title: Pwp2Lib4_BCtoPr

description:
Barcode to promoter assignment
processed data file: pwp2_lib4_results.tab

data_processing:
Library strategy: DNA-seq
Basecalls performed using MiSeq and HiSeq control software.
For reporter assay libraries, fastq files were trimmed to the promoter sequence and aligned to mm9 using bowtie for libraries where the design allowed efficient alignment (See table 2). For mutant promoter libraries, reads were matched to the reference sequences using the "stringdistmatrix" function in R (van der Loo, 2014). The frequency of each barcode sequence was calculated to get counts for each sample. Genomic DNA and RNA samples were scaled to each other by normalizing to the smaller total number of counts. Only barcodes that were sufficiently represented on genomic DNA (more than 20 reads after scaling) were used for further analysis. Enrichments of barcodes in the RNA sample were then calculated as nr/nd + alpha, where nr are the RNA counts and nd the DNA counts for a particular barcode and alpha represents a pseudo-count, set to 0.05.
ChIP-seq samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (Gaidatzis et al, 2015), which internally uses bowtie (Langmead et al, 2009). ChIP-seq peaks were called using Peakzilla with default parameters (Bardet et al, 2013)
For amplicon Bis-seq, sequences were aligned to the mutant promoter libraries using QuasR (Gaidatzis et al, 2015), using default settings for Bis-converted samples. DNA methylation was quantified using qMeth and the average methylation across each promoter was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Activities (Act_*), number of barcodes (nBCs_*), activities relative to the wt sequence (relAct_*), percentage of C+Gs (GC), percentage of dinucleotides that are CpGs (CpG), CpG observed/expected (OE), number of CpGs (nCGs), coordinates (chr, start, end, strand), percentage of CpGs mutated (CpGmut), qPCR values (qPCR), fraction methylated (methylation).

source_name: plasmid

value: plasmid

value: reporter assay


title: clone_2

status: Public on Jan 20 2019

type: SRA

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Bisulfite sequencing
processed data file: HKG_methylation.tab

library_source: genomic

data_processing:
Basecalls performed using MiSeq and HiSeq control software.
For reporter assay libraries, fastq files were trimmed to the promoter sequence and aligned to mm9 using bowtie for libraries where the design allowed efficient alignment (See table 2). For mutant promoter libraries, reads were matched to the reference sequences using the "stringdistmatrix" function in R (van der Loo, 2014). The frequency of each barcode sequence was calculated to get counts for each sample. Genomic DNA and RNA samples were scaled to each other by normalizing to the smaller total number of counts. Only barcodes that were sufficiently represented on genomic DNA (more than 20 reads after scaling) were used for further analysis. Enrichments of barcodes in the RNA sample were then calculated as nr/nd + alpha, where nr are the RNA counts and nd the DNA counts for a particular barcode and alpha represents a pseudo-count, set to 0.05.
ChIP-seq samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (Gaidatzis et al, 2015), which internally uses bowtie (Langmead et al, 2009). ChIP-seq peaks were called using Peakzilla with default parameters (Bardet et al, 2013)
For amplicon Bis-seq, sequences were aligned to the mutant promoter libraries using QuasR (Gaidatzis et al, 2015), using default settings for Bis-converted samples. DNA methylation was quantified using qMeth and the average methylation across each promoter was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Activities (Act_*), number of barcodes (nBCs_*), activities relative to the wt sequence (relAct_*), percentage of C+Gs (GC), percentage of dinucleotides that are CpGs (CpG), CpG observed/expected (OE), number of CpGs (nCGs), coordinates (chr, start, end, strand), percentage of CpGs mutated (CpGmut), qPCR values (qPCR), fraction methylated (methylation).

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured on cell culture plates coated with 0.2% gelatine in DMEM medium with 15% fetal calf serum, 2mM L-glutamine, 1 x non-essential amino acids, LIF and 0.001% b-mercaptoethanol. Cells were incubated at 37 °C with 7% CO2.

extract_protocol:
RNA was isolated from cell lines containing the expression libraries with Quiagen RNeasy Mini Kit with on-column DNase digestion and reverse transcribed using Takara PrimeScript RT Reagent Kit (#RR047A). For DNA isolation cell pellet was resuspended in Bradleys-Buffer, 6 ul RNaseA (10mg/ml) was added and samples were incubated for 1h at 37 degree C. Subsequently 30 ul protease K was added and samples were incubated at 50 degree C over night. Then DNA was extracted using Phenol and Chloroform. Bio-ChIP was performed as previously described (Baubec et al, 2013). For amplicon Bis-seq, cells containing integrated mutant CGI promoter libraries were thawed, plated at low density and 96 clones picked and expanded to a minimum cell number of 20,000 cells. Cells were lysed with Baradley Buffer (10mM Tris-HCl (pH 7.5), 10mM EDTA (pH 8.0), 0.5% SDS, 10mM NaCl) and DNA extracted with beads (Homemade). DNA was Bisulfite converted using Zymo lightning conversion kit (D5046) and cleaned up using MagBeads (Zymno). Bis-converted DNA was amplified with primers RSG353 and RSG354 (Table 1). Amplified DNA was purified with Ampure beads and sequencing libraries were prepared using the Illumina NEBNext ChIP-seq library prep kit with 96 dual indexing.
DNA and cDNA barcodes were amplified with KAPA HIFI Hotstart using Primer DH.P6 and indexing primer (Table 1). PCR products were purified using AmPure XP beads (Beckman Coulter, #A63880) and sequenced using 50 cycle Kit on HiSeq 2500.

treatment_protocol: Mouse embryonic stem cells with a RMCE site in the beta-globin locus were used for integration of expression libraries for the transcriptional reporter assay (Lienert et al, 2011). Dnmt1, Dnmt3a and Dnmt3b was deleted in these cells using CRISPR-Cas9 gene editing as previously described (Domcke et al, 2015). Mouse HA36 ES cells (mixed 129-C57Bl/6 strain) were used for Bio-ChIP (Baubec et al, 2013).

tag: tissue

value: embryonic stem cells

tag: genotype

value: Wild Type

tag: library type

value: amplicon Bis-seq


title: clone_16


title: Snx3lib1_BCtoPr

description:
Barcode to promoter assignment
processed data file: Snx3Lib1_results.tab


title: Pwp2lib3_BCtoPr

description:
Barcode to promoter assignment
processed data file: pwp2_lib3_results.tab


title: HKGlib2_rep1_gDNA

description:
DNA Barcodes
processed data file: HKGlib2_results.tab


title: HKGlib1_rep1_cDNA

description:
RNA Barcodes
processed data file: HKGlib1_results.tab

library_source: transcriptomic

molecule: total RNA


title: HKGlib2_rep1_cDNA

description:
RNA Barcodes
processed data file: HKGlib2_results.tab


title: HKGlib1_BCtoPr

description:
Barcode to promoter assignment
processed data file: HKGlib1_results.tab


title: Input

description: Bio-ChIP

source_name: Mouse HA36 ES cells

value: Mouse HA36 ES cells

value: ChIPseq


title: Gabpa_rep2

description: Bio-ChIP


title: Gabpa_rep3

description: Bio-ChIP


title: Sp3_rep3

description: Bio-ChIP


title: HKGlib2_BCtoPr

description:
Barcode to promoter assignment
processed data file: HKGlib2_results.tab


title: Sp3_rep1

description: Bio-ChIP


title: Sp3_rep2

description: Bio-ChIP


title: Gabpa_rep1

description: Bio-ChIP


title: Pwp2Lib5_BCtoPr

description:
Barcode to promoter assignment
processed data file: pwp2_lib5_results.tab


title: HKGlib1_rep2_gDNA

description:
DNA Barcodes
processed data file: HKGlib1_results.tab


title: Sp1_rep3

description: Bio-ChIP


title: Sp1_rep2

description: Bio-ChIP


title: HKGlib1_rep2_cDNA


title: Sp1_rep1

description: Bio-ChIP


title: CpGdensitylib1_rep2_gDNA_S223

description:
DNA Barcodes
processed data file: CpGDensitylib1_results.tab


title: CpGdensitylib1_rep2_cDNA_S222

description:
RNA Barcodes
processed data file: CpGDensitylib1_results.tab


title: DN1c_D4

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

country: USA

institute: OMRF

data_processing:
Raw fastq files were imported into Strand software (v9.5, Agilent) for trimming, alignment and statistical analysis.  Sequence with a Q score of <30 were discarded, 1 base from the 3’ and 5’, and adaptors sequences were removed.
Reads were aligned to mm10  and duplicate reads were removed. Raw counts  were computed for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

source_name: DN1 thymocytes cultured on OP9-DL1 in ILC2 condition for 4 days

extract_protocol:
trizol was used to extract RNA using standard protocol from the vendor.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: thymus

tag: cell type

value: DN1 thymocytes


title: CpGdensitylib1_rep3_cDNA_S224


title: HKGmutlib3_BCtoPr

description:
Barcode to promoter assignment
processed data file: HKGlib3_results.tab


