title: CAR005

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam
Genome_build: ASM1938v1
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values

organism: Escherichia coli ATCC 8739

source_name: CAR005 strain

growth_protocol: Single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm for 5 h.

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CRISPR_screen_THP-1 Day7- Biorep 1

status: Public on Sep 06 2017

type: SRA

city: Princeton

first: Trinna

middle: L.

last: Cuellar

state: New Jersey

address: Lewis Thomas Lab, Washington Rd/MOF223C

department: Molecular Biology

country: USA

institute: Princeton University

library_source: genomic

data_processing:
Library strategy: DNA sgRNA-Amplicon-Seq
Reads exactly matching gRNAs were counted by a custom script
Genome_build: N/A
Supplementary_files_format_and_content: Excel file including ncounts

molecule: genomic DNA

organism: Homo sapiens

source_name: THP-1 Cells

growth_protocol: Cells were grown in RPMI + 10%FBS + 1X L-glutamine. Puromycin selection was at 1ug/ml.

extract_protocol:
At each time-point, cells were spun down, washed with PBS, flash frozen on dry ice, and genomic DNA was harvested with Qiagen DNeasy Kits and sgRNAs were amplified by PCR. The ~221 bp sgRNA products were isolated.
NGS libraries were prepared with NuGen Ovation low complexity kits, followed by PCR amplification for 6 cycles. 6pM of samples were sequenced on an Illumina MiSeq with reagent kit v3 for 150 cycles.

treatment_protocol: THP-1 cells were transduced with the sgRNA library and an MOI of 0.3. Cells were selected with 1ug/ml 2 days post-transduction. Cells were kept at a 1000X coverage, at least 6X10^6 cells in every flask.

tag: tissue

value: Blood

tag: cell line

tag: disease

value: Acute Myelogenous Leukemia


title: IspG1

country: China

library_source: transcriptomic

molecule: total RNA

source_name: IspG1 strain

tag: strain


title: H-cow_liver2

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

description: Songpan,Sichuan,China,3000m altitude

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to respective genome of the species using Tophat 2.0.11.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Galgal4, UMD3.1, Suscrofa 10.2, Oar_v3.1 and CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Bos grunniens

source_name: liver

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The dUTP based strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols; Strand-specific mRNA-Seq

tag: altitude

value: high

value: liver

tag: age

value: adult(>4 years old)


title: CRISPR_screen_THP-1 Day7- Biorep 3


title: H-cow_spleen1

description: Songpan,Sichuan,China,3000m altitude

source_name: spleen

value: spleen


title: H-sheep_heart2

description: Songpan,Sichuan,China,3000m altitude

organism: Ovis aries

source_name: heart

value: heart

value: adult(>3 years old)


title: H-cow_liver1

description: Songpan,Sichuan,China,3000m altitude


title: H-cow_kidney2

description: Songpan,Sichuan,China,3000m altitude

source_name: kidney

value: kidney


title: rng-interrupted mutant 5 min

city: Madrid

first: Alejandra

middle: Leticia

last: Bernardini

state: Madrid

address: Darwin 3

country: Spain

institute: Centro Nacional de Biotecnología

data_processing:
The trimming and the quality filtering was performed using Fastq_trimmer and Alien_trimmer. The procedure consisted of removing the first 10 bp of all sequences, removing adapters (with no mismatches and with at least 10 bp), removing reads shorter than 30 bp and keeping reads with at least 28 of c quality.
The processed .fastq data files were analyzed using Rockhopper to map reads against the reference genome SMD457 and to obtain the values of gene expression.
The RNA-sequencing data were normalized as the total number of reads mapped to a CDS, and divided by the length of the CDS in kilobases. Rockhopper normalize the expression levels by the upper quartile of gene expression, giving data equivalent to RPKM.
Genome_build: NC_017671
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Stenotrophomonas maltophilia

source_name: Bacteria culture at exponential growth

growth_protocol: Luria Bertani medium at 37ºC 250 rpm until 0,6 OD (600 nm)

extract_protocol:
RNA was extracted every 5 min after rifampicin addition. Five ml samples obtained at any given time were spun down for 20 min at 6,000xg, 4°C and pellets were immediately frozen on dry ice and stored at −80°C. Total RNA was extracted and cleaned up using the RNeasy mini-kit (Qiagen).
Duplicated RNAs from each strain and each time point were pooled. RNA samples (3,5 µg each) were rRNA depleted with RiboZero (Epicentre). RNA was then subjected to RNA library prep using the Ultra Directional RNA Library Prep Kit (Cat no. E7420S, New England Biolabs) following manufacturer recommendations. Libraries were pooled and fragments with lengths between 200 and 500 bp were purified from agarose gels. Remaining adaptor dimers were cleaned with AMPure XP beads (Beckma-Coulter). Libraries were sequenced in a Miseq system (Illumina) using a v3 cartridge and a 150 bp, single-read format at the Parque Científico de Madrid.

treatment_protocol: 200 mg/l of rifampicin was added at cultures at time 0 min

tag: genotype

value: miniTn5 rng-interrupted

tag: time after rifampicin added

value: 5 min


title: rng-interrupted mutant 10 min

value: 10 min


title: WT 15 min

value: wild type

value: 15 min


title: H-cow_kidney3

description: Songpan,Sichuan,China,3000m altitude


title: WT 5 min


title: WT 10 min


title: G4H14

source_name: G4H14 strain


title: H-cow_kidney1

description: Songpan,Sichuan,China,3000m altitude


title: WT 0 min

value: 0 min


title: CRISPR_screen_THP-1 Day 21- Biorep 3


title: Thrombin + SB + AG Replicate 3

status: Public on Sep 05 2017

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

data_processing:
QuadTrim was used for quality trimming of RNA-sequencing reads. Raw reads with Q-score greater than 20 (>Q20) were retained for further analysis.
High quality filtered reads were aligned to the human reference genome (hg19) using Bowtie v2.2.4 and TopHat v2.1.1
Uniquely mapped reads were then used for counting reads using HTSeq
The genes differentially expressed between the different treatments were identified using edgeR v3.0.7, a Bioconductor package of R statistical environment.
This method uses a Poisson distribution to model genic read counts following normalization based on size factors and variance, therefore this software allows normalization of RNA-sequence data based on sequencing depth GC content and gene length for analysis of differentially expressed genes. Differentially expressed genes were defined with log2FC of >0.7 or <-0.7 significant at p value <0.01 (FDR 0.05)
Genome_build: STRING (v10.0) (http://string-db.org), a publically available online database of functional interaction was used to identify gene ontology analysis and networks, the differentially expressed genes were analysed.

source_name: CASMCS (Lonza Cat No. CC-2583, Lot No. 0000317155)

growth_protocol: Human CASMCS (purchased from Lonza Cat No. CC-2583, Lot No. 0000317155). Cells were grown in DMEM (5mM glucose, 10% FBS and 1% antibiotics at 37⁰C in 5% CO2) and were seeded in 60 mm dishes.

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
mRNA library preparation followed the manufacturer’s instructions (Ion Chip Sequencing Kit - Thermo Fisher Scientific).
QuadTrim was used for quality trimming of RNA-sequencing reads. Raw reads with Q-score greater than 20 (>Q20) were retained for further analysis. High quality filtered reads were aligned to the human reference genome (hg19) using Bowtie v2.2.4 and TopHat v2.1.1 [40, 41]. Uniquely mapped reads were then used for counting reads using HTSeq.

treatment_protocol: Cells were grown to confluence then rendered quiescent by serum deprivation for 48 hours. Inhibitors to TGFBR1 (SB431542 10µM) and EGFR (AG1478 5µM) were pre-incubated for 30 mins prior to treatment with thrombin (10 units/ml) for 6  hours.

tag: cell type

value: Coronary Artery Smooth Muscle Cells

tag: treatment

value: Thrombin + SB431542 + AG1478


title: Thrombin + SB + AG Replicate 2


title: cold-tolerant rice

city: Porto Alegre

first: Janette

middle: Palma

last: Fett

state: Rio Grande do Sul

address: Avenida Bento Gonçalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
All low quality reads (FASTq value < 13) were removed, and 3p and 5p adapter sequences were trimmed using Genome Analyzer Pipeline (Fasteris). The remaining low quality reads with ‘n’ were removed using a Python script. After cleaning the data (low quality reads, adapter sequences), the mRNAseq data from the two libraries were aligned to the rice genome using the software Bowtie version 0.12.7. Only sequences with up to two mismatches to the rice reference genome (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/) were used. The SAM files from Bowtie were then processed using Python scripts to assign the frequencies of each read and map them onto references. For data normalization, the scaling normalization method (Robinson et al. 2010) was used.  The R package EdgeR (Robinson et al. 2010) was used to calculate the adjusted p-value.
Robinson MD, McCarthy DJ, Smyth GK (2010) EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/
Supplementary_files_format_and_content: Please note that the identifiers are in the “all.seq.gz” reference genome file.

organism: Oryza sativa Indica Group

source_name: leaves

growth_protocol: Seeds from both selected genotypes were germinated for five days in distilled water and then planted into soil and grown in a greenhouse (temperature range from 20 to 30 °C, full daylight).

extract_protocol:
Total RNA was extracted from rice leaves of nine plants using Concert Plant RNA Reagent (Invitrogen) and treated with DNase I (Invitrogen).
Approximately 20 µg of total RNA was used in high-throughput cDNA sequencing by Illumina HiSeq 2000 technology (Fasteris SA, Plan-les-Ouates, Switzerland - http://www.fasteris.com/). We constructed an individual single-end cDNA library for each rice genotype. The cDNA libraries were prepared according to Illumina’s protocols. Briefly, RNAseq was performed using the following successive steps: poly-A purification; cDNA synthesis using a poly-T primer, shotgun method to generate inserts of approximately 500 bp; 3p and 5p adapter ligations; pre-amplification; colony generation; and Illumina single-end 100 bp sequencing.

treatment_protocol: At the three-leaf stage (approximately 20 days), plants were transferred to a climatic chamber and maintained at 10 °C for 6 h (light intensity of 40 µmol m-2 s-1).

tag: phenotype

value: cold-tolerant

value: leaves


title: Thrombin + SB + AG Replicate 1


title: Thrombin + AG1478 Replicate 1

value: Thrombin + AG1478


title: rng-interrupted mutant 15 min


title: Thrombin + SB431542 Replicate 2

value: Thrombin + SB431542


title: Thrombin Replicate 3

value: Thrombin


title: Thrombin Replicate 1


title: Thrombin + SB431542 Replicate 3


title: Thrombin + SB431542 Replicate 1


title: Basal Replicate 2

value: Basal


title: Thrombin Replicate 2


title: Basal Replicate 3


title: Basal Replicate 1


title: cold-sensitive rice

value: cold-sensitive


title: H2AZac_ChIPseq_VCaP_rep2

city: Darlinghurst

first: Fatima

last: Valdes Mora

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie (version 1.0.1), allowing up to three mismatches. Non-uniquely alignable reads were excluded.
Peaks were called using PeakRanger (version 1.16) with peak size set to broad and with input control set to a pooled control LNCaP or VCaP input.
Bigwig files were generated using a scaling factor of 1,000,000 reads/library size, average fragment length of 300 and duplicates removed.
ChromHMM v.1.10 was used to simultaneoulsy partition the genome of PrEC and LNCaP cell lines into states. The same approach was employed for the VCaP cell line. Redundant states were then collapsed into seven distinct states and manually annotated by comparison to the published ChromHMM model for HMEC cells.
Genome_build: hg19
Supplementary_files_format_and_content: bed file format

source_name: Human cell line

growth_protocol: PrEC cells were growth and maintained in  PrEGM media (Cambrex) at 37ºC with 5% CO2; LNCaP cells were growth and maintained in T-medium (Gibco) and 10% fetal bovine serum (FBS)  at 37ºC with 5% CO2. When reached 70-80% confluence cell were fixed with 1% formaldehyde for 10 min at room temperature.

