: Raw sequence reads were trimmed using Trim Galore (v0.4.2; default parameters). Trimmed sequences were aligned using Bismark (v0.16.3; default parameters). Methylation calls were extracted after duplicate sequences had been excluded (parameters --ignore_r2 2 for paired-end libraries).
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each sample; results for differential gene expression analysis.
Supplementary_files_format_and_content: BS-seq: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

molecule: genomic DNA

organism: Mus musculus

source_name: DR 26m PE BS-seq

extract_protocol:
RNA-seq: RNA from 3 AL and 3 DR animals per time point was isolated from 30 mg of liver tissue using Trizol Reagent (ThermoFisher) according to the manufacturer’s instructions, followed by DNAse treatment with the TURBO DNA-free Kit (ThermoFisher). RNA integrity was analyzed using the Agilent TapeStation System.
BS-seq: DNA of 3 AL and 3 DR animals per timepoint was isolated from 30 mg of liver tissue using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq: TruSeq RNA-seq library preparation was conducted as previously described (Sultan, et al., 2012) using 3 µg of total RNA as input and rRNA depletion. Barcoded libraries were sequenced with 2x40 mio, 100 bp paired-end reads on an Illumina HiSeq2500.
BS-seq: Around 400 ng genomic DNA was used as input for BS-Seq library generation. DNA was sonicated, and end repair and A-tailing were performed using the NEB Next kit according to the manufacturers’ instructions. Illumina’s Early Access Methylation Adaptor Oligo Kit was used for adaptor ligation. Adaptor-ligated DNA was treated with sodium-bisulfite using the Imprint DNA Modification Kit from Sigma-Aldrich according to the manufacturer’s instructions for the one-step protocol. Bisulfite-treated DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase from Agilent Technologies with 14–18 cycles depending on input amount. Size selection was performed by gel extraction for DNA fragments between 200 bp and 250 bp, as adapted from (Seisenberger et al., 2012). Libraries of young samples were sequenced using the paired-end protocol. Old sample libraries were sequenced using single-end protocol and a subsequent re-run using a paired-end protocol to increase coverage.

treatment_protocol: We used females of the long-lived F1 hybrid mouse strain (C3B6F1), which responds to DR with a robust increase in lifespan. To avoid effects on post-natal development, DR treatment was started in 12-week-old animals, by providing DR mice with 40% less food than their AL controls. We collected liver samples of AL and DR animals at the ages of 5 months (young) and 26 months (old).

tag: strain

tag: gender

value: female

tag: diet

value: dietary-restricted (DR)

tag: age

value: 26 months

tag: tissue

value: liver


title: AL 26m SE Rep1 BS-seq

description: Fully-fed

source_name: AL 26m SE BS-seq

value: control-fed (AL)


title: AL 26m SE Rep3 BS-seq

description: Fully-fed


title: DR 26m SE Rep1 BS-seq

description: Dietary restricted

source_name: DR 26m SE BS-seq


title: DR 26m SE Rep2 BS-seq

description: Dietary restricted


title: AL 26m PE Rep3 BS-seq

description: Fully-fed

source_name: AL 26m PE BS-seq


title: AL 26m PE Rep1 BS-seq

description: Fully-fed


title: AL 26m SE Rep2 BS-seq

description: Fully-fed


title: AL 26m PE Rep2 BS-seq

description: Fully-fed


title: DR 26m PE Rep3 BS-seq

description: Dietary restricted


title: DR 5m Rep2 BS-seq

description: Dietary restricted

source_name: DR 5m BS-seq

value: 5 months


title: AL 5m Rep3 BS-seq

description: Fully-fed

source_name: AL 5m BS-seq


title: DR 26m Rep3 RNA-seq

description:
Dietary restricted
processed data file:
Differential_Gene_expression_Analysis_results_ALold-vs-ALyoung.txt
Differential_Gene_expression_Analysis_results_DRold-vs-ALold.txt
Differential_Gene_expression_Analysis_results_DRold-vs-DRyoung.txt
Differential_Gene_expression_Analysis_results_DRyoung-vs-ALyoung.txt
RNA-seq.Readcount_output.txt

library_source: transcriptomic

molecule: total RNA

source_name: DR 26m RNA-seq


title: WTB_time2.5

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

data_processing:
Adapters trimmed with Cutadapt (v1.12)
Aligned to NC_000913.3 with bwa version 0.7.7
Index and sort alignments with samtools version 1.2
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB
Gave a pseudocount of 0.01 to all values of 0
Genome_build: NC_000913.3
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking

extract_protocol:
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays)
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep

treatment_protocol: Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples.

tag: genotype/variation

value: wild type

tag: time point


title: AL 5m Rep1 BS-seq

description: Fully-fed


title: DR 5m Rep1 BS-seq

description: Dietary restricted


title: AL 26m Rep3 RNA-seq

description:
Fully-fed
processed data file:
Differential_Gene_expression_Analysis_results_ALold-vs-ALyoung.txt
Differential_Gene_expression_Analysis_results_DRold-vs-ALold.txt
Differential_Gene_expression_Analysis_results_DRold-vs-DRyoung.txt
Differential_Gene_expression_Analysis_results_DRyoung-vs-ALyoung.txt
RNA-seq.Readcount_output.txt

source_name: AL 26m RNA-seq


title: AL 5m Rep2 BS-seq

description: Fully-fed


title: DR 5m Rep3 BS-seq

description: Dietary restricted


title: G110-M11_PolyA+_Hypophysectomized male + GH 240' pool 1

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Sample name: G110-M11
poly-A selected RNA, strand-specific library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting  sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes any sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using  edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: excel spreadsheet with differential expression results.

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen liver by Trizol per the manufacturer's instructions.
RNA was polyA-selected using the NEBNext Poly(A) mRNA magnetic isolation kit (NEB, Ipswich, MA, Cat# E7490). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: Male and female CD-1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA). Mice were intact or were hypophysectomized by the supplier at 7 wk of age, Hypophysectomized male mice were given a single ip injection of vehicle (control) without or with recombinant rat GH at 125 ng GH/g body weight

value: CD-1 (Charles River)

tag: treatment

value: hypophysectomy + GH pulse

tag: Sex

value: Male

value: 11 weeks


title: G110-M12_PolyA+_Hypophysectomized male + GH 240' pool 2

description:
Sample name: G110-M12
poly-A selected RNA, strand-specific library


title: AL 26m Rep1 RNA-seq


title: AL 26m Rep2 RNA-seq


title: DR 5m Rep3 RNA-seq

source_name: DR 5m RNA-seq


title: G110-M10_PolyA+_Hypophysectomized male + GH 90' pool 2

description:
Sample name: G110-M10
poly-A selected RNA, strand-specific library


title: DR 26m Rep1 RNA-seq


title: DR 5m Rep2 RNA-seq


title: DR 26m Rep2 RNA-seq


title: DR 5m Rep1 RNA-seq


title: AL 5m Rep3 RNA-seq

source_name: AL 5m RNA-seq


title: G7-669 (KO1) RNA-Seq

city: Miami

first: Peng

last: Zhang

state: FL

address: 1011 NW 15th Street

institute: University of Miami Miller School of Medicine

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using STAR version 2.3.1t
Gene count table was generated for samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for samples

source_name: hematopoietic stem/progenitor cells

extract_protocol:
2x10^6 LK cells were harvested and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: BM-derived Lin-Kit+ cells

tag: genotype


title: G110-M9_PolyA+_Hypophysectomized male + GH 90' pool 1

description:
Sample name: G110-M9
poly-A selected RNA, strand-specific library


title: G7-660 (WT2) RNA-Seq

value: Wild type


title: G7-679 (KO2) RNA-Seq


title: G110-M7_ PolyA+_Hypophysectomized male + GH 30' pool 1

description:
Sample name: G110-M7
poly-A selected RNA, strand-specific library


title: AL 5m Rep2 RNA-seq


title: G110-M8_PolyA+_Hypophysectomized male + GH 30' pool 2

description:
Sample name: G110-M8
poly-A selected RNA, strand-specific library


title: AL 5m Rep1 RNA-seq


title: G7-657 (WT1) RNA-Seq


title: G110-M6_PolyA+_Hypophysectomized male pool 2

description:
Sample name: G110-M6
poly-A selected RNA, strand-specific library

value: hypophysectomy


title: T176LyM

city: Buffalo

middle: W

last: Goodrich

state: NY

address: Elm and Carlton

department: Pharmacology&Therapeutics

institute: Roswell Park Cancer Institute

description:
experimental
RawCounts.csv
RPKMedgeR.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed with adaptor sequence using cutadapt v1.2.1  and mapped to mm10 reference with corresponding RefGene GTF annotation using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and RPKM estimation using edgeR_3.12.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with counts and RPKM values of each sample

source_name: Lymph node

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

tag: genetic background

value: Mixed

value: Metastasis


title: T209PT

source_name: Prostate

value: Primary Tumor


title: T812PT


title: G110-M5_PolyA+_Hypophysectomized male pool 1

description:
Sample name: G110-M5
poly-A selected RNA, strand-specific library


title: T643LyM


title: T643PT


title: DR 26m PE Rep1 BS-seq

description: Dietary restricted

value: female


title: T300PT

value: Primary Tumor Castrate Recurrent


title: T176PT


title: mock_antiCD3_8h

city: Lausanne

first: Julia

last: DI IULIO

state: Vaud

address: Bugnon 48

country: Switzerland

institute: Institute of Microbiolgy

data_processing:
The sequencing reads were cleaned before alignment in order to improve the accuracy of downstream analyses. The cleaning steps included the removal of (i) Illumina’s adapter (if present at the 3’ end of the read) with cutadapt v0.9.5 [56], (ii) low quality (PHRED score,6) nucleotides at the 39 or 59 end of the reads, (iii) reads with mean PHRED score lower than 20 and (iv) polyA tails with prinseq v0.17. Only reads of 30 nucleotides or longer after trimming were kept for further analyses.
The cleaned reads were aligned to the reference genome with TopHat v2.0.6 using the ensembl gene GRCh37 release 68 annotation file. The reference genome was built by concatenating the human genome (hg19) and the HIV vector sequence
The number of reads per gene was extracted with a modified version of HTSeq-count v0.5.3 (http://www-huber.embl.de/users/anders/HTSeq/doc/count. html) using the same annotation file and considering the whole HIV vector as a single gene. The modifications allowed multiply aligned reads to be weighted accordingly. Ambiguous reads were randomly attributed to one of the genomic regions they aligned to.
Genome_build: hg19
Supplementary_files_format_and_content: table (tab delimited txt file) with number of mapped reads per gene for each condition