title: CpGdensitylib1_rep1_cDNA_S220


title: HKGlib1_rep1_gDNA


title: DN1a_D4


title: Pwp2lib5_rep3_cDNA_TKO

description:
RNA Barcodes
processed data file: pwp2_lib5_results.tab

value: Dnmt1, Dnmt3a, Dnmt3b triple knock-out


title: Pwp2lib5_rep3_gDNA_TKO

description:
DNA Barcodes
processed data file: pwp2_lib5_results.tab


title: Pwp2lib5_rep2_gDNA_TKO


title: Pwp2lib5_rep1_cDNA_TKO


title: Pwp2lib5_rep1_gDNA_TKO


title: Pwp2lib5_rep2_gDNA


title: CpGdensitylib1_rep1_gDNA_S221


title: Pwp2lib4_rep1_cDNA

description:
RNA Barcodes
processed data file: pwp2_lib4_results.tab


title: Pwp2lib5_rep1_gDNA


title: Pwp2lib5_rep2_cDNA


title: Pwp2lib4_rep3_cDNA


title: Pwp2lib4_rep3_gDNA

description:
DNA Barcodes
processed data file: pwp2_lib4_results.tab


title: Pwp2lib4_rep1_gDNA


title: Pwp2lib4_rep2_cDNA


title: Pwp2lib3_rep3_cDNA_TKO

description:
RNA Barcodes
processed data file: pwp2_lib3_results.tab


title: Pwp2lib3_rep3_gDNA_TKO

description:
DNA Barcodes
processed data file: pwp2_lib3_results.tab


title: Pwp2lib3_rep2_gDNA_TKO


title: Pwp2lib4_rep2_gDNA


title: Pwp2lib3_rep1_gDNA_TKO


title: Pwp2lib3_rep1_cDNA_TKO


title: Pwp2lib3_rep3_gDNA


title: Pwp2lib3_rep2_cDNA_TKO


title: Pwp2lib5_rep2_cDNA_TKO


title: Pwp2lib3_rep3_cDNA


title: Pwp2lib3_rep2_gDNA


title: Pwp2lib3_rep2_cDNA


title: Pwp2lib5_rep3_gDNA


title: Pwp2lib5_rep3_cDNA


title: Pwp2lib3_rep1_gDNA


title: Pwp2lib3_rep1_cDNA


title: Snx3lib1_rep3_gDNA_TKO

description:
DNA Barcodes
processed data file: Snx3Lib1_results.tab


title: Snx3lib1_rep2_gDNA_TKO


title: Snx3lib1_rep1_gDNA_TKO


title: Snx3lib1_rep1_cDNA_TKO

description:
RNA Barcodes
processed data file: Snx3Lib1_results.tab


title: Snx3lib1_rep3_gDNA


title: Snx3lib1_rep3_cDNA_TKO


title: Snx3lib1_rep2_cDNA_TKO


title: Snx3lib1_rep2_cDNA


title: Snx3lib1_rep3_cDNA


title: HKGmutlib3_rep2_gDNA_TKO

description:
DNA Barcodes
processed data file: HKGlib3_results.tab


title: Snx3lib1_rep1_cDNA


title: HKGmutlib3_rep3_cDNA_TKO

description:
RNA Barcodes
processed data file: HKGlib3_results.tab


title: Snx3lib1_rep2_gDNA


title: HKGmutlib3_rep3_gDNA


title: HKGmutlib3_rep1_cDNA_TKO


title: HKGmutlib3_rep1_gDNA_TKO


title: HKGmutlib3_rep2_cDNA_TKO


title: Snx3lib1_rep1_gDNA


title: HKGmutlib3_rep2_cDNA


title: HKGmutlib3_rep1_gDNA


title: HKGmutlib3_rep3_cDNA


title: HKGmutlib3_rep1_cDNA


title: HKGmutlib3_rep2_gDNA


title: HKGlib2gDNA_rep3

description:
DNA Barcodes
processed data file: HKGlib2_results.tab


title: PRIMARY_CHOR_A269A1_H3K27AC (CF_269)

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
All datasets were aligned using Bowtie2 (version 2.2.1) to build version NCBI37/HG19 (Langmead et al., 2009). Alignments were performed using all default parameters except for –N 1.
wiggles were made using MACS 1.4.2 pileups
Genome_build: hg19
Supplementary_files_format_and_content: .wig wiggles of read pileups across the whole genome

organism: Homo sapiens

source_name: patient-derived chordoma CF_269

extract_protocol:
For H3K27ac ChIP of patient-derived tissue: approximately 100 mg of flash-frozen tissue was minced into 1-2 mm pieces and incubated in 1% formaldehyde for 15 minutes, followed by quenching with glycine (125 mM final concentration). Fixed tissue pieces were homogenized with a Tissue Tearor rotor stator homogenizer (Biospec) set to 30,000 RPM for 60 seconds. Homogenate was washed with ice-cold PBS containing 1X HALT protease inhibitor. Homogenized pellets were then resuspended in cytosolic lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL, 0.25% Triton X-100, 1X HALT protease inhibitor) and the protocol was continued as described below. For H3K27ac ChIP of chordoma cell lines: Chordoma cell lines were grown in 175 cm collagen I-coated plates (3 plates per cell line) and cross-linked by adding 1/10 of the cell culture volume of 11% formaldehyde solution (1M HEPES-KOH pH 7.5, 0.5 M EDTA pH 8.0, 0.5 M EGTA pH 8.0, 5 M NaCl, 37% formaldehyde) for 10 minutes, followed by quenching (125 mM glycine). Cells were washed in PBS and harvested by cell scraper in PBS. Cells were centrifuged at 1,350 X g for 5 min at 4°C, washed with PBS, and centrifuged again at 1,350 X g for 5 min at 4°C. Cell pellets were flash frozen and stored at -80°C until further processing.
For both cell line and tissue ChIP-seq: samples were subsequently rotated end-over-end for 10 minutes at 4º C in cytosolic lysis buffer and then collected by spinning at 1,350 x g for 5 minutes. Samples were resuspended in nuclear lysis buffer (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 1X HALT protease inhibitor) and rotated end-over-end for 10 minutes at 4º C and spun at 1,350 x g for 5 minutes. Samples were resuspended in 1 mL sonication buffer ( 0.1% Na-Deoxycholate, 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 1X HALT protease inhibitor) with SDS added to a final concentration of 0.5%. Chromatin was sheared by sonication using a Bioruptor water bath sonicator (Diagenode) for 25 cycles. Samples were clarified by centrifuging 10 minutes at 20,000 x g at 4º C. A 50 uL aliquot of supernatant was set aside as non-IP input control. The remaining sheared chromatin was diluted 1:5 in sonication buffer and each sample was incubated overnight at 4º C with 100 uL of Protein G Dynabeads (Life Technologies) bound with 10 µg of anti-H3K27ac antibody (abcam, #ab4729). Beads were washed while rotating end-over-end at 4º C with the following buffers: twice in sonication buffer, once in sonication buffer with NaCl added to a final concentration of 500 mM, once in LiCl wash buffer (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% IGEPAL, 0.5% Na-Deoxycholate), and once in TE-NaCl buffer (50 mM Tris-HCl pH 8, 50 mM NaCl). Chromatin was eluted by resuspending beads in 200 uL elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) and heating for 15 minutes at 65º C. Beads were pelleted by centrifuging at 20,000 G for 30 seconds and supernatant was collected. Elution buffer (150 uL) was also added to input chromatin samples. Samples were incubated at 65º C overnight to reverse crosslinks. Samples were then incubated with RNAse A (Thermo Scientific) for 2 hours at 37º C, followed by incubation with Proteinase K (Ambion) for 30 minutes at 55º C. DNA isolation was performed via phenol-chloroform extraction and concentrated by ethanol precipitation. Sequencing libraries were generated with the Thruplex DNAseq Single Index Kit (Rubicon) and sequenced on an Illumina NextSeq 500 with single-end, 75 bp reads. ChIP-seq was performed once for each sample.

value: patient-derived chordoma CF_269

tag: antibody

tag: barcode

value: TACAGGAT

tag: antibody maker

value: abcam

tag: antibody catalog number


title: HKGlib2gDNA_rep2


title: HKGlib2cDNA_rep3

description:
RNA Barcodes
processed data file: HKGlib2_results.tab


title: HKGlib2cDNA_rep2


title: HKGlib1_cDNA_rep3

description:
RNA Barcodes
processed data file: HKGlib1_results.tab


title: HKGmutlib3_rep3_gDNA_TKO


title: HKGlib1_gDNA_rep3

description:
DNA Barcodes
processed data file: HKGlib1_results.tab


title: clone_96

description:
Bisulfite sequencing
processed data file: HKG_methylation.tab


title: clone_93


title: clone_92


title: clone_95


title: clone_94


title: h3k4me3_norm3

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

data_processing:
We extended the 34-bp reads toward the 3’ end to cover DNA fragments bound by the specific modified histone proteins. The readout was converted to browser extensible data (BED) files for visualization in the UCSC genome browser (http://genome.ucsc.edu).
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: Normal liver_H3k4me3

extract_protocol:
Small liver pieces were incubated for 10 min at room temperature in 1× phosphate-buffered saline (PBS) containing 1% formaldehyde. The crosslinking reaction was quenched by adding glycine to a final concentration of 0.125 M. After a wash in 1× PBS, liver pieces were homogenized in lysis buffer and incubated for 10 min on ice. Nuclei were pelleted and resuspended in 1× TE buffer. Nuclei were sonicated using a Bioruptor (Diagenode, Liege, Belgium). Chromatin samples were diluted with 2× RIPA buffer to a final 1× concentration. IPs were performed with primary antibody and Dynabeads Protein A complex overnight at 4°C. Immune complexes were washed twice for 10 min in each of the following buffers: 1× RIPA buffer, 1× RIPA + 0.3 M NaCl, LiCl buffer, 1× TE + 0.2% Triton X-100, 1× TE. Then, immune complexes were in 100 μl 1× TE, protease K, and 0.3% sodium dodecyl sulfate (SDS) and incubated at 65°C overnight. Eluted DNA was purified using a QIAGEN PCR purification kit. Buffers were comprised of the following: lysis buffer (10 mM Tris [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1× TE; 10 mM Tris-HCl [pH 7.5], and 1 mM EDTA), 1× RIPA (1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and 10 mM Tris [pH 7.5], 1 mM EDTA), LiCl buffer (0.25 M LiCl, 0.5% NP40, and 0.5% sodium deoxycholate). Every buffer included 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN). The following antibodies were used: H3Ace (06-599, Upstate/Millipore, Temecula, CA), H3K36me3 (ab9050, abcam), H3K27me3 (07-449, Upstate/Millipore, Temecula, CA), H3K4me3 (07-473, Upstate/Millipore, Temecula, CA), RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (abcam, ab5131). RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody (abcam, ab5095), Anti-H3 (millipore 06-755).
Illumina ChIP library prep (Part # 11251892 Rev. A)

tag: phenotype

value: Normal liver

value: Liver

tag: background strain


title: clone_88


title: clone_90


title: h3k36me3_norm3

source_name: Normal liver_h3k36me3


title: clone_89


title: clone_87


title: h3k27me3_norm3

source_name: Normal liver_h3k27me3


title: clone_86


title: clone_85


title: sg-T_2 rep 1

city: Cambridge

first: Tanaz

last: Sharifnia

address: 415 Main Street

department: Chemical Biology and Therapeutics Science Program

institute: Broad Institute

description:
processed data file: all_counts.txt
sgT2_a

data_processing:
Base calls performed with Illumina RTA
Reads were trimmed for adapter sequences with TrimGalore (version 0.4.1)
Reads were aligned to the genome (GRCh38) and quantified with STAR (version 2.4.2) using the Gencode annotation (version 23)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file contains read counts per gene for all samples

source_name: UM-Chor1 chordoma cells

growth_protocol: UM-Chor1 cells were maintained in IMDM/RPMI (4:1) media + 10% fetal bovine serum (FBS) and 1X non-essential amino acids.

