title: H1-1

source_name: Human primed pluripotent stem cells

value: Human primed pluripotent stem cells


title: H1-2

status: Public on Apr 06 2017

type: SRA

city: Beijing

first: Hongkui

last: Deng

address: this is for reviewer only

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using RPKM for mouse samples and FPKM for human samples respectively.
Genome_build: hg19 for human and GRCm38/mm10 for mouse
Supplementary_files_format_and_content: Excel files include the expression values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human primed pluripotent stem cells were maintained in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells in conventional human embryonic stem cell medium.Human extended pluripotent stem cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or or Matrigel-coated plates.

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell type


title: Study patient J

status: Public on Jun 26 2017

type: RNA

city: Madison

first: Jennifer

middle: M

last: Reinhart

state: WI

address: 2015 Linden Dr.

department: Medical Sciences

country: USA

institute: University of Wisconsin-Madison

description:
SPJ
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.

hyb_protocol: Following fragmentation and labeling, 5.0 ug of ss cDNA was hybridized to the Affymetrix Human Transcriptome 2.0 ST array according to manufacturer protocols for each sample.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G with Autoloader. Scanner serial #50208130.

data_processing: The gene data was extracted using RMA-Sketch in Affymetrix Expression Console version 1.14.46. The exon data was extracted using Alt Splice Analysis in Affymetrix Expression Console version 1.14.46.

label: biotin

source_name: CD*+ T cell-enriched peripheral blood mononuclear cells, TOL

label_protocol: Biotinylated ss cDNA was prepared from 5 ng of total RNA using the Affymetrix GeneChip® WT Pico kit.

growth_protocol: 40ml of heparinized whole blood was collected from each patient.

extract_protocol: RNA was extracted using the Trizol/chloroform method, digested for gDNA (TURBO DNA-free, ThermoFisher Scientific), and residual extraction reagents removed using RNeasy MinElute Cleanup (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells were extracted with gradient separation and enriched for CD*+ T cells using an antibody-based, negative selection magnetic bead system (MACS CD8+ T cell Isolation Kit; Miltenyi Biotec Inc.).

tag: sulfonamide antibiotics sensitivity

value: Tolerant (TOL)


title: H1-EPS-2

source_name: Human extended pluripotent stem cells

value: Human extended pluripotent stem cells


title: Cbx1 (DamID)

status: Public on Jun 24 2016

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
processed data file: Franks et al._DamID TSS correlation_062316.xlsx
Sample_DamID_Cbx1-6-1-GCCAAT
Sample_DamID_Cbx1-6-2-GCCAAT

library_source: genomic

data_processing:
Library strategy: DamID-Seq
Reads were aligned to the human genome (hg19, GRCh37) using Bowtie2 (version 2.2.3) (Langmead and Salzberg 2012).  Only reads that aligned uniquely to a single genomic location were used for downstream analysis.  In addition, only reads aligning just downstream of a GATC sequence in the genome were kept for further analysis.  Reads aligning to non-GATC locations were much more likely to represent non-specific noise.  Putative DamID-Seq peaks were identified using HOMER in a manner similar to variable-size ChIP-Seq peaks, with several modifications as described previously (Jacinto et al. 2015).  Duplicate reads, which are normally discarded to avoid artifacts in ChIP-Seq, were retained for DamID-Seq analysis since most of the reads align to a limited number of GATC sites. DamID-Seq peaks regions were required to have 2-fold more normalized reads than GFP DamID-Seq controls.  In addition, peaks were required to contain at least 50 normalized reads per peak (per 10 million reads sequenced) to remove low magnitude sites.  Normalized bedGraph files were created for DamID by extending reads 1 kb both upstream and downstream to reflect the relative size of DamID enriched regions. Annotation and comparisons between ChIP-Seq peaks, DamID-Seq peaks, and other genomics features such as TSS were performed using the ‘mergePeaks’ and ‘annotatePeaks.pl’ programs in HOMER.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: [.xlsx] Correlation with transcription start sites
Supplementary_files_format_and_content: [.xls] Binding sites for DamID tagged proteins

