title: pCIneo transfected human myoblasts [pCINeo-3]

city: Columbus

first: Scott

middle: Q

last: Harper

state: Ohio

address: 700 Children's Drive

department: Gene Therapy

institute: Nationwide Children's Hospital

data_processing:
Paired-end 150 bp sequence reads were generated using the Illumina HiSeq 4000 platform.
The samples were aligned to GRCh38.p6 from NCBI using the RNA-Seq aligner STAR
Feature coverage counts were calculated using HTSeq
Differentially expressed features were calculated using DESeq2
Features were sorted by absolute value of fold change and only features whose absolute value of fold change is greater than 2 and having an adjusted p-value of <= 0.10 are included. In addition to information about the feature (symbol, class, chromosome, start/end/length) and differential expression (fold change, padj), normalized read counts are included for each sample, which give an indication of the level of expression for that sample.
Genome_build: GRCh38.p6
Supplementary_files_format_and_content: unfiltered gene counts for all annotated genes

source_name: human myoblast, WS236 15Vbic

growth_protocol: Human immortalized myoblasts (WS236, 15V, bicep, unaffected control cells) were cultured in media containing DMEM supplemented with 16% Medium 199, 15% fetal bovine serum, 30 ng/ml zinc sulfate, 1.4 µg/ml vitamin B12, 55 ng/ml dexamethasone, 2.5 ng/ml human growth factor, 10 ng/ml fibroblast growth factor, and 20 mM HEPES. Cells were maintained as myoblasts and were not differentiated.

extract_protocol:
Cells were harvested in TRIzol RNA isolation reagent (Life Technologies) 18-20 hours post-transfection. Following assessment of the quality of total RNA using Agilent 2100 bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA), RNA was DNAse treated and 1.5 µg was subjected to rRNA with Ribo-ZeroTM rRNA removal kit for human/mouse/rat (Illumina).
Libraries were constructed from first strand cDNA using ScriptSeqTM v2 RNA-Seq library preparation kit (Epicentre Biotechnologies, WI).  Briefly, 50 ng of rRNA-depleted RNA was fragmented and reverse transcribed using random primers containing a 5’ tagging sequence, followed by 3’end tagging with a terminal-tagging oligo to yield di-tagged, single-stranded cDNA.  Following purification by a magnetic-bead based approach, the di-tagged cDNA was amplified by limit-cycle PCR using primer pairs that anneal to tagging sequences and add adaptor sequences required for sequencing cluster generation.  Amplified RNA-seq libraries were purified using AMPure XP System (Beckman Coulter).  Quality of libraries were determined via Agilent 2200 Tapestation using High Sensitivity D1000 screen tape, and quantified by Qubit flourometer with dsDNA BR assay (Invitrogen by Thermo Fisher Scientific).  Paired-end 150 bp sequence reads were generated using the Illumina HiSeq 4000 platform.

treatment_protocol: Human immortalized myoblasts were transfected with plasmids encoding C-terminal epitope tagged DUX4 and Dux using the Human Dermal Fibroblast Nucleofector kit (Amaxa).

value: pCIneo

value: immortalized human myoblasts:clone WS236 15Vbic (unaffected)


title: pCIneo transfected human myoblasts [pCINeo-2]

status: Public on Aug 24 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: transfection

tag: cell type


title: input_ChIP-seq, 2

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

state: Utah

department: Chemistry

institute: University of Utah

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.8.2
ChIP-exo and ChIP-seq fastq files were aligned to the hg19 genome assembly using Novoalign with the following parameters: -0 SAM –r. Sam files were then sorted and indexed with SAMtools.
Peak calling was performed with and without the input control by MACS2 using the following standard parameters: model fold settings of 5 to 50 q-values with a cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were built with MACS2

molecule: genomic DNA

growth_protocol: Cell were cultured in Dulbecco's Modified Eagle medium supplemented with 4.5 g/L glucose, 10% FBS and 2 nM glutamine in humidified incubator at 37 deg. C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF_DNA complexes were isolated with antibody.
Libraries were prepared according to Active Motif 's ChIP-Exo Kit (Part# 53043) and NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (Part# E6200L).

tag: cell line

value: HeLa S3

tag: passage

value: 4 to 6


title: input_ChIP-seq, 1


title: EpiLC_MS61T88

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from day2 EpiLC
processed data file: SC3seq_Ms_ProcessedData.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 or Macsca fascicularis genome Macaca_fascicularis_5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10, Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample ...

organism: Mus musculus

source_name: EpiLC

growth_protocol:
For cultivation on feeders, cyESCs were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).
For cultivation in feeder free condition, CMK6 was cultured using the same condition applied for human ESC/iPSC as reported previously [Nakagawa, M., et al. (2014). Scientific Reports, 4, 3594.]
The mouse ESC line BVSC R8 was cultured in a 2i+LIF, feeder-free culture condition as reported previously [Hayash, K., et al. (2011). Cell, 146, 519].
The mouse EpiLC was induced from 2i+LIF ESCs for two days in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), and KSR (1%) as reported previously [Hayash, K., et al. (2011). Cell, 146, 519].

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from mouse E5.5 and E6.5 embryos, the embryos were dissected out from decidua and the extra-embryonic ectoderm was removed manually. The EPI/visceral endoderm (VE) were incubated in 0.25% Pancreatin/0.5 % Trypsin/Polyvinylpyrrolidone, and EPI and VE were separated by mild pipetting. For E5.5 embryos, EPI and VE were incubated with 0.25% trypsin/PBS separately for around 10 min at 37℃. For E6.5 EPI, their proximal parts were dissected out manually, and the proximal EPI and whole VE were incubated with 0.25% trypsin/PBS separately for around 10 min at 37℃. The proximal EPI and VE were dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from cyESCs, cells were first detached as clumps with CTK solution, incubated in 0.25% trypsin/PBS (Sigma-Aldrich) for around 10 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632. Cells under feeder-free condition were directly incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632.
For single cell isolation from mESCs and EpiLCs, cells were incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

tag: strain

value: BVSC R8

value: EpiLC


title: input_ChIP-seq, 3


title: input_ChIP-exo, 2

data_processing:
Library strategy: ChIP-exo
Basecalls were performed using CASAVA version 1.8.2
ChIP-exo and ChIP-seq fastq files were aligned to the hg19 genome assembly using Novoalign with the following parameters: -0 SAM –r. Sam files were then sorted and indexed with SAMtools.
Peak calling was performed with and without the input control by MACS2 using the following standard parameters: model fold settings of 5 to 50 q-values with a cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were built with MACS2

value: 6 to 7


title: input_ChIP-exo, 1


title: pCIneo transfected human myoblasts [pCINeo-1]


title: EpiLC_MS61T89


title: EpiLC_MS61T86


title: Mouse Dux transfected human myoblasts [mDUX-1]

value: Mouse Dux


title: E65_MS77T74

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from mouse embryo at E6.5
processed data file: SC3seq_Ms_ProcessedData.txt

source_name: mouse embryo E6.5

tag: tissue

value: embryo

tag: developmental stage


title: E65_MS77T73


title: EpiLC_MS61T85


title: CTCF_ChIP-exo, 1

tag: chip antibody

value: CTCF (Millipore, 07-729, lot 122116)


title: Mouse Dux transfected human myoblasts [mDUX-2]


title: Human DUX4 transfected myoblasts [DUX4-1]

value: Human DUX4


title: CTCF_ChIP-exo, 2


title: Human DUX4 transfected myoblasts [DUX4-3]


title: EpiLC_MS61T84


title: E65_MS77T70


title: Human DUX4 transfected myoblasts [DUX4-2]


title: E65_MS77T71


title: E65_MS77T72


title: Yal2

city: fuzhou

first: peng

last: guo

address: shangxiadian road

country: China

institute: Fujian Agriculture and Forestry University

description: processed data file: Yal.fpkm.xls

data_processing:
Illumina HiSeq 2000 software used for basecalling.
Clean reads were obtained by removing low quality sequences, reads containing adapter and reads containing ploy-N.
In the mapping process, the software Bowtie aligner (Langmead et al., 2009) was used to delete the reads mapping to Ribosomal RNA database.
The remaining reads were mapped to the C. sinensis genome using the software TopHat2 (Kim et al., 2013), and assembled by Cufflinks (Trapnell et al., 2010; PMID:20436464 ) and RABT (reference annotation based transcripts) (Roberts et al., 2011;PMID: 21697122).
The gene expression level was calculated by RPKM (reads per kilobases per millionmapped reads) method (Mortazavi et al., 2008). Differentially expressed genes (DEGs) analysis were performed using EdgeR (version 3.0.0, R version2.1.5), and identified using a FDR (false discovery rate) ≤ 0.05 and an absolute value of the log2 ratio ≥1.
Genome_build: C. sinensis
Supplementary_files_format_and_content: Excel files include FPKM values, description, Pathway, GO Component, GO Function and GO Process for each gene. The identifiers  (e.g. Cs1g01010, Cs1g01015etc.) are searchable at CsiDB (http://citrus.hzau.edu.cn/orange/index.php).

organism: Citrus maxima

source_name: C. grandis_Al_citrus root

extract_protocol:
Equal amounts of frozen roots from five seedlings (one seedling per pot) were pooled as one biological replicate. There were two biological replicates for each treatment. Total RNA was independently extracted twice from ca. 100 - 200 mg frozen control and +Al roots of C. sinensis and C. grandis seedlings using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: Al-intolerant

tag: treated with

value: nutrient solution containing 1.0 mM AlCl3•6H2O for 18wks

value: seedling; root tips


title: Yal1

description: processed data file: Yal.fpkm.xls


title: EpiLC_MS61T87


title: Mouse Dux transfected human myoblasts [mDUX-3]


title: E65_MS77T68


title: E65_MS77T69


title: Yck2

description: processed data file: Yck.fpkm.xls

source_name: C. grandis_control_citrus root

value: nutrient solution containing 0mM AlCl3•6H2O for 18 wks


title: Yck1

description: processed data file: Yck.fpkm.xls


title: E65_MS77T67


title: E65_MS77T65


title: E65_MS77T66


title: E65_MS77T64


title: 15d-PGJ2-PC rep2

city: Shanghai

first: Huiyong

last: Yin

state: Shanghai

address: 320 Yueyang Road

institute: Institute for Nutritional Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA with parameters -o 1 -e 50 -i 50 -L -k 2 -l 31 -t 4 -q 10.
FPKM  method was used in calculated expression level.
NOISeq method  was used to screen differentially expressed genes between two groups.
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text include FPKM values for each Sample.

growth_protocol: BMDMs were cultured in RPMI medium.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 1μM 15d-PGJ2,15d-PGJ2-PC or media control for 6h.