extract_protocol:
Cell pellets were used for RNA extraction using an RNeasy Kit (Qiagen).
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs), and libraries were sequenced using the Illumina HiSeq 2500 instrument (rapid-run mode) with paired-end 100 bp reads.

treatment_protocol: UM-Chor1 cells were incubated with lentivirus corresponding to the pXPR_001 plasmid, encoding either sg-T_1, sg-T_2, or sg-EGFP in the presence of 4 μg/mL polybrene, dispensed in 12-well plates (1.3 x 10^6 cells/well), and spin-infected at 2,000 rpm for 2 h at 30°C. After spin-infection, 2 mL of standard growth media was added to each well, and cells were incubated at 37°C overnight. The following day, cells were trypsinized and expanded in selective media containing puromycin (2 µg/mL). Following selection for infected cells, selective media was replaced with standard growth media, and cells were harvested 2 d later. Two biological replicates were generated for each condition.

tag: disease state

value: chordoma

tag: cell line

value: UM-Chor1 chordoma cells

tag: treatment


title: sg-T_2 rep 2

description:
processed data file: all_counts.txt
sgT2_b


title: clone_84


title: sg-T_1 rep 2

description:
processed data file: all_counts.txt
sgT1_b


title: sg-EGFP rep 2

description:
processed data file: all_counts.txt
sgEGFP_b

value: sg-EGFP


title: sg-T_1 rep 1

description:
processed data file: all_counts.txt
sgT1_a


title: clone_82


title: sg-EGFP rep 1

description:
processed data file: all_counts.txt
sgEGFP_a


title: MB3_C_RNA-seq

first: Cristina

last: Pina

address: Long Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description:
Count_Matrix.csv
sample name in processed data file: CMb3

data_processing:
Illumina software used for base-calling
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using Galaxy bowtie for illumina v1.1.2
BAM files were processed with DESeq by knowngenes, and empty/single read rows were filtered for processing
Genome_build: mm10
Supplementary_files_format_and_content: csv file with raw counts

molecule: polyA RNA

growth_protocol: Mouse embryonic stem cells with GFP reporter expression from a single Nanog locus allele (TNGA cells, Chambers et al., 2007) were grown in the presence of serum and Leukaemia Inhibitory Factor (LIF).

extract_protocol:
Cells were dissociated with Trypsin before RNA harvesting with Trizol, according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TNGA cells were treated in triplicate for 48h with either DMSO (vehicle) or the Gcn5/Kat2a inhibitor MB-3, at a dose of 100uM. All cultures received a final 0.1% volume of DMSO.

value: TNGA

value: embryonic stem cell line

value: Kat2 inhibitor MB-3


title: MB3_B_RNA-seq

description:
Count_Matrix.csv
sample name in processed data file: BMb3


title: h3k27me3_hbx3

source_name: HBx transgenic liver_h3k27me3

value: HBx transgenic liver


title: clone_81

value: embryonic stem cells

value: Wild Type

value: amplicon Bis-seq


title: clone_80


title: clone_91


title: DMSO_C_RNA-seq

description:
Count_Matrix.csv
sample name in processed data file: CDMSO

value: DMSO


title: DMSO_B_RNA-seq

description:
Count_Matrix.csv
sample name in processed data file: BDMSO


title: clone_79


title: MB3_A_RNA-seq

description:
Count_Matrix.csv
sample name in processed data file: AMb3


title: DMSO_A_RNA-seq

description:
Count_Matrix.csv
sample name in processed data file: ADMSO


title: clone_76


title: clone_77


title: DMSO_Input_DNA

data_processing:
Data were aligned to the mm9 genome with BWA before merging replicates together with samtools merge.
H3K9ac peaks were identified from merged samples using MACS2 using a q-value cut-off of 10e-2.
Differentially acetylated regions were determined using Diffbind from the DESeq2 package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bw: Signal tracks (bigwig) were generated from merged BAM aligned files using deepTools bamCoverage function, normalized to 1x sequencing depth, and a binning size of 50bp.
Supplementary_files_format_and_content: *_H3K9ac.bed: Bed files

extract_protocol:
10^7 cells per condition were cross-linked in 1% formaldehyde, lysed and sonicated as described (Tzelepis et al., 2016). Chromatin was immunoprecipitated with an anti-H3K9ac antibody (ab4441, AbCam) and captured with 1:1 protein A and protein G magnetic beads. After reverse cross-linking, immunoprecipitated and input DNA were purified using a Qiagen PCR purification kit.
Standard Illumina ChIP library protocols with Nextera indices.

treatment_protocol: TNGA cells were treated in duplicate for 48h with either DMSO (vehicle) or the Gcn5/Kat2a inhibitor MB-3, at a dose of 100uM. All cultures received a final 0.1% volume of DMSO.

tag: chip antibody


title: clone_75


title: clone_73


title: DMSO_H3K9ac_ChIPSeq

value: H3K9ac (Abcam, ab4441)


title: clone_74


title: Mb3_Input_DNA


title: SEL_KO_rep3

city: Rochester

first: Virginia

middle: Smith

last: Shapiro

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

data_processing:
Base calling and demultiplexing was performed with the Illumina bcl2fastq 1.8.4 software
The paired end reads were aligned by TopHat 2.1.0
QC was performed on the aligned BAM files using RSeQC software (http://rseqc.sourceforge.net/)
Gene counts were generated using Subread featureCounts (http://bioinf.wehi.edu.au/featureCounts/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Thymocytes

extract_protocol:
Thymi were harvested, processed for single cell suspension, and stained with antibody for cell sorting by FACS Aria.  RNA was extracted from FACS sorted cells with Qiazol (Qiagen) and purified using the RNeasy Micro kit (Qiagen) using DNase treatment, according to the manufacturer’s protocol.
TruSeq RNA Library Prep Kit v2

value: TCR-int CD69-pos thymocyte

value: OT-II CD2-icre HDAC3-cKO


title: SEL_KO_rep2


title: clone_70


title: Mb3_H3K9ac_ChIPSeq


title: clone_71


title: clone_83


title: SEL_KO_rep1


title: clone_72


title: clone_69


title: IMM_KO_rep3

value: TCR-lo CD69-neg thymocyte


title: IMM_KO_rep2


title: clone_68


title: IMM_KO_rep1


title: clone_67


title: clone_78


title: clone_66


title: clone_65


title: SEL_WT_rep2

value: OT-II


title: clone_64


title: SEL_WT_rep1


title: clone_63


title: clone_62


title: IMM_WT_rep3


title: IMM_WT_rep1


title: clone_61


title: clone_60


title: KO SEL_Input

data_processing:
ChIP-seq data was analyzed using the HiChIP pipeline (Yan et al., 2014). In a brief, raw reads were mapped to the reference genome (mm10) using BWA (v0.5.9) with default parameters for pair-end reads. Uniquely mapped reads were remained for further analysis.
Base calling and demultiplexing was performed with the Illumina bcl2fastq 1.8.4 software
Peak calling was performed using MASC2 (v2.0.10)
bigwig files were generated from bedGraph files that were generated from MACS.
Genome_build: mm10
Supplementary_files_format_and_content: Peak bed files
Supplementary_files_format_and_content: bigwig files

extract_protocol:
Thymi were harvested, processed for single cell suspension, and stained with antibody for cell sorting by FACS Aria.  Sorted samples were cross-linked with 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature. After washing with TBS, cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspendsion in 200 μL fresh MNase digestion buffer containing a proteinase inhibitor cocktail (Sigma), the lysates were incubated with 2,000 units of MNase (NEB, Cat # M0247S) per 4 x 106 cells at 37 °C for 20 min with continuous mixing in thermal mixer. After adding 200 μL of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 30 min (30 sec on / 30 sec off) using Bioruptor Twin (UCD-400) (Diagenode, Inc.) and centrifuged at 21,130 x g for 10 min. The supernants were collected, and the chromatin content was estimated by the Qubit assay (Invitrogen). For normalization of ChIP efficiency, Drosophila chromatin equivalent to about 5% of total chromatin was added. The chromatin was then incubated with anti-H3K27ac antibody (Abcam, Cat.# ab4729, lot# GR150367) or in-house generated anti-H3K9ac antibody (EDL lot 1) on a rocker overnight. Protein G-magnetic beads (30 μL, Life Technologies) were added, and further incubated for 3 hours. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
ChIP-seq libraries were prepared from about 5 ng ChIP and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to manufacturere protocol.