extract_protocol:
ChIP assays were carried out according to the manufacturer’s protocol (Upstate Biotechnology). Briefly, ~ 2 x 10^6 cells were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibodies specific for Histone H2AZ (Active motif # 39113), acetylated Histone H2AZ (Abcam #ab18262), H3K4Me1 (Active Motif #39297), H3K27ac (Active Motif #39133), H3K9K14ac (Millipore #06-599.) and H3K36Me3 (Abcam ab9050-100). Ten µl of antibody was used for each immunoprecipitation. No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 ul H2O.
TruSeq ChIP sample prep kit

treatment_protocol: Human LNCaP or VCaP prostate cancer cells and were maintained in RPMI Medium 1640 (Gibco), or DMEM media 11995 (Gibco), respectively, and supplemented with 10% fetal bovine serum (FBS) for at least 72 hrs to 70-80% confluence. LNCaP cell were then seeded to 2.5x10^6 cell per 15cm dish and starved for 3 days in RPMI Medium 1640-no-phenol red (Gibco)  and 5% chracoal stripped FBS (CSFBS). Then LNCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 2h, 4h and 16h.  VCaP cell were then seeded to 2.5x10^6 cell per 15cm dish and starved for 3 days in DMEM media 11995 (Gibco)  and 2.5% chracoal stripped FBS (CSFBS). Then VCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 16h. Cells were then fixed with 1% formaldehyde for 10 min at room temperature.

value: VCaP (ATCC # CRL-2876). Androgen-sensitive human prostate adenocarcinoma cells

tag: passage number

tag: chip antibody

value: Abcam Cat #ab18262


title: H2AZac_ChIPseq_VCaP_DHT_16hr


title: H2AZac_ChIPseq_VCaP_Ethanol


title: H2AZac_ChIPseq_VCaP_input


title: H2AZac_ChIPseq_VCaP_rep1


title: PO1P14S

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description:
1139-7
Stranded mRNA-seq

data_processing:
Raw FASTQ files from the sequencing were processed in Illumina BaseSpace to filter reads with a q score < 30.
Alignment was performed to version mm10 of the mouse genome and annotated to RefSeq (5-2-16) using the Bowtie2 algorithm.
BAM files were downloaded into Partek Flow (Partek, Inc., St Louis, MO) for data summarization, quantification, and normalization of RNA counts into total reads per kilobase of gene model per million reads (RPKM).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .alignments.counts.txt: Tab-delimited text files include counts for each sample; abundance measurements.
Supplementary_files_format_and_content: *.alignments.rpkm: Tab-delimited text files include RPKM values for each sample; normalized abundance measurements.

organism: Mus musculus

source_name: Somatosensory cortex, p53 KO, saline

extract_protocol:
Somatosensory cortex was removed from mice on postnatal day 7, flash frozen on dry ice, and RNA extracted using Trizol reagent followed by RNeasy (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: IP injection of ethanol or saline.

tag: strain/background

tag: genotype/variation

value: p53 KO

value: brain

tag: Sex

value: male

value: postnatal day 7

value: Saline


title: PM1P16S

description:
1139-14
Stranded mRNA-seq

source_name: Somatosensory cortex, WT, EtOH

value: WT

value: EtOH


title: PM1P18S

description:
1139-5
Stranded mRNA-seq


title: PM1P6S

description:
1139-1
Stranded mRNA-seq

source_name: Somatosensory cortex, WT, saline


title: PQ1P9S

description:
1139-13
Stranded mRNA-seq


title: Thrombin + AG1478 Replicate 3

value: Coronary Artery Smooth Muscle Cells


title: PL1P13S

description:
1139-10
Stranded mRNA-seq

source_name: Somatosensory cortex, p53 KO, EtOH


title: Thrombin + AG1478 Replicate 2


title: rng-interrupted mutant 0 min

value: miniTn5 rng-interrupted

value: 0 min


title: PJ1P13S

description:
1139-8
Stranded mRNA-seq


title: PE1P17S

description:
1139-4
Stranded mRNA-seq


title: PJ1P5S

description:
1139-9
Stranded mRNA-seq


title: LM1P8S

description:
1139-3
Stranded mRNA-seq


title: LB1P19S

description:
1139-12
Stranded mRNA-seq


title: mESC_4suSeq_UNT_rep3

city: Oxford

first: Vincenzo

last: Di Cerbo

address: South Parks Road

country: United Kingdom

institute: University of Oxford

description:
4sUseq_MERGE_plusStrand.bw
4sUseq_MERGE_minusStrand.bw
4sU-Seq_raw_counts.txt

data_processing:
RNA-seq paired-end reads were initially aligned against the rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment using the STAR RNA-seq aligner (Dobin et al., 2012). To improve mapping of nascent, intronic sequences, reads which failed to map using STAR were aligned against the genome using bowtie2 and reads which mapped more than once were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009).   For calibrated nuclear RNA-seq experiments, in which a spikein D. melanogaster S2 cell line was mixed with mES cells prior extraction, alignements were made against concatenated genomes (mm10+dm6) or concatenated rRNA genomic sequences (GenBank: BK000964.3 and M21017.1), following the same procedure described above. For "input" genomic DNA, alignment against concatenated mm10+dm6 genomes was performed using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options and non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools.
Raw read counts from at least biological triplictes were calculated using custom scripts for a custom-built, non-redundant mm10 gene set.
Read count normalization and differential expression analysis for nuclear RNA-seq were performed in R (v 3.3.0) using the DESeq2 package (Love et al., 2014). Briefly, dm6 counts were used to quantify sizeFactors for subsequent differential expression analysis of raw fragment counts at mm10 RefSeq transcripts. Normalized counts were extracted from the DESeq2 object for each sample and each gene and used in subsequent analysis to calculate FPKM values. FPKM were calculated based on an average library size, due to the nature of already normalized counts. Log2FoldChange counts were extracted from the DESeq2 results table. Significantly differentially expressed genes were defined as having and adjusted p value less than 0.01 and a fold change in expression of at least 1.5x.
Genome_build: mm10, dm6
Supplementary_files_format_and_content: Stranded bigWig files representing genome coverage for merged biological replicates and read count results.

source_name: Embryonic stem cells, 4sU RNA-Seq

growth_protocol: Mouse embryonic stem cells containing conditional alleles for CFP1 (CFP1 fl/fl) were grown on gelatin-coated plates in DMEM (Gibco, Carlsbad, CA) supplemented with 15 % FBS, 10 ng/mL leukemia-inhibitory factor, penicillin/streptomycin, beta-mercaptoethanol, L-glutamine and non-essential amino-acids. Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider Drosophila Medium (Gibco), supplemented with 1x penicillin-streptomycin solution and 10% fetal bovine serum (Biosera) that was previously heat-inactivated at 60°C for 30 min.

extract_protocol:
4 × 10^6 cells were resuspended in 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature to isolate nuclei. Nuclei were centrifuged at 1000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer. Nuclei were then resuspended in 1mL of TriZOL reagent (ThermoScientific) according to the manufacturer’s protocol. Nuclear RNA was treated with the TURBO DNA-free Kit (ThermoScientific) and depleted for rRNA using the NEBNext rRNA Depletion Kit (NEB).   Nascent RNA sequencing was performed by pulse labelling with 4-thiouridine (4sU) as previously described (Rädle B. et al., 2013). Confluent 15 cm plates were treated with 500 µM 4sU in 10 ml culture medium for 20 min. The 4sU-containing media was then aspirated and immediately replaced with 5 ml TRIZOL (Thermo Fisher Scientific). RNA was isolated by phenol-chloroform extraction using phase lock tubes (Eppendorf) and resuspend in nuclease-free water. Total RNA aliquots were treated with 6U Turbo DNase (Ambion) and incubated at 37°C for 30 min, followed by inactivation of the DNase according to the manufacturer’s instructions. 300 μg of the resulting total RNA were incubated with 2 μg Biotin-HPDP/μg RNA in biotinylation buffer (10 mM Tris-HCl pH 7.4 and 1 mM EDTA) under rotation for 1.5 h at RT. Unincorporated biotin-HPDP was removed by chloroform/isoamylalcohol extraction. To capture biotinylated RNA, μMACS streptavidin beads (Miltenyi) were added to the RNA suspension (1 μl of beads/ μg RNA) and rotated for 15 min at room temperature prior to loading onto μMACS minicolumns. Unlabelled RNA was removed by washing three times with 900 µl of wash buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween20) pre-heated at 65°C, then three more times with wash buffer at room temperature. Biotinylated RNA was then eluted in two rounds with 100 mM DTT and purified using an RNeasy miniElute kit (Qiagen).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB), whereas gDNA libraries were prepared using NEBNext Ultra DNA Library Prep Kit (NEB). Libraries were sequenced on the Illumina NextSeq500 with 80bp paired-end reads.

treatment_protocol: CFP1 fl/fl ESCs were treated with 4-hydroxytamoxifen (TAM) for 96 h to ablate CFP1 protein levels. For 4sU-seq, CFP1 fl/fl cells were treated with 500 μM 4-thiouridine for 20 minutes prior to extraction.

value: CFP1 fl/fl (CFP1 conditional)

tag: replicate


title: mESC_4suSeq_UNT_rep2


title: mESC_4suSeq_UNT_rep1


title: mESC_gDNA_TAM_rep2

source_name: Embryonic stem cells with Drosophila S2 line (SG4) spike-in


title: mESC_gDNA_TAM_rep3


title: mESC_gDNA_UNT_rep4


title: mESC_gDNA_UNT_rep3


title: mESC_gDNA_TAM_rep4


title: mESC_gDNA_TAM_rep1


title: PP1P4S

description:
1139-18
Stranded mRNA-seq

tag: tissue


title: mESC_gDNA_UNT_rep1

tag: cell line


title: mESC_nucRNA-Seq_TAM_rep3

description:
nuclear RNA
nucRNA_TAM_MERGE_plusStrand.bw
nucRNA_TAM_MERGE_minusStrand.bw
nucRNA_seq_DeSEQ2_normalized_counts.txt


title: mESC_nucRNA-Seq_TAM_rep2


title: mESC_nucRNA-Seq_TAM_rep4


title: mESC_nucRNA-Seq_UNT_rep2

description:
nuclear RNA
nucRNA_UNT_MERGE_plusStrand.bw
nucRNA_UNT_MERGE_minusStrand.bw
nucRNA_seq_DeSEQ2_normalized_counts.txt


title: mESC_nucRNA-Seq_UNT_rep1


title: mESC_gDNA_UNT_rep2


title: mESC_nucRNA-Seq_UNT_rep4


title: mESC_nucRNA-Seq_UNT_rep3


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep1_TAM

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged when an internal calibration control was not available. ChIP-seq experiments which contained a spike-in genome (D. melanogaster) were aligned against a concatenated genome of the two genome sequences (mm10+dm6) using bowtie2  with the "--no-mixed" and "--no-discordant" options, and reads which mapped more than once were discarded. PCR duplicates were removed using samtools.
Spiking an identical concentration of D. melanogaster cells into our quantitative ChIP-seq experiments allows for calibration of each sample for IP efficiency and total mouse cell number. When comparing ChIP-seq for untreated and tamoxifen-treated cell lines using an internal calibration, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 reads in that sample. Furthermore, to adjust for variation in the dm6/mm10 ratio between biological replicates, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in each sample's input DNA.
Calibrated native H3K4me3 ChIP-seq tracks were generated using DANPOS2 (Chen et al., 2013), whereas CFP1 and T7 ChIP-seq tracks were made using the pileup function of MACS2 (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage for merged biological replicates.