molecule: genomic DNA

growth_protocol: cDNA corresponding to sPom121, Nup98, Nup98ΔCTD, or GFP was cloned into MSCV-DamID-Gateway using the gateway system.  5ug of the MSCV-DamID vector of choice and 5ug of Ampho were co-transfected into 293T cells.  After 2 days the media was collected from the 293T cells and placed onto HeLa-C cells for 6hrs in the presence of polybrene.   After 48hrs, cells were placed in media containing 2ug/mL puromycin.  After 7-10 days, stable cell lines were obtained.  DNA was harvested from 2 million cells using the Qiagen DNAeasy Blood and Tissue Kit (cat # 69504).  2.5ug of DNA was digested in a 20uL reaction containing 1uL of Dpn1 enzyme (NEB) and NEB buffer 4 at a 1x concentration for > 4 hrs.  The Dpn1 digested DNA was next ligated with the DamID adapter primer duplex.  The sequences of the adapter duplex are: AdR top 5’- CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA- 3’ and AdR-bottom 5’- TCCTCGGCCG-3’.  To make the AdR duplex, 200pmol of each primer were placed in an eppendorf tube together and sample was diluted such that each primer was at a final concentration of 20pmol/uL.  The duplex was next heated at 95°C for 3 min and allowed to slowly cool to room temperature for 15 min.  The resulting DNA duplex was placed in a ligation reaction with the Dpn1 digested DNA (20uL Dpn1 digested sample, 3uL T4 ligase buffer (NEB), 3uL AdR duplex primers, 4 uL ddH2O) at 16°C for > 4hrs.  5uL of the ligation sample was amplified by PCR with KOD DNA polymerase (Toyobo) using manufacturers guidelines.  The primer used to amplify the DNA fragments is: bio-Adr-PCR 5’ bio-GGTCGCGGCCGAGGATC-3’.  Note: the 5’ end of this primer contains a biotin label to be used in later purification steps.  The resulting amplified DNA was diluted to 250uL in binding and washing buffer (5mM Tris-HCL pH 7.5, 0.5mM EDTA) and sonicated in eppendorf tubes for 15 minutes using a bioruptor sonicator (15 cycles of 30 seconds on / 30 seconds off).  The size of sonicated DNA was verified to be 200-500 bp before moving on to the next step.  Next, biotinylated ends were pulled down using Invitrogen Dynabeads MyOne Streptavidin T1.  50uL were washed 3x in binding and washing buffer containing 1M NaCl.  Then the sonicated DNA was added to the 50uL of washed dynabeads.  NaCl was added to the sample at this step to bring the concentration to 1M.  The DNA-bead mixture was rotated at 4°C for 30 minutes.  The beads were then washed 3x with binding and washing buffer + 1M NaCl.  The bound DNA was digested from the beads in a 20uL DpnII digestion reaction at 37°C for 2 hrs.   The sample was cleaned using a Qiagen MinElute Reaction CleaNup Kit.  The DNA was eluted in 20uL and libraries were prepared according to Illumina specifications.

extract_protocol: Standard Illumina Truseq LT

tag: cell line

value: HeLa cells

tag: dam-fusion protein


title: Nup98dCTD (DamID)

description:
processed data file: Franks et al._2016_DamID peaks.xls
processed data file: Franks et al._DamID TSS correlation_062316.xlsx
Sample_DamID_Nup98dCTD-19-1-GTGAAA
Sample_DamID_Nup98dCTD-19-2-GTGAAA


title: Study patient 51

description:
SP51
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: sPom121 (DamID)

description:
processed data file: Franks et al._2016_DamID peaks.xls
processed data file: Franks et al._DamID TSS correlation_062316.xlsx
Sample_DamID_Pom121S-13-1-AGTCAA
Sample_DamID_Pom121S-13-2-AGTCAA


title: Study patient B

description:
SPB
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.