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary CD4+ T cells

growth_protocol: Primary CD4+ T cells were purified by Ficoll gradient separation followed by negative selection and magnetic separation using the human CD4+ T Cell Isolation kit II (Miltenyi Biotec) (Fig. S1). Cells were activated using CD3/CD28 co-stimulation in presence of IL-2 (mimicking TCR stimulation) as described previously [10]. Briefly, anti-CD3 antibodies (10 µg) were plated in 1 ml PBS per well of a 6-well plate and incubated for 1–2 h at 37°C. Wells were then washed once with 3 ml of PBS and filled with 10e6 cells/ml of primary CD4+ T cells supplemented with 1 µg/ml anti-CD28 antibodies in Optimizer CTS T-Cell expansion SFM culture medium containing 5% heat-inactivated fetal calf serum (FCS) and 100 U/ml human recombinant IL-2 (Opti/FCS/IL-2 culture medium). Three days post-stimulation, cells were collected, washed and resuspended at 10e6 cells/ml in Opti/FCS/IL-2 for infection with an HIV-based vector (NL4-3-Δ6-drEGFP/CXCR4; a kind gift from R.F. Siliciano). This HIV vector uses a CXCR4 tropic HIV envelope for entry, contains functional tat and rev genes, as well as a gfp reporter gene containing a PEST sequence (yielding a protein half time of ∼6 hours); this vector contains mutations (stop codons, frameshift or deletion) in gag, vif, vpr, vpu, env and nef and is thus less cytotoxic for the infected cell, thereby promoting latency in a higher proportion of infected cells [10]. HIV particles were produced by transfection of HEK293T cells as previously described [22]. Infection was carried out by spinoculation for 3 hours at 25°C and at 1500 g using 50 µg p24 equivalent HIV vector/10e6 cells in presence of 5 µg/ml polybrene. After spinoculation, cells were washed and resuspended at 10e6 cells/ml in Opti/FCS/IL-2. Forty-eight hours post-infection, cells were resuspended in PBS/FCS (to eliminate the interference of phenol red) and sorted by FACS according to GFP expression, yielding a typical purity of >98%. FACS sorting was performed with a Mo-Flo Astrios instrument. Upon sorting, successfully infected GFP+ cells were further processed to investigate HIV latency.Establishment and maintenance of HIV latency was mostly carried out as previously described [19], [20] (Fig. S1). Infected GFP+ cells stimulated using anti-CD3 and anti-CD8 antibodies in presence of IL-2 as described above were expanded in Opti/FCS/IL-2 for ∼3 weeks, typically allowing ∼2 log of cell multiplication. At this time (week 0), cells were washed, resuspended in R-10/IL-2 (RPMI-1640 culture medium supplemented with 10% heat-inactivated FCS and 40 U/ml IL-2) and added to an adherent H80 feeder cell layer. The H80 human brain tumor cell line, known to promote ex vivo survival of primary CD4+ T cells, were prepared by plating 10e6 cells/25 cm2 flask (T25) or 3×10e6 cells/75 cm2 flask (T75) the day before starting co-culture with primary CD4+ T cells. CD4+ T cells were resuspended in R-10/IL-2 and added on top of the feeder cell layer, in 16 ml R-10/IL-2 in T75 if 30-100×10e6 primary CD4+ T cells or in 5 ml R-10/IL-2 if >30×10e6 cells. Culture medium was changed three times a week by renewing half of it. Every two weeks, CD4+ T cells were collected and transferred onto a new feeder cell layer flask. During this transfer, cell samples were collected for analyses (see below). The co-culture of primary CD4+ T cells with H80 feeder cells was carried over a period of 10 weeks to allow CD4+ T cells to revert to a resting phenotype and to ensure entry into and maintenance of latency. Collected samples were used for: (i) assessing the expression of virally-encoded GFP and of the marker of activation IL2Rα (CD25) by FACS analysis, and (ii) assessing dynamic changes of the cellular and viral transcriptomes using mRNA-Seq. This analysis allowed for (a) following the cellular dynamic process from activated to resting state at the transcriptional level in non-infected as well as infected cells, (b) highlighting genes differentially expressed in HIV-infected cells as compared to mock cells, and (c) measuring concomitant viral transcriptional activity in resting CD4+ T cells. The latency process was also repeated using H80 supernatant as alternative to cell-to-cell contact conditions.

extract_protocol:
Cell samples were stored in RNALater at the time of collection. Once all samples, from week 0 to week 10, were collected, total RNA extraction was performed using Illustra RNAspin mini isolation kit (GE Healthcare) and further processed for mRNA-Seq library preparation (TruSeq RNA sample prep kit, Illumina – that starts with capture of polyA-containing transcripts), followed by cluster generation (TruSeq single-end cluster generation kit, Illumina) and high-throughput sequencing on Illumina HiSeq2000 at the Genomics Technology Facility, University of Lausanne. Addition of RNA spike-ins were also added according to manufacturer's instructions (ERCC Exfold RNA Spike-in Mixes, Life Technologies and Loven et al.)
total RNA extraction was performed using Illustra RNAspin mini isolation kit (GE Healthcare) and further processed for mRNA-Seq library preparation (TruSeq RNA sample prep kit, Illumina – that starts with capture of polyA-containing transcripts), followed by cluster generation (TruSeq single-end cluster generation kit, Illumina) and high-throughput sequencing on Illumina HiSeq2000 at the Genomics Technology Facility, University of Lausanne. Addition of RNA spike-ins were also added according to manufacturer's instructions (ERCC Exfold RNA Spike-in Mixes, Life Technologies and Loven et al.)

treatment_protocol: We included pharmacological and immunological agents that affect HIV transcriptional activity by different mechanisms of action and that are currently under clinical consideration. Specifically, we used a histone deacetylase inhibitor (vorinostat or SAHA, 0.5 µM), a DNA methylation inhibitor (5′-azacytidine, 1 µM), an alcohol dehydrogenase inhibitor (disulfiram, 0.5 µM). All drugs were suspended in dimethyl sulfoxyde (DMSO), thus DMSO was used as a negative control (of note, final DMSO concentration was 0.0033% corresponding to 1∶30,000 dilution). We also used immunological stimulation by interleukin-7 cytokine (100 ng/ml), and a full TCR stimulation using anti-CD3/anti-CD28 antibodies in presence of interleukin-2. At 8 h and 24 h after treatment, cells were analyzed for GFP expression by FACS and for transcriptome composition as described below.

tag: Stage

value: reactivation

tag: cell infection

value: mock

tag: treatment time

value: TCR (anti-CD3/anti-CD28/IL-2)


title: mock_disu_24h

value: disulfiram


title: T298PT


title: mock_disu_8h


title: mock_SAHA_24h

value: SAHA


title: T297PT


title: mock_SAHA_8h


title: mock_DMSO_8h

value: DMSO (neg control)


title: mock_DMSO_24h


title: HIV_antiCD3_24h

value: HIV vector


title: mock_antiCD3_24h


title: T596PT


title: mock_antiCD3_72h


title: T655PT


title: HIV_IL-7_24h

value: Interleukin-7 (IL-7)


title: T57LyM


title: HIV_IL-7_8h


title: HIV_antiCD3_8h


title: HIV_disu_24h


title: HIV_aza_8h


title: HIV_disu_8h


title: HIV_aza_24h


title: T735PT


title: T57LiM

source_name: Liver


title: HIV_SAHA_8h


title: T569PT


title: ZUMA-0047-0048

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

description: Tests on paired end sequencing

data_processing:
NSUMA technique is described in (Jordà, 2017) PMID:27999094
Pre-processing. Sequences were obtained from the Illumina instruments as fastq
Mapping. Paired-end reads were locally aligned against the hg19 canonocal chromosomes (22 autosomal, 2 sex) using bowtie2-2.2.6 with the -q --local --phred33 --sensitive-local  --no-discordant  --no-unal flags.
Post-processing. Primary aligned reads from concordant pairs (unaligned and discordant pairs discarded during mapping) were assigned to the NSUMA canonical universe using featureCounts from subread-1.5.1 with the following flags:  -F SAF -f -O -a slois_amplicons.saf –primary.
Genome_build: hg19
Supplementary_files_format_and_content: fastq, read counts (text files)