title: IMM_WT_rep2


title: clone_59


title: KO SEL_H3K27ac


title: clone_58


title: clone_57


title: KO IMM_H3K27ac


title: KO IMM_Input


title: KO SEL_H3K9ac

value: H3K9ac (in-house generated, EDL lot 1)


title: clone_56


title: KO IMM_H3K9ac


title: clone_54


title: WT SEL_Input


title: clone_55


title: clone_53


title: clone_52


title: SEL_WT_rep3


title: WT SEL_H3K27ac


title: clone_51


title: clone_50


title: WT SEL_H3K9ac


title: WT IMM_Input


title: clone_49


title: clone_48


title: WT IMM_H3K27ac


title: WT IMM_H3K9ac


title: S_SSc1120

status: Public on Jan 19 2019

type: RNA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro

source_name: biopsy from Systemic Sclerosis (SSc) patient

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

value: skin

source_name: Universal Human Reference

value: UHR cell line


title: S_SSc1215


title: S_SSc1138


title: NormN0903

source_name: biopsy from control


title: NormN1002


title: S_SSc0916


title: s15

city: Minneapolis

first: Rachel

middle: Stegeman

last: Graham

address: 2101 6th St SE

department: Pediatrics

institute: University of Minnesota

description: s15 control mouse, ultrasound treatment

data_processing:
Basecalling performed by NovaSeq 6000 software RTA3
Reads aligned to mm10 genome using Cell Ranger 2.1.0 using STAR 2.5.1b
Data was filtered: genes in detected in >0.1% cells per sample, and cells with detected genes >200 and <3000, <0.075 mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include filtered, normalized and scaled count values for each cell (UMI) in each sample

source_name: dissected spleen

extract_protocol:
extraction occurs similtaneously with library prep on a cell-by-cell basis
10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (v2) per manufactures instructions
All samples pooled and sequenced on 2 lanes of Illumina NovaSeq 6000 Sequencer

treatment_protocol: ultrasound treatment parameters: 1 MHz ultrasound at 350 kPa using 1s on/5s off bursts for a total of 12 minutes

tag: Sex

value: male

tag: age

value: 6 weeks

tag: serum injected

value: C57BL/6J mouse serum

value: ultrasound


title: s16

description: s16 arthritic mouse, ultrasound treatment

value: K/B.g7 mouse serum


title: s14

description: s14 arthritic mouse, sham treatment

value: sham


title: S_SSc0918

tag: tissue


title: S_SSc0920


title: S_SSc1205


title: NormN0901


title: NormN1003


title: S_SSc0882


title: DLL4-OMP-JeKo 48h

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

country: Spain

institute: IDIBAPS-HOSPITAL CLINIC

description: gene expression data in Jeko cells stimulated with DLL4 and treated with OMP-52M51  48h

hyb_protocol: RNA samples were processed in  Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA)  algorithm if the bioconductor Affy package

label: biotin

source_name: DLL4-OMP-JeKo 48h

label_protocol: Biotinylated cRNA  was prepared according affymetrix protocols fron 150 ng total RNA

growth_protocol: cells culured with RPMI 1640 supplemented with 10-20 % FCS. 2 mM Glutamine And 50 ug/ml penicillin/streptomycin

extract_protocol: Trizol extraction  of total RNA was done according manufacturer's instructions

treatment_protocol: cells were stimulated with DLL4  4 ug/mL and treated  with 25 ug/mL OMP-52M51

value: jeKo

value: Notch1 wt MCL cell line


title: DLL4--JeKo 48h

description: gene expression data in JeKo cells stimulated with DLL4  48h

source_name: DLL4--JeKo 48h


title: OMP--JeKo 48h

description: gene expression data in JeKo cells treated with OMP-52M51  48h

source_name: OMP--JeKo 48h


title: DLL4-OMP MINO 48H

description: gene expression data in Mino cells stimulated with DLL4 and treated with OMP-52M51  48h

source_name: DLL4-OMP MINO 48H

value: Mino

value: Notch1 mutated MCL cell line


title: DLL4-MINO 48H

description: gene expression data in Mino cells stimulated with DLL4  48h

source_name: DLL4-MINO 48H


title: Control-JeKo 48h

description: gene expression data in JeKo cells  48h

source_name: Control-JeKo 48h


title: LV, WT3

city: Kyoto

first: Masahiro

last: Nishi

address: Kajii-cho 465, Kawaramachi Hirokoji, Kamigyo

department: Cardiology

country: Japan

institute: Kyoto prefectural university of medicine

description: Gene exprssion data from WT adult mouse heart

hyb_protocol: RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: WT mouse heart

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total

growth_protocol: 10-13 week old C57BL/6 background male mice (wild-type and MURC knockout) were prepared.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Left ventricule tissue from 10–13-week-old wild type (WT) and MURC knockout (KO) male mouse hearts. After sacrificing the mice, the hearts were excised by cervical dislocation and stored at -80 °C. Total RNA was extracted from the tissue using TRIzol reagent according to the manufacturer’s instructions.

tag: gender

value: left ventricle

value: 12 week-old

tag: genotype

value: wild type (WT)


title: LV, MURCKO2

description: Gene exprssion data from MURCKO adult mouse heart

source_name: MURCKO mouse heart

tag: strain

value: 11 week-old

value: MURC knockout (KO)


title: LV, WT1

value: 13 week-old


title: LV, MURCKO1


title: LV, MURCKO3


title: OMP-MINO 48H

description: gene expression data in Mino cells treated with OMP-52M51  48h

source_name: OMP-MINO 48H


title: LV, WT2


title: Control- MINO 48H

description: gene expression data in Mino cells  48h

source_name: Control- MINO 48H


title: s12

description: s12 arthritic mouse, ultrasound treatment

tag: cell type


title: s10

description: s10 arthritic mouse, sham treatment


title: s09

description: s09 control mouse, sham treatment


title: s05

description: s05 control mouse, sham treatment


title: s06

description: s06 arthritic mouse, sham treatment


title: s08

description: s08 arthritic mouse, ultrasound treatment


title: s04

description: s04 arthritic mouse, ultrasound treatment


title: s07

description: s07 control mouse, ultrasound treatment


title: s03

description: s03 control mouse, ultrasound treatment


title: OA model_Lentiviruses expressing CBX4 rep3

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: Lentiviruses expressing CBX4

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: knee joints

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: An OA mouse model was generated as previously described. Briefly, anterior cruciate ligament transection (ACLT) was performed on male C57BL/6 mice aged 8 weeks. For the ACLT surgery, after opening the joint capsule, the ACL was transected with microscissors under a surgical micro-scope. One week after surgery, lentiviruses expressing Luc, CBX were injected into the articular cavity. Eight weeks after lentivirus injection, the mice were euthanized and the joints were collected for RNA extraction. The RNA samples of one treatment group were mixed and three technical repeats were performed for RNA-seq.

value: OA mouse model

value: knee joints

value: Lentiviruses expressing CBX4


title: OA model_Lentiviruses expressing CBX4 rep2

description: Lentiviruses expressing CBX4


title: OA model_Lentiviruses expressing Luc rep3

description: Lentiviruses expressing Luc

value: Lentiviruses expressing Luc


title: OA model_Lentiviruses expressing Luc rep2

description: Lentiviruses expressing Luc


title: OA model_Non surgery rep3

description: Non surgery

value: Non surgery


title: OA model_Lentiviruses expressing Luc rep1

description: Lentiviruses expressing Luc


title: OA model_Lentiviruses expressing CBX4 rep1

description: Lentiviruses expressing CBX4


title: s02

description: s02 arthritic mouse, sham treatment

value: male

value: 6 weeks

value: K/B.g7 mouse serum


title: s13

description: s13 control mouse, sham treatment

value: C57BL/6J mouse serum

value: sham


title: s11

description: s11 control mouse, ultrasound treatment

value: ultrasound


title: SRS5

city: Paris

first: Walid

last: Abi Habib

address: 28 avenue du dr arnold netter

country: France

data_processing:
Reads from each Fastq file was aligned to the reference human genome hg19/GRCh37 with tophat2 to determine insert sizes with Picard. Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2
We used HTSeq to obtain the number of reads associated to each gene in the Gencode v19 database, restricting to protein-coding genes, antisense and lincRNAs.
We used the Bioconductor DESeq package to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
After normalizing for library size, we normalized the count matrix by the coding length of genes to compute FPKM scores
Genome_build: human genome hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: SRS patient

growth_protocol: Skin-derived fibroblasts from patients and controls were cultured to confluence in RPMI 1640 (Gibco, Cergy Pontoise, France) supplemented with 10% fetal calf serum and 50 U/ml ampicillin/50 μg/ml streptomycin at 37°C

extract_protocol:
mRNA wasextracted from cultured fibroblasts with the NucleoSpin miRNA kit for the isolation of small and large RNAs (Macherey-Nagel, France).
Libraries were prepared with TruSeq Stranded mRNA kit protocol according supplier recommendations.

treatment_protocol: no treatment

value: skin-derived fibroblasts culture

tag: genomic defect

value: IGF2/H19 hypomethylation


title: SRS/TS14

source_name: SRS/TS14 patient

value: IGF2/H19 and DLK1/MEG3 hypomethylations


title: TS14-4

source_name: TS14 patient

value: DLK1/MEG3 hypomethylation


title: TS14-3


title: Doxycycline-rep1

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
sample name in raw data files:
DXP1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data are included in the files: Gene_Profile.txt and Probe_Profile.txt.
The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: AW8507-tet-ON-shYY1 oral cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: AW8507 and AW8507-tet-ON-shYY1 cells were grown in DMEM with 10% FBS and PSA antibiotic, antimycotic solution

extract_protocol: Total RNA was harvested using TRIzol reagent and isolated using PCI precipitation method

treatment_protocol: AW8507-tet-ON-shYY1 cells were treated with 2µg/ml doxycycline for 72h and cells for both the control and doxycycline group were collected in TRIzol

value: oral cancer

value: YY1 knockdown


title: TS14-1


title: Control-rep1

description:
sample name in raw data files:
DXM1

value: wildtype


title: Doxycycline-rep2

description:
sample name in raw data files:
DXP2


title: TSMC_2_RNA-seq

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: Tracheal smooth muscle cells

growth_protocol: The isolated primary cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: No treatment