source_name: CD*+ T cell-enriched peripheral blood mononuclear cells, HS

value: Hypersensitive (HS)


title: Nup98 (DamID)

description:
processed data file: Franks et al._2016_DamID peaks.xls
processed data file: Franks et al._DamID TSS correlation_062316.xlsx
Sample_DamID_Nup98-12-1-CTTGTA
Sample_DamID_Nup98-12-2-CTTGTA


title: Study patient 113

description:
SP113
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 37

description:
SP37
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: mRNA_ColorectalCancer_rep8

status: Public on Aug 31 2017

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

molecule: polyA RNA

source_name: fresh frozen colorectal tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

tag: tissue

value: colorectal tumor

tag: age

tag: gender

value: female


title: Study patient 120

description:
SP120
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 45

description:
SP45
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 294

description:
SP294
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 226

description:
SP226
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: IMR90-Nup98 siRNA (RNA-Seq)

status: Public on Jun 22 2016

description:
Data-IMR90-RNAseq-siNup98-150715
processed data file: Franks et al._2016_IMR90 RNAseq.xlsx

data_processing:
Libraries were prepared using the Illumina RNA Library Prep Kit. Reads were aligned to the human genome (hg19, GRCh37) using STAR (version 2.2.0.c) (Dobin et al. 2013). Only reads that aligned uniquely to a single genomic location were used for downstream analysis (MAPQ > 10). Gene expression values were calculated for annotated RefSeq genes using HOMER by counting reads found overlapping exons (Heinz et al. 2010). Differentially expressed genes were found using EdgeR (Robinson et al. 2010). Genes that were significantly misregulated by sPom121 depletion (p-value < 0.01 in Figure 3E and adjusted p-value < 0.05 in Figure 3F) were used for analysis. They were compared with genes that were misregulated by Nup98 knockdown (p-value < 0.01). Gene Ontology functional enrichment analysis was performed using DAVID (Dennis et al. 2003).
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: Excel spreadsheets with FPKM normalized expression values

source_name: IMR90-Nup98 siRNA

growth_protocol:
DMEM 10% for HepG2
DMEM 15% + amino acids for IMR90

extract_protocol:
RNAeasy
Illumina Truseq LT

treatment_protocol: siRNA transfection with RNAimax (Biorad)

value: Lung fibroblast

value: IMR90 cells

tag: treatment

value: Nup98 siRNA transfection


title: HepG2-Nup98 siRNA (RNA-Seq)

description:
Hetzer0150626-TobyHepG2-Nup98
processed data file: Franks et al._2016_HepG2 RNAseq.xlsx

source_name: HepG2-Nup98 siRNA

value: Liver

value: HepG2 cells


title: IMR90-sPom121 siRNA (RNA-Seq)

description:
Hetzer0150626-TobyIMR90-sPom121
processed data file: Franks et al._2016_IMR90 RNAseq.xlsx

source_name: IMR90-sPom121 siRNA

value: sPom121 siRNA transfection


title: GFP (DamID)

description:
processed data file: Franks et al._2016_DamID peaks.xls
processed data file: Franks et al._DamID TSS correlation_062316.xlsx
Sample_DamID_GFP-5-1-ACAGTG
Sample_DamID_GFP-5-2-ACAGTG

source_name: GFP

value: Dam-GFP


title: HepG2-sPom121 siRNA (RNA-Seq)

description:
Hetzer0150626-TobyHepG2-sPom121
processed data file: Franks et al._2016_HepG2 RNAseq.xlsx

source_name: HepG2-sPom121 siRNA


title: IMR90-Fluc siRNA (RNA-Seq)

description:
Hetzer0150626-TobyIMR90-Fluc
processed data file: Franks et al._2016_IMR90 RNAseq.xlsx

source_name: IMR90-Fluc siRNA

value: Fluc siRNA transfection


title: HepG2-Fluc siRNA (RNA-Seq)

description:
Hetzer0150626-TobyHepG2-Fluc
processed data file: Franks et al._2016_HepG2 RNAseq.xlsx