source_name: Mouse embryonic stem cells with Drosophila S2 line (SG4) spike-in

extract_protocol:
ChIP sequencing for H3K4me3 in mouse ES cells was performed by calibrated native ChIP sequencing. Calibrated ChIP-seq was carried out in biological triplicate for each cell line and condition. This was achieved by adding 2.5x10^6 Drosophila S2 (SG4) cells to 10x10^6 untreated or tamoxifen treated Cfp1 fl/fl cells. Nuclei were released by resuspending the mixed cell mixture in ice cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40). Nuclei were then washed, and resuspended in 1 ml (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 1x protease inhibitors, and incubated with 100U of MNase (Fermentas) at 37°C for 5 min followed by the addition of EDTA to halt the digestion. The supernatant was collected following centrifugation at 1500 g for 5 min at 4°C. The remaining pellet was incubated with 300 ul of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x PIC) at 4°C for 1 h, then passed through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The two supernatants were combined. For each immunoprecipitation 20 µl of IPA300 agarose beads (RepliGen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton X-100). Native chromatin was then diluted 10-fold in (70 mM NaCl, 10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 1x PIC) and incubated with 20 µl of blocked beads per 1 ml of diluted chromatin at 4°C for 1 h. Beads were washed four times with native ChIP wash buffer (20 mM Tris-HCl pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100), and once with 1 ml ice cold TE buffer. DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo Research). For CFP1 and T7-SET1A ChIP-seq in ES cells, an equal number of untreated and treated cells were resuspended in 10 mL of PBS and subjected to crosslink with 1% methanol-free formaldehyde (ThermoFisher) for 10 min at 25°C and quenched with 150 mM glycine for 10 min at RT. For T7-SET1A ChIP, cells were first crosslinked in 2 uM disuccinimidyl glutarate (DSG, ThermoFisher) at 25° C for 50 mins and then 1% formaldehyde was added for 10 min at 25°C. Cells were lysed on ice for 10 min in 1 mL of lysis buffer (50 mM HEPES pH7.9, 300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x Complete EDTA-free inhibitor cocktail, 1 mM AEBSF) and then sonicated with Bioruptor Pico (Diagenode) for 20 min with 30s ON/OFF cycles (for double crosslinked chromatin, cells were sonicated for 23 min). Lysates were centrifuged for 10 min at 16000 g and the cleared chromatin was recovered and DNA quantified. For each IP, 300 ug of chromatin was diluted to 1 mL of lysis buffer and pre-cleared for 1 h at 4°C with IPA 300 resin beads (Repligen) blocked with yeast tRNA and BSA. Antibodies were then added to each IP and incubated overnight, followed by isolation of antibody-chromatin complexes with 40 uL of 50% blocked slurry beads per IP. Immunoprecipitates were washed 1x with lysis buffer, 1x with lysis buffer at 500 mM NaCl, 1x DOC buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-deoxycholate), 2x with TE pH 8. Chromatin was then eluted in 200 uL of elution buffer (1% SDS, 0.1 M NaHCO3) for 30 min at 30°C with vigorous shaking. Eluates and inputs were treated with DNase-free RNase (ThermoFisher) and crosslinks were reversed at 65 ˚C overnight with 200 mM NaCl and ProteinaseK solution (Sigma). DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo Research). For massively parallel sequencing, DNAs were post-sonicated with Bioruptor Pico (Diagenode) to a DNA fragment size of 200-300 bp as determined by Bioanalyser analysis.
Libraries were prepared with NEBNext Ultra DNA Library Prep Kit or with NEBNext EndPrep Dual Index for H3K4me3 ChIP-seq and quantified by qPCR using KAPA Illumina DNA standards as reference. Libraries were sequenced on an Illumina NextSeq500 platform.

treatment_protocol: CFP1 fl/fl ESCs were treated with 4-hydroxytamoxifen (TAM) for 96 h to ablate CFP1 protein levels.

value: In-house rabbit polyclonal α‑H3K4me3


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep2_TAM


title: mESC_Inp_CFP1-GFP_SIDmut_rep3_TAM


title: mESC_nucRNA-Seq_TAM_rep1


title: mESC_Inp_CFP1-GFP_SIDmut_rep2_TAM


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep3_UNT


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep1_UNT


title: mESC_Inp_CFP1-GFP_SIDmut_rep1_TAM


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep2_UNT


title: mESC_Inp_CFP1-GFP_SIDmut_rep2_UNT


title: mESC_Inp_CFP1-GFP_SIDmut_rep3_UNT


title: mESC_Inp_CFP1-GFP_PCmut_rep3_TAM


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep1_TAM


title: mESC_Inp_CFP1-GFP_PCmut_rep2_TAM


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep2_TAM


title: mESC_Inp_CFP1-GFP_SIDmut_rep1_UNT


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep3_TAM


title: mESC_Inp_CFP1-GFP_PCmut_rep1_TAM


title: mESC_H3K4me3_CFP1-GFP_SIDmut_rep3_TAM


title: mESC_Inp_CFP1-GFP_PCmut_rep3_UNT


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep1_UNT


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep2_UNT


title: mESC_H3K4me3_CFP1-GFP_PCmut_rep3_UNT


title: mESC_H3K4me3_CFP1-GFP_rep3_UNT


title: mESC_Inp_CFP1-GFP_PCmut_rep2_UNT


title: mESC_Inp_CFP1-GFP_rep3_TAM


title: mESC_Inp_CFP1-GFP_rep1_TAM


title: mESC_H3K4me3_CFP1-GFP_rep1_TAM


title: mESC_H3K4me3_CFP1-GFP_rep2_UNT


title: mESC_H3K4me3_CFP1-GFP_rep2_TAM


title: mESC_H3K4me3_CFP1-GFP_rep1_UNT


title: mESC_H3K4me3_CFP1-GFP_rep3_TAM


title: mESC_Inp_CFP1-GFP_rep3_UNT


title: mESC_Inp_CFP1-GFP_rep1_UNT


title: mESC_Inp_EV-GFP_rep3_TAM


title: mESC_H3K4me3_EV-GFP_rep1_TAM


title: mESC_H3K4me3_EV-GFP_rep2_TAM


title: mESC_Inp_EV-GFP_rep2_TAM


title: mESC_H3K4me3_EV-GFP_rep3_UNT


title: mESC_H3K4me3_EV-GFP_rep1_UNT


title: mESC_Inp_EV-GFP_rep1_TAM


title: mESC_Inp_CFP1-GFP_PCmut_rep1_UNT


title: mESC_Inp_CFP1-GFP_rep2_TAM


title: mESC_Inp_EV-GFP_rep2_UNT


title: mESC_Inp_EV-GFP_rep1_UNT


title: mESC_H3K4me3_EV-GFP_rep2_UNT


title: mESC_Inp_EV-GFP_rep3_UNT


title: mESC_H3K4me3_EV-GFP_rep3_TAM


title: mESC_H3K4me3_parental_rep1_TAM

description: mESC_H3K4me3_MERGED_Parental_TAM.DANPOS.bw


title: mESC_Inp_parental_rep1_TAM


title: mESC_H3K4me3_parental_rep2_UNT

description: mESC_H3K4me3_MERGED_Parental_UNT.DANPOS.bw


title: mESC_H3K4me3_parental_rep3_UNT


title: mESC_Inp_parental_rep2_TAM


title: mESC_Inp_parental_rep2_UNT


title: mESC_Inp_parental_rep1_UNT


title: mESC_Inp_parental_rep3_UNT


title: mESC_Inp_rep2_TAM


title: mESC_Inp_rep1_TAM


title: mESC_H3K4me3_parental_rep2_TAM


title: mESC_CFP1_rep1_UNT

value: In-house rabbit polyclonal α‑CFP1f


title: mESC_Inp_rep2_UNT


title: mESC_H3K4me3_parental_rep3_TAM


title: mESC_Inp_CFP1-GFP_rep2_UNT


title: mESC_CFP1_rep2_UNT


title: mESC_H3K4me3_parental_rep1_UNT


title: mESC_Inp_rep1_UNT


title: mESC_CFP1_rep1_TAM


title: mESC_CFP1_rep2_TAM


title: mESC_T7MOCK

source_name: Mouse Embryonic stem cells

value: α‑T7-Tag XP® (Cell Signaling, D9E1X)


title: mESC_T7SET1A_rep2_UNT

value: CFP1 fl/fl line, with 3xT7-Strep2 tag knockin at SET1A N-ter


title: mESC_InpT7


title: mESC_T7SET1A_rep1_TAM


title: mESC_T7SET1A_rep1_UNT


title: mESC_Inp_parental_rep3_TAM


title: C127_H3K4me_input

data_processing:
Single-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Peakcalling was performed with MACS2 using  samples in biological triplicate and input control as background.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files representing genome coverage of input and ChIP samples. Interval file with peak set for H3K4me3 in C127 cells.

source_name: Mouse mammary epithelial cell line

growth_protocol: Mouse C127 cells were grown at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Biosera) and 1x penicillin-streptomycin solution (Gibco).

extract_protocol:
H3K4me3 ChIP was performed by crosslinking cells in PBS with 1% formaldehyde for 15 min at 25˚C and was quenched with 150 mM glycine. For CFP1, KDM2B and RNAPII ChIP-seq, cells were fixed with 2 µM EGS for 1 h prior to the formaldehyde crosslinking. All ChIP-sequencing experiments were carried out as at least biological duplicate. Crosslinked cells were incubated in lysis buffer (50 mM HEPES KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA,10% Glycerol, 0.5% NP40, 0.25% TritonX-100) for 10 minutes at 4˚C. The released nuclei were then washed (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 minutes at 4˚C. Chromatin was resuspended (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na Deoxycholate, 0.5% N-lauroylsarcosine), and sonicated for 50 min using a BioRuptor sonicator (Diagenode), shearing genomic DNA into 0.5–1 kb fragments. After sonication, TritonX-100 was added to a final concentration of 1.5%. Following centrifugation at 19000 g for 10 min at 4˚C, the supernatant containing soluble chromatin was isolated from the insoluble fraction. The relevant  antibodies were incubated with 750 µl of ProteinA Dynabeads (Novex) in PBS/BSA 0.5% rotating at 4˚C for 4 h. The beads were then washed three times in PBS/BSA 0.5%, to remove unbound antibody. Prior to immunoprecipitation, chromatin was diluted (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% TritonX-100) 10-fold (or 50-fold for H3K4me3). Immunoprecipitations were performed using 1 ml of diluted chromatin per 25 µl of antibody coated beads, and rotated overnight at 4˚C. This is equivalent to 5x10^6 cells (or 1x10^6 for H3K4me3 ChIP).  The IP was then washed one time with each of the following buffers: low salt buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1% Triton X-100, 2 mM EDTA, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8, 500 mM NaCl, 1% Triton X-100, 2 mM EDTA, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8, 0.25 M LiCl, 1% NP-40, 1 mM EDTA, 1% Na-deoxycholate), followed by two washes with TE buffer. Elution was performed in 100 µl of elution buffer (100 mM NaCO3, 0.1% SDS) by vigorous shaking for 30 min at 30°C. Crosslinks were reversed by the addition of 4 µl of 5M NaCl and 2 µl of 500 µg/ml RNaseA (Roche) at 65˚C followed by incubation at 42˚C for 1.5 h with 1 µl of 20 mg/ml proteinaseK. ChIP DNA was purified ChIP DNA Clean & Concentrator kit (Zymo Research).
ChIP-seq libraries were generated as described previously (Blackledge et al., 2010) by the High-Throughput Sequencing centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol.


title: C127 H3K4me3 rep1

description:
C127_H3K4me3_merged_triplicate.bigwig
C127_H3K4me3_peaks.bed

value: In-house


title: C127 H3K4me3 rep2


title: C127_ATAC input

data_processing:
For BioCAP and ATAC-seq, paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options and non-uniquely mapping reads were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.  Nascent RNA-seq (4sU-Seq) paired-end reads were initially aligned against rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment against mm10  genome using the STAR RNA-seq aligner (Dobin et al., 2013). To improve mapping of nascent, intronic sequences, reads which failed to map using STAR were aligned against the genome using bowtie2 and reads which mapped more than once were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009).Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Peakcalling of non-methylated islands from BioCAP data was performed using MACS2.  ATAC-seq merged BAM files were used to make a genome tracks using DANPOS2, with the Tn5 control provided as background.  Merged nascent RNA-seq bam files were used to generate genome coverage tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome tracks for data visualisation. Peak file generated from BioCAP data to identify non-methylated island (NMI) intervals.