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a  Illumina Hi-Seq 2000instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits.

value: Blood


title: HIV_antiCD3_72h


title: T173PT


title: HIV_DMSO_8h


title: mock_week_10

value: latency

value: 10 weeks


title: HIV_week_8

value: 8 weeks


title: T456PT

value: Mixed


title: HIV_week_6

value: 6 weeks


title: mock_week_8


title: mock_week_6


title: T433PT

value: Ptenf/f

value: Primary Tumor


title: HIV_week_4

value: 4 weeks


title: mock_week_4


title: HIV_SAHA_24h

value: reactivation


title: HIV_week_2

value: 2 weeks


title: T326PT


title: HIV_week_0


title: T104PT


title: mock_week_2

value: mock


title: T410PT


title: Mock_week_0


title: T173LyM


title: ZUMA-0045__LoVo

description: NSUMA technique to assess the methylation status of Alu repeats

data_processing:
NSUMA technique is described in: PMID:27999094
Pre-processing. Reads sequences were obtained from the Illumina instruments in qseq format and were pre-processed in different steps in order to remove misleading reads and improve the mapping accuracy. Bases at the 3’ end of the reads with low quality (PHRED score <= 2) were end clipped. The adapters sequence used in the PCR amplification were also removed using iterative searches of 5’ to 3’ fragments. Ambiguous bases (Ns) at both ends of the read were also removed. Finally, reads shorter than 10 bp or with more than 30% of ambiguous bases were filtered out from the analysis.
Mapping. Once trimmed and cleaned, reads were mapped to the human reference genome (build GRCh37/hg19) with Bowtie 0.12.7 using the following parameters: -S –p 8 –v 2 –phred64-quals –best –l 28 –k 2. The value of option v is the number of mismatches allowed.
Post-processing. Once mapped, ambiguous reads (those that are mapped in several genome locations) were disambiguated when the number of mismatches allowed the assignment of a unique position in the human genome with a higher probability, otherwise they were rejected. Reads mapped in unknown chromosome were annotated as chrUn (scaffolds and contigs which could not be placed on chromosomes) and excluded from further analyses. The unambiguous reads (including uniquely mapped reads) were selected for further analysis. The information was stored using the standard SAM/BAM format. Counting of reads in regions of interest (NSUMA universe) was performed using coverageBed of the bedtools suite 2.16.2
Genome_build: hg19
Supplementary_files_format_and_content: qseq, coverage text files

source_name: LoVo

growth_protocol: Human embryonic stem cells: HUES (MEF conditioned), matrigel, trypsin subculture. Keratinocytes from human foreskin: HUES (MEF conditioned), matrigel, trypsin subculture. Differentiated cells (K1,K2, K3, MMTA): EpiLife+supplements, Tryp-LE Express subculture. Colorectal cancer cell lines: Human colon cancer cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA). All cell lines were grown in DMEM:F12 medium plus 10% heat-inactivated FBS, L-glutamine and pyruvate (Invitrogen)

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer II or Illumina Hi-Seq 2000instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits. Each flow cell ran on the Genome Analyzer IIx contained a PhiX control lane (loaded at a concentration of 4pM) that was used to monitor run quality.

treatment_protocol: CaCo-2 were cultured to confluence (day 0), or for 10, 20 or 40 days post-confluence, with medium changed every second or third day.

value: Colon adenocarcinoma cell line SW480

value: cell line

tag: cell line

value: LoVo


title: ZUMA-0044__HT29

value: Colorectal carcinoma cell line HT29


title: HIV_DMSO_24h

value: HIV vector

value: DMSO (neg control)


title: ZUMA-0043__SW480_test3


title: HIV_week_10

value: latency


title: DR 26m SE Rep3 BS-seq

description: Dietary restricted

value: female

value: dietary-restricted (DR)

value: 26 months

value: liver


title: ZUMA-0042__SW480_test2

description: NSUMA technique test without ssDNA


title: T57PT

value: Mixed


title: Cpos-deficient-18hpi-replicate3

city: Durham

first: Raphael

middle: H

last: Valdivia

state: NC

address: 207 Research Drive

department: Department of Molecular Genetics and Microbiology

institute: Duke University

description: polyA RNA (eukaryotic mRNA)

data_processing:
Basecalls were performed on the sequencing instrument using RTA version 1.18.61 software
reads were demultiplexed using software bcl2fastq and trimmed with software fastq-mcf (-q 20 -x 0.5)
reads were mapped to human genome using TopHat 2.0.9 (--transcriptome-max-hits 1 --max-multihits 1)
number of reads mapped to each gene was assessed using HTSeq 0.6.1p1
normalization and differential expression analysis were carried out using the DESeq2 R package (DESeq 1.8.1, R 3.2.1)
Genome_build: GRCh38.81 (dowloaded from Ensembl on Sept 22 2015)
Supplementary_files_format_and_content: csv file including normalized read counts for each sample

source_name: endocervical epithelial cell line (A2EN cells)

growth_protocol: A2EN cells were maintained at 37°C, 5%CO2 in keratinocyte-SFM medium (Life technologies) supplemented with 10% FBS (Sigma-Aldrich) and 0.3 mM CaCl2 in 6-well tissue culture plates

extract_protocol:
Total RNA was isolated using the RNeasy Mini Plus kit (Qiagen) including an additional on-column DNase treatment, as described in the manual of the RNeasy Mini kit (Qiagen).
Sequencing libraries were prepared using the Kapa Stranded mRNA-Seq kit (Kapa Biosystems)

treatment_protocol: 6 h or 18 h prior to RNA extraction cells were infected by addition of the indicated Chlamydia strain (20 inclusion-forming units/cell) followed by centrifugation (1500 x g, 30 min, 23°C)

tag: infection group

value: infected with CpoS-deficient C .trachomatis

tag: infection time

tag: replicate


title: ZUMA-0041__SW480_test1

description: NSUMA technique est without purification beads


title: WT_PRO3

description:
control
RawCounts.csv
RPKMedgeR.csv

value: Wild Type

value: Normal


title: Cpos-deficient-18hpi-replicate2

description: polyA RNA (eukaryotic mRNA)


title: WT_PRO2

description:
control
RawCounts.csv
RPKMedgeR.csv


title: WT_PRO1

description:
control
RawCounts.csv
RPKMedgeR.csv


title: Cpos-deficient-6hpi-replicate3

description: polyA RNA (eukaryotic mRNA)

value: 6 h


title: Cpos-deficient-6hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: Wildtype-18hpi-replicate2

description: polyA RNA (eukaryotic mRNA)

value: infected with wild-type C .trachomatis


title: Wildtype-18hpi-replicate3

description: polyA RNA (eukaryotic mRNA)


title: Wildtype-18hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: Wildtype-6hpi-replicate3

description: polyA RNA (eukaryotic mRNA)


title: Wildtype-6hpi-replicate2

description: polyA RNA (eukaryotic mRNA)


title: Uninfected-6hpi-replicate2

description: polyA RNA (eukaryotic mRNA)

value: uninfected


title: Uninfected-18hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: Uninfected-6hpi-replicate3

description: polyA RNA (eukaryotic mRNA)


title: AML8_LMPP_99L

city: New York

first: Stephen

middle: Shiu-Wah

last: Chung

state: NY- NEW YORK

address: 1275 York Avenue, Box 443

department: Leukemia Service

institute: Memorial Sloan Kettering Cancer Center

data_processing:
trim_glaie (trimming adaptor sequences)
picard (remove duplicates)
htseq_count (read numbers for each gene)
paired analysis of CD99 high and low from same population in each patient (t-test)

source_name: AML blasts

growth_protocol: Cryopreserved primary AML specimens were thawed, and CD99 high and low (top and bottom 10%, respectively) expressors were FACS-purified from either the bulk (CD45 low SSC low) or leukemic stem cell enriched LMPP/MLP fraction (CD34+CD38-CD45RA+CD90-).

extract_protocol:
FACS-purified cells were lysed in Trizol LS, from which RNA extractions were performed.
Libraries were prepared using SMARTer amplification

value: Primary AML cells

tag: leukemia fraction

value: Bulk (CD45 low SSC low)

tag: cd99 expression

value: Bottom 10%


title: AML6_LMPP_99L

value: LMPP/MLP (CD34+CD38-CD45RA+CD90-)


title: AML7_LMPP_99H

value: Top 10%


title: Uninfected-6hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: AML8_LMPP_99H


title: AML7_LMPP_99L


title: Uninfected-18hpi-replicate3

description: polyA RNA (eukaryotic mRNA)


title: AML4_LMPP_99H


title: AML6_LMPP_99H


title: AML5_LMPP_99L


title: AML3_LMPP_99L


title: AML5_LMPP_99H


title: AML4_LMPP_99L


title: AML3_LMPP_99H


title: Cpos-deficient-18hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: WT_PRO4

description:
control
RawCounts.csv
RPKMedgeR.csv

tag: tissue


title: AML2_LMPP_99H


title: Cpos-deficient-6hpi-replicate2

description: polyA RNA (eukaryotic mRNA)


title: AML1_LMPP_99L


title: Wildtype-6hpi-replicate1

description: polyA RNA (eukaryotic mRNA)


title: Uninfected-18hpi-replicate2

description: polyA RNA (eukaryotic mRNA)


title: AML6_Bulk_99H


title: AML1_LMPP_99H


title: AML5_Bulk_99L


title: AML6_Bulk_99L


title: AML4_Bulk_99H


title: AML4_Bulk_99L


title: AML2_Bulk_99H


title: AML1_Bulk_99H


title: AML2_Bulk_99L


title: AML1_Bulk_99L


title: Hu_Afib_ex

city: Taipei

first: Mai-Yi

last: Fan

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

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were aligned to hg19 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: dermal fibroblast of adult skin cultured in E16.5 skin extract

growth_protocol: All fibroblasts and DP cells were expanded and cultured in DMEM with 10% FBS