source_name: HepG2-Fluc siRNA


title: K1-H8

status: Public on Mar 09 2016

description: C57Bl/6-derived cells

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the edgeR package v3.6.8 using duplicates to copute within-group dispersion. FDR < 0.05 and log2 fold change greater than 0.5
GO term and KEGG pathway enrichment analysis was carried out on differentially expressed genes using the HOMER analysis package and Benjamini and Yekutieli general correction for multiple testing. Alternatively, Gene Set Enrichment Analysis was carried out using pre-ranked lists generated from either FDR or log2fold change values, setting gene set permutations to 1000 and using the c2 and c6 collections in MSigDB v5.0. DAVID enrichment analysis was performed using the online DAVID tool with default settings.
Differences of CLEAR network genes were calculated uisng the R 3.1.1 language and statistical signficance for differences between conditions were evaluated using a one-sample t-test for non-zero mean.
Clustering was performed with Gene Cluster 3.0 and visualized using heat maps generated with Java TreeView (version 1.1.6r4).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RPKM normalized gene expression table (Excel spreadsheet).

organism: Mus musculus

source_name: Embryoid Bodies (EBs)

growth_protocol: ESCs were passaged on gelatinized plates containing irradiated DR4 feeders in standard ES media (DMEM (Mediatech) supplemented with 15% FBS (Hyclone ES-grade),  1X MEM non-essential amino acids (Mediatech), 100 uM β-mercaptoethanol (Sigma), 100 U/mL penicillin; 100μg/mL streptomycin (Life Technologies) and 1000 U/mL ESGRO-LIF  (EMD Millipore) in 5% CO2 at 37°C. Fresh media was added daily. Prior to mRNA extraction and/or EB formation, mESCs were depleted of feeders for two passages. EBs were generated by typsinizing feeder-free mESC cultures and plating single cell suspensions at 5-6 x 10,000/cm2 on low attachment tissue culture plates (Corning) in ES-media lacking ESGRO-LIF. Media was changed every other day. For high glucose vs. low glucose experiments, ES media was made with no glucose-DMEM (Life Technologies), adding D-(+)-glucose (Sigma) to final concentrations of 25mM (high) or 2.5mM (low).

extract_protocol:
Snap frozen ESC and EB pellets were homogenized in Qiazol (Qiagen), and the resulting aqueous phase was further purified by the RNA clean and concentrator kit (Zymo Reasearch) and digested with DNAse (Qiagen). RNA integrity (RIN) numbers were determined using the Agilent TapeStation prior to library preparation.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina);  non-stranded mRNA-seq

value: mESC-derived EBs

tag: genotype

value: AMPK DKO

tag: background strain

tag: day of differentiation

tag: glucose concentration

value: HG


title: K1-HES

description: C57Bl/6-derived cells

source_name: mouse embryonic stem cells (mESCs)

value: ESCs


title: K1-H4-2

description: C57Bl/6-derived cells


title: K1-H4

description: C57Bl/6-derived cells


title: K1-H2

description: C57Bl/6-derived cells


title: 9301 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

status: Public on Mar 27 2016

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: AML experimental mouse #9301 ckit+ splenocytes

data_processing:
FASTQ sequence files were aligned to the mouse genome version 10 (mm10) using TopHat2 with de novo junction discovery and separately to mm9 using RSEM.
The fastq files were aligned to mouse genome mm10 using BowTie 2 and TopHat 2 (Kim et al., 2013; Trapnell et al., 2009). BAM files were further processed in AltAnalyze 2.0.9 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold. RSEM gene-expression TPM values were all subjected to the same defaults in AltAnlayze for statistical analysis.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005). All gene set enrichment analyses were performed using GSEA v.2.2.0 (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: primary AML

growth_protocol: Mice were euthanized with carbon dioxide and cervical dislocation. Spleens were harvested from moribund Flt3ITD/ITD;Dnmt3afl/- MxCre and  Flt3ITD/ITD;Dnmt3afl/fl controls.  Splenocytes were isolated from freshly sacrificed mice and crushed between two glass slides. Red blood cells were lysed using Ammonium-Chloride-Potassium (ACK) buffer (Gibco), washed, and filtered to obtain single cells suspensions for downstream applications.