extract_protocol:
For each individual Bio-CAP experiment, 25 μl of NeutrAvidin Agarose Resin (Thermo Scientific, 29200) was washed with BC100 buffer and then incubated with 50 μl of 0.5 μg/μl biotinylated hKDM2b-CxxC protein diluted in BC100 buffer for 1 h at 4°C. The conjugated resin/CxxC protein was then washed with CAP100 buffer (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 100 mM NaCl). Genomic DNA was sonicated to an average size of 150-250 bp using a Diagenode Bioruptor. Sonicated DNA was then diluted in CAP100 buffer to a concentration of 16 μg/ml and a 100 μl Input sample was retained. For each Bio-CAP experiment, 500 μl of diluted sonicated DNA, corresponding to approximately 8 μg of DNA, was added to the conjugated CxxC resin. The DNA and resin were incubated at 4°C for 1 h with gentle mixing. The resin was then collected by centrifugation at 1500 g for 3 min at 4°C and the unbound flowthrough (FT) material was removed. The resin and any associated DNA was washed twice with 1 ml of CAP100 buffer, before the first elution was performed by adding 50 μl of CAP300 (12.5% glycerol, 0.1% Triton-x-100, 20 mM HEPES pH 7.9, 300 mM NaCl) to the resin and incubating at room temperature for 10 min. Following centrifugation a 50 μl elution fraction was carefully collected. The elution process was repeated using another 50 μl of CAP300 and the 300 mM elution fractions were pooled (giving a total volume of 100 μl). Subsequent elutions were performed in the same way using buffers with 500 mM, 700 mM and 1 M NaCl sequentially. Each 100 μl elution fraction, together with 100 μl of both the Input and FT samples, was purified using a PCR purification column (Qiagen) and DNA was eluted in a volume of 50 μl. The 700 mM and 1 M fractions were pooled for sequencing. Bio-CAP material was quantified using the High Sensitivity Qubit system (Invitrogen) and the fragmentation profile was assessed using a DNA HS Agilent 2200 TapeStation chip.   Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al., 2013). Briefly, 5 × 10^6 cells were harvested, washed with PBS and nuclei were isolated using 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10mM NaCl, 10mM Tris (pH 7.4), 3mM MgCl2), to remove as much of contaminating cytoplasmic and mitochondrial material as possible. Nuclei were then counted, and 5×10^4 nuclei were resuspended in Tn5 reaction buffer (10mM TAPS, 5mM MgCl2, 10% dimethylformamide) and 2 µl of Tn5 transposase (25 µM) made in house according to the previously described protocol (Picelli et al., 2014). Nuclei were then incubated for 30 min at 37°C, before isolation and purification of tagmented DNA using QiaQuick MinElute columns (Qiagen). To control for sequence bias of the Tn5 transposase, an ATAC “input” sample was generated, by tagmenting genomic DNA from ESCs with Tn5 for 30 min at 55°C.  Nascent RNA sequencing was performed by pulse labelling with 4-thiouridine (4sU) as previously described (Rädle B. et al., 2013). Confluent 15 cm plates were treated with 500 µM 4sU in 10 ml culture medium for 20 min. The 4sU-containing media was then aspirated and immediately replaced with 5 ml TRIZOL (Thermo Fisher Scientific). RNA was isolated by phenol-chloroform extraction using phase lock tubes (Eppendorf) and resuspend in nuclease-free water. Total RNA aliquots were treated with 6U Turbo DNase (Ambion) and incubated at 37°C for 30 min, followed by inactivation of the DNase according to the manufacturer’s instructions. 300 μg of the resulting total RNA were incubated with 2 μg Biotin-HPDP/μg RNA in biotinylation buffer (10 mM Tris-HCl pH 7.4 and 1 mM EDTA) under rotation for 1.5 h at RT. Unincorporated biotin-HPDP was removed by chloroform/isoamylalcohol extraction. To capture biotinylated RNA, μMACS streptavidin beads (Miltenyi) were added to the RNA suspension (1 μl of beads/ μg RNA) and rotated for 15 min at room temperature prior to loading onto μMACS minicolumns. Unlabelled RNA was removed by washing three times with 900 µl of wash buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween20) pre-heated at 65°C, then three more times with wash buffer at room temperature. Biotinylated RNA was then eluted in two rounds with 100 mM DTT and purified using an RNeasy miniElute kit (Qiagen).
BioCAP libraries were generated by the High-Throughput Sequencing centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol and sequenced on the Illumina HiSeq2000 platform with 51 bp reads.   ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes previously described (Buenrostro et al., 2013) and the NEBNext® High-Fidelity 2X PCR Master Mix. ATAC-seq libraries were sequenced on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.  For RNA-seq library generation, nascent RNA samples were initially depleted of ribosomal RNAs using the Low Input RiboMinus Eukaryote System v2 kit (Thermo Fisher). The recovered rRNA-depleted nascent RNA was used to prepare the cDNA libraries with NEBNext Ultra Directional RNA Library Prep Kit for Illumina and subject to sequencing on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.


title: C127_RNAseq rep3

description:
Nascent RNA from pulse labelling experiments with 4-thiouridine.
C127_4SU_merged_plusStrand.bw
C127_4SU_merged_minusStrand.bw


title: C127_RNAseq rep1


title: C127_ATAC rep3


title: C127_ATAC rep1


title: C127_ATAC rep2


title: 3'-end mRNA-seq ES cells 4dRA 4hr DOX

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
ChIP-seq: Mapping using Bowtie to the mouse genome (mm9). Mapping only unique hits with up to 3 mismatches.
RNA-seq: Reads were mapped using TopHat to the mouse genome (mm9), and expression levels were calculated using cufflinks (with default parameters).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Following mapping, reads were extended to length of 500bp and genome-wide read coverage was calculated, normalized to 10M mapped reads per experiment, and saved as bigWig files.
Supplementary_files_format_and_content: RNA-seq:fpkm_tracking

source_name: 3'-end mRNA-seq ES cells 4dRA 4hr DOX

growth_protocol: Cells were cultured on gelatinized tissue culture plates in ESC media supplemented with LIF and the 2i inhibitors cocktail (mitogen activated protein kinase (MAPK)/extracellular-signal-regulated kinase (ERK) kinase (MEK) inhibitor PD0325901 and the glycogen synthase kinase 3 (GSK3) inhibitor CHIR99021). This media was shown to maintain mES cell self-renewal without the addition of exogenous factors. hygromycin b was also added as selection against loss of the HA-H3.3 construct for several passages.

extract_protocol:
ChIP-seq: was performed as described in Schlesinger and Goff, 2013. In short, cells from different time points after dox addition, with and without 4 days retinoic acid (4dRA) treatment, were collected and fixed. IP was done using Magna ChIP kit (Millipore) and DNA was purified using QIAquick PCR purification kit (Qiagen). ChIP Grade HA tag antibody was used (ab9110 from Abcam).
3'-end RNA-seq: Extraction, library preparation and sequencing was done using the RNesay kit (Qiagen) according to the manufacturer’s instructions, library preparation was done with QuantSeq 3′ mRNA-Seq Library Prep Kit by Lexogen.  Four RNA libraries were prepared: from ESCs and 4dRA cells without or with 4h Dox addition. Libraries were subjected to single-end sequencing using Illumina Next-Seq 500 platform.
ChIP-seq: Libraries were prepared as previously described (Blecher-Gonen et al., 2013).

treatment_protocol: For retinoic acid (RA) induced differentiation, cells were grown on gelatin-coated dishes for 4 days in ESC media with 1µM RA.

value: mESC 4dRA


title: mESC_T7SET1A_rep2_TAM


title: 3'-end mRNA-seq ES cells

source_name: 3'-end mRNA-seq ES cells

value: mESC


title: 3'-end mRNA-seq ES cells 4hr DOX

source_name: 3'-end mRNA-seq ES cells 4hr DOX


title: H3K4Me1_ChIPseq_PrEC_rep1

description: processed data file: PrEC_ChromHMM.bed.gz

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie (version 1.0.1), allowing up to three mismatches. Non-uniquely alignable reads were excluded.
Peaks were called using PeakRanger (version 1.16) with peak size set to broad and with input control set to a pooled control LNCaP or VCaP input.
Bigwig files were generated using a scaling factor of 1,000,000 reads/library size, average fragment length of 300 and duplicates removed.
ChromHMM v.1.10 was used to simultaneously partition the genome of PrEC and LNCaP cell lines into states. The same approach was employed for the VCaP cell line. Redundant states were then collapsed into seven distinct states and manually annotated by comparison to the published ChromHMM model for HMEC cells.
genome_build = hg19
processed data files format and content: bed file format

extract_protocol: ChIP assays were carried out according to the manufacturer's protocol (Upstate Biotechnology). Briefly, ~ 2 x 10^6 cells were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibodies specific for Histone H2AZ (Active motif # 39113), acetylated Histone H2AZ (Abcam #ab18262), H3K4Me1 (Active Motif #39297), H3K27ac (Active Motif #39133), H3K9K14ac (Millipore #06-599.) and H3K36Me3 (Abcam ab9050-100). Ten ul of antibody was used for each immunoprecipitation. No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 ul H2O.

treatment_protocol: Human LNCaP or VCaP prostate cancer cells and were maintained in RPMI Medium 1640 (Gibco), or DMEM media 11995 (Gibco), respectively, and supplemented with 10% fetal bovine serum (FBS) for at least 72 hrs to 70-80% confluence. LNCaP cell were then seeded to 2.5x106 cell per 15cm dish and starved for 3 days in RPMI Medium 1640-no-phenol red (Gibco)  and 5% chracoal stripped FBS (CSFBS). Then LNCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 2h, 4h and 16h.  VCaP cell were then seeded to 2.5x106 cell per 15cm dish and starved for 3 days in DMEM media 11995 (Gibco)  and 2.5% chracoal stripped FBS (CSFBS). Then VCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 16h. Cells were then fixed with 1% formaldehyde for 10 min at room temperature.

value: Primary prostate epithelial cells. Cambrex Bio Science Cat. No. CC-2556

value: Active Motif Cat #39297


title: H3K36Me3_ChIPseq_PrEC


title: C127 H3K4me3 rep3


title: H2AZac_ChIPseq_LNCaP_rep2

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells

value: Abcam Cat #ab18262


title: H2AZac_ChIPseq_PrEC_rep2


title: H2AZ_ChIPseq_PrEC_rep1

value: Primary prostate epithelial cells. Cambrex Bio Science Cat. No. CC-2555

value: Active Motif Cat #39113


title: H2AZ_ChIPseq_LNCaP_rep1


title: C127_RNAseq rep2


title: H3K36Me3_ChIPseq_LNCaP

description: processed data file: LNCaP_ChromHMM.bed.gz


title: MACPL000029CAC

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

description:
cell free DNA
Processed_Data
1849

data_processing:
Read-through sequences within raw sequencing reads were trimmed using Trimmomatic version 0.35. Low quality bases at the 5' (Phred quality score <5) and 3' (5bp-sliding window Phred score< 15) were also trimmed. Reads with a minimum length of 50bp were aligned to the human genome assembly GRCh37 using Bowtie2 version 2.2.6 with end-to-end alignment mode. For paired-end sequencing data, read pairs were concordantly aligned with fragment length <500bp and with up to 1 ambiguous base and four mismatched bases per 100bp length.
Raw sequencing reads profiled for 5mC were trimmed and aligned to GRCh37 using Bismark version 0.15.0 according to previously published data processing procedures.
Alignments with Mapping Quality Score (MAPQ) ≥10 were counted for overlap with genomic features using featureCounts of subread version 1.5.0-p1, without strand information.
Gene regions were defined as the regions between gene start sites and gene end sites annotated by GENCODE release 19.
CpG islands were annotated CpG islands by UCSC Table Browser plus +/- 1kb regions.
Genome_build: GRCh37
Supplementary_files_format_and_content: Plain text format. Processed_Data is a data frame with fields: 1) gene (official gene symbol; for 23 pairs of genes sharing the same official gene symbol, one from each pair assigned a new gene symbol as original_gene_symbol.dup); 2) pos (chr_start_stop) of genes; 3) raw counts of samples at genes. Reports hydroxy-methylation levels.
Supplementary_files_format_and_content: Plain text format. Processed_5mc_Data is a data frame with fields: 1) pos (chr_start_stop) of CpG islands; 2) raw counts of samples at CpG islands. Reports methylation levels.