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

treatment_protocol: Fibroblasts were cultured with the indicated E16.5 skin extract (2 μg/ml) for 3 days.

value: dermal fibroblast of adult skin

value: male

tag: passages


title: AML3_Bulk_99H


title: AML2_LMPP_99L


title: Hu_DP

source_name: hair follicle dermal papilla of adult skin


title: Y-55-30617697

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

description: FINAL_master_list_of_genes_counts_MIN.RNA_Pooling_Experiment_29_samples.highExp.txt

data_processing:
Basecalls performed using CASAVA
Alignment using STAR 2.4.1d
Normalized using PORT (https://github.com/itmat/Normalization), v0.8-beta for fibroblast and IMR, v0.7.5-beta for stem
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files

source_name: Stem cell

growth_protocol: Subcutaneous abdominal adipose tissues were excised from informed and consented donors during abdominoplasties (University of Pennsylvania IRB approval Protocol number 812150).  The tissues were immediately transferred to the laboratory on ice.  Adipose tissue were dissected from skin and stored at -70oC until ASC isolations.  ASCs were isolated from 29 tissue samples of female individual between 24 to 39 years, according to a protocol described in (Percec, Stem Cells International 2015).  Fibroblasts were isolated from 7 procured specimens of female donors with age between 25 and 64, using the method described in (Huschtscha et al., 2012).

extract_protocol:
ASCs and fibroblasts were detached from culture plates by trypsin digestion at confluence and cell numbers were counted using Countess Automated Cell Counter (Invitrogen, Carlsbad, CA).  Approximately 500,000 cells from each sample were collected and frozen at -80oC until RNA isolation.  Total RNA was extracted from the cells using TRIzol (Thermo Fisher Scientific, Grand Island, NY) and quality was examined by electrophoresis.
Poly (A)+RNA were isolated from the total RNA samples using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA).  RNA-seq libraries were generated for each sample from 1 ug of mRNA using the NEBNext Ultra Directional RNA Library Prep Kit with NEBNext® Multiplex Oligos for Ilumina according to the manufacture’s protocol (New England Biolabs, Ipswich, MA).  Size distribution of the libraries was determined using the Agilent Bioanalyzer High Sensitivity Chip on Agilent Bioanalyzer 2100 (Santa Clara, CA).  The concentration of the libraries were quantified by quantitative PCR using the the KAPA SYBR® FAST ABI Prism qPCR Kit and Applied Biosystems® 7500 Real-Time PCR System (Thermo Fisher Scientific, Grand Island, NY).  The libraries were pooled and diluted to 1.8 pM with sequencing reagents from the Illumina NextSeq 500/550 High Output kit and sequenced on the NextSeq 500 desktop sequencer (Illumina Inc., San Diego, CA)

value: Stem cell

tag: age


title: X-52-30344430


title: Hu_Afib

source_name: dermal fibroblast of adult skin


title: Z-53-30637609


title: V-33-30339426


title: Input_CTCF_Pool3

city: Kowloon

first: Jian

last: Yan

address: 83 Tat Chee Ave

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq
Genome_build: hg19

growth_protocol: Mouse embryonic stem cell lines E14 and Mll3/4 double knockout were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.

extract_protocol:
The ChIP-seq has been carried out as previously described6,7. Briefly, 2 million cells were crosslinked with 1% formadehyde for 10 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit.
TruSeq

value: C-terminal Flag tagging of SP1, pool 3


title: Input_CTCF_Pool2

value: C-terminal Flag tagging of SP1, pool 2


title: U-40-30348412


title: T-50-30355433


title: R-64-30625665


title: Input_CTCF_Pool1

value: C-terminal Flag tagging of SP1, pool 1


title: S-27-30639611


title: AML5_Bulk_99H


title: Flag_CTCF_Pool2

value: C-terminal Flag tagging of SP1, clone 2


title: Flag_CTCF_Pool1

value: C-terminal Flag tagging of SP1, clone 1


title: Flag_CTCF_Pool3

value: C-terminal Flag tagging of SP1, clone 3


title: AML3_Bulk_99L


title: P-39-30345425


title: O-37-30336420


title: M-50-30351437


title: L-33-30622637


title: N-35-30339427


title: I-34-30613727


title: J-24-30330415


title: K-42-30613728


title: H-49-30628647


title: F-48-30345427


title: G-41-30625666


title: W-53-30616706


title: E-64-30336421


title: D1-61-30640612


title: C-39-30640611


title: C1-47-30622638


title: B-44-30352423


title: siControl P2

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

data_processing:
RNA-Seq reads were first mapped to the human genome hg19 using TopHat2 (Kim et al., 2013).
Raw read counts for each gene were quantified by using featureCounts software (Liao et al., 2014) that uses GENCODE v.22 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Genes with counts below 5 for at least 2 samples out of 3 within each group were filtered out. Then the counts were normalized toward the common library size. The count data were assumed to follow a negative binomial distribution.
To improve the estimate of over-dispersion and to identify genes differentially expressed between samples, R package DESeq2 (Love et al., 2014) was used to estimate the smoothed over-dispersion parameters and to calculate p-values with Wald test for group comparison under a generalized linear model. The p-value cut-offs were determined by controlling the mean number of false positives (Gordon et al., 2007).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized abundance measurements

source_name: thyroid primary cells

growth_protocol: Human primary thyroid cells were cultured in 6H medium after digested from the fresh thyroid tissue. 6H medium was made from modified F-12M medium (Coon’s modification of Ham’s F-12 medium) by adding 5% Heat Inactivated FBS, 2 mM Glutamine, 2.6 g/l NaHCO3, 5 ug/ml gentamicin, 1% NEAA and six nutrition factors: 10mU/ml TSH, 10 mU/ml Insulin, 1 nM Hydrocortisone, 2 ng/ml Glycyl-Histidyl-L-Lysine Acetate, 5µg/ml Transferrin and 10ng/ml Somatostatin.

extract_protocol:
The total RNA samples for RNA-seq were extracted by TRIzol reagent (Invitrogen) and then treated byDNase-1 (Ambion) in order to eliminate the DNA contamination. Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (catalog #RS-122-2201) was used to transform RNA into cDNA after removing rRNA and mitochondrial RNA. The RNA-seq libraries were prepared according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary cells were electroporated by Nucleofector®II device (Amaxa) with 75pmol Human FOXE1 siRNA (ON-TARGET plus SMART pool) or negative control siRNA (ON-TARGET plus control pool)  in 100μl of Basic Nucleofector Medium for Primary Mammalian Epithelial Cells (Lonza, VPI-1005) for each well of 6-well plates. Cells were then resuspended in 6H medium, incubated for 24 hours and used for further analysis.

tag: cultured stage

value: thyroid primary cells on Day 5

tag: sirnas target genes

value: nontumorous fresh thyroid tissue


title: siControl P1


title: Q-30-30616705

tag: cell type


title: siFOXE1 P2


title: siFOXE1 P1


title: siControl P3


title: IMR-90_p55-33420507

description: FINAL_master_list_of_genes_counts_MIN.IMR-90_PORT.txt


title: A1-43-30345426


title: siFOXE1 P3


title: A-42-30353428


title: IMR-90_p19-33429497


title: 259-34-33423513

description: FINAL_master_list_of_genes_counts_MIN.Fibroblasts_PORT.txt

source_name: Fibroblasts

value: Fibroblasts


title: 257-32-33429496


title: 254-64-33409572


title: 244-27-33422502


title: 247-59-33434476


title: D-63-30332398


title: Input_ChIPseq

data_processing:
Basecalls performed using Illumina NextSeq 500
ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings
Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using SICER version 1.1 with the following setting:Threshold for redundancy allowed for ChIP reads(1),window size(200bp) ,FDR cutoff(1E-10)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file

extract_protocol:
LK cells were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Protein-DNA complexes were isolated with specific antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.