extract_protocol:
RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant Bioanalyzer. Then samples with a RIN>8.0 were processed by poly-A selection, stranded True-seq, paired-end 75 base pair (bp), 40 million reads.
RNAs were detected by RNAseq analysis using paired-end 75 nucleotide (nt) sequencing and 40 million reads for all samples. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

treatment_protocol: To isolated c-Kit+ leukemic stem/progenitor populations, freshly isolated single cells suspensions were incubated with CD117 MicroBeads and separated on an AutoMACS Pro separator (Miltenyi, San Diego, CA) according to manufacturer specifications. RNA was extracted from cKit+ purified splenocytes using TriZol (Invitrogen) according to manufacturers instructions.

value: cKit+ splenocytes

value: acute myeloid leukemia


title: K1-H12

description: C57Bl/6-derived cells


title: 8303 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

description: AML experimental mouse #8303 ckit+ splenocytes


title: 9797 Flt3ITD/ITD,Dnmt3afl/- MxCre AML

description: AML experimental mouse #9797 ckit+ splenocytes


title: K1-L4

description: C57Bl/6-derived cells

value: LG


title: K1-L8

description: C57Bl/6-derived cells


title: K1-L2

description: C57Bl/6-derived cells


title: K1-L4-2

description: C57Bl/6-derived cells


title: K3-H12

description: C57Bl/6-derived cells


title: K3-H4

description: C57Bl/6-derived cells


title: K3-HES

description: C57Bl/6-derived cells


title: K3-H8

description: C57Bl/6-derived cells


title: K1-L12

description: C57Bl/6-derived cells


title: K3-L2

description: C57Bl/6-derived cells


title: K3-L12

description: C57Bl/6-derived cells


title: W1-H12

description: C57Bl/6-derived cells

value: WT


title: W1-HES

description: C57Bl/6-derived cells


title: W1-H4

description: C57Bl/6-derived cells


title: K3-L8

description: C57Bl/6-derived cells


title: K3-L4

description: C57Bl/6-derived cells


title: K3-H2

description: C57Bl/6-derived cells


title: W1-H2

description: C57Bl/6-derived cells


title: W1-L4-2

description: C57Bl/6-derived cells


title: W1-L2

description: C57Bl/6-derived cells


title: W2-H2

description: C57Bl/6-derived cells


title: W2-H8

description: C57Bl/6-derived cells


title: W1-L12

description: C57Bl/6-derived cells


title: W2-L4-2

description: C57Bl/6-derived cells


title: W2-H4

description: C57Bl/6-derived cells


title: W2-HES

description: C57Bl/6-derived cells


title: W2-L12

description: C57Bl/6-derived cells


title: W2-H4-2

description: C57Bl/6-derived cells


title: W2-H12

description: C57Bl/6-derived cells


title: W2-L8

description: C57Bl/6-derived cells


title: W2-L2

description: C57Bl/6-derived cells


title: W2-L4

description: C57Bl/6-derived cells


title: W1-H4-2

description: C57Bl/6-derived cells


title: W1-H8

description: C57Bl/6-derived cells


title: W1-L4

description: C57Bl/6-derived cells


title: MCF10A_input_R2

status: Public on Feb 10 2016

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
MCF10A SAMPLE 6
genomic DNA control

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with STAR v2.4, splicing disabled with '--alignIntronMax 1'.
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals).