source_name: blood

growth_protocol: A total of 4ml of peripheral blood was collected from subject individuals using EDTA anticoagulant tubes. Tissue samples, including tumor and adjacent tissue samples, from patients were stocked at -80°C after surgical operation.

extract_protocol:
The plasma cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s protocol. Genomic DNA from tissues was isolated using the ZR Genomic DNA-Tissue Kits (Zymo Research) according to the manufacturer’s protocol.
First, the genomic DNA is fragmented using an enzymatic reaction. Next, the fragmented genomic DNA or the cfDNA were repaired and installed with the Illumina compatible adaptors. The glucosylation reactions were performed in a 25 μL solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 μM N3-UDP-Glc, and 1 μM βGT, at 37°C for 1 hr. The reaction was purified by Micro Bio-Spin 30 Column (Bio–Rad) into ddH2O. After that, 1 μL DBCO-PEG4-DBCO (Click Chemistry Tools, 4.5 mM stock in DMSO) was added to the reaction mixture. The reactions were incubated at 37°C for 2 hr. Next, the DNA was purified by Micro Bio-Spin 30 Column (Bio-–Rad). The purified DNA was incubated with 5 µL C1 Streptavidin beads (Life Technologies) in 2X buffer (1X buffer: 5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl) for 15 min according to the manufacturer’s instruction. The beads were subsequently washed eight times for 5 -min with 1X buffer. All binding and washing was done at room temperature with gentle rotation. The captured DNA fragments were amplified with 14-16 cycles of PCR amplification. The PCR products were purified using AMPure XP beads according to the manufacturer’s instructions. DNA concentration of each library was measured with a Qubit fluorometer (Life Technologies) and sequencing was performed on the Illumina Hi-Seq platform or NextSeq 500 platform.

treatment_protocol: Plasma sample was prepared within 6h by centrifuging twice at 1,350g for 12min, and then centrifuging at 13,500g for 12min. The prepared plasma samples (about 2ml/subject) were immediately stored at -80°C. About 10-25 mg tissue was collected using a scalpel after sample unfreezing.

tag: gender (1=male, 2=female)