tag: age

value: 8 weeks

value: bone marrow-derived macrophage (BMDM)

value: 1μM 15d-PGJ2-PC  for 6h


title: 15d-PGJ2 rep3

value: 1μM 15d-PGJ2 for 6h


title: 15d-PGJ2-PC rep1


title: E65_MS77T63


title: 15d-PGJ2 rep2


title: E65_MS77T61


title: 15d-PGJ2 rep1


title: control rep2

value: media control for 6h


title: control rep1


title: E65_MS77T62


title: control rep3


title: E65_MS77T58


title: E65_MS77T56


title: E65_MS77T57


title: E65_MS77T59


title: IL15_Polysomal_A _1

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA-seq reads mapping to ribosomal RNA were filtered using HISAT  (0.1.6-beta) on all ribosomal sequences with parameter --un
Filtered RNA-seq reads were mapped to the hg19 genome assembly using HISAT (0.1.6-beta)
Reads were quantified using the python script rpkmforgenes.py with parameters -bamu -bothends -rmnameoverlap (Ramsköld et al., 2009, PLOS Comp. Biol.)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file datCount.csv consists of the read counts as given by rpkmforgenes.py

source_name: NK Cells

extract_protocol:
Cytosolic and polysome-associated RNA was collected from 2-4 million NK cells per donor and treatment  (as described in Gandin et al.,  J. Vis. Exp. 2014). Briefly, total cytosolic mRNA was extracted (10% of the resulting input was kept as “cytosolic RNA”) and sedimented on a 5%-50% sucrose gradient to separate mRNA according to the number of associated ribosomes as described. Gradient fractions were collected and UV absorbance at 254 nm was measured. Fractions corresponding to >2 ribosomes (“polysome-associated RNA”) were collected. RNA was extracted using Tri reagent (Sigma, manufacturer’s protocol) and fractions were pooled followed by a column-based cleanup using the RNeasy MinElute Cleanup kit (Qiagen).
smartSeq2 RNA-sequencing libraries were prepared as described in Picelli et al., 2013 Nat Methods (from step 5)

tag: cytokine

tag: treatment

value: A

tag: rna

value: Polysomal

tag: donor

value: NK cells


title: IL15_Cytosolic_A _1

value: Cytosolic


title: 15d-PGJ2-PC rep3


title: E65_MS77T55


title: IL15_Cytosolic_A _2


title: IL15_Polysomal_A _2


title: E65_MS77T54


title: IL15_Cytosolic_W_4

value: W


title: IL15_Polysomal_W_4


title: IL2_Cytosolic_A _5


title: E55_MS11T75

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from mouse embryo at E5.5
processed data file: SC3seq_Ms_ProcessedData.txt

source_name: mouse embryo E5.5

value: embryo


title: E55_MS11T76


title: IL2_Cytosolic_W_3b


title: IL2_Polysomal_A _5


title: E65_MS77T60


title: E65_MS77T51


title: IL2_Polysomal_W_3b


title: IL2_Cytosolic_W_5


title: IL15_Polysomal_A _3a


title: E55_MS11T74


title: IL2_Polysomal_W_5


title: E55_MS11T72


title: IL2_Polysomal_W_2


title: E55_MS11T69


title: IL2_Cytosolic_W_2


title: IL2_Cytosolic_A _3a


title: E65_MS77T53


title: IL2_Polysomal_A _3a


title: E55_MS11T67


title: E55_MS11T70


title: RNASeq_F5C2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
Expression estimation: Tophat 2.0.9.
Depth of reads= 30 million/sample, Genes excluded if RPKM was <1 in all samples
genome build: hg19
processed data files format and content: text file with RPKM values.

growth_protocol:
RPMI-B27
Cardiac differentiation of iPSCs grown in E8 media, using RPMI-B27 medium with 6uM CHIR induction for 2 days (d0-d2) and 2.5uM C59 treatment for two days (d3-d5)

extract_protocol:
QIAGEN RNeasy Mini Kit
RNA-Seq libraries prepared from 100ng RNA, Sequencing data was un-stranded, ERCC spike-in (Ambion) used for data normalization.

treatment_protocol: Daily for 7 days

value: Untreated

tag: reagent/antibody (company

value: cat #):Not applicable

value: hiPSC-derived cardiomyocytes


title: E65_MS77T52


title: RNASeq_F5C1


title: IL15_Cytosolic_W_5


title: E55_MS11T66


title: E55_MS11T64


title: IL15_Cytosolic_A _5


title: IL15_Cytosolic_A _3a


title: RNASeq_F4C1


title: E55_MS11T63


title: E55_MS11T73


title: E55_MS11T71


title: E55_MS11T65


title: RNASeq_F3C2


title: RNASeq_F4C2


title: E55_MS11T68


title: IL2_Cytosolic_W_4


title: IL2_Polysomal_W_4


title: E55_MS11T60


title: RNASeq_F2C1


title: RNASeq_F2C2


title: RNASeq_F1C2


title: E55_MS11T61


title: E55_MS11T59


title: IL2_Cytosolic_A _1


title: IL2_Polysomal_A _1


title: IL2_Cytosolic_A _4


title: RNASeq_F1C1


title: E55_MS11T58


title: RNASeq_hESC

value: hESC-derived cardiomyocytes, H7 line


title: E55_MS11T57


title: IL15_Polysomal_W_5


title: RNASeq_F3C1


title: IL15_Polysomal_A _5


title: IL2_Polysomal_A _4


title: E55_MS11T56


title: E55_MS11T62


title: E55_MS11T55


title: E55_MS11T54


title: IL15_Cytosolic_A _4


title: IL2_Cytosolic_A _2


title: NHBE 8h rep1

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Paired-end sequencing (101 x 2) was performed using a Hiseq-2000 (Illumina).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). The reference genome index was built using SAMtools (v. 0.1.19) and the Bowtie2-build component of Bowtie2 (v. 2.1.0). Reads were mapped to the reference genome using Tophat2 (v. 2.0).
The number of reads per kilobase per million mapped reads (rpkm) for each gene of 46,895 RefSeq (UCSC hg19) gene models was calculated using Cufflinks (v. 2.2.1).
Heat maps were constructed using Mev (v. 4.9.0). Statistical analyses and graph construction were performed using R (v. 3.1.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Primary normal human bronchial epithelial (NHBE) cells

growth_protocol: Primary normal human bronchial epithelial were grown in keratinocyte serum-free medium with 5 ng/ml human recombinant epidermal growth factor, 0.05 mg/ml bovine pituitary extract, 0.005 mg/ml insulin, and 500 ng/ml hydrocortisone.

extract_protocol:
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
The sequencing library was prepared using the TruSeq RNA sample preparation kit v2 (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Cells were infected with 1 MOI of A/PR8/34 influenza virus for 8 or 24 h.

tag: time

value: 8 hour infection

value: infected A/PR/8/34 influenza virus (MOI = 1)


title: IL15_Polysomal_A _4


title: E55_MS11T53


title: NHBE 8h rep2

value: Primary normal human bronchial epithelial (NHBE) cells


title: NHBE 24h rep1

value: 24 hour infection


title: NHBE 24h rep2


title: IL2_Polysomal_A _2


title: NHBE 0h rep2

value: control


title: Xal2

description: processed data file: Xal.fpkm.xls

organism: Citrus sinensis

source_name: C. sinensis_Al_citrus root

value: Al-tolerant

value: nutrient solution containing 1.0 mM AlCl3•6H2O for 18wks

value: seedling; root tips


title: E55_MS11T52


title: IL15_Cytosolic_W_1


title: NHBE 0h rep1


title: IL15_Cytosolic_W_2


title: IL15_Polysomal_W_2

value: Polysomal


title: IL2_Cytosolic_W_1

value: NK cells


title: Xck1

description: processed data file: Xck.fpkm.xls

source_name: C. sinensis_control_citrus root

value: nutrient solution containing 0mM AlCl3•6H2O for 18 wks


title: IL15_Polysomal_W_1

value: W


title: Xck2

description: processed data file: Xck.fpkm.xls


title: Xal1

description: processed data file: Xal.fpkm.xls


title: IL15_Cytosolic_W_3b

value: Cytosolic


title: IL15_Polysomal_W_3b


title: RNAseq-NPC-ZIKVM-2

status: Public on Aug 23 2016

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

data_processing:
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq gene expression value in cufflink fpkm_tracking file format

source_name: hNPC

extract_protocol:
RNA was extracted by Trizol.
RNA-seq libraries were constructed with Illumina True-seq kit

tag: virus

value: ZIKVM


title: IL2_Polysomal_W_1

tag: cell type


title: RNAseq-NPC-ZIKVC-2

value: ZIKVC


title: RNAseq-NPC-Mock-4

value: mock


title: MF200402

city: Hohhot

first: Junjie

last: Wang

state: Inner Mongolia

address: 306 Zhaowuda Road

department: College of Ecology and Environmental Science

institute: Inner Mongolia Agricultural University

description: Sample 3

data_processing:
filter_fq (BGI unpublished software)
Remove reads with adaptors, unknown nucleotides larger than 5%, low quality reads which the percentage of low quality bases(base quality≤10) is more than 20%
Trinity release-20121005
--seqType fq --min_contig_length 100
--group_pairs_distance 250 --path_reinforcement_distance 85
--min_kmer_cov 2
TGICL v2.1;
-l 40 -c 10 -v 20
Phrap Release 23.0
-repeat_stringency 0.95 -minmatch 35 -minscore 35
BLAST v2.2.26+x64-linux
-F F -e 1e-5 -p blastn
NT
-F F -e 1e-5 -p blastx
NR, KEGG, Swiss-Prot, COG
Genome_build: None (de novo assembly)
Supplementary_files_format_and_content: txt file includes FPKM values for each sample and each transcript (with blast annotation)

organism: Medicago sativa

source_name: Root, stem, leaf cells

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instruction and treated with RNase-free DNase I (Takara Biotechnology, Dalian, China).
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subspecies