tag: strain

value: Bone Marrow

value: BM-derived Lin-Kit+ cells


title: 242-58-33426499


title: 245-25-33426501


title: SMC1A_KO_ChIPseq


title: RAD21_WT_ChIPseq


title: RAD21_KO_ChIPseq


title: ASXL1_WT_ChIPseq


title: SMC1A_WT_ChIPseq


title: DLYM-1117

status: Public on Feb 23 2017

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
TopHat v1.4.1
Cuffdiff
Genome_build: canfam3.1
Supplementary_files_format_and_content: matrix of fpkm values per sample

organism: Canis lupus familiaris

source_name: lymphoma

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits

tag: tumor

value: tumor

tag: phenotype

value: T cell

tag: breed

value: Golden Retriever

tag: gender (neuter status)

value: M

tag: age (yr) at diagnosis


title: DLYM-1111

value: MN


title: DLYM-1102

value: B cell


title: DLYM-1007


title: DLYM-1020


title: DLYM-1014


title: DLYM-1113

value: FS


title: DLYM-1021

value: F


title: DLYM-0905


title: 255-25-33409574


title: DLYM-0904


title: DLYM-0802


title: DLYM-0902

value: B-cell


title: DLYM-0801


title: 252-53-33426503


title: DLYM-0702


title: DLYM-0602


title: DLYM-0601

value: T-cell


title: DLYM-0603


title: DLYM-0405


title: DLYM-0404


title: DLYM-0908


title: DLYM-0401


title: DLYM-1112


title: DLYM-0302


title: DHSA-1203

source_name: hemangiosarcoma

value: abdominal mass, metastatic

value: Lab/Husky Mix


title: DHSA-0908

value: abdominal mass

value: Boxer


title: DLYM-0903


title: DLYM-0102


title: DHSA-1112

value: spleen

value: Portuguese Water Dog


title: DHSA-1114


title: DHSA-1106


title: DHSA-1202


title: DHSA-1109

value: heart


title: DHSA-1110

value: tumor

value: metastatic tumor


title: DHSA-1111

value: Golden Retriever


title: DLYM-0701


title: DHSA-1103


title: DHSA-1016

value: M


title: DLYM-0504


title: DLYM-0502


title: DLYM-0501

value: T cell


title: DHSA-1014


title: DHSA-1015

value: liver

value: Wolf Mix


title: DHSA-1010


title: DHSA-1011

value: FS


title: DHSA-1009

value: German Shepherd Dog


title: DHSA-1008


title: DHSA-1007

value: Gordon Setter


title: DHSA-1006


title: DHSA-0910

value: Keeshond

value: MN


title: DHSA-1107


title: DHSA-1108

value: Labrador retriever


title: DHSA-1017

value: Briard

value: F


title: DHSA-0909

value: spleen


title: DHSA-0805


title: DHSA-0803

value: heart


title: DHSA-0906

value: tumor


title: DHSA-0903


title: DHSA-0905


title: DHSA-0804


title: DHSA-0907

value: Portuguese Water Dog


title: DHSA-1113

value: Saluki


title: DHSA-1013

value: Labrador Retriever


title: DHSA-1002

value: Golden Retriever


title: DHSA-0702

value: Bullmastiff


title: DHSA-0606


title: DHSA-0605

value: undetermined histogenic origin


title: DHSA-0602


title: DHSA-0604


title: DHSA-0601


title: DHSA-0603

value: FS


title: CHAD-P9

value: M


title: CHAD-G6


title: CHAD-G8


title: CHAD-G3


title: CHAD-G4


title: DHSA-0501

value: Bernese Mountain Dog


title: CNOB

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000> and masked genes with length <200
Genome_build: CanFam3
Supplementary_files_format_and_content: matrix of fpkm values per sample

source_name: osteoblast

extract_protocol:
total RNA was extracted using Thermo Fisher TotalRNA kit
TruSeq RNA v2
average insert size of 200 selected

value: osteoblast

tag: tumor type

value: cell line


title: OSCA.8

source_name: bone tumor

value: bone tumor


title: CHAD-B7

value: Border Collie Mix

value: MN


title: DHSA-0701

value: cutaneous

value: Bichon Frise


title: DOS.90

value: tumor


title: DOS.85


title: DOS.84


title: DOS.81


title: DOS.76


title: DOS.75


title: DOS.78


title: OSCA.78


title: DOS.8


title: DOS.6M

value: metastasis


title: DOS.73


title: DOS.6


title: DOS.70


title: DHSA-0502

value: spleen

value: F


title: DOS.57

value: Golden Retriever


title: DOS.46.2


title: DOS.32


title: DOS.46


title: DOS.37


title: DOS.24


title: DOS.114


title: DOS.28


title: DOS.112


title: DOS.116


title: DOS.11


title: DOS.105


title: DOS.115


title: DOS.113


title: DOS.101


title: DOS.111


title: DOS.56


title: P72L

city: Shanghai

first: Kunshan

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Clean reads were aligning to rn5 with TopHat2 (Kim et al., 2013). Gene expression levels were estimated by Cufflinks (Ghosh and Chan 2016). Genome DNA sequence and gene annotation were download from UCSC genome browser.
Genome_build: rn5
Supplementary_files_format_and_content: BED format file that annotate novel lncRNAs. Tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: cerebral ischemia_left_brain tissue

extract_protocol:
Total RNA was extract by standard TriZol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

tag: gender

value: male

tag: time point

value: after 24 hrs of middle cerebral artery occlusion (MCAO)

value: brain tissue

tag: side

value: Left


title: P71L


title: P52R

source_name: cerebral ischemia_right_brain tissue

value: Right


title: P45L


title: P61L


title: P45R


title: P52L


title: 120min Total LTP 3

city: Los Angeles

first: Patrick

last: Chen

address: 615 Charles E. Young Dr. S.

department: Biological Chemistry

institute: UCLA

description: Total RNA

data_processing:
raw sequencing output files (.bcl) were demultiplexed and adaptors were trimmed using the default BaseSpace apps (GenerateFASTQ)
fastq files were aligned to mm10 using STAR aligner with default parameters
HTS-seq was used to count aligned fragments/reads. For paired-end reads, if one read of a fragment is aligned that was counted. Read counts were normalized by the trimmed mean method for each time point before differential expression analysis.
FDR values for differential expression of counts between corresponding LTP/basal replicates was calculated using edgeR with default parameters.
What we deemed significant was an FDR < 0.1 and a log2FC of +0.4. This was done independently for each gene for TRAP-seq and RNA-seq results.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with normalized counts and raw read numbers for each replicate in both TRAP-seq and RNA-seq, fold-changes between expression levels of corresponding LTP/basal replicates, and FDR values from edgeR for the indicated time point

source_name: Acute hippocampal slice

extract_protocol:
Tissue was flash frozen in crushed dry ice, followed by homogenization in TRAP homogenization buffer. Debris was pelleted, RNA was extracted from 10% of the homogenate at this step using a combined Trizol/kit purification while the remaining homogenate was incubated with anti-HA agarose beads overnight at 4C. Beads were washed, followed by removal of RNA from beads with vortexing in buffer RLT from Qiagen RNEasy Micro Kit. This was followed by the standard RNEasy kit protocol.
rRNA was first depleted with RiboZero Gold, followed by standard Illumina TruSeq library prep
Libraries were made from both TRAP and total RNA, for all basal and LTP samples, for each time point on the same day with the same master mix of reagents. All samples at a given time point were processed, multiplexed, and sequenced together.

value: Acute hippocampal slice

value: 120 minutes post-induction


title: P71R


title: DOS.110

value: bone tumor


title: 120min Total basal 3

description: Total RNA


title: 120min Total LTP 2

description: Total RNA


title: 120min Total LTP 1

description: Total RNA


title: P61R


title: 120min Total basal 2

description: Total RNA


title: 120min TRAP LTP 3

description: TRAP RNA

data_processing:
Library strategy: TRAP-Seq
raw sequencing output files (.bcl) were demultiplexed and adaptors were trimmed using the default BaseSpace apps (GenerateFASTQ)
fastq files were aligned to mm10 using STAR aligner with default parameters
HTS-seq was used to count aligned fragments/reads. For paired-end reads, if one read of a fragment is aligned that was counted. Read counts were normalized by the trimmed mean method for each time point before differential expression analysis.
FDR values for differential expression of counts between corresponding LTP/basal replicates was calculated using edgeR with default parameters.
What we deemed significant was an FDR < 0.1 and a log2FC of +0.4. This was done independently for each gene for TRAP-seq and RNA-seq results.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with normalized counts and raw read numbers for each replicate in both TRAP-seq and RNA-seq, fold-changes between expression levels of corresponding LTP/basal replicates, and FDR values from edgeR for the indicated time point
For this time point, there is a probable artifact when comparing between basal and LTP samples; Lars2, Mir6236, Rn45s show differential expression but this is likely due to a difference in rRNA depletion. When using this data, filter out the reads belonging to these genes or disregard these genes.


title: DOS.100


title: P72R


title: 120min TRAP basal 1

description: TRAP RNA


title: 60min Total LTP 3

description: Total RNA

value: 60 minutes post-induction


title: 120min TRAP basal 3

description: TRAP RNA


title: 120min TRAP basal 2

description: TRAP RNA


title: 60min Total LTP 1

description: Total RNA


title: 60min Total basal 3

description: Total RNA


title: 120min TRAP LTP 1

description: TRAP RNA


title: 60min Total LTP 2

description: Total RNA


title: 120min TRAP LTP 2

description: TRAP RNA


title: 60min Total basal 1

description: Total RNA


title: 60min TRAP LTP 3

description: TRAP RNA

data_processing:
Library strategy: TRAP-Seq
raw sequencing output files (.bcl) were demultiplexed and adaptors were trimmed using the default BaseSpace apps (GenerateFASTQ)
fastq files were aligned to mm10 using STAR aligner with default parameters
HTS-seq was used to count aligned fragments/reads. For paired-end reads, if one read of a fragment is aligned that was counted. Read counts were normalized by the trimmed mean method for each time point before differential expression analysis.
FDR values for differential expression of counts between corresponding LTP/basal replicates was calculated using edgeR with default parameters.
What we deemed significant was an FDR < 0.1 and a log2FC of +0.4. This was done independently for each gene for TRAP-seq and RNA-seq results.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with normalized counts and raw read numbers for each replicate in both TRAP-seq and RNA-seq, fold-changes between expression levels of corresponding LTP/basal replicates, and FDR values from edgeR for the indicated time point