value: Tracheal smooth muscle cells

tag: cell subtype

value: Primary isolated cells


title: Control-rep2

description:
sample name in raw data files:
DXM2


title: s01

description: s01 control mouse, sham treatment

source_name: dissected spleen


title: SRS2


title: ISMC_2_RNA-seq

source_name: Intestinal smooth muscle cells

value: Intestinal smooth muscle cells


title: TSMC_3_RNA-seq


title: OA model_Non surgery rep2

description: Non surgery

value: OA mouse model

value: knee joints

value: Non surgery


title: TS14-2


title: SRS1


title: ISMC_1_RNA-seq


title: ISMC_3_RNA-seq


title: Pwp2lib5_rep1_cDNA

description:
RNA Barcodes
processed data file: pwp2_lib5_results.tab

data_processing:
Basecalls performed using MiSeq and HiSeq control software.
For reporter assay libraries, fastq files were trimmed to the promoter sequence and aligned to mm9 using bowtie for libraries where the design allowed efficient alignment (See table 2). For mutant promoter libraries, reads were matched to the reference sequences using the "stringdistmatrix" function in R (van der Loo, 2014). The frequency of each barcode sequence was calculated to get counts for each sample. Genomic DNA and RNA samples were scaled to each other by normalizing to the smaller total number of counts. Only barcodes that were sufficiently represented on genomic DNA (more than 20 reads after scaling) were used for further analysis. Enrichments of barcodes in the RNA sample were then calculated as nr/nd + alpha, where nr are the RNA counts and nd the DNA counts for a particular barcode and alpha represents a pseudo-count, set to 0.05.
ChIP-seq samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (Gaidatzis et al, 2015), which internally uses bowtie (Langmead et al, 2009). ChIP-seq peaks were called using Peakzilla with default parameters (Bardet et al, 2013)
For amplicon Bis-seq, sequences were aligned to the mutant promoter libraries using QuasR (Gaidatzis et al, 2015), using default settings for Bis-converted samples. DNA methylation was quantified using qMeth and the average methylation across each promoter was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Activities (Act_*), number of barcodes (nBCs_*), activities relative to the wt sequence (relAct_*), percentage of C+Gs (GC), percentage of dinucleotides that are CpGs (CpG), CpG observed/expected (OE), number of CpGs (nCGs), coordinates (chr, start, end, strand), percentage of CpGs mutated (CpGmut), qPCR values (qPCR), fraction methylated (methylation).

source_name: embryonic stem cells

extract_protocol:
RNA was isolated from cell lines containing the expression libraries with Quiagen RNeasy Mini Kit with on-column DNase digestion and reverse transcribed using Takara PrimeScript RT Reagent Kit (#RR047A). For DNA isolation cell pellet was resuspended in Bradleys-Buffer, 6 ul RNaseA (10mg/ml) was added and samples were incubated for 1h at 37 degree C. Subsequently 30 ul protease K was added and samples were incubated at 50 degree C over night. Then DNA was extracted using Phenol and Chloroform. Bio-ChIP was performed as previously described (Baubec et al, 2013). For amplicon Bis-seq, cells containing integrated mutant CGI promoter libraries were thawed, plated at low density and 96 clones picked and expanded to a minimum cell number of 20,000 cells. Cells were lysed with Baradley Buffer (10mM Tris-HCl (pH 7.5), 10mM EDTA (pH 8.0), 0.5% SDS, 10mM NaCl) and DNA extracted with beads (Homemade). DNA was Bisulfite converted using Zymo lightning conversion kit (D5046) and cleaned up using MagBeads (Zymno). Bis-converted DNA was amplified with primers RSG353 and RSG354 (Table 1). Amplified DNA was purified with Ampure beads and sequencing libraries were prepared using the Illumina NEBNext ChIP-seq library prep kit with 96 dual indexing.
DNA and cDNA barcodes were amplified with KAPA HIFI Hotstart using Primer DH.P6 and indexing primer (Table 1). PCR products were purified using AmPure XP beads (Beckman Coulter, #A63880) and sequenced using 50 cycle Kit on HiSeq 2500.

value: embryonic stem cells

value: Wild Type

tag: library type

value: reporter assay


title: Control 4

source_name: Control


title: TSMC_1_RNA-seq


title: SRS4


title: Control 3


title: Control 1


title: rs.d2 DDT

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: RS.ddt.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. Genomic windows with no CpG or ambiguous base within 1000 bp were identified in the reference genome and used as control genes to perform RUVg normalization (R package RUVSeq). The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with DDT. The control and DDT lineage rats were housed in the same room with lighting, food and water.

extract_protocol:
Pregnant rats were euthanized when fetuses reached embryonic day 16 (E16) of gestation, and fetal gonads were collected for germ cell preparations. In addition, postnatal day 10 (P10) testes were obtained and used for spermatogonia cell isolation. At E16, sex was determined on the basis of gonadal morphology as previously described (30).  Germ cells were isolated exclusively from males.  Purified populations of male type T1 prospermatogonia (at E16) or postnatal day 10 (P10) spermatogonia were prepared using a mini StaPut gradient method as previously described (30, 43, 44). Briefly, fetal (E16) or postnatal (P10) testes were pooled and dissociated by incubation in 0.25% trypsin-EDTA (Sigma) with vigorous pipetting using a 1000 microliter pipette tip, and the resulting cell solution was filtered through 100 micron nylon mesh to yield a single cell suspension. This cell suspension was then loaded onto a 50 ml 2-4% bovine serum albumen (BSA) gradient prepared in KREBS buffer, and the cells were allowed to sediment at unit gravity at 4˚C for two hours as described (43, 44). The gradient was then fractionated and aliquots of the fractions were examined under phase optics to identify those enriched for the appropriate prospermatogonial or spermatogonial cell types on the basis of morphological characteristics. The enriched fractions were pooled to yield the final sample which was >85% pure for the desired male germ cell type in each case. The pooled samples were then stored at -80°C prior to processing for DNA preparations.  The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1x PBS solution for up to 24 hours at 4°C.  The epididymal tissue was minced and the released sperm was centrifuged at 6,000 x g, then the supernant removed, and the pellet resuspended in NIM buffer, to be stored at -80O C until further use. One hundred µl of sperm suspension was sonicated, spun down at 6,000 g, the pellet washed with 1x PBS once, and then combined with 820 µL DNA extraction buffer and 80 µl 0.1M DTT. The sample was incubated at 65ºC for 15 minutes. Following this incubation 80 µl proteinase K (20 mg/ml) was added and the sample incubated at 55ºC for at least 2 hours under constant rotation. Then 300 µl of protein precipitation solution (Promega, A7953) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 14,000 rpm for 30 minutes at 4ºC. One ml of the supernatant was transferred to a 2 ml tube and 2 µl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20ºC freezer for at least one hour. After precipitation the sample was centrifuged at 14,000 rpm for 20 min at 4ºC. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500 µl of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4ºC at 14,000 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 µl of nuclease free water. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat sperm DNA pools were generated using the appropriate amount of genomic DNA from each individual for 3 pools each of control and vinclozolin lineage animals. Genomic DNA was sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95˚C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ C and then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight.  The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. NGS was performed by the WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application.

treatment_protocol: On days 8 through 14 of gestation, the females received daily intraperitoneal injections of DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO). The DDT (dichlorodiphenyltrichloroethane) was obtained from Chem Service Inc. (West Chester, PA) and reported to have a purity of 98.2%. DDT were dissolved and injected in DMSO vehicle as previously described.

tag: development stage

value: RS

tag: lineage

value: DDT


title: VSMC_2_RNA-seq

source_name: Vascular smooth muscle cells

value: Vascular smooth muscle cells


title: Control 2

value: skin-derived fibroblasts culture


title: VSMC_3_RNA-seq


title: rs.d3 DDT

description: RS.ddt.csv.gz


title: VSMC_1_RNA-seq


title: rs.c2 DDT

description: RS.ddt.csv.gz

value: control


title: Genome DNA_G2

city: Tokyo

first: Takashi

last: Sutani

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

description: genome DNA

data_processing:
Basecalls was performed using CASAVA version 1.8
Reads were aligned to the fission yeast genome (ASM294v2.19) using Bowtie2 (version 2.1.0) aligner
Binning, ChIP/input ratio calculation, normalization and peak-calling were conducted using Drompa2 ChIP-seq analysis package (version 2.5.1)
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: A ChIP-seq read file and the corresponding input DNA file were fed into Drompa2 tool to generate ChIP fold-enrichment profile in wig format (Orc4 and Mcm2 ChIP-seq). LOOESS smoothened DNA copy number profile (DNA copy number ratio between early S and G2) was calculated and outputed  in bedgraph format using an script in R.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

growth_protocol: YPD complete medium, standard yeast cultivation protocol.

extract_protocol:
Fixed yeast cells were mechanically disrupted with zirconium beads, and the released chromatin was sheared by sonication.
Libraries were prepared according to an instruction accompanying an NEB library preparation kit (cat# E7645L)

value: cdc25-22 leu1

tag: cell cycle point

tag: antibody


title: Mcm2-PK_input

description: input DNA (DNA before ChIP)

value: cdc10-V50 mcm2+-9PK


title: Mcm2-PK_ChIPseq

description: ChIP-purified DNA

value: anti-PK (SV5-Pk1)


title: Genome DNA_earlyS

description: genome DNA

value: early S (released from G2 arrest to 26C medium with 11 mM hydroxyurea and incubated for 2.5 hrs)


title: Germ_3_RNA-seq

source_name: Germ cells

value: Germ cells

value: Primary isolated cells


title: Orc4-PK_input

description: input DNA (DNA before ChIP)

value: cdc10-V50 orc4+-9PK


title: rs.c1 DDT

description: RS.ddt.csv.gz


title: rs.d1 DDT

description: RS.ddt.csv.gz


title: Germ_1_RNA-seq


title: Germ_2_RNA-seq


title: Orc4-PK_ChIPseq

description: ChIP-purified DNA


title: pachy.d3 DDT

description: Pachy.ddt.csv.gz

value: Pachy


title: Leydig_3_RNA-seq

source_name: Leydig cells

value: Leydig cells


title: rs.c3 DDT

description: RS.ddt.csv.gz


title: Leydig_2_RNA-seq


title: pachy.d2 DDT

description: Pachy.ddt.csv.gz


title: pachy.d1 DDT

description: Pachy.ddt.csv.gz


title: Leydig_1_RNA-seq


title: Sertoli_3_RNA-seq

source_name: Sertoli cells

value: Sertoli cells


title: pachy.c2 DDT

description: Pachy.ddt.csv.gz


title: pachy.c1 DDT

description: Pachy.ddt.csv.gz


title: Sertoli_2_RNA-seq


title: Sertoli_1_RNA-seq


title: 9-control

city: Indianapolis

first: Sunil

middle: S

last: Badve

state: IN

address: 635 Barnhill Drive, MS A-128

department: Pathology

institute: Indiana University

description: control vector

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 Hg19 whole genome using bowtie/cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM

source_name: LCC9-empty vector

growth_protocol: Charcoal stripped media

extract_protocol:
Ambion RNA kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit . Pair-end sequencing was performed as per manusfacturers protocols.