value: falcata

tag: sample group

value: grazing intolerant and grazed

value: root, stem, leaf cells


title: MCF-7 wildtype RUNX1 ChIPseq Replicate2 Input

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

data_processing:
RNA-seq: For  RNA-Seq analysis, first, the adapter sequences were removed from the RNA-seq reads.  Ribosomal RNA reads were then filtered out using Bowtie (Song et al. 2014).  After these filtration and adapter removal steps, the reads were aligned to a transciptome and quantified using RSEM v1.2.7 (Li and Dewey 2011). Differential gene expression was calculated by using the Deseq2 package in R 3.1.0 by using the mean value of gene-wise dispersion estimates (Love et al. 2014).
ChIP-seq: ~1x107 parental MCF-7 cells were crosslinked with formaldehyde at room temperature for 10 minutes.  Then, the cells were lysed using lysis buffer A (50mM HEPES, 140mM NaCl, 1mM EDTA pH=8, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100), and the residual cytoplasmic protein was removed using lysis buffer B (10mM Tris-HCl pH=8, 200mM NaCl, 1mM EDTA, 1mM EGTA).  The nuclear fraction was released using lysis buffer C (10mM Tris-Hcl pH=8, 100mM NaCl, 1mM EDTA, 1mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine).  The chromatin was then sheared by using a Covaris S2 instrument with 10% duty cycle, 5 intensity, 200 cycles per burst, frequency sweeping mode, 60 second process time and for 4 cycles. The pull-down was performed by using the RUNX1 antibody (Cell Signaling #4334).  Samples were washed three times with RIPA buffer (Tris-HCl pH=8, 150mM NaCl, 1mM EDTA, 1% NP-40, 0.25% Sodium deoxycholate, 0.1% SDS) and were eluted.  The pull-down and input control sequencing libraries were generated by using the NEXTflex Rapid DNA Sequencing Kit (Bioo Scientific #5144-02) and were sequenced by using SE100 reads with a HiSeq 2000 instrument.
data processing step: The Hi-C data were mapped with Bowtie and  binned at 6.5Mb, 1Mb, 250kb, 100kb and 40kb non-overlapping genomic intervals.  Iterative mapping and correction of Hi-C data were performed as previously described (Imakaev et al. 2012).  Biological replicates showed high reproducibility (Pearson's correlation coefficient > 0.9 for 1Mb resolution data).  Similarly, the first eigenvector comparison of the replicates showed high reproducibility.  For the downstream analyses, sequences obtained from both biological replicates were pooled and ICE-corrected to serve as a combined dataset.
Compartment analysis: First, the z-scores of the interaction matrices at 250kb resolution were generated as described previously (Lieberman, 2009).  Then, Pearson Correlation on the Z-score matrices was calculated.  By performing principal component analysis (Lieberman-Aiden et al. 2009; Zhang et al. 2012), the first eigenvector typically represents the compartment profile(Lieberman-Aiden et al. 2009), where the positive and negative 1st eigenvalues represent different compartments.   Gene density for each compartment was calculated to call the “A” and “B” compartmentalization.
TAD Calling : TAD calling was performed as calculating the “insulation” score of each bin using the 40kb resolution combined Hi-C data (as previously described.  The mean of the interactions across each bin were calculated.  By sliding a 1Mb x 1Mb (25bins x 25bins) square along the diagonal of the interaction matrix for every chromosome, we obtained the “insulation score” of the interaction matrix.  Valleys in the insulation score indicated the depletion of Hi-C interactions occurring across a bin.  These 40kb valleys represent the TAD boundaries.  Based on the variation of boundaries between replicates, we chose to add a total of 160kb (80kb to each side) to the boundary to account for replicate variation.  The final boundaries span a 200kb region. All boundaries with a boundary strength < 0.15 were excluded as they were considered weak and non-reproducible.  The insulation plots for the biological replicates showed high reproducibility, suggesting the robustness of the method.  Similarly, the overlap of detected boundaries also showed high reproducibility between the biological replicates.  Therefore, we used the combined Hi-C replicates for the TAD analyses.
Z-Score Calculation: We modeled the overall Hi-C decay with distance using a modified LOWESS method (alpha = 1%, IQR filter), as described previously (Sanyal et al. 2012).  LOWESS calculates the weighted-average and weighted-standard deviation for every genomic distance and therefore normalizes for genomic distance signal bias.
Genome_build: hg19
Supplementary_files_format_and_content: HiC: Interaction matrices at 2.5Mb, 1Mb, 250kb and 40kb resolution; RNA-seq: Expected count file for all genes and a txt file showing the shRUNX1/shNS log2 Fold Change and pvalues for all genes; ChIP-seq: BedGeapgh UCSC visualization files and the MCF7 RUNX1 peak bed file
Supplementary_files_format_and_content: MCF7_shRUNX1_shNS_processed_HiC_files - all normalized/corrected Hi-C data matrices binned at 40kb/250kb/1Mb/2.5Mb
Supplementary_files_format_and_content: MCF7_RUNX1_ChIPseq_peaks.bed - BED file of RUNX1 ChIP-seq peaks
Supplementary_files_format_and_content: MCF7_shNS_shRUNX1_genes_expression_expected_count.tsv - TSV file showing the RNA-seq counts for each gene
Supplementary_files_format_and_content: MCF7_shRUNX1_shNS_RNAseq_log2_foldchange.txt - TSV file showing the log2 fold change of all  genes between shRUNX1 and shNS samples

source_name: Human breast cancer cell line

growth_protocol: The MCF-7 cells were obtained from ATCC and were cultured in DMEM supplemental with 10% fetal bovine serum and 5% penicillin/streptomycin. For shRNA-mediated knockdown of Runx1 expression, MCF7 cells were plated in six-well plates (1x105 cells per well) and infected 24 h later with lentivirus expressing shRunx1 or nonspecific shRNA (Thermo Scientific).  Briefly, cells were treated with 0.5 ml of lentivirus and 1.5 ml complete fresh DMEM high glucose per well with a final concentration of 4 μg/ml polybrene. Plates were centrifuged upon addition of the virus at 1460 × g at 37 C for 30 min. Infection efficiency was monitored by GFP co-expression at 2 days after infection. Cells were selected with 2 μg/ml puromycin for at least two additional days. After removal of the floating cells, the remaining attached cells were passed and analyzed.

extract_protocol: Hi-C was sequenced using PE100 reads; RNA-seq and ChIP-seq were sequenced using SE100 reads by using a HiSeq 2000 instrument

tag: cell line


title: MCF-7 shRUNX1  RNA-seq Replicate3


title: MF200401

description: Sample 1

value: grazing tolerant and grazed

tag: tissue


title: MF200401-1

description: Sample 2

value: grazing tolerant and not grazed


title: EHEC plus Symbioflor

city: Freising

first: Klaus

last: Neuhaus

address: Weihenstephaner Berg 3

department: Core Facility Microbiome/NGS

country: Germany

institute: Technische Universität München

data_processing:
conversion: Convert SOLiD output to fastq (Galaxy Version 1.0.0); default parameters.
mapping: bowtie (Galaxy Version 1.1.2); 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions.
counting: countOverlaps of Iranges; default parameters
normalizing: convert counts in RPKM using Excel
differential expression: Bioconductor package edgeR (version 3.2.3); default parameters
Genome_build: NC_002655
Supplementary_files_format_and_content: xlsx: logFC and p-value

organism: Escherichia coli O157:H7 str. EDL933

source_name: plus Symbioflor

growth_protocol: LB agar plates, 37°C for 18 h

extract_protocol:
scraping bacteria, opening with bead beating, Trizol-based RNA isolation, rRNA depletion with RiboZero, DNA digest, SoLiD seq by CeGaT (Tübingen, Germany)
conducted by CeGaT (Tübingen, Germany) according to SOLiD standard protocols for RNA-seq

treatment_protocol: EHEC either grown on plain LB plates or LB plates containing Symbioflor within the agar

tag: culture

value: 18 h at 37°C

tag: medium

value: LB

tag: symbioflor status

value: with Symbioflor


title: MCF-7 wildtype RUNX1 ChIPseq Replicate2 Pulldown


title: MCF-7 wildtype RUNX1 ChIPseq Replicate1 Pulldown


title: EHEC

source_name: without Symbioflor

value: without Symbioflor


title: MCF-7 shRUNX1 Hi-C Replicate2


title: RNAseq-NPC-ZIKVM-1


title: Am

city: Pingtung County

first: Chi-Chu

last: Tsai

address: 2-6 Dehe Rd., Dehe Village, Changjhih Township

department: Crop Improvement Section

country: Taiwan

institute: Kaohsiung District Agricultural Research and Extension Station

data_processing:
Illumina Casava v1.8.2 software was used for basecalling.
The fastq quality was assessed using FastQC v0.11.2, then the reads were processed to trim adaptor sequences and low-quality ends via Trimmomatic v0.32 with parameters "ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25".
Trimmed reads from all three samples were de novo assembled together using Trinity v2.1.0 with defalut k-mer of 25 and minimum assembled contig length of 200.
Quantification of transcripts and genes were estimated across all samples using the RSEM v1.2.23 and EdgeR package to obtain TMM-normalized FPKM values.
Transcripts with zero TMM-normalized FPKM values for all three samples, and the rest with longest length per component (i.e. gene locus) defined by Trinity were interpreted to represent "unigenes" for downstream analysis.
Each pairwise comparison of differential expression analysis was performed using the R package LIMMA with upper-quantile normalization.
Supplementary_files_format_and_content: fasta format files of nucleotide and amino acid sequences; tab-delimited text file of TMM-normalized FPKM values for each Sample.

organism: Armillaria mellea

source_name: Armillaria mellea

growth_protocol: Both vegetative propagation corms and tubers of G. elata are cultivated in sand with some wood. Armillaria mellea is cultured in PDA medium

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260 by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using TruSeq RNA Library Preparation Kit v2 with standard Illumina protocols

value: Armillaria mellea


title: MCF-7 shNS  RNA-seq Replicate3


title: MCF-7 shNS Hi-C Replicate1


title: MCF-7 shRUNX1  RNA-seq Replicate2


title: SRBC_DZ_AP4–_RNAseq_rep3

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
Read tags from ChIP-seq and RNA-seq were mapped to the mm9 mouse genome with Bowtie2-2.1.0 and TopHat, respecitvely, and further analyzed using Homer to generate bedgraph files and Cufflinks for transcript assembly and RPKM estimation, respectively.
Peak calling was performed using Homer for ChIP-seq data
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Bedgraph files for read histograms normalized to 10,000,000 reads) for ChIP-seq data and RPKM estimation output from Cufflinks for RNA-seq data

source_name: Germinal center dark zone AP4– cells

extract_protocol:
For RNA-seq, MYC–AP4– LZ and MYC+AP4+ LZ cells, AP4+ DZ, and AP4– DZ GC B cells were purified by cell sorting  from AP4-mCherry c-MYC-GFP dual reporter mice 8 days after immunization with SRBC.
For RNA-seq, total RNA was reverse transcribed and amplified (SMART-Seq v4 Ultra Low Input RNA Kit, Clonetech), followed by library construction using a Nextera DNA Library Prep Kit (Illumina).

tag: strain

value: AP4-mCherry c-MYC-GFP knockin

value: lymph node

value: Germinal center dark zone AP4-- cells


title: SRBC_DZ_AP4+_RNAseq_rep3

source_name: Germinal center dark zone AP4+ cells

growth_protocol: For RNA-seq, MYC–AP4– LZ and MYC+AP4+ LZ cells, AP4+ DZ, and AP4– DZ GC B cells were purified by cell sorting  from AP4-mCherry c-MYC-GFP dual reporter mice 8 days after immunization with SRBC.

value: Germinal center dark zone AP4+ cells


title: MCF-7 shNS  RNA-seq Replicate1


title: MCF-7 shRUNX1 Hi-C Replicate1


title: MCF-7 shNS Hi-C Replicate2


title: SRBC_LZ_c-MYC+AP4+_RNAseq_rep3

source_name: Germinal center light zone c-MYC+AP4+ cells


title: MCF-7 wildtype RUNX1 ChIPseq Replicate1 Input


title: MCF-7 shRUNX1  RNA-seq Replicate1


title: MCF-7 shNS  RNA-seq Replicate2


title: SRBC_DZ_AP4–_RNAseq_rep2


title: SRBC_LZ_c-MYC+AP4+_RNAseq_rep2

value: Germinal center light zone c-MYC+AP4+ cells


title: HCC1419 Replicate 1

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
bcl2fastq was used to convert the bcl files into fastq format.
Reads were mapped to the reference genome using TopHat
Allele-specific expression was called with ABC
Genome_build: hg19
Supplementary_files_format_and_content: ABC output file:
SNV=SNV Identifier; CHR=Chromosome; BP=Position on chromosome; REF=Reference allele; OBS=Observed alleles; A1=Allele 1; N_A1=Number of reads containing A1; F_A1=Frequency of A1; N_A1_POS=Number of reads aligned to the +ve strand containing A1; N_A1_NEG=Number of reads aligned to the -ve strand containing A1; A2=Allele 2; N_A2=Number of reads containing A2; F_A2=Frequency of A2; N_A2_POS=Number of reads aligned to the +ve strand containing A2; N_A2_NEG=Number of reads aligned to the -ve strand containing A2; N_TOTAL=Total number of reads overlapping a SNV, including: N_ERRORS, N_OMITTED, MISSING_N; N_ERRORS=Number of reads containing a nucleotide other than A1 or A2; N_OMITTED=Number of reads where the SNV falls within a clipped or deleted region; MISSING_N=Number of reads containing an ambiguous nucleotide N; MAX=The maximum value of from the .bedgraph file (if specified) within the 2x read length window centered on the SNV; P_BINOM=The P-value used to call allele-specific binding; P_MANN_WHIT=The P-value used to call a bias in read position between alleles; P_FISHER=The P-value used to call a bias in the strand distribution between alleles; P_CHISQ=(Same as P_FISHER greater number of reads required); P_STRAND=A binomial p-value of the differences in strand abundance; A1_Position=Position of A1 within reads; A1_Strand=Strand of reads containing A1; A2_Position=Position of A2 within reads; A2_strand=Strand of reads containing A2

growth_protocol: HCC1419 cells were grown to 95% confluence in RPMI 1640 medium supplemented with 10% foetal bovine serum.