tag: disease site

value: colon

tag: disease state

value: cancer

value: plasma


title: MAZPL000027HEA

description:
cell free DNA
Processed_Data
1853

tag: age

value: healthy


title: MACPL000028CAC

description:
cell free DNA
Processed_Data
1848


title: MAZPL000029HEA

description:
cell free DNA
Processed_Data
1855


title: MACPL000025CAC

description:
cell free DNA
Processed_Data
1845


title: MAZPL000026HEA

description:
cell free DNA
Processed_Data
1852


title: MAZPL000030HEA

description:
cell free DNA
Processed_Data
1856


title: MACPL000026CAC

description:
cell free DNA
Processed_Data
1846


title: MAZPL000028HEA

description:
cell free DNA
Processed_Data
1854


title: MAZPL000031HEA

description:
cell free DNA
Processed_Data
1857


title: SHDPL000055CAC

description:
cell free DNA
Processed_Data
1336

value: liver


title: MACPL000027CAC

description:
cell free DNA
Processed_Data
1847


title: SHDPL000056CAC

description:
cell free DNA
Processed_Data
1337


title: SHDPL000050CAC

description:
cell free DNA
Processed_Data
1331


title: SHDPL000049CAC

description:
cell free DNA
Processed_Data
1330


title: SHDPL000045CAC

description:
cell free DNA
Processed_Data
1326


title: SHDPL000036CAC

description:
cell free DNA
Processed_Data
1323


title: SHDPL000048CAC

description:
cell free DNA
Processed_Data
1329


title: SHDPL000031CAC

description:
cell free DNA
Processed_Data
1321


title: SHDPL000047CAC

description:
cell free DNA
Processed_Data
1328


title: SHDPL000029CAC

description:
cell free DNA
Processed_Data
1320


title: SHDPL000020CAC

description:
cell free DNA
Processed_Data
1315


title: SHDPL000046CAC

description:
cell free DNA
Processed_Data
1327


title: SHDPL000033CAC

description:
cell free DNA
Processed_Data
1322


title: SHDPL000021CAC

description:
cell free DNA
Processed_Data
1316


title: SHDPL000027CAC

description:
cell free DNA
Processed_Data
1319


title: SHDPL000019CAC

description:
cell free DNA
Processed_Data
1314


title: SHDPL000006CAC

description:
cell free DNA
Processed_Data
1050


title: SHDPL000005CAC

description:
cell free DNA
Processed_Data
1049


title: HXJPL000062CAC

description:
cell free DNA
Processed_Data
880

value: thyroid


title: SHDPL000026CAC

description:
cell free DNA
Processed_Data
1318


title: HXJPL000057CAC

description:
cell free DNA
Processed_Data
875


title: HXJPL000059CAC

description:
cell free DNA
Processed_Data
877


title: HXJPL000054CAC

description:
cell free DNA
Processed_Data
872


title: HXJPL000055CAC

description:
cell free DNA
Processed_Data
873


title: HXJPL000060CAC

description:
cell free DNA
Processed_Data
878


title: SHDPL000044CAC

description:
cell free DNA
Processed_Data
1325


title: HXJPL000061CAC

description:
cell free DNA
Processed_Data
879


title: SHDPL000013CAC

description:
cell free DNA
Processed_Data
1313


title: SHDPL000001CAC

description:
cell free DNA
Processed_Data
1045


title: HXJPL000053CAC

description:
cell free DNA
Processed_Data
871


title: SHDPL000010CAC

description:
cell free DNA
Processed_Data
1054


title: HXJPL000056CAC

description:
cell free DNA
Processed_Data
874


title: HXJPL000049CAC

description:
cell free DNA
Processed_Data
867


title: HXJPL000051CAC

description:
cell free DNA
Processed_Data
869


title: HXJPL000050CAC

description:
cell free DNA
Processed_Data
868


title: SHDPL000002CAC

description:
cell free DNA
Processed_Data
1046


title: HXJPL000047CAC

description:
cell free DNA
Processed_Data
865


title: HXJPL000043CAC

description:
cell free DNA
Processed_Data
861


title: HXJPL000041CAC

description:
cell free DNA
Processed_Data
860


title: HXJPL000046CAC

description:
cell free DNA
Processed_Data
864


title: HXJPL000040CAC

description:
cell free DNA
Processed_Data
859


title: HXJPL000037CAC

description:
cell free DNA
Processed_Data
857


title: HXJPL000038CAC

description:
cell free DNA
Processed_Data
858


title: HXJPL000036CAC

description:
cell free DNA
Processed_Data
856


title: HXJPL000052CAC

description:
cell free DNA
Processed_Data
870


title: SHDPL000003CAC

description:
cell free DNA
Processed_Data
1047


title: HXJPL000035CAC

description:
cell free DNA
Processed_Data
854


title: HXJPL000029CAC

description:
cell free DNA
Processed_Data
848


title: HXJPL000031CAC

description:
cell free DNA
Processed_Data
850


title: HXJPL000166CAC

description:
cell free DNA
Processed_Data
855


title: HXJPL000033CAC

description:
cell free DNA
Processed_Data
852


title: HXJPL000034CAC

description:
cell free DNA
Processed_Data
853


title: HXJPL000022CAC

description:
cell free DNA
Processed_Data
841


title: HXJPL000024CAC

description:
cell free DNA
Processed_Data
843


title: HXJPL000025CAC

description:
cell free DNA
Processed_Data
844


title: HXJPL000027CAC

description:
cell free DNA
Processed_Data
846


title: HXJPL000023CAC

description:
cell free DNA
Processed_Data
842


title: HXJPL000021CAC

description:
cell free DNA
Processed_Data
840


title: HXJPL000011CAC

description:
cell free DNA
Processed_Data
218


title: HXJPL000014CAC

description:
cell free DNA
Processed_Data
221


title: HXJPL000017CAC

description:
cell free DNA
Processed_Data
224


title: HXJPL000032CAC

description:
cell free DNA
Processed_Data
851


title: HXJPL000008CAC

description:
cell free DNA
Processed_Data
215


title: HXJPL000003CAC

description:
cell free DNA
Processed_Data
210


title: HXJPL000030CAC

description:
cell free DNA
Processed_Data
849


title: HXJPL000012CAC

description:
cell free DNA
Processed_Data
219


title: HXJPL000010CAC

description:
cell free DNA
Processed_Data
217


title: HXJPL000028CAC

description:
cell free DNA
Processed_Data
847


title: HXGPL000079CAC

description:
cell free DNA
Processed_Data
838

value: pancreas


title: HXJPL000004CAC

description:
cell free DNA
Processed_Data
211


title: HXGPL000069CAC

description:
cell free DNA
Processed_Data
836


title: HXGPL000068CAC

description:
cell free DNA
Processed_Data
835


title: HXGPL000067CAC

description:
cell free DNA
Processed_Data
834


title: HXJPL000009CAC

description:
cell free DNA
Processed_Data
216


title: HXGPL000064CAC

description:
cell free DNA
Processed_Data
833


title: HXGPL000063CAC

description:
cell free DNA
Processed_Data
832


title: HXJPL000006CAC

description:
cell free DNA
Processed_Data
213


title: HXGPL000060NOR

description:
cell free DNA
Processed_Data
829


title: HXGPL000062NOR

description:
cell free DNA
Processed_Data
831


title: HXGPL000046CAC

description:
cell free DNA
Processed_Data
203


title: HXGPL000050CAC

description:
cell free DNA
Processed_Data
207


title: HXGPL000041CAC

description:
cell free DNA
Processed_Data
198


title: HXGPL000052CAC

description:
cell free DNA
Processed_Data
824


title: HXGPL000058CAC

description:
cell free DNA
Processed_Data
827


title: HXGPL000059NOR

description:
cell free DNA
Processed_Data
828


title: HXGPL000049CAC

description:
cell free DNA
Processed_Data
206


title: HXGPL000037CAC

description:
cell free DNA
Processed_Data
194


title: HXGPL000038CAC

description:
cell free DNA
Processed_Data
195


title: HXGPL000023CAC

description:
cell free DNA
Processed_Data
180


title: HXGPL000039CAC

description:
cell free DNA
Processed_Data
196


title: HXGPL000030CAC

description:
cell free DNA
Processed_Data
187


title: HXGPL000025CAC

description:
cell free DNA
Processed_Data
182


title: HXGPL000028CAC

description:
cell free DNA
Processed_Data
185


title: HXGPL000026CAC

description:
cell free DNA
Processed_Data
183


title: HXGPL000015CAC

description:
cell free DNA
Processed_Data
172


title: HXGPL000018CAC

description:
cell free DNA
Processed_Data
175


title: HXGPL000024CAC

description:
cell free DNA
Processed_Data
181


title: HXGPL000004CAC

description:
cell free DNA
Processed_Data
161


title: HXGPL000002CAC

description:
cell free DNA
Processed_Data
159


title: HXGPL000008CAC

description:
cell free DNA
Processed_Data
165


title: HXGPL000014CAC

description:
cell free DNA
Processed_Data
171


title: HXGPL000007CAC

description:
cell free DNA
Processed_Data
164


title: HXGPL000019CAC

description:
cell free DNA
Processed_Data
176


title: SHZPL000100HEA

description:
cell free DNA
Processed_Data
1385


title: SHZPL000099HEA

description:
cell free DNA
Processed_Data
1384


title: HXGPL000035CAC

description:
cell free DNA
Processed_Data
192


title: SHZPL000098HEA

description:
cell free DNA
Processed_Data
1383


title: HXGPL000010CAC

description:
cell free DNA
Processed_Data
167


title: SHZPL000090HEA

description:
cell free DNA
Processed_Data
1376


title: SHZPL000092HEA

description:
cell free DNA
Processed_Data
1378


title: SHZPL000091HEA

description:
cell free DNA
Processed_Data
1377


title: SHZPL000095HEA

description:
cell free DNA
Processed_Data
1380


title: SHZPL000088HEA

description:
cell free DNA
Processed_Data
1374


title: SHZPL000096HEA

description:
cell free DNA
Processed_Data
1381


title: SHZPL000094HEA

description:
cell free DNA
Processed_Data
1379


title: SHZPL000084HEA

description:
cell free DNA
Processed_Data
1370


title: SHZPL000087HEA

description:
cell free DNA
Processed_Data
1373


title: SHZPL000083HEA

description:
cell free DNA
Processed_Data
1369


title: SHZPL000086HEA

description:
cell free DNA
Processed_Data
1372


title: SHZPL000076HEA

description:
cell free DNA
Processed_Data
1362


title: SHZPL000078HEA

description:
cell free DNA
Processed_Data
1364


title: SHZPL000071HEA

description:
cell free DNA
Processed_Data
1357


title: SHZPL000074HEA

description:
cell free DNA
Processed_Data
1360


title: SHZPL000067HEA

description:
cell free DNA
Processed_Data
1353


title: SHZPL000068HEA

description:
cell free DNA
Processed_Data
1354


title: SHZPL000082HEA

description:
cell free DNA
Processed_Data
1368


title: SHZPL000072HEA

description:
cell free DNA
Processed_Data
1358


title: SHZPL000075HEA

description:
cell free DNA
Processed_Data
1361


title: SHZPL000065HEA

description:
cell free DNA
Processed_Data
1351


title: SHZPL000066HEA

description:
cell free DNA
Processed_Data
1352


title: SHZPL000069HEA

description:
cell free DNA
Processed_Data
1355


title: SHZPL000064HEA

description:
cell free DNA
Processed_Data
1350


title: SHZPL000062HEA

description:
cell free DNA
Processed_Data
1348


title: SHZPL000063HEA

description:
cell free DNA
Processed_Data
1349


title: SHZPL000061HEA

description:
cell free DNA
Processed_Data
1347


title: SHZPL000058HEA

description:
cell free DNA
Processed_Data
1344


title: SHZPL000055HEA

description:
cell free DNA
Processed_Data
1341


title: SHZPL000056HEA

description:
cell free DNA
Processed_Data
1342


title: SHZPL000081HEA

description:
cell free DNA
Processed_Data
1367


title: SHZPL000085HEA

description:
cell free DNA
Processed_Data
1371


title: SHZPL000080HEA

description:
cell free DNA
Processed_Data
1366


title: SHZPL000054HEA

description:
cell free DNA
Processed_Data
898


title: SHZPL000053HEA

description:
cell free DNA
Processed_Data
897


title: SHZPL000060HEA

description:
cell free DNA
Processed_Data
1291


title: SHZPL000050HEA

description:
cell free DNA
Processed_Data
894


title: SHZPL000052HEA

description:
cell free DNA
Processed_Data
896


title: SHZPL000047HEA

description:
cell free DNA
Processed_Data
891


title: SHZPL000045HEA

description:
cell free DNA
Processed_Data
889


title: SHZPL000046HEA

description:
cell free DNA
Processed_Data
890


title: SHZPL000049HEA

description:
cell free DNA
Processed_Data
893


title: SHZPL000043HEA

description:
cell free DNA
Processed_Data
887


title: SHZPL000042HEA

description:
cell free DNA
Processed_Data
886


title: SHZPL000039HEA

description:
cell free DNA
Processed_Data
549


title: SHZPL000035HEA

description:
cell free DNA
Processed_Data
545


title: SHZPL000037HEA

description:
cell free DNA
Processed_Data
547


title: SHZPL000036HEA

description:
cell free DNA
Processed_Data
546


title: SHZPL000038HEA

description:
cell free DNA
Processed_Data
548


title: SHZPL000033HEA

description:
cell free DNA
Processed_Data
543


title: SHZPL000051HEA

description:
cell free DNA
Processed_Data
895


title: SHZPL000032HEA

description:
cell free DNA
Processed_Data
542


title: SHZPL000048HEA

description:
cell free DNA
Processed_Data
892


title: SHZPL000031HEA

description:
cell free DNA
Processed_Data
541


title: SHZPL000029HEA

description:
cell free DNA
Processed_Data
539


title: SHZPL000044HEA

description:
cell free DNA
Processed_Data
888


title: SHZPL000027HEA

description:
cell free DNA
Processed_Data
537


title: SHZPL000026HEA

description:
cell free DNA
Processed_Data
536


title: SHZPL000028HEA

description:
cell free DNA
Processed_Data
538


title: SHZPL000040HEA

description:
cell free DNA
Processed_Data
550


title: SHZPL000023HEA

description:
cell free DNA
Processed_Data
533


title: SHZPL000025HEA

description:
cell free DNA
Processed_Data
535


title: SHZPL000041HEA

description:
cell free DNA
Processed_Data
551


title: SHZPL000019HEA

description:
cell free DNA
Processed_Data
271


title: SHZPL000022HEA

description:
cell free DNA
Processed_Data
532


title: SHZPL000017HEA

description:
cell free DNA
Processed_Data
269


title: SHZPL000016HEA

description:
cell free DNA
Processed_Data
268


title: SHZPL000015HEA

description:
cell free DNA
Processed_Data
267


title: SHZPL000020HEA

description:
cell free DNA
Processed_Data
530


title: SHZPL000011HEA

description:
cell free DNA
Processed_Data
263


title: SHZPL000014HEA

description:
cell free DNA
Processed_Data
266


title: SHZPL000013HEA

description:
cell free DNA
Processed_Data
265


title: SHZPL000012HEA

description:
cell free DNA
Processed_Data
264


title: SHZPL000034HEA

description:
cell free DNA
Processed_Data
544


title: SHZPL000010HEA

description:
cell free DNA
Processed_Data
262


title: SHZPL000030HEA