title: 60min TRAP basal 2

description: TRAP RNA


title: 60min TRAP basal 3

description: TRAP RNA


title: 60min Total basal 2

description: Total RNA


title: 30min Total LTP 2

description: Total RNA

value: 30 minutes post-induction


title: 30min Total LTP 3

description: Total RNA


title: 30min Total LTP 1

description: Total RNA


title: 60min TRAP LTP 1

description: TRAP RNA


title: 60min TRAP LTP 2

description: TRAP RNA


title: 60min TRAP basal 1

description: TRAP RNA


title: 120min Total basal 1

description: Total RNA


title: 30min Total basal 3

description: Total RNA


title: 30min Total basal 2

description: Total RNA


title: 30min TRAP LTP 2

description: TRAP RNA


title: 30min Total basal 1

description: Total RNA


title: 30min TRAP basal 3

description: TRAP RNA


title: 30min TRAP LTP 1

description: TRAP RNA


title: 30min TRAP LTP 3

description: TRAP RNA


title: 30min TRAP basal 2

description: TRAP RNA


title: 30min TRAP basal 1

description: TRAP RNA


title: S3 rep3

city: Shenyang

first: xue

last: zhou

state: Liaoning

address: No. 120, Dongling Road, Shenhe District

department: Department of Horticulture

institute: Shenyang Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The gene expression level was calculated by using RPKM method.
Genome_build: http://brassicadb.org/brad/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Brassica rapa subsp. pekinensis

source_name: Chinese cabbage

growth_protocol: The seeds were sowed in the greenhouse after vernalization.

extract_protocol:
Total RNA was isolated from fertile and sterile flower buds using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA quality and DNA contamination was monitored by electrophoresis on 1% agarose gels. RNA concentration was measured using the Qubit RNA Assay Kit and a Qubit 2.0 Flurometer (Life Technologies, Carlsbad, CA, USA). Finally, RNA integrity was assessed using the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bud

tag: genotype

value: sterile


title: S2 rep2

tag: tissue


title: S1 rep1


title: F1 rep1

value: fertile


title: F2 rep2


title: Neuro_H3K27me3_Rep2_TCLSeq

city: Stanford

first: Mark

middle: A

last: Zarnegar

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: Native chromatin TCL-seq using 1,000 cells

data_processing:
Sequence reads were generated by Illumina's NextSeq500 platform.
MCF7 reads were aligned to the hg19 genome using Bowtie 1.1.2 with the following parameters: (-5 = 15; -e = 40; -v = 2; -m = 1). Neurosphere reads were aligned to the mm9 genome using Bowtie 2.2.6.2 using -very-fast-local.
Samtools was used to convert and/or filter alignements to BAM files containing all reads with MAPQ > 1
BAM files were then used with Deeptools bamCoverage to produce normalized (RPKM) BigWig signal tracks using 100 bp bins.  Reads were extended to 500 bp.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: BigWig files contain RPKM nnormalized genome-wide signals generated with bamCoverage verison 2.3.6.0.  Scores were calculated using 100 bp bins after extending reads to 500 bp.

source_name: Neurosphere cells

growth_protocol: MCF7 were grown according to ATCC instructions. To produce neurospheres, mice (Black6 from a mixed C57Bl6 and B6C3 background) were euthanized by CO2, decapitated, and their brains immediately removed. The subventricular zone (SVZ) was micro-dissected and stored in ice-cold PBS for further processing. The tissue was digested using Liberase DH (Roche) and DNase I (250 U ml−1) at 37 °C for 20 min followed by trituration. Digested tissue was washed in ice-cold HBSS without calcium and magnesium, filtered through a 40-μm filter and FACS-sorted as Lineage−CD24− cells into neurosphere growth media that is, Neurobasal-A (Invitrogen) supplemented with Glutamax (Life Technologies), 2% B27-A (Invitrogen), mouse recombinant epidermal growth factor (EGF; 20 ng ml−1) and basic fibroblast growth factor (bFGF; 20 ng ml−1) (Shenandoah Biotechnology). Lineage cells were depleted using mouse CD45, CD31, and Ter119 (Biolegend).

extract_protocol:
For ChIP samples,unfixed cells were clarified after enzymmatically digesting and lysing cells, then histone-DNA complexes were isolated with antibody. For TCL samples, cells were permeablized and treated with restriction enzymes to fragment chromatin, then diluted with lysis buffer.  Antibody-adapter complexes were added to chromatin fragment solution, then a ligation mix was added to facilitate proximity ligation of the antibody bound adapter.  DNA was puried and ligated DNA was amplified prior to library construction.
Libraries were prepared with Illumina's NEXTERA DNA prep kit (FC-121-1031)

value: brain

value: Brain-derived neurosphere cells

tag: chip antibody

value: H3K27me3 (Active Motif #39155)


title: F3 rep3


title: Pollen_bioreplicate_5

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
Illumina software was used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were filtered for reads 18-28 nt in size, only genome matching reads retained (UEA small RNA tool v 2.5.0 used)
Only small RNAs that perfectly match the genome are reported
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

organism: Arabidopsis thaliana

source_name: pollen

growth_protocol: Plants were grown on soil in 18 hour long days at 23C

extract_protocol: For the Inflorescence libraries, total RNA was extracted using Trizol reagent and enriched using a the MirVana microRNA isolation kit. For the pollen libraries sRNA enrichment was performed through gel purification and elution of the fraction containing the 20-26 nt range as determined by a sRNA size marker (miRNA Ladder,New England Biolabs). For the IP libraries, small RNAs were extracted from proteins using Trizol LS. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit.

tag: ecotype

tag: genotype/variation

value: wild type

value: mature pollen

tag: molecule subtype

value: small RNA


title: Neuro_H3K4me3_Rep2_TCLSeq

tag: cell type

value: H3K4me3 (Abcam ab8580)


title: Pollen_bioreplicate_3


title: Neuro_H3K36me3_Rep2_TCLSeq

value: H3K36me3 (Abcam ab9050)


title: Neuro_H3K27me3_Rep1_TCLSeq


title: Neuro_H3K36me3_Rep1_TCLSeq


title: MCF7_H3K4me3_Rep1_TCLSeq

description: Native chromatin TCL-seq using 2,000 cells

source_name: Breast cancer cells

tag: cell line

value: breast


title: MCF7_200_H3K27ac_Rep2_TCLSeq

description: Native chromatin TCL-seq using 200 cells

value: H3K27ac (Active Motif #39133)


title: MCF7_2K_H3K27ac_Rep2_TCLSeq

description: Native chromatin TCL-seq using 2000 cells


title: MCF7_400_H3K27ac_Rep1_TCLSeq

description: Native chromatin TCL-seq using 400 cells


title: MCF7_2K_H3K27ac_Rep1_TCLSeq


title: MCF7_10K_H3K27ac_Rep1_TCLSeq

description: Native chromatin TCL-seq using 10,000 cells


title: MCF7_10K_H3K27ac_Rep2_TCLSeq


title: MCF7_H3K27me3_Rep1_TCLSeq


title: MCF7_400_H3K27ac_Rep2_TCLSeq


title: MCF7_H3K36me3_Rep2_TCLSeq


title: Neuro_H3K4me3_Rep1_TCLSeq


title: MCF7_H3K27me3_Rep3_TCLSeq


title: DHSA-0904

tag: tumor

value: tumor

value: heart

value: Golden Retriever

value: M


title: Pollen_bioreplicate_4


title: MCF7_H3K4me3_Rep2_TCLSeq


title: MCF7_200_H3K27ac_Rep1_TCLSeq


title: MCF7_H3K27me3_Rep2_ChIPSeq

description: Native chromatin ChIP-seq using 1 million cells


title: MCF7_H3K27ac_Rep1_ChIPSeq


title: MCF7_H3K36me3_Rep2_ChIPSeq


title: MCF7_H3K27me3_Rep1_ChIPSeq


title: MCF7_H3K36me3_Rep1_TCLSeq


title: mv411_input_Rx

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: input sample for background measurement

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: MLL-AF4 rearranged acute myeloid leukemia

growth_protocol:
RPMI, 10% FBS
MV4;11 cells (obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin. ENL-FKBP(F36V)-expressing MV4;11 cells were selected with 2 µg/mL puromycin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

treatment_protocol: ENL-FKBP(F36V) was degraded with addition of 500 nM dTAG-13 (final DMSO concentration of 0.01%). Control treatments were performed with 0.01% DMSO

value: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)

tag: input

tag: treatment

tag: sequencing barcode

value: TCAGATTC

tag: antibody

tag: antibody manufacturer

tag: antibody catalog number


title: mv411_dTAG_6h_CDK9_Rx

description: Chromatin IP against CDK9

value: 0.01% DMSO, 500 nM dTAG-13 for 6 hr

value: TCTCACGG

value: Santa Cruz


title: MCF7_H3K36me3_Rep1_ChIPSeq


title: mv411_DMSO_6h_AFF4_Rx

description: Chromatin IP against AFF4

value: 0.01% DMSO for 6 hr

value: TTGGTATG

value: Abcam


title: mv411_DMSO_24h_pSer2_Rx

description: Chromatin IP against RNA Pol II pSer2

value: 0.01% DMSO for 24 hr

value: ATCACGTT

value: RNA Pol II pSer2

value: Active Motif


title: mv411_DMSO_6h_CDK9_Rx

description: Chromatin IP against CDK9

value: GGCACAAC


title: MV411_H3K18ac

description: Chromatin IP against H3K18ac

value: GTGCTACC

value: Millipore


title: mv411_dTAG_24h_pSer2_Rx

description: Chromatin IP against RNA Pol II pSer2

value: 0.01% DMSO, 500 nM dTAG-13 for 24 hr

value: CGATGTTT


title: mv411_dTAG13_96h_r3

description: RNA-seq after 96 hr dTAG-13 (500 nM) treatment

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: ENL_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

growth_protocol: MV4;11 (Cas9; ENL-FKBP(F36V); ENL -/-) cells (MV4;11 parent cell line obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin.