extract_protocol:
Total RNA was extracted from HCC1419 cells using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
Two RNA-seq libraries were prepared using the Truseq Stranded mRNA kit (Illumina).

value: breast cancer cell line

tag: source tissue info.

value: TNM stage IIIA, grade 3, primary ductal carcinoma


title: SRBC_DZ_AP4+_RNAseq_rep1


title: SRBC_DZ_AP4+_RNAseq_rep2


title: SRBC_LZ_c-MYC+AP4+_RNAseq_rep1


title: IgM+CD40L_H3K27ac_ChIPSeq_rep2

source_name: Splenic B cells activated in vitro

growth_protocol: For anti-MYC and anti-H3K27ac ChIP-seq, splenic B cells from naïve C57BL/6 mice were activated with anti-IgM for two days, followed by activation with CD40L expressed on NIH-3T3 feeder cells for 24 hours. For anti-AP4 ChIP-seq,  light zone (LZ) and dark zone (DZ) germinal center (GC) B cells were pirified by cell sorting from C57BL/6 mice 8 days after immunization with sheep red blood cells (SRBC).

extract_protocol:
For ChIP-seq, cells were fixed with 1% paraformaldehyde for 10 minutes at room temperature. Soluble chromatin was prepared as described by Ciofani et al (Cell,2012, PubMed ID: 23021777), and immunoprecipitated with antibodies.
Immunoprecipitated DNA and input DNA were used for library preparation according to the Illumina ChIP-seq protocol. After end-repair and indexed adapter ligation, fragments were size-selected using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) prior to amplification. The size-selected and amplified fragment libraries were verified on a 2100 Bioanalyzer (Agilent) prior to being pooled and sequenced.

tag: chip antibody

value: Anti-H3K27ac (Abcam ab4729)

value: spleen

value: Splenic B cells activated in vitro


title: IgM+CD40L_input_rep1


title: SGE

organism: Gastrodia elata

source_name: vegetative propagation corms

value: vegetative propagation corms


title: SRBC_LZ_c-MYC–AP4–_RNAseq_rep2

source_name: Germinal center light zone c-MYC–AP4– cells

value: Germinal center light zone c-MYC--AP4-- cells


title: SRBC_LZ_c-MYC–AP4–_RNAseq_rep1


title: SRBC_LZ_c-MYC–AP4–_RNAseq_rep3


title: IgM+CD40L_MYC_ChIPSeq

value: Anti-c-MYC (Santa cruz sc-764)


title: BGE

source_name: tubers

value: tubers


title: HCC1419 Replicate 2


title: SRBC_DZ_input

source_name: Germinal center dark zone cells

value: Germinal center dark zone cells


title: IgM+CD40L_input_rep2


title: SRBC_LZ_AP4_ChIPSeq

source_name: Germinal center light zone cells

value: anti-AP4 (in house)

value: Germinal center light zone cells


title: RNAseq-NPC-Mock-1

value: mock


title: RNAseq-NPC-ZIKVM-3

value: ZIKVM


title: SRBC_LZ_input

value: lymph node


title: IgM+CD40L_H3K27ac_ChIPSeq_rep1


title: Twist Chip-Seq Rep1

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

description: ChIp with abcam anti-TWIST1 monoclonal antibody

data_processing:
Adaptors removed and quality <30 filtered with cutadept
Reads aligned with bowtie2 using parameters --end-to-end --sensitive
Duplicate reads removed with Picard MarkDuplicates
Peak calling with MACS2 parameters: -p 0.01 --nomodel --extsize (fragment size determined by MACS2 predictd function with band width (-bw) 300 and mfold range 10,30)
IDR analysis of the two replicates performed using the p.value
Genome_build: CanFam3.1
Supplementary_files_format_and_content: MACS2 narrowPeak file

organism: Canis lupus familiaris

source_name: MDCK cells modified to constitutively express human TWIST1, Twist ChIP

growth_protocol: Parental Madin-Darby Canine Kidney (MDCK) cells and MDCK cells that were modified to constitutively express human TWIST1 (Xue et al. 2012) and were maintained in DMEM, 10% Fetal bovine serum (FBS), 1% Penicillin/Streptomycin and 50μM β-mercaptoethanol at 370C and 5% CO2. TWIST1-expressing cells were maintained under selection with 2-4µg/mL of puromycin (Xue et al. 2012) (reference Xue G, Restuccia DF, Lan Q, Hynx D, Dirnhofer S, Hess D, Ruegg C, Hemmings BA. 2012. Akt/PKB-mediated phosphorylation of Twist1 promotes tumor metastasis via mediating cross-talk between PI3K/Akt and TGF-beta signaling axes. Cancer Discov 2: 248-259.)

extract_protocol:
Cells were cross-linked in 1% formaldehyde/PBS (EM grade; ThermoScientific) for 10 minutes, quenched with glycine (0.25M) and washed in cold PBS. Frozen cells were thawed on ice and lysed in 1mL Lysis Buffer 1 (50mM HEPES-KOH pH8.0, 1mM EDTA, 140mM NaCl, 0.25%Triton X-100, 0.5% Igepal CA-630, 10% glycerol) on ice for 10 min, dissociated by pipetting and pelleted by centrifugation at 800g for 5min at 4°C. The pellet was resuspended in 1mL lysis buffer 3 (10mM Tris-HCl [pH 8], 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-lauroylsarcosine) and sonicated (Diagenode Bioruptor). Effective sonication was confirmed by Bioanalyzer analysis. An aliquot (10% of total volume?) was removed for use as the Input sample and the remaining extract was pre-cleared by incubation with 60μL protein A/G Dynabead magnetic beads (Dynal) for 3 hours. Beads for immunoprecipitation were blocked in 0.5% BSA, 0.5% Tween-20 in PBS overnight at 4°C. The cleared chromatin extract was incubated with an anti-TWIST1 monoclonal antibody (ChIP-grade Abcam) overnight at 4°C and the blocked beads added for 3 hours at 4°C. Beads were washed five times in RIPA buffer, twice in RIPA buffer containing 500mM NaCl , twice in LiCl washing buffer (10mM Tris-HCl pH8.0, 1mM EDTA, 250mM LiCl, 0.5% Igepal Ca-630, 0.5% Na-deoxycholate) and once in TE buffer.
Illumina unstranded TruSeq ChIP sample preps

treatment_protocol: No treatments

value: MDCK cells constitutively expressing human TWIST1

tag: phenotype

value: TWIST1-induced mesenchymal phenotype

value: anti-TWIST1 monoclonal antibody (Abcam, cat# ab50887, lot# unknown)


title: SRBC_DZ_AP4_ChIPSeq


title: RNAseq-NPC-ZIKVC-1

value: ZIKVC


title: RNAseq-NPC-DENV-1

value: DENV


title: RNAseq-NPC-DENV-Mock-1


title: RNAseq-NPC-Mock-3


title: TY1SD

status: Public on Aug 22 2016

city: Changsha

first: Miao

last: Bai

state: Hunan

address: Hunan Agricultural University, No. 1 Nongda Road, Furong

institute: Hunan Agricultural University

description: degradome

data_processing:
Illumina Casava1.7 software used for basecalling.
The data is processed by the following steps: 1) Getting rid of low quality reads; 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Supplementary_files_format_and_content: The .fa files report the host plant sRNAs (from MMC and TY1C samples only) and virus sRNAs (from MMS and TY1S samples).  't0xxxxxx' is a custom ID number for unique sequence filter from .fq files.

organism: Solanum lycopersicum

source_name: TYLCV infected leaves

growth_protocol: Inoculated plants and controls were kept in an insect-free chamber at 25~27℃ with a 16 h/day light.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol and DNA was removed with DNase I (Takara, JAPAN) treatment.
small RNA library: After total RNA isolation, low molecular weight RNAs (LMW) were isolated as described Hafner et al., 2008.By polyacrylamide gel electrophoresis, the sRNAs were purified and ligated to 5’ and 3’ RNA adapter. A reverse transcription reaction followed by low cycle PCR was performed to obtain sufficient product for Solexa sequencing. PCR products were collected by gel purification and analysis based on Solexa high-throughput sequencing takes the SBS-sequencing by synthesis.
degradome library: The tomato degradome library was constructed as previously described German et al., 2009. In this study, we utilizing identical copy of samples which proposed for sRNA deep sequencing to identify degradome by parallel analysis of RNA ends (PARE) in high-throughput sequencing. The degradome data of MMC and TY1C were marked as MMCD and TY1CD, respectively; in addition, we balanced mix DNA of 21dpi and 30dpi samples of MMS or TY1S, and marked MMCD and TY1CD, respectively.

treatment_protocol: Tomato 'Moneymaker' and ‘FL505’at 6~8 leaf stages (5-week-old) were agroinoculated with infectious clones of the pBinPLUS-SH2-1.4A which contain TYLCV-[CN:SH2] (AM282874) as described previously (Zhang H et al., 2009). The two samples were called as ‘MMS’ and ‘TY1S’, respectively. Mock-inoculations was performed by inoculating plants with Agrobacterium tumefaciens strain GV3101 containing pBinPLUS, that samples were called ‘MMC’ and ‘TY1C’, respectively.

tag: host variety

tag: inoculum

value: TYLCV

tag: inoculation method

value: Agrobacterium-mediated inoculation

value: 21 and 30 days post-inoculation

value: leaf


title: RNAseq-NPC-Mock-2

source_name: hNPC


title: SRBC_DZ_AP4–_RNAseq_rep1

value: AP4-mCherry c-MYC-GFP knockin

value: Germinal center dark zone AP4-- cells


title: Twist Chip-Seq Rep2

value: anti-TWIST1 monoclonal antibody (Abcam, cat# ab50887, lot# GR100488-11)


title: RNAseq-NPC-DENV-Mock-3


title: RNAseq-NPC-DENV-Mock-2


title: Input DNA Rep1

description: DNA isolated from input chromatin. Not subjected to ChIP

source_name: MDCK cells modified to constitutively express human TWIST1, Input


title: RNAseq-NPC-DENV-2


title: TY1CD

description: degradome

source_name: Mock infected leaves

value: Mock

tag: time

value: 21 days post-inoculation


title: MMCD

description: degradome

value: Moneymaker


title: TY1S_30dpi

description: small RNA

value: 30 days post-inoculation


title: MMSD

description: degradome


title: Input DNA Rep2


title: MMS_30dpi

description: small RNA


title: RNAseq-NPC-DENV-3

tag: virus


title: TY1C

description: small RNA


title: MMS_21dpi

description: small RNA


title: MMC

description: small RNA


title: SMARCB1_Null-B

city: stanford

first: Rajat

last: Rohatgi

state: California

address: 279 campus drive

department: Biochemistry

data_processing:
FASTQ files obtained from Stanford Functional Genomics Facility server were downloaded to desktop. These files were then uploaded to the Partek Flow Server
The raw data obtained was aligned, quantified and analyzed by using Partek Flow software, version 4.0, Partek Inc., St. Louis, MO, USA. Reads were aligned to human reference genome build hg19 using STAR Align and Quantify pipeline in Partek Flow. Differential gene expression (GSA) analysis was done using RPKM normalization.
Genome_build: hg19
Supplementary_files_format_and_content: This is an excel (xslx) file generated by Partek Flow software as explained above. The file has gene expression data for the samples compared to wildtype cells.