description:
cell free DNA
Processed_Data
540


title: SHZPL000009HEA

description:
cell free DNA
Processed_Data
261


title: SHZPL000007HEA

description:
cell free DNA
Processed_Data
260


title: SHZPL000024HEA

description:
cell free DNA
Processed_Data
534


title: SHZPL000021HEA

description:
cell free DNA
Processed_Data
531


title: SHZPL000004HEA

description:
cell free DNA
Processed_Data
257


title: SHZPL000006HEA

description:
cell free DNA
Processed_Data
259


title: SHZPL000018HEA

description:
cell free DNA
Processed_Data
270


title: SHZPL000005HEA

description:
cell free DNA
Processed_Data
258


title: SHZPL000002HEA

description:
cell free DNA
Processed_Data
255


title: SHZPL000003HEA

description:
cell free DNA
Processed_Data
256


title: SHZPL000001HEA

description:
cell free DNA
Processed_Data
254


title: SHCPL000150CAC

description:
cell free DNA
Processed_Data
1757


title: SHCPL000155CAC

description:
cell free DNA
Processed_Data
1754


title: SHCPL000151CAC

description:
cell free DNA
Processed_Data
1758


title: SHCPL000152CAC

description:
cell free DNA
Processed_Data
1741


title: SHCPL000153CAC

description:
cell free DNA
Processed_Data
1742


title: SHCPL000141NOR

description:
cell free DNA
Processed_Data
1557

value: benign


title: SHCPL000128NOR

description:
cell free DNA
Processed_Data
1574


title: SHCPL000135NOR

description:
cell free DNA
Processed_Data
1535


title: SHCPL000125NOR

description:
cell free DNA
Processed_Data
1527


title: SHCPL000145NOR

description:
cell free DNA
Processed_Data
1519


title: SHCPL000149NOR

description:
cell free DNA
Processed_Data
1517


title: SHCPL000140NOR

description:
cell free DNA
Processed_Data
1513


title: SHCPL000130NOR

description:
cell free DNA
Processed_Data
1515


title: SHCPL000129NOR

description:
cell free DNA
Processed_Data
1555


title: SHCPL000124NOR

description:
cell free DNA
Processed_Data
1500


title: SHCPL000139NOR

description:
cell free DNA
Processed_Data
1506


title: SHCPL000123NOR

description:
cell free DNA
Processed_Data
1509


title: SHCPL000126NOR

description:
cell free DNA
Processed_Data
1496


title: SHCPL000133CAC

description:
cell free DNA
Processed_Data
1499


title: SHCPL000131NOR

description:
cell free DNA
Processed_Data
1495


title: SHCPL000112NOR

description:
cell free DNA
Processed_Data
1487


title: SHCPL000154CAC

description:
cell free DNA
Processed_Data
1744


title: SHCPL000134CAC

description:
cell free DNA
Processed_Data
1484


title: SHCPL000132CAC

description:
cell free DNA
Processed_Data
1482


title: SHCPL000114NOR

description:
cell free DNA
Processed_Data
1490


title: SHCPL000146CAC

description:
cell free DNA
Processed_Data
1480


title: SHCPL000143CAC

description:
cell free DNA
Processed_Data
1476


title: SHCPL000136NOR

description:
cell free DNA
Processed_Data
1502


title: SHCPL000137CAC

description:
cell free DNA
Processed_Data
1477


title: SHCPL000138CAC

description:
cell free DNA
Processed_Data
1481


title: SHCPL000142CAC

description:
cell free DNA
Processed_Data
1426


title: SHCPL000095NOR

description:
cell free DNA
Processed_Data
1346


title: SHCPL000127CAC

description:
cell free DNA
Processed_Data
1419


title: SHCPL000113CAC

description:
cell free DNA
Processed_Data
1417


title: SHCPL100100NOR

description:
cell free DNA
Processed_Data
1310


title: SHCPL100102NOR

description:
cell free DNA
Processed_Data
1312


title: SHCPL000122NOR

description:
cell free DNA
Processed_Data
1309


title: SHCPL000121NOR

description:
cell free DNA
Processed_Data
1308


title: SHCPL100101NOR

description:
cell free DNA
Processed_Data
1311


title: SHCPL000116NOR

description:
cell free DNA
Processed_Data
1304


title: SHCPL000119NOR

description:
cell free DNA
Processed_Data
1306


title: SHCPL000115NOR

description:
cell free DNA
Processed_Data
1303


title: SHCPL000111NOR

description:
cell free DNA
Processed_Data
1302


title: SHCPL000117NOR

description:
cell free DNA
Processed_Data
1305


title: SHCPL000120CAC

description:
cell free DNA
Processed_Data
1307


title: SHCPL000110NOR

description:
cell free DNA
Processed_Data
1301


title: SHCPL000109NOR

description:
cell free DNA
Processed_Data
1300


title: SHCPL000107NOR

description:
cell free DNA
Processed_Data
1299


title: SHCPL000106NOR

description:
cell free DNA
Processed_Data
1298


title: SHCPL000098NOR

description:
cell free DNA
Processed_Data
1295


title: SHCPL000097NOR

description:
cell free DNA
Processed_Data
1294


title: SHCPL000104NOR

description:
cell free DNA
Processed_Data
1296


title: SHCPL000105NOR

description:
cell free DNA
Processed_Data
1297


title: SHCPL000096NOR

description:
cell free DNA
Processed_Data
1293


title: SHCPL000093NOR

description:
cell free DNA
Processed_Data
1292


title: SHCPL000092NOR

description:
cell free DNA
Processed_Data
1289


title: SHCPL000089NOR

description:
cell free DNA
Processed_Data
1287


title: SHCPL000087CAC

description:
cell free DNA
Processed_Data
1285


title: SHCPL000088CAC

description:
cell free DNA
Processed_Data
1286


title: SHCPL000083NOR

description:
cell free DNA
Processed_Data
1281


title: SHCPL000086CAC

description:
cell free DNA
Processed_Data
1284


title: SHCPL000085NOR

description:
cell free DNA
Processed_Data
1283


title: SHCPL000094NOR

description:
cell free DNA
Processed_Data
1345


title: SHCPL000080NOR

description:
cell free DNA
Processed_Data
1278


title: SHCPL000081CAC

description:
cell free DNA
Processed_Data
1279


title: SHCPL000079NOR

description:
cell free DNA
Processed_Data
1277


title: SHCPL000077CAC

description:
cell free DNA
Processed_Data
1275


title: SHCPL000069NOR

description:
cell free DNA
Processed_Data
1273


title: SHCPL000064NOR

description:
cell free DNA
Processed_Data
1269


title: SHCPL000067CAC

description:
cell free DNA
Processed_Data
1271


title: SHCPL000059CAC

description:
cell free DNA
Processed_Data
1264


title: SHCPL000063NOR

description:
cell free DNA
Processed_Data
1268


title: SHCPL000056CAC

description:
cell free DNA
Processed_Data
1262


title: SHCTU000054CAC

description:
Processed_Data
1239

source_name: tissue

value: tumor


title: SHCTU000051CAC

description:
Processed_Data
1238


title: SHCPL100053CAC

description:
cell free DNA
Processed_Data
1043


title: SHCTI000054CAC

description:
Processed_Data
1237

value: adjacent tissue


title: SHCTI000051CAC

description:
Processed_Data
1236


title: SHCPL000054CAC

description:
cell free DNA
Processed_Data
1044


title: SHCPL000051CAC

description:
cell free DNA
Processed_Data
1041


title: SHCPL000052CAC

description:
cell free DNA
Processed_Data
1042


title: SHCPL000050CAC

description:
cell free DNA
Processed_Data
915


title: SHCTU000047CAC

description:
Processed_Data
769


title: SHCTU000042CAC

description:
Processed_Data
764


title: SHCTU000046CAC

description:
Processed_Data
768


title: SHCTU000045CAC

description:
Processed_Data
767


title: SHCPL000073CAC

description:
cell free DNA
Processed_Data
1274


title: SHCTI000046CAC

description:
Processed_Data
761


title: SHCTU000044CAC

description:
Processed_Data
766


title: SHCTI000047CAC

description:
Processed_Data
762


title: SHCPL000060CAC

description:
cell free DNA
Processed_Data
1265


title: SHCPL000068NOR

description:
cell free DNA
Processed_Data
1272


title: SHCPL000058CAC

description:
cell free DNA
Processed_Data
1263


title: SHCTI000044CAC

description:
Processed_Data
759


title: SHCTU000043CAC

description:
Processed_Data
765


title: SHCPL000046CAC

description:
cell free DNA
Processed_Data
718


title: SHCPL000044CAC

description:
cell free DNA
Processed_Data
717


title: SHCPL000041CAC

description:
cell free DNA
Processed_Data
714


title: SHCPL000042CAC

description:
cell free DNA
Processed_Data
715


title: SHCPL000039CAC

description:
cell free DNA
Processed_Data
713


title: SHCPL000036CAC

description:
cell free DNA
Processed_Data
710


title: SHCPL000037CAC

description:
cell free DNA
Processed_Data
711


title: SHCPL000034CAC

description:
cell free DNA
Processed_Data
708


title: SHCPL000033CAC

description:
cell free DNA
Processed_Data
707


title: SHCPL000035CAC

description:
cell free DNA
Processed_Data
709


title: SHCPL000030CAC

description:
cell free DNA
Processed_Data
704


title: SHCPL000049CAC

description:
cell free DNA
Processed_Data
914


title: SHCPL000029CAC

description:
cell free DNA
Processed_Data
703


title: SHCTU000039CAC

description:
Processed_Data
763


title: SHCPL000031CAC

description:
cell free DNA
Processed_Data
705


title: SHCPL000038CAC

description:
cell free DNA
Processed_Data
712


title: SHCPL000032CAC

description:
cell free DNA
Processed_Data
706


title: SHCPL000026CAC

description:
cell free DNA
Processed_Data
701


title: SHCPL000027CAC

description:
cell free DNA
Processed_Data
702


title: SHCPL000025CAC

description:
cell free DNA
Processed_Data
700


title: SHCPL000021CAC

description:
cell free DNA
Processed_Data
698


title: SHCPL000020CAC

description:
cell free DNA
Processed_Data
697


title: SHCTI000045CAC

description:
Processed_Data
760


title: SHCTI000043CAC

description:
Processed_Data
666


title: SHCTU000040CAC

description:
Processed_Data
528


title: SHCPL000018CAC

description:
cell free DNA
Processed_Data
695


title: SHCTI000042CAC

description:
Processed_Data
665


title: SHCTU000041CAC

description:
Processed_Data
529


title: SHCPL000019CAC

description:
cell free DNA
Processed_Data
696


title: SHCPL000043CAC

description:
cell free DNA
Processed_Data
716


title: SHCTU000036CAC

description:
Processed_Data
525


title: SHCTU000037CAC

description:
Processed_Data
526


title: SHCTU000038CAC

description:
Processed_Data
527


title: SHCTU000035CAC

description:
Processed_Data
524


title: SHCTU000034CAC

description:
Processed_Data
523


title: SHCTU000030CAC

description:
Processed_Data
519


title: SHCTU000028CAC

description:
Processed_Data
517


title: SHCTU000027CAC

description:
Processed_Data
516


title: SHCTU000031CAC

description:
Processed_Data
520


title: SHCTU000029CAC

description:
Processed_Data
518


title: SHCTU000025CAC

description:
Processed_Data
514


title: SHCTU000032CAC

description:
Processed_Data
521


title: SHCPL000023CAC

description:
cell free DNA
Processed_Data
699


title: SHCTU000024CAC

description:
Processed_Data
513


title: SHCTI000041CAC

description:
Processed_Data
511


title: SHCTU000023CAC

description:
Processed_Data
512


title: SHCTU000026CAC

description:
Processed_Data
515


title: SHCTI000039CAC

description:
Processed_Data
509


title: SHCTI000038CAC

description:
Processed_Data
508


title: SHCTI000037CAC

description:
Processed_Data
507


title: SHCTI000034CAC

description:
Processed_Data
504


title: SHCTI000035CAC

description:
Processed_Data
505


title: SHCTI000033CAC

description:
Processed_Data
503


title: SHCTI000036CAC

description:
Processed_Data
506


title: SHCTU000033CAC

description:
Processed_Data
522


title: SHCTI000029CAC

description:
Processed_Data
499


title: SHCTI000031CAC

description:
Processed_Data
501


title: SHCTI000027CAC

description:
Processed_Data
497


title: SHCTI000026CAC

description:
Processed_Data
496


title: SHCTI000030CAC

description:
Processed_Data
500


title: SHCTI000028CAC

description:
Processed_Data
498


title: SHCTI000023CAC

description:
Processed_Data
493


title: SHCTU000020CAC

description:
Processed_Data
389


title: SHCTI000022CAC

description:
Processed_Data
386


title: SHCTI000021CAC

description:
Processed_Data
385


title: SHCTI000024CAC

description:
Processed_Data
494


title: SHCTU000022CAC

description:
Processed_Data
391


title: SHCTI000020CAC

description:
Processed_Data
384


title: SHCTI000018CAC

description:
Processed_Data
381


title: SHCTU000021CAC

description:
Processed_Data
390


title: SHCTU000019CAC

description:
Processed_Data
388


title: SHCTU000018CAC

description:
Processed_Data
387


title: SHCTI000019CAC

description:
Processed_Data
383


title: SHCTI000032CAC

description:
Processed_Data
502


title: SHCTU000017CAC

description:
Processed_Data
312


title: SHCTU000015CAC

description:
Processed_Data
311


title: SHCTU000014CAC

description:
Processed_Data
310


title: SHCTI000040CAC

description:
Processed_Data
510


title: SHCTU000012CAC

description:
Processed_Data
307


title: SHCTU000008CAC

description:
Processed_Data
300


title: SHCTU000009CAC

description:
Processed_Data
301


title: SHCTU000006CAC

description:
Processed_Data
297


title: SHCTU000004CAC

description:
Processed_Data
295


title: SHCTU000003CAC

description:
Processed_Data
294


title: SHCTU000001CAC

description:
Processed_Data
292


title: SHCTU000002CAC

description:
Processed_Data
293


title: SHCTU000005CAC

description:
Processed_Data
296


title: SHCTI000014CAC

description:
Processed_Data
288


title: SHCTI000015CAC

description:
Processed_Data
289


title: SHCTI000012CAC

description:
Processed_Data
286


title: SHCTI000006CAC

description:
Processed_Data
277


title: SHCTI000005CAC

description:
Processed_Data
276


title: SHCTI000001CAC

description:
Processed_Data
272


title: SHCTI000002CAC

description:
Processed_Data
273


title: SHCTI000008CAC

description:
Processed_Data
279


title: SHCPL000017CAC

description:
cell free DNA
Processed_Data
253


title: SHCTI000004CAC

description:
Processed_Data
275


title: SHCTI000003CAC

description:
Processed_Data
274


title: SHCPL000016CAC

description:
cell free DNA
Processed_Data
252


title: SHCTI000009CAC

description:
Processed_Data
280


title: SHCPL000015CAC

description:
cell free DNA
Processed_Data
251


title: SHCPL000014CAC

description:
cell free DNA
Processed_Data
250


title: SHCPL000011CAC

description:
cell free DNA
Processed_Data
248


title: SHCPL000009CAC

description:
cell free DNA
Processed_Data
246


title: SHCPL000007CAC

description:
cell free DNA
Processed_Data
244


title: SHCPL000013CAC

description:
cell free DNA
Processed_Data
249


title: SHCPL000004CAC

description:
cell free DNA
Processed_Data
241


title: SHCPL000008CAC

description:
cell free DNA
Processed_Data
245


title: SHCPL000003CAC

description:
cell free DNA
Processed_Data
240


title: SHCPL000002CAC

description:
cell free DNA
Processed_Data
239


title: SHCPL000006CAC

description:
cell free DNA
Processed_Data
243


title: SHCTI000017CAC

description:
Processed_Data
290


title: SHCPL000005CAC

description:
cell free DNA
Processed_Data
242


title: SHCPL000001CAC

description:
cell free DNA
Processed_Data
238


title: SHBPL000108NOR

description:
cell free DNA
Processed_Data
1534

value: stomach


title: SHBPL000111NOR

description:
cell free DNA
Processed_Data
1530


title: SHBPL000103NOR

description:
cell free DNA
Processed_Data
1556


title: SHBPL000106NOR

description:
cell free DNA
Processed_Data
1514


title: SHBPL000099NOR

description:
cell free DNA
Processed_Data
1528


title: SHBPL000107NOR

description:
cell free DNA
Processed_Data
1503


title: SHBPL000100NOR

description:
cell free DNA
Processed_Data
1510


title: SHBPL000113CAC

description:
cell free DNA
Processed_Data
1485


title: SHCTI000025CAC

description:
Processed_Data
495


title: SHBPL000115CAC

description:
cell free DNA
Processed_Data
1497


title: SHBPL000104CAC

description:
cell free DNA
Processed_Data
1486


title: SHBPL000110CAC

description:
cell free DNA
Processed_Data
1483


title: SHBPL000098CAC

description:
cell free DNA
Processed_Data
1261


title: SHBPL000109CAC

description:
cell free DNA
Processed_Data
1478


title: SHBPL000097NOR

description:
cell free DNA
Processed_Data
1260


title: SHBPL000096NOR

description:
cell free DNA
Processed_Data
1259


title: SHBPL000090CAC

description:
cell free DNA
Processed_Data
1254


title: SHBPL000095NOR

description:
cell free DNA
Processed_Data
1258


title: SHBPL000088NOR

description:
cell free DNA
Processed_Data
1252


title: SHBPL000094NOR

description:
cell free DNA
Processed_Data
1257


title: SHBPL000112NOR

description:
cell free DNA
Processed_Data
1498


title: SHBPL000093NOR

description:
cell free DNA
Processed_Data
1256


title: SHBPL000087NOR

description:
cell free DNA
Processed_Data
1251


title: SHBPL000086CAC

description:
cell free DNA
Processed_Data
1250


title: SHBPL000083NOR

description:
cell free DNA
Processed_Data
1247


title: SHBPL000091NOR

description:
cell free DNA
Processed_Data
1255


title: SHBPL000114NOR

description:
cell free DNA
Processed_Data
1508


title: SHBPL000080NOR

description:
cell free DNA
Processed_Data
1245


title: SHBPL000081CAC

description:
cell free DNA
Processed_Data
1246


title: SHBPL000089NOR

description:
cell free DNA
Processed_Data
1253


title: SHBPL000075NOR

description:
cell free DNA
Processed_Data
1243


title: SHBTU000068CAC

description:
Processed_Data
1235


title: SHBPL000074CAC

description:
cell free DNA
Processed_Data
1242


title: SHBPL000084CAC

description:
cell free DNA
Processed_Data
1248


title: SHBTI000066CAC

description:
Processed_Data
1232


title: SHBTI000068CAC

description:
Processed_Data
1233


title: SHBPL000076CAC

description:
cell free DNA
Processed_Data
1244


title: SHBPL000085NOR

description:
cell free DNA
Processed_Data
1249


title: SHBPL000068CAC

description:
cell free DNA
Processed_Data
1039


title: SHBPL000066CAC

description:
cell free DNA
Processed_Data
1037


title: SHBPL100067CAC

description:
cell free DNA
Processed_Data
1038


title: SHBPL000069CAC

description:
cell free DNA
Processed_Data
1040


title: SHBTU000063CAC

description:
Processed_Data
1025


title: SHBTU000062CAC

description:
Processed_Data
1024


title: SHBTU000061CAC

description:
Processed_Data
1023


title: SHBTU000066CAC

description:
Processed_Data
1234


title: SHBTU000060CAC

description:
Processed_Data
1022


title: SHBTU000059CAC

description:
Processed_Data
1021


title: SHBTI000061CAC

description:
Processed_Data
1017


title: SHBTI000060CAC

description:
Processed_Data
1016


title: SHBTI000058CAC

description:
Processed_Data
1014


title: SHBPL000064CAC

description:
cell free DNA
Processed_Data
913


title: SHBPL000062CAC

description:
cell free DNA
Processed_Data
911


title: SHBPL000057CAC

description:
cell free DNA
Processed_Data
909


title: SHBPL000065CAC

description:
cell free DNA
Processed_Data
1036


title: SHBPL000056CAC

description:
cell free DNA
Processed_Data
908


title: SHBPL000063CAC

description:
cell free DNA
Processed_Data
912


title: SHBPL000058CAC

description:
cell free DNA
Processed_Data
910


title: SHBPL000055CAC

description:
cell free DNA
Processed_Data
907


title: SHBTU000053CAC

description:
Processed_Data
755


title: SHBPL000049CAC

description:
cell free DNA
Processed_Data
902


title: SHBTU000052CAC

description:
Processed_Data
754


title: SHBPL000054CAC

description:
cell free DNA
Processed_Data
906


title: SHBPL000051CAC

description:
cell free DNA
Processed_Data
904


title: SHBPL000050CAC

description:
cell free DNA
Processed_Data
903


title: SHBTU000058CAC

description:
Processed_Data
1020


title: SHBTU000048CAC

description:
Processed_Data
750


title: SHBTU000049CAC

description:
Processed_Data
751


title: SHBTI000062CAC

description:
Processed_Data
1018


title: SHBTU000046CAC

description:
Processed_Data
748


title: SHBTI000059CAC

description:
Processed_Data
1015


title: SHBTU000050CAC

description:
Processed_Data
752


title: SHBTI000063CAC

description:
Processed_Data
1019


title: SHBTU000044CAC

description:
Processed_Data
746


title: SHBTU000041CAC

description:
Processed_Data
744


title: SHBTU000040CAC

description:
Processed_Data
743


title: SHBTU000045CAC

description:
Processed_Data
747


title: SHBTU000039CAC

description:
Processed_Data
742


title: SHBTU000038CAC

description:
Processed_Data
741


title: SHBPL000052CAC

description:
cell free DNA
Processed_Data
905


title: SHBPL000047CAC

description:
cell free DNA
Processed_Data
900


title: SHBTU000054CAC

description:
Processed_Data
756


title: SHBTI000054CAC

description:
Processed_Data
734


title: SHBTU000033CAC

description:
Processed_Data
736


title: SHBTU000036CAC

description:
Processed_Data
739


title: SHBTU000035CAC

description:
Processed_Data
738


title: SHBTU000051CAC

description:
Processed_Data
753


title: SHBTI000049CAC

description:
Processed_Data
729


title: SHBTI000052CAC

description:
Processed_Data
732


title: SHBTI000051CAC

description:
Processed_Data
731


title: SHBTI000046CAC

description:
Processed_Data
726


title: SHBTI000044CAC

description:
Processed_Data
724


title: SHBTI000045CAC

description:
Processed_Data
725


title: SHBTI000041CAC

description:
Processed_Data
722


title: SHBTI000040CAC

description:
Processed_Data
721


title: SHBTI000039CAC

description:
Processed_Data
720


title: SHBPL000046CAC

description:
cell free DNA
Processed_Data
694


title: SHBPL000045CAC

description:
cell free DNA
Processed_Data
693


title: SHBPL000044CAC

description:
cell free DNA
Processed_Data
692


title: SHBPL000042CAC

description:
cell free DNA
Processed_Data
691


title: SHBPL000036CAC

description:
cell free DNA
Processed_Data
687


title: SHBPL000039CAC

description:
cell free DNA
Processed_Data
688


title: SHBPL000041CAC

description:
cell free DNA
Processed_Data
690


title: SHBTU000037CAC

description:
Processed_Data
740


title: SHBPL000040CAC

description:
cell free DNA
Processed_Data
689


title: SHBPL000035CAC

description:
cell free DNA
Processed_Data
686


title: SHBTU000034CAC

description:
Processed_Data
737


title: SHBPL000027CAC

description:
cell free DNA
Processed_Data
679


title: SHBPL000029CAC

description:
cell free DNA
Processed_Data
681


title: SHBPL000031CAC

description:
cell free DNA
Processed_Data
683


title: SHBPL000033CAC

description:
cell free DNA
Processed_Data
685


title: SHBPL000025CAC

description:
cell free DNA
Processed_Data
677


title: SHBPL000032CAC

description:
cell free DNA
Processed_Data
684


title: SHBTI000048CAC

description:
Processed_Data
728


title: SHBTI000053CAC

description:
Processed_Data
733


title: SHBPL000023CAC

description:
cell free DNA
Processed_Data
675


title: SHBPL000028CAC

description:
cell free DNA
Processed_Data
680


title: SHBTI000050CAC

description:
Processed_Data
730


title: SHBPL000022CAC

description:
cell free DNA
Processed_Data
674


title: SHBPL000017CAC

description:
cell free DNA
Processed_Data
672


title: SHBPL000010CAC

description:
cell free DNA
Processed_Data
667


title: SHBPL000013CAC

description:
cell free DNA
Processed_Data
669


title: SHBPL000016CAC

description:
cell free DNA
Processed_Data
671


title: SHBTI000036CAC

description:
Processed_Data
662


title: SHBTI000038CAC

description:
Processed_Data
664


title: SHBPL000014CAC

description:
cell free DNA
Processed_Data
670


title: SHBTI000035CAC

description:
Processed_Data
661


title: FLAG1 (FA)

city: Rochester

first: Benoit

last: Biteau

address: KMRB 2-9905 601 Elmwood Ave

department: Genetics

institute: University of Rochester

description: mRNA-FLAG enriched

data_processing:
Illumina MiSeq was used for sequencing. Default base calling parameters were used.
Fastq files were analyzed using a standard Tuxedo pipeline, using Tophat for mapping reads to Drosphila genome release 5.57
Genome_build: Drosophila melanogaster genome release 5.57
Supplementary_files_format_and_content: excel file containing matrix table of RPKM values for each sample

organism: Drosophila melanogaster

source_name: whole fly lysate

growth_protocol: flies were raised on standard yeast and molasses-based food and 65% humidity, on a 12-hour light/dark cycle.

extract_protocol:
Flies with intestinal progenitor cells expressing FLAG-Tis11 were snap frozen in liquid nitrogen and crushed.  Pulverized tissue was resuspended in polysome lysis buffer.  Protein G Dynabeads (Invitrogen) were coated with either 2.5 µg Mouse anti-FLAG antibodies (Sigma-Aldrich) or 2.5 µg Mouse IgG2A proteins (Sigma-Aldrich).   Fly lysates were added to prepared beads, in duplicate (FLAG1, FLAG2, IgG1, IgG2), and incubated as directed.  Following the IP, beads were washed and a fraction was set aside to analyze for the enrichment of Tis11 protein.  The remainder was treated with Trizol (Invitrogen) to extract the Tis11-bound mRNAs
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: transgenes were expressed for 3 days, 3 days after adult flies emerged from pupae, before harvesting material.  Twenty-four hours prior to harvesting material, flies were infected with Erwinia carotovora carotovora (OD100).

tag: genetic background

tag: rip antibody

value: anti-FLAG monoclonal (sigma-aldrich)


title: FLAG2 (FB)

description: mRNA-FLAG enriched


title: SHBTI000034CAC

description:
Processed_Data
660


title: SHBTI000033CAC

description:
Processed_Data
659


title: IgG1 (IA)

description: mRNA-FLAG enriched

value: mouseIgG monoclonal (sigma-aldrich)


title: SHBTU000032CAC

description:
Processed_Data
492


title: IgG2 (IB)

description: mRNA-FLAG enriched


title: SHBTU000029CAC

description:
Processed_Data
491


title: SHBPL000018CAC

description:
cell free DNA
Processed_Data
673


title: SHBTU000028CAC

description:
Processed_Data
490


title: SHBTU000027CAC

description:
Processed_Data
489


title: Tis11RNAi infection (ISCs expressing Tis11RNAi)

description: mRNA-total

source_name: intestinal stem cells

extract_protocol:
intestines with GFP labled progenitor cells were dissected and trypsinized to yield a single cell suspension. Progenitors were then sorted by FACs and mRNA was extracted with trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: not applicable


title: SHBPL000011CAC

description:
cell free DNA
Processed_Data
668


title: SHBTU000024CAC

description:
Processed_Data
486


title: FLAGTis11 infection  (ISCs overexpressing Tis11)

description: mRNA-total


title: control zebrafish embryos transcriptome

city: Beijing

first: Lu

last: WANG

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: control zebrafish embryos transcriptome

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat2 for RNA-seq and BWA for MeDIP-seq,respectively.
For each sample, reads counts of all genes were computed using HTSeq 0.6.1
Genome_build: zv9
Supplementary_files_format_and_content: Transcriptome_ExpLevel.xls: Reads count for each gene of all samples
Supplementary_files_format_and_content: MeDIP_Peak.xls: 5mC peaks indentified by macs2 software

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
For MeDIP-seq, genome DNA was isolate from whole embryos at 80% epi stage using phenol-chloroform extraction. For RNA-seq, RNA was isolated from whole embryos of control and dnmt1 morphant zebrafish embryos using Trizol(Tiangen) by following the company manual.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole embryos

tag: cell type

value: normal zebrafish embryos cells

tag: developmental stage

value: 10 somite stage


title: dnmt1 morphants zebrafish embryos MeDIP rep2

value: dnmt1 morphants zebrafish embryos cells

value: 80%epi stage


title: SHBTI000037CAC

description:
Processed_Data
663

value: cancer


title: dnmt1 morphants zebrafish embryos  transcriptome


title: dnmt1 morphants zebrafish embryos MeDIP rep1


title: control zebrafish embryos MeDIP rep2

description: control zebrafish embryos MeDIP rep2


title: SHBTU000025CAC

description:
Processed_Data
487


title: SHBTU000023CAC

description:
Processed_Data
485


title: SHBTU000022CAC

description:
Processed_Data
484


title: SHBTU000020CAC

description:
Processed_Data
482


title: SHBTU000021CAC

description:
Processed_Data
483


title: control zebrafish embryos MeDIP rep1

description: control zebrafish embryos MeDIP rep1


title: w118 infection (control)

description: mRNA-total