extract_protocol:
Prior to RNA isolation, cell were counted and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)

treatment_protocol: Cell were treated with 500 nM dTAG-13 (0.1% DMSO final concentration) for 8, 24, or 96 hours; 500 nM EPZ-5676 (0.1% DMSO final concentration) for 96 hours; or DMSO (0.1%) for 24 or 96 hours

value: MV4;11 (Cas9; ENL-FKBP(F36V); ENL-/-)

tag: bar code

value: GGCTAC


title: MV411_H3K9ac

description: Chromatin IP against H3K9ac

value: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)

value: GGTTGGAC


title: mv411_dTAG13_96h_r2

value: TAGCTT


title: mv411_dTAG13_8h_r2

description: RNA-seq after 8 hr dTAG-13 (500 nM) treatment

value: CAGATC


title: MOLM13_input

description: input sample for background measurement

source_name: MLL-AF9 rearranged acute myeloid leukemia

value: TAGTGACT


title: mv411_dTAG13_8h_r3

value: CTTGTA


title: mv411_dTAG13_96h_r1

value: GATCAG


title: mv411_dTAG13_8h_r1

value: GCCAAT


title: mv411_dTAG13_24h_r2

description: RNA-seq after 24 hr dTAG-13 (500 nM) treatment

value: TGACCA


title: mv411_dTAG13_24h_r3

value: ACAGTG


title: MCF7_H3K27ac_Rep2_ChIPSeq

value: breast

value: H3K27ac (Active Motif #39133)


title: mv411_dTAG13_24h_r1

value: CGATGT


title: MOLM13_ENL

description: Chromatin IP against ENL

value: TTGGAGGT

value: ENL

value: Cell Signalling


title: mv411_dTAG_6h_AFF4_Rx

description: Chromatin IP against AFF4

value: 0.01% DMSO, 500 nM dTAG-13 for 6 hr

value: TGAACTGG

value: Abcam


title: mv411_EPZ5676_96h_r3

description: RNA-seq after 96 hr EPZ-5676 (500 nM) treatment

value: MV4;11 (Cas9; ENL-FKBP(F36V); ENL-/-)

value: CGTACG


title: mv411_EPZ5676_96h_r2

value: GTTTTG


title: mv411_DMSO_96h_r1

description: RNA-seq after 96 hr DMSO (0.1%) treatment

value: ATCACG


title: mv411_DMSO_96h_r2

value: TTAGGC


title: mv411_EPZ5676_96h_r1

value: GTGGCC


title: mv411_DMSO_24h_Pol2_Rx

description: Chromatin IP against RNA Pol II

value: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)

value: 0.01% DMSO for 24 hr

value: TAGTCGTG

value: RNA Pol II

value: Diagenode


title: mv411_DMSO_24h_r3

description: RNA-seq after 24 hr DMSO (0.1%) treatment

value: ATTCCT


title: mv411_DMSO_24h_r1

value: GAGTGG


title: mv411_DMSO_24h_r2

value: ACTGAT


title: mv411_H3K4me3

description: Chromatin IP against H3K4me3

growth_protocol: MV4;11 cells (obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin. ENL-FKBP(F36V)-expressing MV4;11 cells were selected with 2 µg/mL puromycin

treatment_protocol: ENL-FKBP(F36V) was degraded with addition of 500 nM dTAG-13 (final DMSO concentration of 0.1%). Control treatments were performed with 0.1% DMSO

tag: input sample

tag: growth protocol

value: RPMI, 10% FBS

value: TCCAGTCG

value: Millipore


title: mv411_DMSO_96h_H3K79me2

description: Chromatin IP against H3K79me2

value: 0.1% DMSO for 96 hr

value: TCTCACGG

value: abcam


title: mv411_dTAG_96h_H3K79me2

description: Chromatin IP against H3K79me2

value: 0.1% DMSO, 500 nM dTAG-13 for 96 hr

value: TCAGGAGG


title: mv411_H3K27ac

description: Chromatin IP against H3K27ac

value: TGTATGCG


title: mv411_ENL

description: Chromatin IP against ENL

value: TAAGCTTT

value: ENL

value: Cell Signalling


title: mv411_input

description: input sample for background measurement

value: GGCTACAG


title: MOLM13.POL2_sgENL5

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers

growth_protocol: Cells were maintained in RPMI with 10% FBS, 5% CO2, 37oC.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.

treatment_protocol: For Flag-tagged stable cell selection, 10 ug/ml blasticidin was used for stable cells selection. For iCas9 induced ENL CRISPR knockout, 1ug/ml of doxycycline was used for induction of 5days before collecting for ChIP.

value: ENL Knock Down

value: Santa Cruz sc-899X


title: MOLM13.POL2-S2P_sgENL1

value: abcam ab5095


title: MOLM13.POL2-S2P_sgENL5


title: MOLM13.POL2-S2P_sgGFP

value: Control


title: ZUMA-0051__h_KiPS4F1

description: NSUMA technique to assess the methylation status of Alu repeats

data_processing:
NSUMA technique is described in (Jordà, 2017) PMID:27999094
Pre-processing. Reads sequences were obtained from the Illumina instruments in fastaQ or qseq format and were pre-processed in different steps in order to remove misleading reads and improve the mapping accuracy. Bases at the 3’ end of the reads with low quality (PHRED score <= 2) were end clipped. The adapters sequence used in the PCR amplification were also removed using iterative searches of 5’ to 3’ fragments. Ambiguous bases (Ns) at both ends of the read were also removed. Finally, reads shorter than 10 bp or with more than 30% of ambiguous bases were filtered out from the analysis.
Mapping. Once trimmed and cleaned, reads were mapped to the human reference genome (build GRCh37/hg19) with Bowtie 0.12.7 using the following parameters: -S –p 8 –v 2 –phred64-quals –best –l 28 –k 2. The value of option v is the number of mismatches allowed.
Post-processing. Once mapped, ambiguous reads (those that are mapped in several genome locations) were disambiguated when the number of mismatches allowed the assignment of a unique position in the human genome with a higher probability, otherwise they were rejected. Reads mapped in unknown chromosome were annotated as chrUn (scaffolds and contigs which could not be placed on chromosomes) and excluded from further analyses. The unambiguous reads (including uniquely mapped reads) were selected for further analysis. The information was stored using the standard SAM/BAM format. Counting of reads in regions of interest (NSUMA universe) was performed using coverageBed of the bedtools suite 2.16.2
Genome_build: hg19
Supplementary_files_format_and_content: qseq, text files

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer II or Illumina Hi-Seq 2000 instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits. Each flow cell ran on the Genome Analyzer IIx contained a PhiX control lane (loaded at a concentration of 4pM) that was used to monitor run quality.

value: Human induced pluripotent stem cells (iPSCs) from hair

tag: tissue

value: iPSC

tag: source

value: Hair-derived


title: ZUMA-0005__hES_r1

value: Human stem cells (hESC)

value: cell line


title: mv411_DMSO_96h_r3

value: MV4;11 (Cas9; ENL-FKBP(F36V); ENL-/-)

value: ACTTGA


title: ZUMA-0037__K3

value: Human keratinocytes cell line K3

value: Keratinocyte-derived


title: ZUMA-0046__h_KiPS4F1


title: ZUMA-0038__CaCO2_wt

value: Colon adenocarcinoma cell line CaCO2 wt


title: ZUMA-0036__K1

value: Human keratinocytes cell line K1


title: ZUMA-0040__CaCO2_20d

value: Colon adenocarcinoma cell line CaCO2 differentiation time course:day 20


title: ZUMA-0039__CaCO2_11d

value: Colon adenocarcinoma cell line CaCO2 differentiation time course:day 11


title: ZUMA-0035__MMTA

source_name: MMTA

value: Human keratinocytes cell line MMTA


title: ZUMA-0032__KiPS4F1

value: Human induced pluripotent stem cells (iPSCs) from foreskin

value: Foreskin-derived


title: mv411_ENL_FKBP

description: Chromatin IP against HA tag of ENL-FKBP(F36V)

value: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)

value: RPMI, 10% FBS

value: TAAGTTCG

value: preconjugated anti-HA beads

value: Pierce


title: ZUMA-0031__ES6

value: Human stem cells (hESC)

value: cell line


title: ZUMA-0030__ES2


title: MOLM13.H3K79me3_sgGFP

value: control

tag: chip antibody

value: Abcam ab2621


title: MOLM13.POL2_sgGFP

value: Control

value: Santa Cruz sc-899X


title: MV411.F-ENL.Flag

value: Sigma F1804


title: MOLM13.H3K79me3_sgENL5

value: ENL-KO


title: Col_AGO1-IP_2

description: small RNA

source_name: unopened flower buds

growth_protocol: Plants were grown on soil in 18 hour long days at 23C.