tag: condition

value: breast cancer

value: endocrine resistance

tag: vector

value: lenti-viral


title: p10.d3 DDT

value: DDT


title: 9C2

description: ESRP1 vector

source_name: LCC9-ESRP1 kd


title: shRNA-LUC_ctr-1

city: Stanford

first: Stephen HK

last: WONG

state: California

address: G2035 SIM1 Bldg

institute: Stanford University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw microarray image processing, normalization and expression calling were performed by the R-Bioconductor package  affy  using RMA function module.

label_protocol: Affymetrix protocol

growth_protocol: RPMI

extract_protocol: Trizol

treatment_protocol: shRNA transduction by lentivirus

tag: cell line

value: RCH-ACV

tag: genotype/variation


title: shRNA-216-1

value: SETDB2 knockdown


title: 2C3

description: ESRP1 vector

source_name: LCC2-ESRP1 kd


title: shRNA-LUC_ctr-3

value: control


title: p10.d2 DDT


title: pachy.c3 DDT

description: Pachy.ddt.csv.gz


title: 2-control

description: control vector

source_name: LCC2-empty vector


title: p10.d1 DDT


title: PTM_3_RNA-seq

source_name: Peritubular myoid (PTM) cells

value: Peritubular myoid (PTM) cells


title: PTM_2_RNA-seq


title: PTM_1_RNA-seq


title: shRNA-216-3


title: p10.c3 DDT


title: DONOR 106 IFNB 24H

city: Los Angeles

first: Priscila

middle: Ribeiro

last: Andrade

state: CALIFORNIA

address: 615 Charles E Young Drive South, room 246

department: Medicine

institute: UCLA

description:
processed data file: DeSeq Normalized counts IFNB.csv
processed data file: Raw_counts_IFNB_all_donors_24h.csv

data_processing:
Sequenced reads were demultiplexed and aligned to the human reference genome hg19 (UCSC) using TopHat (version 2.0.6) and Bowtie2 (version 2.0.2).
The HTseq package was then used to assign uniquely mapped reads to exons and genes using the gene annotation file for build hg19 from Ensembl in order to generate raw count data.
Once raw count data was generated, data normalization and differential expression analysis using a negative binomial model were performed in the R statistical programming environment using the DESeq (version 1.5) Bioconductor package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Raw_counts_IFNB_all_donors_*.csv: Comma-separated text files include raw counts from all samples and 5 donors.
Supplementary_files_format_and_content: DeSeq_Normalized_counts_IFNB.xlsx: Excel file of DESeq normalized counts.

source_name: CD14+ cells stimulated with 50ng/ml MCSF

growth_protocol: Human CD14+ cells were obtained by magnetic bead separation of PBMCs from 5 healthy donors and differentiated in vitro for 5 days with 50ng/ml of MCSF into macrophages.

extract_protocol:
Total RNA was harvested using RLT buffer (1% β-mercaptoethanol supplemented) from RNeasy Micro kit (Qiagen) at 2, 6, and 24 hours. RNA extraction was performed according to manufacturer’s instructions, which included the on-column DNase treatment step.
Extracted RNA was quantified with Quant-iT RiboGreen RNA Assay Kit (Invitrogen) and RNA quality was assessed using the Agilent 2200 Tapestation. Total RNA was subjected to poly-A-selection to purify messenger RNA, then fragmented and converted into double stranded cDNA. Library construction was then done using TruSeq Sample Preparation Kit (Illumina) according to manufacturer’s instructions. This included the ligation of sequencing adapters containing 7 nucleotide indexes for multiplexing. Libraries were quantified using PicoGreen (Invitrogen) and quality was assessed using the Agilent 2200 Tapestation.
Library samples were pooled (4 per lane) at equimolar quantities (10uM each library) and sequenced on a HiSeq 2000 sequencer (Illumina) with 100bp single-end protocol.

treatment_protocol: MDMs from each donor were treated with interferon-beta (285u/ml) for 2, 6 and 24h. RNA was harvested at each time point. Media control samples were also harvested at each time point and can found at series GSE82227.

tag: donor

tag: disease status

value: Healthy

value: Monocyte-derived macrophages (MDMs)

tag: treatment

value: Interferon-beta

tag: time


title: shRNA-LUC_ctr-2


title: DONOR 106 IFNB 2H

description:
processed data file: DeSeq Normalized counts IFNB.csv
processed data file: Raw_counts_IFNB_all_donors_2h.csv


title: TSMC_3_miRNA-seq

data_processing:
Experiment Pipeline Steps for Small RNA Sequencing: 1) Filter small RNA: separate 18-30nt RNA segment by PAGE gel. 2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3'  end of selected small RNAs from step 1. 3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is cross-linked to the 3' adapter of RNAs and excessive free 3' adapter. 4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The connection (5鈥 adaptor) will be attached to the 5鈥 end only, but it is not c onnected to the 3' adaptor or RT primer hybrid chain. This greatly reduces self-ligation. 5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand cDNA. 6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with both 3' and 5' adaptor. 7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts. 8) Library quantitative and pooling cyclization.
Bioinformatics Analysis Pipeline for Small RNA Sequencing: 1. Eliminate the low-quality reads, adaptors and other contaminants to get clean reads 2. Summarize the length distribution of the clean tags, common and specific sequences between samples 3. Annotate the clean tags into different categories 4. Predict the novel miRNA 5. Function annotation of known miRNAs
Data Filtering: 1) Remove low quality tags 2) Remove tags with 5' primer contaminants 3) Remove tags without 3' primer 4) Remove tags without insertion 5) Remove tags with poly A 6) Remove tags shorter than 18nt 7) Summarize the length distribution of the clean tags. After filtering, the remaining tags are called 'clean tags' and stored in FASTQ format.
Reads Mapping: Bowtie2 : -q -L 16 --phred64 -p 6 cmsearch: --cpu 6 --noali
sRNA Classification: MiRbase > pirnabank > snoRNA(human/plant) > Rfam > other sRNA. sRNA Prediction: miRDeep2, Piano,
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: counts + TPMs

source_name: Tracheal smooth muscle cells

extract_protocol:
Total RNA (including small RNA) was extracted using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols

value: Tracheal smooth muscle cells

tag: strain


title: DONOR 106 IFNB 6H

description:
processed data file: DeSeq Normalized counts IFNB.csv
processed data file: Raw_counts_IFNB_all_donors_6h.csv

tag: cell type


title: p10.c2 DDT


title: TSMC_2_miRNA-seq

value: Primary isolated cells


title: p10.c1 DDT


title: DONOR 100 IFNB 24H


title: e16.d3 DDT


title: DONOR 100 IFNB 2H


title: DONOR 100 IFNB 6H


title: e16.d2 DDT


title: ISMC_2_miRNA-seq

value: Intestinal smooth muscle cells


title: ISMC_3_miRNA-seq


title: e16.d1 DDT


title: DONOR 97 IFNB 24H


title: DONOR 97 IFNB 6H


title: e16.c3 DDT


title: e16.c2 DDT


title: e16.c1 DDT


title: U937_shKDM6A_CHD4_ChIPSeq

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

data_processing:
ChIp seq reads were aligned to hg19 genome assembly using Bowtie,with following parameters -n,-a,-S
Peaks were called using MACS1.4 version with following settings : Pvalue(0.5),mfold(10,30)
Peaks were annotated using PeakAnalyzer1.4 tool
Genome_build: GrCh37/hg19
Supplementary_files_format_and_content: Bed files were genearted using MACS1.4 version

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 280 ± 8bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

value: Pro-monocytic, human myeloid leukemia cell line

tag: chip antibody

value: CHD4 (Abcam, Cat. ab70469, Clone:3F2/4)


title: DONOR 95 IFNB 24H


title: U937_shKDM6A_2% Input

source_name: U937_shKDM6A_2% Input

value: 2% Input


title: U937_shControl_CHD4_ChIPSeq

value: shControl


title: cauda.d3 DDT

description: Caput.ddt.csv.gz

value: Cauda


title: DONOR 97 IFNB 2H


title: VSMC_2_miRNA-seq

value: Vascular smooth muscle cells

tag: cell subtype


title: DONOR 95 IFNB 6H


title: U937_shControl_2% Input

source_name: U937_shControl_2% Input


title: Germ_3_miRNA-seq

value: Germ cells


title: cauda.d2 DDT

description: Caput.ddt.csv.gz

value: DDT


title: TSMC_1_miRNA-seq


title: DONOR 95 IFNB 2H


title: cauda.d1 DDT

description: Caput.ddt.csv.gz


title: Germ_2_miRNA-seq


title: shRNA-216-2

value: RCH-ACV

value: SETDB2 knockdown


title: DONOR 94 IFNB 24H


title: cauda.c3 DDT

description: Caput.ddt.csv.gz

value: control


title: DONOR 94 IFNB 6H

value: Healthy


title: cauda.c2 DDT

description: Caput.ddt.csv.gz


title: Leydig_3_miRNA-seq

value: Leydig cells


title: VSMC_1_miRNA-seq


title: PD2

city: Chengdu

first: Jie

last: Luo

state: Sichuan

address: Huimin road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description: mRNA derived from liver tissue of common carp fed with duckweed (PD)

data_processing:
The Illumina Hiseq 4000 platform generated the mRNA-Seq raw reads was processed with Perl scripts to ensure the quality of data used in further analysis.
Genome_build: The reads were mapped to the carp genome (cyprinus carpio from http://www.carpbase.org/download_home.php)
Supplementary_files_format_and_content: Reads Count for each gene in each sample was counted by (HTSeq v0.6.0), and RPKM (Reads Per Kilo base Million Mapped Reads) was then calculated to estimate the expression level of genes.