extract_protocol:
Nuclei were isolated using a modification of the Dignam method (Dignam et al Nucleic Acids Res. 1983) and pellets were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin ranging from 200-800 bp with an average peak size of 500 bp.  For immunoprecipitation, 30 μg of sheared chromatin was incubated with 10 ug of anti H3K4me3 (Abcam, ab1012 lot#GR80367-1) or H3K4ac (Active Motif -39382 lot#29108001) overnight at 4°C and then incubated with 50 μl Protein-G Dynabeads (Life Technologies 10004D lot#123085320) for 4 h at 4°C.
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range.
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and crosslinked with 0.8% formaldehyde (Thermo Scientific Cat no. 28908) in PBS for 10 minutes at room temperature with continuous shaking

value: mammary gland/breast epithelial cell

tag: neoplasia type

value: luminal ductal cells

tag: atcc id

value: fibrocystic disease; ATCC CRL-10317


title: Naive_RNAseq_technicalReplicate2

status: Public on Nov 21 2015

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
RNA-seq alignment and quantification were performed using the TopHat and Cufflinks software tools. RNA-seq reads were first aligned to the human genome (build hg19, GRCh37) using Tophat v2.0.13 (Trapnell et al., 2009) with the parameters: --solexa-quals --no-novel-juncs and using RefSeq gene annotations. The expression levels of RefSeq transcripts were calculated using Cufflinks v2.2.1 (Trapnell et al., 2010). Aligned reads were used to generate wiggle files using RSeQC with the parameters: -t 40000000 -d '+-,-+'.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 25 bp bins. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cells

growth_protocol: cultured in naive ES medium

extract_protocol:
6 million naive or primed hESCs were used for each RNA extraction.
Total RNA was purified using the mirVana™ miRNA Isolation Kit (Life Technologies, AM1560) following the manufacturer’s instructions. 1 μg of total RNA was used for the RNA-seq library construction. A technical replicate was performed for both naïve and primed hESCs. Polyadenylated RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101). The RNA-seq libraries were sequenced on the Illumina HiSeq 2000.

treatment_protocol: None.

value: naive hESC


title: Primed_RNAseq_technicalReplicate2

growth_protocol: cultured in primed ES cells medium

value: primed hESC


title: H1 4iLIF rep2

status: Public on Nov 17 2015

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
mRNA aligned using Tophat 2.0.13
human mRNA reads counted using Ensembl 72 annotations; mouse mRNA reads counted using NCBIM37 annotations
Genome_build: hg19; mm9
Supplementary_files_format_and_content: read counts for mRNA  in tab deliminated format

source_name: embryonic stem cell

growth_protocol: Lis1 was cultured as previously described in Gafni et al, Nature, 2013. H1 4iLIF was cultured in the following conditions:DMEM/F12 media, 20% knock-out serum replacer (KSR), 1mM sodium pyruvate, 0.1mM nonessential amino acids (NEAA), 50U/ml (penicillin), 50µg/ml (streptomycin), 0.1mM β-mercaptoethanol, 1µM GSK3 inhibitor (CHIR99021), 1µM MEK inhibitor (PD0325901), 10µM JNK inhibitor (SB600125), 10µM p38 inhibitor (SB203580),10ng/ml human LIF, 5ng/ml IGF1 and 10ng/ml bFGF

extract_protocol:
Total RNA was extracted using trizol
Standard Illumina protocol

value: H1 embryonic stem cell

tag: pluripotency state

value: naïve


title: Primed_RNAseq_technicalReplicate1


title: Naive_RNAseq_technicalReplicate1


title: MCF10A_input_R1

description:
MCF10A SAMPLE 5
genomic DNA control


title: H1 4iLIF rep1


title: H1 mRNA rep 1

description:
h1-1
processed data file: mrna-counts.tsv

data_processing:
smRNA counts generated using the miRExpress pipeline
mRNA aligned using gsnap
mRNA reads counted using Ensembl 72 annotations
H3K27me3 ChIP-seq read depth counted using samtools mpileup
Genome_build: hg19
Supplementary_files_format_and_content: read counts for mRNA and smRNA in tab deliminated format
Supplementary_files_format_and_content: wiggle file with a ChIP-seq read count every 10bp window and with a minimum depth of 3