extract_protocol: For the Inflorescence libraries, total RNA was extracted using Trizol reagent and enriched using a the MirVana microRNA isolation kit. For the pollen libraries  sRNA enrichment was performed through gel purification and elution of the fraction containing the 20-26 nt range as determined by a sRNA size marker (miRNA Ladder,New England Biolabs). For the IP libraries, small RNAs were extracted from proteins using Trizol LS. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit.

tag: genotype

value: wild type

value: unopened flower buds

tag: sample type

value: total small RNAs

tag: ecotype background


title: ago1_Pollen

description: small RNA

value: pollen


title: ddm1_AGO1-IP_1

description: small RNA


title: ddm1_AGO1-IP_2

description: small RNA


title: Col_Pollen_2

description: small RNA


title: ZUMA-0017__hES_r2

tag: cell type


title: MV411.ENL-F59A_Flag

tag: cell line

value: F59A mutation


title: Col_Inflorescence

description: small RNA


title: Col_AGO1-IP_1

description: small RNA


title: MV411.ENL-Y78A_Flag

value: Y78A mutation


title: HeLa.ENL_Flag

source_name: HeLa

growth_protocol: Cells were maintained in DMEM with 10% FBS, 5% CO2, 37oC.

value: HeLa


title: ZUMA-0033__KiPS4F8

value: Human induced pluripotent stem cells (iPSCs) from foreskin

value: iPSC

value: Foreskin-derived


title: MOLM13.H3K79me2_sgENL5

value: abcam ab3594


title: MOLM13.H3K79me2_sgGFP

value: control


title: Col_Pollen_1

description: small RNA


title: SW1116-Vector

city: Dalian

first: Jinsong

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

data_processing:
alignment: TopHat v2.0.14 using default settings
expression levels: Cufflinks v2.2.1, Cuffdiff and Cuffnorm using default settings
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: control, SW1116 cells

extract_protocol:
DMEM medium were removed, PBS was washed three times, and RNA was harvested using Trizol reagent. RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We used Ajuba OE and Vector virus to infect SW-1116 cells.

value: colorectal cancer line SW1116

tag: genotype/variation


title: SW1116- AJUBA OE

source_name: AJUBA OE, SW1116 cells

value: AJUBA OE


title: WKY rep3

city: Singapore

first: Enrico

last: Petretto

address: 8 College Road, Level 8

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke‐NUS Graduate Medical School

data_processing:
Illumina Casava1.7 software used for basecalling
Reads were pre-processed by in silico conversion of C bases to T bases in read 1 and G bases to A bases in read 2 and the first base of all reads removed
Alignment was via BWA 0.6.1 with 3' end quality trimming using -I -t 8 -q 20 parameters. Reads 1 & 2 were mapped to in silico bsulfite converted rn4 references
unmethylated phage lambda control DNA was used to assay bisulfite conversion efficiency
Following alignment we removed CpG sites where less than 50% of the samples contain reads
split the WGBS data into chunks where distance between last CpG in one chunk & the 1st CpG in the next chunk is greater than 3,000bp
Genome_build: rn4
Supplementary_files_format_and_content: [Processed_Data.tar.bz2] Compressed directories, one per chromosome containing the preprocessed data split into chunks ready to be used by our software (see biorxiv http://dx.doi.org/10.1101/041715)

source_name: WKY, macrophages

growth_protocol: Primary bone marrow-derived macrophages from WKY and Lewis rats were cultured exactly as described in PMID 18443593

extract_protocol:
WKY and Lew genomic DNA was extracted from macrophages using the Qiamp DNA  mini kit (Qiagen, UK) according to manufacturers instructions
DNA libraries were produced as described in PMID: 22870857, with the following modifications: DNA was bisulfite converted using the epitect bisulfite kit (qiagen) and bisulfite converted libraries were purified by use of Agencourt AMPure XP beads

treatment_protocol: DNA from macrophages was extracted without any treatment distinct from that used in derivation

tag: strain

value: WKY

tag: disease state

value: glomerulonephritis

value: Primary macrophages

tag: age


title: WKY rep4


title: WKY rep2


title: Lewis rep4

source_name: Lewis, macrophages

value: Lewis


title: MV411.POL2_Control

tag: treatment

value: Control

tag: antibody

value: Santa Cruz sc-899x


title: MV411.Input


title: MV411.H3K9ac

value: Active motif,  61251


title: Lewis rep2


title: Input DNA – Control Replicate 2

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

description:
antibody: none
siControl-B-Input

data_processing:
Raw fastq files containing reads from HiSeq Illumina 2500, single-end reads
Reads were aligned using Bowtie on human hg19 release, with default settings
Output files (SAM format) were converted into BAM files and indexed using the SAMTools program
Peak calling was performed with Sicer software with a window of 200 nt and a gap of 600 nt (cut off 10-3 p-value) ,normalized by corresponding “inputs “files
Genome_build: hg19
Supplementary_files_format_and_content: 1 wig file (final yH2AX profile on hg19), 1 bed file (peaks related to profile)

source_name: Primary fibroblast transformed with hTERT and SV40 early region

growth_protocol: Cells were grown in DMEM media supplemented with 10% fetal calf serums

extract_protocol:
Lysates were clarified from sonicated nuclei and yH2AX-DNA complexes were isolated with antibody.
Libraries were prepared according to standards Illumina's instructions. yH2AX antibody from Abcam (ab2893), rabbit polyclonal

treatment_protocol: Cells were transfected for 72 hrs with either siControl or siTRF2

value: BJ-HELT

tag: transfection

value: siControl

value: human foreskin fibroblast


title: Input DNA – siTRF2 Replicate 1

description:
antibody: none
siTRF2-A-Input


title: Input DNA – siTRF2 Replicate 2

description:
antibody: none
siTRF2-B-Input


title: MOLM13.Input


title: MOLM13.POL2_Control


title: MOLM13.H3K9ac

value: Active motif  #61251


title: MOLM13.H3K4me3

value: Abcam, ab8580


title: Input DNA – Control Replicate 1

description:
antibody: none
siControl-A-Input


title: TRF2 downregulation Replicate 2

description:
antibody: yH2AX antibody (Abcam;ab2893)
siTRF2-B-γH2AX


title: MOLM13.H3K4me1

value: Abcam, ab8895


title: MV411.H3K27ac

value: Abcam, ab4729


title: Lewis rep3

value: control


title: MOLM13.H3K27ac


title: WKY rep1


title: TRF2 downregulation Replicate 1

description:
antibody: yH2AX antibody (Abcam;ab2893)
siTRF2-A-γH2AX


title: Control situation Replicate 2

description:
antibody: yH2AX antibody (Abcam;ab2893)
siControl-B-γH2AX


title: MOLM13.ENL-Y78A_Flag

value: Y78A mutation

value: Flag M2, Sigma F3165


title: MOLM13.ENL-F59A_Flag

value: F59A mutation


title: Control situation Replicate 1

description:
antibody: yH2AX antibody (Abcam;ab2893)
siControl-A-γH2AX


title: MOLM13.CDK9_ENLKO

value: ENL Knock Down

value: Santa Cruz, sc-484


title: Lewis rep1

value: Lewis

value: Primary macrophages


title: CE1_Del_clone3_TSS1

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

data_processing:
Reads were aligned to the reference human genome (build hg19) with Bowtie2 2.2.9.
Reads per million for each HindIII fragment were calculated using r3Cseq 1.18.0 and normalized using DESeq2 1.14.
Statistical analysis for differential interactions between genotypes were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files include average reads per HindIII fragment normalized by DESeq2 in wildtype samples, deletion samples, and the differential signal between deletion and wild-type samples. Bed files include HindIII fragments with significant difference in normalized read counts between genotypes as generated by DESeq2.

extract_protocol:
3C DNAs were digested with a second restriction enzyme, DpnII, religated, and purified using Qiagen PCR purification columns. The circularized DNA was amplified using inverse PCR and nested inverse PCR reactions with primers in the anchor HindIII-DpnII fragment. PCR products were used to prepare indexed sequencing libraries. Twelve to fourteen libraries were pooled in one lane for 50 bp single-end deep sequencing (Illumina HiSeq2500).
4C libraries were prepared for sequencing using standard Illumina protocols

value: Transformed B lymphoblastoid cells

value: NEK6 CE1 homozygote


title: MOLM13.CDK9_Control

value: Control


title: CE1_Del_clone3_CE1


title: CE1_Del_clone2_TSS1


title: HT29 RPL27 siRNA

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

institute: Psomagen Inc

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: colorectal cancer cell line

growth_protocol: HCT116 and HT29 cell lines were cultured with RPMI media

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

treatment_protocol: 15nM of NC siRNA and RPL9, RPL17, RPL27 siRNA transfected with lipofectamine 2000. 48h after transfection cell's total RNA was harvested

value: colon

value: colorectal cancer cell line

value: RPL27 siRNA treated


title: CE1_Del_clone2_CE1


title: HT29 RPL17 siRNA

value: RPL17 siRNA treated


title: HT29 RPL9 siRNA

value: RPL9 siRNA treated


title: CS2-4_Del_clone3_TSS1

value: NEK6 CS2-4 homozygote


title: HCT116 RPL27 siRNA


title: CE1_WT_clone1_TSS1

value: NEK6 CE1 wild-type


title: CE1_WT_clone2_CE1


title: HT29 NC siRNA

value: Negative control siRNA treated


title: HCT116 RPL9 siRNA


title: CS2-4_WT_clone2_TSS1

value: NEK6 CS2-4 wild-type


title: CS2-4_Del_clone3_CE1


title: HCT116 RPL17 siRNA