organism: Cyprinus carpio

source_name: liver

growth_protocol: Common carp (body weight 492.6 ± 30g) were randomly divided into three groups (n = 90 for each group), three repetitions in each group. Group AD, MD, PD fed with earthworm, earthworm+ duckweed (1:1) and duckweed, respectively.

extract_protocol:
total RNA was harvested using Trizol reagent.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sampled after fasting for 24h, the fish were anesthetized with MS-222. Their livers were collected from three groups  and immediately snap-frozen in liquid nitrogen, stored at -80? until use.

tag: tissue

value: liver

tag: developmental stage

value: adult


title: DONOR 94 IFNB 2H

value: Monocyte-derived macrophages (MDMs)

value: Interferon-beta


title: MD3

description: mRNA derived from liver tissue of common carp fed with earthworm + duckweed(MD)


title: SV40-RNA

city: BOSTON

first: Dandi

last: Qiao

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital and Harvard Medical School

description: The SV40 MPRA library was transfected into Beas-2B cells. Twenty-four hours later, cells were harvested for mRNA isolation (Qiagen). After reverse transcription, the cDNA was amplified with barcoded primers by PCR, and sequenced using 36nt single-end sequencing on Illumina HiSeq 2000.

data_processing:
Read counts were obtained by matching all base pairs in the barcode dictionary to the FASTQ reads using a python script.
Supplementary_files_format_and_content: The FAM13A_MPRA.txt file contains the read counts for each barcode, with the corresponding oligonucleotide listed in the oligo column. For each SNP, there are two alleles, two orientations (F: forward, RC: reverse), and three locations (L: left; C: center; R: right). The files is space-delimited.

source_name: human bronchial epithelial cell line

growth_protocol: Beas-2B cells were purchased from ATCC and cultured in Dulbecco's Modified Eagle Medium (DMEM), supplemented with 10% fetal bovine serum, penicillin (50 units/ml) and streptomycin (50 ug/ml).

extract_protocol:
Twenty-four hours post transfection with MPRA library, cells were harvested for mRNA isolation (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The MPRA library was transfected into Beas-2B cells using a Nucleofector II Device with P3 Primary Cell 4D-Nucleofector® X Kit (Lonza).

value: Beas2B cells

tag: processing

value: Transfection

tag: product

value: PCR products


title: cauda.c1 DDT

description: Caput.ddt.csv.gz

source_name: Sperm

tag: development stage

tag: lineage


title: caput.d3 DDT

description: Caput.ddt.csv.gz

value: Caput


title: Leydig_1_miRNA-seq

value: Primary isolated cells


title: MD2


title: MD1

description: mRNA derived from liver tissue of common carp fed with earthworm + duckweed (MD)


title: caput.d2 DDT

description: Caput.ddt.csv.gz


title: Sertoli_3_miRNA-seq

value: Sertoli cells


title: minP-RNA

description: The minP MPRA library was transfected into Beas-2B cells. Twenty-four hours later, cells were harvested for mRNA isolation (Qiagen). After reverse transcription, the cDNA was amplified with barcoded primers by PCR, and sequenced using 36nt single-end sequencing on Illumina HiSeq 2000.


title: Leydig_2_miRNA-seq


title: PD3


title: SV40-Input

description: MPRA oligonucleotides were synthesized on a 244K Agilent array and cloned into the pGL4.10M2 backbone MPRA library vector containinga a strong promoter (simian virus 40 promoter, i.e. SV40) to test enhancer activities. MPRA libraries were amplified by PCR as input control. 36nt single-end sequencing was performed using Illumina HiSeq 2000.


title: caput.d1 DDT

description: Caput.ddt.csv.gz


title: AD3

description: mRNA derived from liver tissue of common carp fed with earthworm(AD)


title: Sertoli_2_miRNA-seq


title: Germ_1_miRNA-seq

value: Germ cells


title: SRS3

source_name: SRS patient

value: skin-derived fibroblasts culture

tag: genomic defect

value: IGF2/H19 hypomethylation


title: minP-Input

description: MPRA oligonucleotides were synthesized on a 244K Agilent array and cloned into the pGL4.10M2 backbone MPRA library vector containinga a relatively weak promoter (minimal promoter, i.e. minP) to test enhancer activities. MPRA libraries were amplified by PCR as input control. 36nt single-end sequencing was performed using Illumina HiSeq 2000.


title: caput.c3 DDT

description: Caput.ddt.csv.gz


title: Sertoli_1_miRNA-seq


title: caput.c2 DDT

description: Caput.ddt.csv.gz


title: PTM_3_miRNA-seq

value: Peritubular myoid (PTM) cells


title: AD2


title: AD1


title: Young_rep3

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

description: single cell RNA seq

data_processing:
Reads of RNA-seq were mapped to the human genome (GRCh38) with STAR
Mapped reads were subsequently assembled into transcripts guided by the reference annotation (GENCODE gene models) with Stringtie
Gene differential expression analysis using DESeq2 based on the reads count file obtained by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each gene, FPKM

source_name: young MII_oocyte

extract_protocol:
The RNAs in individual oocyte or embryo were reverse transcribed and amplified using the single RNA-seq method we recently developed.
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)

tag: age

value: young

tag: maternal age

value: :metaphase II


title: PTM_2_miRNA-seq


title: caput.c1 DDT

description: Caput.ddt.csv.gz

value: control


title: PTM_1_miRNA-seq


title: Young_rep2

description: single cell RNA seq


title: Old_rep3

description: single cell RNA seq

source_name: old MII_oocyte

value: old


title: 48hours after NG treatment

city: shanghai

first: manli

last: Yu

address: No.168 Changhai road

department: Department of Cardiology

institute: Changhai Hospital of Shanghai

data_processing:
Sequencing raw reads were preprocessed by FASTX-Toolkit filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Tophat v2.1.0 to map the cleaned reads to the rat rn6 reference genome with two mismatches. Cufflinks was used to assemble reads into transcripts.
We used DEGseq software package with the known lncRNAs previously annotated by NONCODE v4.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample. The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Neonatal rat cardiomyocytes

growth_protocol: Neonatal rat cardiomyocytes were isolated from 1- to 2-day-old Sprague-Dawley rats.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions. The RNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, USA).

treatment_protocol: Cells were plated to culture medium M199 supplemented with carnitine (2 mM), creatine (5 mM), and taurine (5 mM). NG: 5 mmol/l glucose, the osmolality was equal by adding 28 mmol/l of mannitol; HG: 33 mmol/l glucose.

tag: strain/background

value: Sprague-Dawley

value: 1-2 days

value: Primary neonatal cardiomyocytes

value: normal glucose (NG)

tag: time point

value: 48 hours


title: MICE HFD POOL

city: Rome

first: Valentina

last: Roglia

address: Via della Ricerca Scientifica, 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

description: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php

scan_protocol: Applied Biosystems® models 7500

data_processing:
https://dataanalysis.sabiosciences.com/pcr/arrayanalysis.php?wuid=8fa7191b-bb49-409d-b896-8ce28966b04e&logindata=&customerdata=&customeremail=&platform=customArray&format=X
For the normalization it uses the average of five housekeeping genes:ACTB. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)] The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.Fold Change worksheet reports test/control ratios average.

label: sybr green

source_name: livers

label_protocol: To study the effects of MOES on the characteristic mechanisms that leads to the neoplastic transformation in hepatic cells, like the deregulation of adipogenesis and lipogenesis, the expression of 84 metabolic genes involved in these mechanisms were analysed. The analysis was performed on mice’s livers after a different high fat diet in presence or not of mol-sRs using Mouse Adipogenesis RT2 Profiler PCR Array (PAMM-049Z; Qiagen).  The Real-time PCR was performed with 7500 Fast Real-Time (Applied Biosystems) using Sybr green detection according with manufacture instructions.

extract_protocol: The livers from mice were prepared in TRIzol reagent (Invitrogen, CA) according to manifacture’s instruction The RNA was dosed with a spectrophotometer (Pharmacia Biotech Ultrospec® 3000) and stored at –20 ° C until used.

treatment_protocol: In vivo experiment was conducted in accordance with accepted standard of humane animal care after the approval by relevant local (Institutional Animal Care and Use Committee, Tor Vergata University) and national (Ministry of Health) committees with authorization n°378/2017-PR. A total of 12 young, 2 months-age-old male C57BL/6J mice (purchased from Harlan Laboratories S.r.l., 91 Urbino, Italy) were randomly divided in two groups (n = 6 mice/group): mice fed with normal calorie diet (ND) group (3.85 kcal/g among which 10% kcal from fat, 20% from protein and 70% from carbohydrate). Mice fed with high fat diet (HFD: 5.24 kcal/g among which 60% kcal from fat, 20% from protein, and 20% from carbohydrate). Three mice for each group (ND and HFD) group were treated with Moringa oleifera sR pool fed by oral gavage every two days. Overall dietary treatments were maintained for 5 weeks.

value: livers


title: 24hours after HG treatment

tag: treatment

value: high glucose (HG)

value: 24 hours


title: Old_rep1

description: single cell RNA seq


title: MICE POOL ND


title: 24hours after NG treatment


title: MICE HFD


title: MICE CTR ND


title: Old_rep2

description: single cell RNA seq


title: HEPg2 CTR

data_processing: https://dataanalysis.sabiosciences.com/pcr/arrayanalysis.php?wuid=8fa7191b-bb49-409d-b896-8ce28966b04e&logindata=&customerdata=&customeremail=&platform=customArray&format=X. For the normalization it uses the average of five housekeeping genes:ACTB. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_HKG)] The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.Fold Change worksheet reports test/control ratios average.