source_name: HAP1 Cell Line

growth_protocol: Cells were grown in IMDM medium supplemented with 10% FBS, 2mM L-Glutamine and 1x PenStrep. For RNAseq experiments cells were plated in 6 well plates. RNA was extratced when cells were 70% confluent.

extract_protocol:
Cells were grown to 70% confluency and RNA was extracted using Trizol (Invitrogen).
Library preparation and sequencing was done in Stanford Functional Genomics Facility. In brief, KapaBiosystem Stranded mRNA kit was used for library preparation. Four uunique Illumina adapters (Bar Coded) for multiplexing were used

tag: passage

tag: mutation

value: SMARCB1 Null (CRISPR-2)


title: SMARCB1_Null-A

description: Sample 3 and 4 are biological replicates created from two different CRISPR guide sequences

value: SMARCB1 Null (CRISPR-1)


title: WT_B

value: Wildtype


title: RNAseq-NPC-ZIKVM-4

value: ZIKVM


title: WT_A

description: Sample 1 and 2 are two different passages of the same cell line (wildtype HAP1)


title: SMARCA4_Null-A

description: Sample 5 and 6 are biological replicates created from two different CRISPR guide sequences

value: SMARCA4 Null (CRISPR-1)


title: Donnor1 d28 ChronicTcf1-

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3) (Martin et al., 2011) and filtered for low complexity with seq crumbs (v. 0.1.8).
Reads were aligned against Mus musculus (version GRCm38) genome using STAR (v. 2.4.2a) (Dobin et al., 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) (Anders et al., 2015) using M. musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include htseq gene counts for each sample.

source_name: Tcf1-GFP- P14 cells at d28 of LCMV c13 infection (chronic)

extract_protocol:
Cells were lysed and stored in Trizol before extraction of total cellular RNA using the Direct-zol™ RNA MiniPrep kit (Zymo Research).
RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA reagents (# 634888, Clontech) according to the protocol provided with the reagents beginning with 5ng of total RNA and using 9 cycles of PCR.  150 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (# 15032354, Illumina).

treatment_protocol: Splenocytes were enriched for CD8 T-cells using the EasySep Mouse CD8+ T Cell Isolation Kit (StemCell Technologies) and  GFP+ and GFP- CD8+ CD45.2+ CD45.1- cells were flow sorted.

tag: cell type

value: CD8 T cells expressing a P14 TCR and a Tcf1-GFP reporter

tag: genotype

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf1GFP)WHe


title: Donnor4 d28 Memory Tcf1+

source_name: Tcf1-GFP+ P14 cells at d28 of LCMV Arm infection (acute resolved)


title: Donnor1 d28 Chronic Tcf1+

source_name: Tcf1-GFP+ P14 cells at d28 of  LCMV c13 infection (chronic)


title: Donnor4 d28 Chronic Tcf1-

source_name: Tcf1-GFP- P14 cells at d28 of  LCMV c13 infection (chronic)


title: SMARCB1-SMARCA4_Null-A

description: Sample 7 and 8 are two different passages of the same cell line (SMARCB1-SMARCA4 double null)

value: SMARCB1 Null (CRISPR-1) SMARCA4 Null (CRISPR-2)

tag: cell line


title: Donnor4 d28 Chronic Tcf1+

source_name: Tcf1-GFP+ P14 cells  at d28 of  LCMV c13 infection (chronic)


title: Donnor3 d28 Memory Tcf1-

source_name: Tcf1-GFP- P14 cells at d28 of  LCMV Arm infection (acute resolved)


title: Donnor3 d28 Memory Tcf1+

source_name: Tcf1-GFP+ P14 cells at d28 of  LCMV Arm infection (acute resolved)


title: Donnor2 d28 Chronic Tcf1+

source_name: Tcf1-GFP+ P14 cells  at d28 o  LCMV c13 infection (chronic)


title: Donnor3 Naive

source_name: Tcf1-GFP+ P14 cells


title: TY1S_21dpi

description: small RNA

value: TYLCV

value: Agrobacterium-mediated inoculation

tag: tissue


title: Donnor2 Naive


title: SMARCB1-SMARCA4_Null-B


title: IP12_miR22_Esp2

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

data_processing:
Alignment of reads to mm10 with SOAPSplice
Bam to bed transformation with Bedtools
Peaks were called using macs2 with default parameters
Peaks were filtered by a log10pvalue > 20
Genome_build: mm10
Supplementary_files_format_and_content: Bed files of macs2 called peaks. Fifth column is log10p.value of peak calling

source_name: RISC-IP from mouse myotubes

growth_protocol: Primary mouse satellite cells (MSC) were grown in Ham’s medium supplemented with 20% FBS, 3% chicken embryo extract and 2.5 ng/ml bFGF on collagen-coated dishes.  Differentiation of MSC myoblasts was induced by incubating the cultures in DMEM supplemented with 2% heat-inactivated Horse Serum.

extract_protocol:
After cell lysis, two lysate aliquotes were taken to analyze total RNAs and proteins and the remaining was immunoprecipitated with anti-Ago2 antibody using the RNA-binding protein immunoprecipitation Magna RIP Kit (Merck Millipore, USA) following the manufacturer’s instructions. Ago2 bound RNA was extracted using TRIzol reagent (Invitrogen, Thermo Scientific, USA).
Amplification of cDNA from Ago-2 co-immunoprecipitated RNA was performed using the Ovation RNA-Seq system V2 (Nugen), then cDNA was fragmented and ligated into a sequencing library using Ovation Ultralow library system (Nugen)

treatment_protocol: MSC myocytes kept in DM for 30 h were transfected with 10 nM miR-222 or siGFP duplex RNAs using Lipofectamine 2000 reagent (Invitrogen, Thermo Scientific, USA) and maintained in DM for a further 16 h.

tag: condition

tag: experiment

value: Primary mouse satellite cells


title: IP11_siGFP_Esp2

value: control


title: IP10_siGFP_Esp2


title: IP8_siGFP_Esp1


title: Donnor2 d28 Memory Tcf1-

source_name: Tcf1-GFP- P14 cells at d28 of LCMV Arm infection (acute resolved)

tag: strain


title: Donnor4 Naive


title: PGCLC, derived from ESC clone 1, DNA methylation

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
ES_v65_PGCLC_Me
DNA methylation; PGCLC (ESC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig

data_processing:
The SOLiD 5500xl sequncer-generated raw binary files (XSQ format) were converted into csfasta/QV.qual color-space ASCII text raw read files using the ABI XSQ tool.
The csfasta/QV.qual files were mapped to the mouse mm9 reference sequence using novoalignCS.
The aligned sequence data (bam files) were subjected to quality control analysis using FastQC.
The QC-passed aligned sequence data (bam files) were subjected to DNA methylation/hydroxymethylation enrichment analysis using the MEDIPS R/Bioconductor package.
Genome_build: mouse NCBI37/mm9
Supplementary_files_format_and_content: The wig files contain locations and strengthes of peaks reflecting DNA methylation (MBD-seq) or DNA hydroxymethylation (hydroxymethylcytosine chemical tagging seq).

source_name: Embryoid Body, 6-day culture in the PGCLC induction medium

growth_protocol: Mouse embryonci PGCs were isolated from E12.5 embryos of the C57BL/6 strain; sex of the embryos were unknown. PGCLCs and EpiLCs were generated from mouse embryonic stem cells or iPS cells (C57BL/6 x 129/Sv background; all males) following the protocol published by Hayashi et al (2011, Cell 146:519-532).

extract_protocol: Genomic DNA fragments (~ 150 bp)  converted to ABI SOLiD 5500xl deep sequencing libraries using SOLiD Fragment Library Core Kit with barcodes.

tag: strain background

tag: Sex

value: male

tag: cell/tissue type

value: primordial germ cell-like cells (PGCLCs)

tag: facs enrichment


title: PGCLC, derived from ESC clone 1, DNA hydroxymethylation

description:
ES_v65_PGCLC_OHM
DNA hydroxymethylation; PGCLC (ESC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig

data_processing:
library strategy: hydroxymethylcytosine chemical tagging seq
The SOLiD 5500xl sequncer-generated raw binary files (XSQ format) were converted into csfasta/QV.qual color-space ASCII text raw read files using the ABI XSQ tool.
The csfasta/QV.qual files were mapped to the mouse mm9 reference sequence using novoalignCS.
The aligned sequence data (bam files) were subjected to quality control analysis using FastQC.
The QC-passed aligned sequence data (bam files) were subjected to DNA methylation/hydroxymethylation enrichment analysis using the MEDIPS R/Bioconductor package.
Genome_build: mouse NCBI37/mm9
Supplementary_files_format_and_content: The wig files contain locations and strengthes of peaks reflecting DNA methylation (MBD-seq) or DNA hydroxymethylation (hydroxymethylcytosine chemical tagging seq).


title: EpiLC, derived from ESC clone 1, DNA hydroxymethylation

description:
ES_v65_EpiLC_OHM
DNA hydroxymethylation; EpiLC (ESC derived)
processed data file: epilcs_OHM_MEDIPS_norm.RPM.wig

source_name: EpiLC cell culture

value: epiblast-like cells (EpiLCs)


title: EpiLC, derived from ESC clone 1, DNA methylation

description:
ES_v65_EpiLC_Me
DNA methylation; EpiLC (ESC derived)
processed data file: epilcs_methyl_MEDIPS_norm.RPM.wig


title: ESC, clone 1, DNA methylation

description:
ES_v65_Me
DNA methylation; ESC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig

source_name: ESC cell culture

value: embryonic stem cells (ESCs)


title: OCI-AML2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Fusion detection; Analysis pipeline #2

data_processing:
pipeline #1: The high-quality reads were aligned to human genome assembly Hg19 using TopHat (v2)
pipeline #1: Read counts were normalized to ERCC RNA spike-in controls
pipeline #1: Calculation of differential gene expression was performed using Deseq (v2)
Supplementary_files_format_and_content: Table_OCI2_OCI3_readcounts.txt: tab-delimited text files with normalized read counts per gene for all samples
pipeline #2: The high-quality reads were aligned to human genome assembly Hg19 using TopHat (v2)
pipeline #2: Fusion detection was performed using Defuse v.2
Supplementary_files_format_and_content: OCI-AML2_Defuse_result_file.txt: tab-delimited text files with sequences of predicted fusion transcripts
Genome_build: hg19

growth_protocol: Cells were maintained in RPMI-1640 with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
Rneasy mini kit, Qiagen, including DNAse treatment
RNA quantification protocol: Quant-IT RiboGreen RNA Assay Kit
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

value: Acute myeloid leukemia cell line

tag: treated with

value: none (control)


title: OCI-AML2_EPZ4777_replicate1

description: Analysis pipeline #1

source_name: OCI-AML2_EPZ4777 [10µM] treated_7 days

treatment_protocol: 7 days treatment with EPZ4777 [10µM]

value: EPZ004777, DOT1L inhibitor


title: Donnor2 d28 Chronic Tcf1-


title: OCI-AML2_EPZ4777_replicate2

description: Analysis pipeline #1


title: Donnor2 d28 Memory Tcf1+


title: OCI-AML2_EPZ4777_replicate3

description: Analysis pipeline #1


title: Mouse E12.5 embryonic PGC, DNA hydroxymethylation

description:
invivoPGC_OHM
DNA methylation; iPSC

source_name: E12.5 mouse embryonic gonads (genital ridges)

value: unknown

value: E12.5 embryonic PGC


title: PGCLC, derived from iPSC clone 4, DNA methylation

description:
R21-6_PGCLC_Me
DNA methylation; PGCLC (iPSC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig


title: OCI-AML2_DMSO_replicate2

description: Analysis pipeline #1

source_name: OCI-AML2_DMSO treated_7 days

treatment_protocol: 7 days treatment with DMSO

value: DMSO, vehicle control


title: OCI-AML2_DMSO_replicate1

description: Analysis pipeline #1


title: OCI-AML2_DMSO_replicate3

description: Analysis pipeline #1


title: IP7_siGFP_Esp1


title: PGCLC, derived from iPSC clone 4, DNA hydroxymethylation

description:
R21-6_PGCLC_OHM
DNA hydroxymethylation; PGCLC (iPSC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig


title: OCI-AML3_EPZ4777_replicate2

description: Analysis pipeline #1

source_name: OCI-AML3_EPZ4777 [10µM] treated_7 days


title: EpiLC, derived from iPSC clone 4, DNA methylation

description:
R21-6_EpiLC_Me
DNA methylation; EpiLC (iPSC derived)
processed data file: epilcs_methyl_MEDIPS_norm.RPM.wig


title: OCI-AML3_EPZ4777_replicate1

description: Analysis pipeline #1


title: IP9_miR222_Esp1


title: OCI-AML3_EPZ4777_replicate3

description: Analysis pipeline #1


title: OCI-AML3_DMSO_replicate3

description: Analysis pipeline #1

source_name: OCI-AML3_DMSO treated_7 days


title: OCI-AML3_DMSO_replicate2

description: Analysis pipeline #1


title: ESC, clone 1, DNA hydroxymethylation

description:
ES_v65_OHM
DNA hydroxymethylation; ESC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: OCI-AML3_DMSO_replicate1

description: Analysis pipeline #1


title: Mouse E12.5 embryonic PGC, DNA methylation

description:
invivoPGC_Me
DNA hydroxymethylation; E12.5 embryonic PGC


title: EpiLC, derived from iPSC clone 4, DNA hydroxymethylation

description:
R21-6_EpiLC_OHM
DNA hydroxymethylation; EpiLC (iPSC derived)
processed data file: epilcs_OHM_MEDIPS_norm.RPM.wig


title: Mouse C57BL/6 female mouse resequencing, no enrichment

description:
no_enrichment_mouse_genome
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig

source_name: C57BL/6 mouse liver

value: female

value: total liver tissue


title: iPSC, clone 4, DNA methylation

description:
R21-6_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig

source_name: iPCS cell culture

value: induced pluripotent stem cells (iPSCs)


title: G180_CIN3

city: Bronx

first: Neil

middle: Ari

last: Wijetunga

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Libraries were multiplexed for 50 bp single-end sequencing on the Illumina HiSeq 2000 platform.  Illumina CASAVA pipeline 1.8 was used to generate fastq files.
Alignment was completed with ELAND allowing at most 3 mismatches. Reads flanking HpaII sites were quantified with a custom script.
The read counts were log transformed and normalized before taking the ratio of the normalized HpaII count to normalized MspI count at each assayed HpaII site.  The CDF of the Cauchy distribution was used to obtain methylation probabilities.
Mixture modeling of the distribution assuming three composite distributions was performed to scale the probabilities between 0 and 1.  HpaII sites with less than 5 read counts were removed from the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Combined_processed_HELP_tagging_data.txt.gz: Matrix with columns corresponding to each sample and rows corresponding to assayed HpaII sites. NOTE: Values are probablity of no methylation so will need to be complemented to find probability of methylation.  Hcount files: Quantification of the number reads with an end located at a HpaII site for the positive strand, negative strand, and total.

source_name: Cervical biopsy of CIN3

extract_protocol:
We extracted genomic DNA using proteinase K and RNase A digestion followed by phenol/chloroform extraction and ethanol precipitation.
We characterized DNA methylation patterns using the HELP-tagging assay, a massively parallel sequencing-based restriction enzyme approach described previously.  To minimize potential batch effects, HELP-tagging libraries were processed in batches that balanced by patient age, disease grade, HIV viral load, and HPV genotype. Genomic DNA was digested with the methylation sensitive restriction enzyme, HpaII for comparison with a reference genome digested with the methylation insensitive restriction enzyme, MspI.  Digested DNA was ligated to a custom Illumina sequencing adapter containing a T7 transcriptional promoter and an EcoP15I restriction site at the 3’ end, allowing digestion with EcoP15I.  A second Illumina sequencing adapter with a unique sequencing index was then added and after in vitro transcription, reverse transcription, and PCR amplification, the library was sequenced on the Illumina HiSeq 2000 platform.

value: cervical biopsy

tag: type

tag: age

tag: batch


title: PGCLC, derived from iPSC clone 3, DNA hydroxymethylation

description:
R21-5_PGCLC_OHM
DNA hydroxymethylation; PGCLC (iPSC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig


title: SMARCA4_Null-B

source_name: HAP1 Cell Line

tag: passage

value: SMARCA4 Null (CRISPR-2)


title: iPSC, clone 4, DNA hydroxymethylation

description:
R21-6_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: EpiLC, derived from iPSC clone 3, DNA methylation

description:
R21-5_EpiLC_Me
DNA methylation; EpiLC (iPSC derived)
processed data file: epilcs_methyl_MEDIPS_norm.RPM.wig


title: G174_CIN3


title: G176_CIN3


title: G179_CIN3


title: G172_CIN3


title: G170_CIN3


title: G169_CIN3


title: EpiLC, derived from iPSC clone 3, DNA hydroxymethylation

description:
R21-5_EpiLC_OHM
DNA hydroxymethylation; EpiLC (iPSC derived)
processed data file: epilcs_OHM_MEDIPS_norm.RPM.wig


title: G164_CIN1

source_name: Cervical biopsy of CIN1


title: G156_CIN3


title: G154_CIN1


title: G162_CIN1


title: G153_CIN3


title: iPSC, clone 3, DNA hydroxymethylation

description:
R21-5_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G182_CIN1


title: PGCLC, derived from iPSC clone 2, DNA methylation

description:
R21-4_PGCLC_Me
DNA methylation; PGCLC (iPSC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig


title: PGCLC, derived from iPSC clone 2, DNA hydroxymethylation

description:
R21-4_PGCLC_OHM
DNA hydroxymethylation; PGCLC (iPSC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig


title: G146_CxCa

source_name: Cervical biopsy of CxCa

value: CxCa


title: PGCLC, derived from iPSC clone 3, DNA methylation

description:
R21-5_PGCLC_Me
DNA methylation; PGCLC (iPSC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig


title: G160_CIN1


title: G145_Normal

source_name: Cervical biopsy of Normal

value: Normal


title: G143_Normal


title: EpiLC, derived from iPSC clone 2, DNA methylation

description:
R21-4_EpiLC_Me
DNA methylation; EpiLC (iPSC derived)
processed data file: epilcs_methyl_MEDIPS_norm.RPM.wig

value: male


title: G184_CIN1


title: iPSC, clone 3, DNA methylation

description:
R21-5_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: EpiLC, derived from iPSC clone 2, DNA hydroxymethylation

description:
R21-4_EpiLC_OHM
DNA hydroxymethylation; EpiLC (iPSC derived)
processed data file: epilcs_OHM_MEDIPS_norm.RPM.wig


title: iPSC, clone 2, DNA methylation

description:
R21-4_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: G144_Normal


title: iPSC, clone 2, DNA hydroxymethylation

description:
R21-4_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G141_Normal


title: G140_Normal


title: G138_Normal


title: G139_Normal


title: G150_CxCa


title: G136_CxCa


title: PGCLC, derived from iPSC clone 1, DNA methylation

description:
R21-2_PGCLC_Me
DNA methylation; PGCLC (iPSC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig

value: primordial germ cell-like cells (PGCLCs)


title: PGCLC, derived from iPSC clone 1, DNA hydroxymethylation

description:
R21-2_PGCLC_OHM
DNA hydroxymethylation; PGCLC (iPSC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig


title: G133_CxCa


title: G128_CxCa


title: G130_CxCa


title: G126_CxCa


title: G125_CxCa


title: G123_CxCa


title: EpiLC, derived from iPSC clone 1, DNA methylation

description:
R21-2_EpiLC_Me
DNA methylation; EpiLC (iPSC derived)
processed data file: epilcs_methyl_MEDIPS_norm.RPM.wig

value: epiblast-like cells (EpiLCs)


title: G122_CxCa


title: G120_CxCa


title: EpiLC, derived from iPSC clone 1, DNA hydroxymethylation

description:
R21-2_EpiLC_OHM
DNA hydroxymethylation; EpiLC (iPSC derived)
processed data file: epilcs_OHM_MEDIPS_norm.RPM.wig


title: G115_CxCa


title: G148_CxCa


title: iPSC, clone 1, DNA methylation

description:
R21-2_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: G117_CxCa


title: G118_CxCa


title: G113_CxCa


title: iPSC, clone 1, DNA hydroxymethylation

description:
R21-2_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G111_CIN1


title: G105_CIN1


title: G107_CIN1


title: G103_Normal


title: G110_Normal


title: G109_Normal


title: G104_Normal


title: G097_CIN3


title: iPSC, clone 6, DNA hydroxymethylation

description:
iPS_PPF159-3_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: iPSC, clone 5, DNA hydroxymethylation

description:
iPS_PPF159-2_OHM
DNA hydroxymethylation; iPSC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G101_CIN3


title: iPSC, clone 5, DNA methylation

description:
iPS_PPF159-2_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: G095_CIN3


title: G089_Normal


title: PGCLC, derived from ESC clone 3, DNA hydroxymethylation

description:
ES1_5_PGCLC_OHM
DNA hydroxymethylation; PGCLC (ESC derived)
processed data file: pgclcs_OHM_MEDIPS_norm.RPM.wig


title: G091_Normal


title: ESC, clone 3, DNA methylation

description:
ES1_5_Me
DNA methylation; ESC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig

value: embryonic stem cells (ESCs)


title: G092_Normal


title: PGCLC, derived from ESC clone 3, DNA methylation

description:
ES1_5_PGCLC_Me
DNA methylation; PGCLC (ESC derived)
processed data file: pgclcs_methyl_MEDIPS_norm.RPM.wig


title: G078_CIN1


title: ESC, clone 2, DNA methylation

description:
ES1_2_Me
DNA methylation; ESC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: G084_Normal


title: G086_CIN3


title: ESC, clone 3, DNA hydroxymethylation

description:
ES1_5_OHM
DNA hydroxymethylation; ESC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G082_Normal


title: ESC, clone 2, DNA hydroxymethylation

description:
ES1_2_OHM
DNA hydroxymethylation; ESC
processed data file: pluri_OHM_MEDIPS_norm.RPM.wig


title: G088_Normal


title: iPSC, clone 6, DNA methylation

description:
iPS_PPF159-3_Me
DNA methylation; iPSC
processed data file: pluri_methyl_MEDIPS_norm.RPM.wig


title: G067_CxCa


title: G061_2_CxCa


title: G075_CIN3


title: G059_CxCa


title: G063_CxCa


title: G080_Normal


title: vm2

city: Irvine

first: Kitt

middle: D.

last: Paraiso

state: CA

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
RNAseq reads were aligned using RSEM v1.2.12 using default parameters. RSEM returned the RNA expression from each gene model in both read counts and transcripts per million.
Genome_build: Xenopus tropicalis version 9.0
Supplementary_files_format_and_content: rsem_v9_counts.txt contains the RNA expression in the number of reads that aligned to the gene models in all 12 RNAseq samples. Each row in the file is a gene model and each column is the RNA expression. The file is tab-delimited.
Supplementary_files_format_and_content: rsem_v9_tpm.txt contains the RNA expression in transcripts per million in all 12 RNAseq samples. Each row in the file is a gene model and each column is the RNA expression. The file is tab-delimited.

molecule: polyA RNA

organism: Xenopus tropicalis

source_name: embryo_ventral marginal zone

extract_protocol:
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4oC in 2.5M LiCl to remove contaminating genomic DNA). Agilent Bioanalyzer analysis revealed all RIN scores to be above 9.
The Illumina TruSeq kit was used to isolate polyA+ RNA and construct non-stranded libraries. All cleanup steps used Ampure XP beads. Library quality was assessed by Agilent Bioanalyzer and KAPA qPCR, they were multiplex sequenced and bar-codes on Illumina adaptors were used for de-multiplexing.

treatment_protocol: Early gastrula stage (N&F stage 10-10.25) Xenopus tropicalis embryos were dissected into dorsal, lateral and ventral marginal zones, animal caps and vegetal masses. Pooled explants (~30 explants for each region except lateral marginal zones, which used double this number due to 2 lateral explants per embryos) were used to generate RNA for libraries.

tag: developmental stage

tag: embryo region

value: ventral marginal zone

tag: illumina rna-seq bar codes

value: ACAGTG


title: G019_CIN1


title: G073_CIN3


title: we2

source_name: embryo_whole embryo

value: Early gastrula stage (N&F stage 10-10.25)

value: whole embryo

value: CTTGTA


title: vg2

source_name: embryo_vegetal mass

value: vegetal mass

value: CGATGT


title: G077_Normal


title: G065_CxCa


title: G012_CIN1


title: lm2

source_name: embryo_lateral marginal zone

value: lateral marginal zone

value: TGACCA


title: G061_CxCa

value: cervical biopsy


title: G014_CIN1


title: G057_CxCa


title: G034_CIN1


title: BJ-OSK-DMSO-2_KH0005

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: cultured as described in treatment protocol

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped to hg19 using STRA
read counting performed using HT-seq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name type=exon)
Normalization and Deferential expression analysis performed using DEseq v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (read counts for genomic features) and normalized count tables

source_name: BJ-OSK-DMSO

growth_protocol:
Fibroblast growth protocol: human fibroblasts were cultured in the following fibroblast media: DMEM, 10% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM MEM NEAA and 10 ng/ml human bFGF
human pluripotent stem cell culture protocol: iPSCs were maintained in E8 medium on Matrigelcoated tissue culture vessels. E8 medium contained DMEM/F12, 64 mg/L Lascorbic acid 2-phosphate sesquimagnesium, 13.6 µg /L sodium selenium, 1.7 g/L NaHCO3, 1 g/L sodium chloride, 10 ng/ml FGF2, 20 µg/ml insulin, 10 µg/ml transferrin and 2 µg/L TGF.

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the Direct-zolTM Miniprep kit (R2052).
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques.  The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity.  A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment.  The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

treatment_protocol: Seed BJ cells into 6-well plate at 100,000 cells/well. Twenty-four hours post plating, add OSK (OCT4, 10 MOI; SOX2, 5 MOI and KLF4, 5 MOI) viruses into respective wells. Incubate  overnight. Next morning, remove viruses by replacing virus-containing media with fresh fibroblast media' On day 3 replace fibroblast media with E7 media, and start treating the reprogramming cells with JQ1. RNA was harvest at 48 hours of treatment

tag: cell line

value: BJ (ATCC, CRL-2522)

tag: cell type origin

value: human foreskin fibroblast

tag: transduced with

value: OCT4 (10 MOI), SOX2 (5 MOI), KLF4 (5 MOI)

tag: cell subtype

value: reprogramming fibroblasts

tag: passage number

value: DMSO for 48hrs

tag: harvest time

value: at 48 hours of treatment


title: we1


title: G026_CIN1

tag: tissue


title: JQ10iPSC

description: iPSCs were maintained in E8 medium on Matrigelcoated tissue culture plates. E8 medium contained DMEM/F12, 64 mg/L Lascorbic acid 2phosphate sesquimagnesium, 13.6 µg /L sodium selenium, 1.7 g/L NaHCO3, 1 g/L sodium chloride, 10 ng/ml FGF2, 20 µg/ml insulin, 10 µg/ml transferrin and 2 µg/L TGF

value: induced pluripotent stem cells

value: 80% confluence


title: JQ1iPSC5_KH0009

description: iPSCs were maintained in E8 medium  on Matrigelcoated tissue culture plates. E8 medium contained DMEM/F12, 64 mg/L Lascorbic acid 2phosphate sesquimagnesium, 13.6 µg /L sodium selenium, 1.7 g/L NaHCO3, 1 g/L sodium chloride, 10 ng/ml FGF2, 20 µg/ml insulin, 10 µg/ml transferrin and 2 µg/L TGF


title: BJ-OSK-DMSO-1_KH0003


title: G008_CIN1


title: BJ-OSK-JQ1-2_KH0006

value: 50nM JQ1 for 48 h


title: dm2

source_name: embryo_dorsal marginal zone

value: Early gastrula stage (N&F stage 10-10.25)

value: dorsal marginal zone

value: GCCAAT


title: lm1

value: CAGATC


title: BJ-OSK-JQ1-1_KH0004


title: G035_CIN1


title: vg1

value: vegetal mass

value: CTTGTA


title: G001_CIN1


title: MN-1044_TUMOR_Input

status: Public on Aug 21 2016

city: New Haven

first: Victoria

middle: Elizabeth

last: Clark

state: CT

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University School of Medicine

data_processing:
Reads were aligned uniquely with bowtie (0.12.7) to the human genome (hg19)
Regions of enrichment (peak calling) were identified with MACS (v1.4)
Peaks within 12.5kb were stitched together, and peaks were excluded if completely contained within a region +/- 2 kb of a gene transcription start site. The resulting enhancer list was ranked based on the H3K27ac signal minus the signal of the input, scaled so that the x- (enhancer) and y- (ChIP signal intensity) axes ranged from 0-1, and plotted. The cutoff between “super-enhancer” and “typical enhancer” was geometrically defined as the point at which a line with a slope of 1 was tangent to the curve generated by plotting the ranked enhancer list by ChIP signal intensity.
Genome_build: hg19
Supplementary_files_format_and_content: .bed files: Super-enhancer calls. All bed files are available on the ChIP sample pages.

source_name: meningioma

extract_protocol:
10-15 frozen sections of each tumor block or dura sample were collected for ChIPseq experiments. Tissue was crosslinked with 1% formaldehyde, quenched with glycine, and washed with PBS. Nuclei were extracted by dounce homogenization and resuspended in nuclear lysis buffer containing 0.3% SDS. Chromatin was sheared by sonication with a Misonix S4000 in a 430A cup horn (60 minutes total, amplitude 30, 10 second pulses, 10 second rest). Soluble chromatin was incubated with magnetic beads coated with H3K27ac antibody (Abcam ab4729) overnight at 4°C. Chromatin was precipitated with magnet, washed extensively, and eluted with TE+1%SDS. Crosslinks were reversed and DNA was purified.
Standard Illumina paired-end multiplexed library construction.  H3K27ac ChIP and input samples were sequenced for each tumor (1x75bp, HiSeq 2000).

value: meningioma

tag: mutation group

value: SMO

tag: who grade

tag: histology

value: meningothelial

tag: radiated

value: N

tag: gender

value: F


title: MN-79_TUMOR_ChIP-seq

tag: age


title: BJ-JQ1_KH0002

description: cells were cultured in human fibroblast media as described in fibroblast culture protocol.

value: BJ (ATCC, CRL-2522)

value: human foreskin fibroblast

tag: treated with


title: MN-1044_TUMOR_ChIP-seq


title: ac1

source_name: embryo_animal cap

tag: developmental stage

value: animal cap

value: TGACCA


title: MN-79_TUMOR_Input


title: G071_CIN3

value: cervical biopsy

tag: type

tag: batch


title: MN-296_TUMOR_Input


title: MN-24_TUMOR_ChIP-seq

value: not determined

value: M


title: MN-296_TUMOR_ChIP-seq


title: G002_CIN1


title: ac2

value: Early gastrula stage (N&F stage 10-10.25)

tag: embryo region

tag: illumina rna-seq bar codes


title: MN-64273_TUMOR_Input


title: vm1

value: ventral marginal zone

value: GCCAAT


title: MN-63670_TUMOR_Input

value: psammomatous


title: MN-60355_TUMOR_Input


title: MN-63670_TUMOR_ChIP-seq


title: dm1

value: dorsal marginal zone

value: ACAGTG


title: MN-60355_TUMOR_ChIP-seq

value: meningioma


title: MN-63345_TUMOR_ChIP-seq

value: meningothelial


title: MN-297_TUMOR_Input

value: fibrous

value: N


title: BJ-DMSO_KH0001

source_name: BJ-DMSO

tag: cell line

value: BJ (ATCC, CRL-2522)

tag: cell type origin

tag: transduced with

value: DMSO for 48hrs

value: at 48 hours of treatment


title: MN-291_TUMOR_Input

value: F


title: MN-63345_TUMOR_Input


title: MN-297_TUMOR_ChIP-seq


title: MN-291_TUMOR_ChIP-seq


title: MN-288_TUMOR_Input

value: transitional


title: MN-169_TUMOR_ChIP-seq

value: fibrous+psammomatous


title: MN-1066_TUMOR_Input

value: not determinednknown


title: MN-249_TUMOR_Input

value: secretory


title: G006_CIN1

value: cervical biopsy


title: MN-201_TUMOR_Input


title: MN-191_TUMOR_Input

value: M


title: MN-288_TUMOR_ChIP-seq


title: MN-64273_TUMOR_ChIP-seq


title: MN-1200_TUMOR_ChIP-seq


title: MN-191_TUMOR_ChIP-seq


title: MN-1200_TUMOR_Input


title: MN-1037_TUMOR_Input


title: MN-1037_TUMOR_ChIP-seq


title: MN-1066_TUMOR_ChIP-seq


title: DURA_2_Input

source_name: meninges_normal control

value: meninges

value: not determined


title: MN-249_TUMOR_ChIP-seq


title: MN-163_TUMOR_Input


title: MN-82152_TUMOR

description: other-ribozero depleted RNA

data_processing:
RNA-seq reads were aligned using TopHat2, transcripts were assembled using Cufflinks, a merged assembly file was created using Cuffmerge, abundance calculations were peformed using Cuffquant, differential expression was analyzed using Cuffdiff, and CummeRbund was used to visualize the Cuffdiff ouput.
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking-Cufflinks gene-level expression output files

extract_protocol:
Meningioma mRNA was extracted using the Allprep DNA/RNA Mini Kit (Qiagen Science, MD). RNA Integrity Number (RIN) was assessed using an Agilent Bioanalyzer 2100, and samples with RIN<5.7 were excluded.
Standard Illumina paired-end multiplexed library construction.  Ribozero depletion was performed, and samples were loaded 4 per HiSeq2500 lane (paired-end, 75bp sequencing)