source_name: hepatoma cell line

label_protocol: To study the effects of MOES on the characteristic mechanisms that leads to the neoplastic transformation in hepatic cells, like the deregulation of adipogenesis and lipogenesis, the expression of 84 metabolic genes involved in these mechanisms were analysed. The analysis was performed on the cDNA of control HepG2 cells, and on the cDNA of HepG2 treated with 2.5 mg/mL of MOES, using Human Adipogenesis RT2 Profiler PCR Array (PAHS-049Z; Qiagen)  The Real-time PCR was performed with 7500 Fast Real-Time (Applied Biosystems) using Sybr green detection according with manufacture instructions.

growth_protocol: HepG2 culture  Human hepatocellular carcinoma cells were maintained in Dulbecco's modified Eagle's medium (DMEM, BioWhittaker™) with 1 g/L glucose, supplemented with 10% Fetal Bovine Serum Good, EU approved, filtrated bovine serum (FBS, PAN-Biotech, Germany), 2 mM of L-glutamine (BioWhittaker™), 100 U/mL penicillin/streptomycin (BioWhittaker™) (changed every 2-3 days) and incubated at 37 °C with 100% relative humidity (RH) under 5% CO2 until near confluence.

extract_protocol: The HepG2 cells were prepared in TRIzol reagent (Invitrogen, CA) according to manifacture’s instruction The RNA was dosed with a spectrophotometer (Pharmacia Biotech Ultrospec® 3000) and stored at –20 ° C until used.

treatment_protocol: The response of human hepatocarcinoma cell line HepG2 to the aqueous extract of Moringa oleifera’s seeds (MOES) was tested. The HepG2 were placed in a 24-well plate with 1 mL of culture medium per well and treated with the different concentration (2.5 mg/mL, 5mg/mL and 10 mg/mL) of MOES, for 72 hours. The HepG2 were incubated for 24 hours to allow their adhesion before treatment.

tag: cell line


title: AD_037_chronic_lesion

status: Public on Jan 18 2019

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: b37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: skin biopsy

extract_protocol:
5mm skin punch biopsies were stored in PaxGene tissue containers (PreAnalytiX) at -80°C until isolation of total RNA with the Qiagen AllPrep DNA/RNA Mini Kit preceded by an additional disruption/homogenization step with innuSPEED Lysis Tubes W (Analytik Jena) and Qiagen QIAshredder spin-columns.
RNA samples were prepared for sequencing using the Illumina Truseq® Stranded total RNA Protocol in combination with the RiboZero rRNA removal Kit and sequenced on the HiSeq2500 with 2x125bp.

tag: patient's condition

value: AD

tag: skin type


title: OA model_Non surgery rep1

description: Non surgery

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: knee joints

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: disease state

value: OA mouse model

value: knee joints

value: Non surgery


title: AD_036_non-lesional

value: non-lesional


title: AD_035_chronic_lesion


title: AD_035_non-lesional


title: HEPg2 MOES 5MG/ML


title: AD_036_chronic_lesion


title: AD_037_non-lesional


title: 48hours after HG treatment

tag: cell type


title: AD_034_chronic_lesion


title: AD_032_chronic_lesion


title: AD_033_chronic_lesion


title: PSO_037_non-lesional

value: PSO


title: AD_033_non-lesional


title: AD_034_non-lesional


title: PSO_037_lesional

value: lesional


title: PSO_036_lesional


title: PSO_033_lesional


title: PSO_033_non-lesional


title: PSO_035_lesional


title: PSO_034_lesional


title: PSO_035_non-lesional


title: PSO_031_non-lesional


title: Young_rep1

description: single cell RNA seq

value: young

value: :metaphase II


title: PSO_030_non-lesional


title: PSO_029_lesional


title: PSO_030_lesional


title: PSO_028_non-lesional


title: PSO_027_lesional


title: PSO_028_lesional


title: PSO_027_non-lesional


title: PSO_024_lesional


title: PSO_023_lesional


title: PSO_024_non-lesional


title: PSO_020_non-lesional


title: PSO_018_lesional


title: PSO_020_lesional


title: PSO_023_non-lesional


title: PSO_036_non-lesional


title: PSO_017_lesional


title: PSO_031_lesional


title: PSO_017_non-lesional


title: PSO_015_non-lesional


title: PSO_016_non-lesional


title: PSO_029_non-lesional


title: PSO_014_non-lesional


title: PSO_012_lesional


title: PSO_011_lesional


title: PSO_009_non-lesional


title: PSO_011_non-lesional


title: PSO_009_lesional


title: PSO_007_non-lesional


title: PSO_008_lesional


title: PSO_007_lesional


title: PSO_008_non-lesional


title: PSO_018_non-lesional


title: PSO_006_lesional


title: PSO_006_non-lesional


title: PSO_012_non-lesional


title: PSO_005_lesional


title: PSO_003_non-lesional


title: PSO_015_lesional


title: PSO_002_non-lesional


title: PD1

tag: tissue

value: liver

value: adult


title: PSO_016_lesional


title: PSO_003_lesional


title: PSO_002_lesional


title: PSO_001_lesional


title: PSO_001_non-lesional


title: PSO_014_lesional


title: CTRL_044_healthy

value: CTRL

value: healthy


title: CTRL_045_healthy


title: CTRL_043_healthy


title: CTRL_042_healthy


title: CTRL_046_healthy


title: CTRL_041_healthy


title: CTRL_035_healthy


title: CTRL_036_healthy


title: CTRL_039_healthy


title: CTRL_037_healthy


title: CTRL_040_healthy


title: CTRL_034_healthy


title: CTRL_033_healthy


title: CTRL_038_healthy


title: CTRL_031_healthy


title: CTRL_032_healthy


title: CTRL_029_healthy


title: CTRL_026_healthy


title: CTRL_030_healthy


title: CTRL_019_healthy


title: CTRL_025_healthy


title: CTRL_022_healthy


title: CTRL_018_healthy


title: CTRL_015_healthy


title: CTRL_024_healthy


title: CTRL_017_healthy


title: CTRL_013_healthy


title: CTRL_016_healthy


title: CTRL_020_healthy


title: CTRL_009_healthy


title: CTRL_010_healthy


title: CTRL_014_healthy


title: CTRL_011_healthy


title: CTRL_004_healthy


title: CTRL_008_healthy


title: CTRL_002_healthy


title: CTRL_003_healthy


title: AD_032_non-lesional


title: AD_031_lesional


title: AD_029_lesional


title: AD_029_non-lesional


title: CTRL_006_healthy


title: AD_028_lesional


title: AD_027_non-lesional


title: AD_027_lesional


title: AD_028_non-lesional


title: AD_026_non-lesional


title: AD_025_lesional


title: AD_026_lesional


title: ISMC_1_miRNA-seq

source_name: Intestinal smooth muscle cells

value: Intestinal smooth muscle cells

tag: cell subtype

value: Primary isolated cells

tag: strain


title: AD_024_non-lesional


title: AD_025_non-lesional


title: AD_021_non-lesional


title: AD_023_non-lesional


title: AD_021_lesional


title: AD_023_lesional


title: VSMC_3_miRNA-seq

source_name: Vascular smooth muscle cells

value: Vascular smooth muscle cells


title: AD_031_non-lesional


title: AD_017_lesional


title: AD_030_lesional


title: AD_030_non-lesional


title: AD_016_lesional


title: AD_016_non-lesional


title: AD_014_non-lesional


title: AD_024_lesional


title: AD_011_non-lesional


title: AD_019_lesional


title: AD_011_lesional


title: AD_009_non-lesional


title: AD_007_non-lesional


title: AD_007_lesional


title: AD_006_lesional


title: AD_005_lesional


title: AD_020_non-lesional


title: AD_005_non-lesional


title: AD_019_non-lesional


title: AD_004_lesional


title: AD_020_lesional


title: AD_014_lesional


title: AD_017_non-lesional


title: AD_009_lesional


title: AD_006_non-lesional


title: DMSO_U251 Hi-C part 2

city: Tianjin

first: Bohan

address: NO.94 Weijin Road

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Hi-C were mapped to hg19 with HIC-Pro (2.11.1). Then we obtained the matrix
Clean reads of Capture Hi-C were cut into two pieces in the DpnII sites
All the reads were mapped to hg19 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values, Hi-C matrixes and Capture Hi-C signal peaks for each Sample

source_name: U251_Cell line

growth_protocol: U251 cell line was cultured in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA-seq:Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit. Hi-C and Capture Hi-C: Cells were fixed in formalin for 10min and DNA was isolated and digested with Dpn II then sheared to 200-300bp fragments by sonication. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs).
RNA, Hi-C and Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TMZ_U251 groups were 1mM TMZ treated for 72h,and DMSO_U251 groups were control groups for the same conditions

value: glioblastoma cells

tag: agent

value: DMSO


title: DMSO_U251 Hi-C part 1


title: TMZ_U251 Capture Hi-C

data_processing:
Library strategy: Capture Hi-C
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Hi-C were mapped to hg19 with HIC-Pro (2.11.1). Then we obtained the matrix
Clean reads of Capture Hi-C were cut into two pieces in the DpnII sites
All the reads were mapped to hg19 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values, Hi-C matrixes and Capture Hi-C signal peaks for each Sample

value: TMZ


title: TMZ_U251 Hi-C part 2


title: DMSO_U251 Hi-C part 3


title: DMSO_U251 Hi-C part 4


title: TMZ_U251 Hi-C part 1


title: AD_004_non-lesional

value: AD


title: 2018HC067 [I]

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

institute: Ajou University School of Medicine

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Colorectal carcinoma samples

extract_protocol:
Total RNA was extracted from each samples using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: genotype

value: p16INK4A positive expression

value: Colorectal carcinoma


title: 2017HC070 [I-2]

value: Colorectal carcinoma


title: 2018HC100 [I]


title: DMSO_U251 Capture Hi-C


title: 2018HC067 [C]

value: p16INK4A negative expression