value: unknown


title: MN-61690_TUMOR

description: other-ribozero depleted RNA

value: meningioma


title: MN-105_TUMOR_ChIP-seq


title: MN-69_TUMOR

description: other-ribozero depleted RNA

value: secretory+meningothelial


title: MN-163_TUMOR_ChIP-seq

value: meningothelial


title: MN-105_TUMOR_Input

value: N


title: MN-201_TUMOR_ChIP-seq


title: DURA_1_ChIP-seq


title: MN-60_TUMOR

description: other-ribozero depleted RNA

value: fibrous


title: MN-60355_TUMOR

description: other-ribozero depleted RNA

source_name: meninges


title: MN-63730_TUMOR

description: other-ribozero depleted RNA

value: U


title: MN-169_TUMOR_Input


title: MN-249_TUMOR

description: other-ribozero depleted RNA


title: MN-1268_TUMOR

description: other-ribozero depleted RNA


title: MN-63670_TUMOR

description: other-ribozero depleted RNA

value: psammomatous


title: MN-1237_TUMOR

description: other-ribozero depleted RNA

value: F


title: DURA_1_Input


title: DURA_2_ChIP-seq


title: MN-63345_TUMOR

description: other-ribozero depleted RNA


title: MN-1137_TUMOR

description: other-ribozero depleted RNA


title: MN-1161_TUMOR

description: other-ribozero depleted RNA


title: MN-60835_TUMOR

description: other-ribozero depleted RNA


title: MN-5_TUMOR

description: other-ribozero depleted RNA


title: MN-24_TUMOR_Input

value: SMO


title: MN-1037_TUMOR

description: other-ribozero depleted RNA


title: gi-2_S24

status: Public on Aug 20 2016

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

description:
Gibbon
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

data_processing:
Quality and adaptor trimming was performed using TrimGalore! with default parameters
Reads were mapped to the respective reference genomes (hg19, pantro4,rheMac3,macFas5 and nomLeu3) with bwa
Duplicate reads were removed using Picard
Identified SNPs using GATK v3.4 and standard hard filtering parameters ("QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0").
Genome_build: hg19, pantro4,rheMac3,macFas5 and nomLeu3
Supplementary_files_format_and_content: vcf (variant format files)

organism: Hoolock leuconedys

source_name: Prefrontal Cortex

extract_protocol:
Genomic DNA was extracted according to the DNeasy Blood&Tissue Kit (QIAGEN) protocol.
DNA libraries were prepared for sequencing using Nextera XT DNA Sample Preparation protocol

value: Prefrontal Cortex

value: 6 years


title: chB-1_S47

description:
Ch-B
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

organism: Pan troglodytes

value: 2 years


title: MN-1236_TUMOR

description: other-ribozero depleted RNA


title: MN-1076_TUMOR

description: other-ribozero depleted RNA


title: RVP3_rep3 (mRNA)

city: Los Angeles

first: Marlin

last: Touma

address: 650 Charles E Young drive- MRL 3760

department: UCLA-Cardiovascular Research Laboratory

institute: UCLA

description: right ventricle, postnatal day 3

data_processing:
RNAseq reads were aligned to the mm10 genome assembly using STAR_2.4.0j with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Deep RNA-seq was performed using total RNA isolated from male C57B/6 mouse left ventricle (LV) and right ventricle (RV) at postnatal day 0 (P0, prior to the ductal closure), day 3 (P3, transition), and day 7 (P7, terminal differentiation of the vast majority of cardiomyocytes). Strand specific cDNA libraries were constructed from three LV and RV total RNAs samples (biological replicate) at each time point with the exception of only two RV samples for day 7.

extract_protocol:
Total RNA was isolated from LV and RV of male newborn mouse using the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Starnd Specific libraries. Paired- end RNAseq

tag: strain

value: male

tag: ventricle

value: RV

value: transition


title: RVP7_rep2 (mRNA)

description: right ventricle, postnatal day 7

value: terminal differentiation of the vast majority of cardiomyocytes


title: MN-1071_TUMOR

description: other-ribozero depleted RNA

tag: tissue

tag: mutation group

value: Y


title: gi-1_S23


title: chB-2_S48


title: chA-2_S46

description:
Ch-A
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: RVP0_rep1 (mRNA)

description: right ventricle, postnatal day 0

value: prior to the ductal closure


title: RVP7_rep1 (mRNA)

description: right ventricle, postnatal day 7


title: LVP7_rep3 (mRNA)

description: left ventricle, postnatal day 7

value: LV


title: LVP7_rep2 (mRNA)

description: left ventricle, postnatal day 7


title: RVP3_rep2 (mRNA)

description: right ventricle, postnatal day 3


title: LVP0_rep2 (mRNA)

description: left ventricle, postnatal day 0


title: RVP3_rep1 (mRNA)

description: right ventricle, postnatal day 3


title: LVP3_rep1 (mRNA)

description: left ventricle, postnatal day 3


title: RVP0_rep2 (mRNA)

description: right ventricle, postnatal day 0


title: chA-1_S45


title: LVP7_rep1 (mRNA)

description: left ventricle, postnatal day 7


title: LVP3_rep3 (mRNA)

description: left ventricle, postnatal day 3


title: RVP3_rep2 (lncRNA)

description: right ventricle, postnatal day 3

extract_protocol:
Total RNA was isolated from LV and RV of male newborn mouse using the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand specific libraries. Paired-end RNAseq


title: RVP3_rep1 (lncRNA)

description: right ventricle, postnatal day 3


title: LVP0_rep3 (mRNA)

description: left ventricle, postnatal day 0


title: LVP0_rep1 (mRNA)

description: left ventricle, postnatal day 0


title: LVP3_rep2 (mRNA)

description: left ventricle, postnatal day 3


title: RVP0_rep2 (lncRNA)

description: right ventricle, postnatal day 0


title: RVP0_rep1 (lncRNA)

description: right ventricle, postnatal day 0


title: RVP7_rep2 (lncRNA)

description: right ventricle, postnatal day 7


title: RVP7_rep1 (lncRNA)

description: right ventricle, postnatal day 7


title: Activated KO MBD enriched replicate 2 DNA library

city: Baltimore

first: Christopher

middle: Jordan

last: Gamper

state: MD

address: 1650 Orleans St., CRB I, Rm. 209

department: Oncology

institute: Johns Hopkins University

description:
processed data file:
011_012_merged_KO_D8_enrich_vs_005_006_merged_KO_D8_total_mm9.50_peaks.bed

data_processing:
Bases were called using Bioscape Software using default parameters.  XSQ output was converted to csfasta and qual files using XSQ tools with default parameters.
SOLiD BioScope Software was used for sequence alignment to the mm9 reference genome using default parameters.  Output was processed to sorted SAM and BAM files.
Visualization of coverage was performed using the IGVTools package (count command) with default parameters to generate a tiled data file (TDF) file for faster display in IGV.
Replicate activated samples were merged for analysis.  Methylated regions were identified as peaks of aligned sequencing tags in the MBD enriched compared with total input fraction using MACS v1.4.1 with parameters -s 50 --nomodel --shiftsize=90 -g mm.  Output files were generated in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files depict aligned read counts versus genome position.  BED files with header (chr, start, stop, peak, pVal) depict genomic intervals of MACS peaks sorted by chr position and numbered sequentially.  pVal = -10*log10(MACS p value).

source_name: Day 8 DNMT3a KO OT1 CD8 T cells MBD enriched DNA

growth_protocol: Splenocytes from DNMT3a WT and KO OT1 Thy1.1 mice were stained for CD8, CD62L, and CD44 and naive T cells were sorted as CD8+CD62L(high)CD44(low).

extract_protocol:
Genomic DNA was isolated from sorted T cells using the DNEasy kit (Qiagen) using the manufacturer's protocol for cultured cells and submitted for MBD-seq analysis by The Next Generation Sequencing Center at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins.
Two micrograms of DNA were sonicated to a modal size of ~150–250 bp, and end-repaired using the NEBNext SOLiD DNA library preparation kit end-repair module following the manufacturer’s protocol (New England Biolabs). After column-purification (using the Qiagen PCR purification kit), SOLiD P1 and P2 adapters lacking 5’ phosphate groups (Life Technologies) were ligated using the NEBNext adaptor ligation module and column-purified, and subjected to nick-translation by treating with Platinum Taq polymerase to remove the nick. Methylated regions were affinity enriched using 6xHis-MBD2-MBD protein immobilized on magnetic beads. (Guerrero-Preston, R. et al. (2014) Epigenetics, 9:7, 1031-1046, DOI: 10.4161/epi.29025). The methylation-enriched fraction was amplified using 10-12 cycles using the NEBNext amplification module and a non-enriched input fraction underwent 4-6 cycles of amplification.  Library fragments that were between 200–300 bp were size selected after agarose gel electrophoresis.

treatment_protocol: A portion of the cells were immediately processed for genomic DNA extraction as naive CD8 samples.  Aliquots of 500 cells were transferred by retroorbital vein injection into Thy1.2+ WT C57BL/6 recipients that were infected with 1e6 pfu Vaccinia-Ova to IV activate the T cells in vivo.  Activated cells were isolated 8 days after adoptive transfer by staining splenocytes and FACS sorting for CD8+Thy1.1+ cells.

tag: strain background

tag: genotype/variation

value: OT1 TCR transgenic; DNMT3a KO

tag: cell type

value: CD8 T cell

tag: activation

value: Day 8 post Vaccinia Ova


title: Activated KO MBD enriched replicate 1 DNA library


title: RVP0_rep3 (mRNA)

description: right ventricle, postnatal day 0

tag: gender

tag: age


title: Activated WT MBD enriched replicate 1 DNA library

description:
processed data file:
009_010_merged_WT_D8_enrich_vs_003_004_merged_WT_D8_total_mm9.50_peaks.bed

source_name: Day 8 DNMT3a WT OT1 CD8 T cells MBD enriched DNA

value: OT1 TCR transgenic; DNMT3a WT


title: RVP3_rep3 (lncRNA)

description: right ventricle, postnatal day 3

tag: developmental stage


title: LVP7_rep3 (lncRNA)

description: left ventricle, postnatal day 7


title: LVP3_rep3 (lncRNA)

description: left ventricle, postnatal day 3


title: LVP7_rep1 (lncRNA)

description: left ventricle, postnatal day 7


title: RVP0_rep3 (lncRNA)

description: right ventricle, postnatal day 0


title: LVP0_rep3 (lncRNA)

description: left ventricle, postnatal day 0


title: LVP3_rep2 (lncRNA)

description: left ventricle, postnatal day 3


title: LVP7_rep2 (lncRNA)

description: left ventricle, postnatal day 7


title: Naive KO MBD enriched DNA library

description:
processed data file:
008_KO_Naive_enrich_vs_002_KO_Naive_total_mm9.50_peaks.bed

source_name: Naive DNMT3a KO OT1 CD8 T cells MBD enriched DNA

value: Naive


title: Activated WT MBD enriched replicate 2 DNA library


title: LVP3_rep1 (lncRNA)

description: left ventricle, postnatal day 3


title: LVP0_rep1 (lncRNA)

description: left ventricle, postnatal day 0


title: ma16_S40

description:
ce071454
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue

organism: Macaca fascicularis

value: 7 years


title: Naive WT MBD enriched DNA library

description:
processed data file:
007_WT_Naive_enrich_vs_001_WT_Naive_total_mm9.50_peaks.bed

source_name: Naive DNMT3a WT OT1 CD8 T cells MBD enriched DNA


title: Activated KO input replicate 2 DNA library

source_name: Day 8 DNMT3a KO OT1 CD8 T cells input DNA


title: ma15_S39

description:
ce071410
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue


title: Activated WT input replicate 1 DNA library

source_name: Day 8 DNMT3a WT OT1 CD8 T cells input DNA


title: Activated KO input replicate 1 DNA library


title: Naive KO input DNA library

source_name: Naive DNMT3a KO OT1 CD8 T cells input DNA


title: ma14_S38

description:
ce080366
PCR products mix
pooling PCR products from  DNA that extracted from prefrontal cortex tissue