growth_protocol: Primed human ESCs [H1 (WA-01) and H7 (WA-07)] and naïve hESCs [Elf-1(NIHhESC-12- 0156)] were cultured as previously described. Briefly, the cells were cultured on a feeder layer of irradiated primary mouse embryonic fibroblasts (MEF) in hESC media: high glucose (3.151g/L) DMEM/F-12 media supplemented with 20% serum replacer, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin (all from Invitrogen, Carlsbad, CA) and 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO). hESC media was supplemented with 4 ng/ml basic fibroblast growth factor (bFGF) for primed hESCs and 1μM GSK3 inhibitor (CHIR99021, Selleckchem), 1μM of MEK inhibitor (PD0325901, Selleckchem), 10ng/mL human LIF (Chemicon), 5ng/mL IFG1 (Peprotech), 10ng/mL bFGF for naïve hESCs, Elf1 (2iLIF). One passage prior to the experiments, the cells were transferred to growth factor reduced Matrigel (Becton Dickinson, Moutainview, CA) in MEF conditioned media (CM). Dispase and Trypsin/EDTA (Invitrogen) were used to passage primed and naïve hESCs, respectively.

value: primed


title: W1-L8

description: C57Bl/6-derived cells


title: SID [S9622]

status: Public on Sep 24 2014

type: genomic

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

description: HumanMethylation450 BeadChip - standard protocol

hyb_protocol: According to HumanMethylation450 protocol

scan_protocol: BeadStudio

data_processing: background subtracted beta-values

source_name: Saliva

extract_protocol: Invitrogen Puregene Genomic DNA kit

tag: sid

tag: Sex

value: Female


title: SID [S9646]

label_protocol: According to HumanMethylation450 protocol

value: Male


title: SID [S9938]


title: SID [S9157]


title: SID [S9169]


title: SID [S9318]


title: SID [S9048]


title: SID [S8834]


title: SID [S9603]


title: SID [S9552]


title: SID [S9465]


title: SID [S9377]


title: SID [S8993]


title: SID [S8845]


title: SID [S8962]


title: SID [S8883]


title: SID [S8874]


title: SID [S8722]


title: SID [S9599]


title: SID [S8928]


title: SID [S9139]


title: SID [S9116]


title: SID [S9233]


title: SID [S9433]


title: SID [S9076]


title: SID [S9167]


title: SID [S8977]


title: SID [S9215]


title: SID [S8697]


title: SID [S9304]


title: SID [S9403]


title: SID [S8543]


title: SID [S8497]


title: SID [S8710]


title: SID [S8240]


title: SID [S8489]


title: SID [S8467]


title: SID [S8453]


title: SID [S8269]


title: SID [S7858]


title: SID [S8158]


title: SID [S7941]


title: SID [S7683]


title: SID [S7326]


title: SID [S6828]


title: SID [S7862]


title: SID [S7228]


title: SID [S6111]


title: SID [S7144]


title: SID [S7811]


title: SID [S5996]


title: SID [S10585]


title: SID [S10175]


title: SID [S10388]


title: SID [S8073]


title: SID [S10284]


title: SID [S5965]


title: SID [S10307]


title: SID [S7005]


title: SID [S6033]


title: SID [S10132]


title: SID [S7759]


title: SID [B9646]

source_name: Blood


title: SID [S10073]


title: SID [S10072]


title: SID [B9465]


title: SID [B9599]


title: SID [B9603]


title: SID [B9552]


title: SID [B9622]


title: SID [B9433]


title: SID [B9318]


title: SID [B9403]


title: SID [B9938]


title: SID [B9304]


title: SID [B9116]


title: SID [B9139]


title: SID [B8962]


title: SID [B9377]


title: SID [B9157]


title: SID [B8883]


title: SID [B8928]


title: SID [B9215]


title: SID [B9048]


title: SID [B9169]


title: SID [B9167]


title: SID [B8874]


title: SID [B8834]


title: SID [B8977]


title: SID [B9233]


title: SID [B8497]


title: SID [B9076]


title: SID [B8467]


title: SID [B8993]


title: SID [B8845]


title: SID [B8543]


title: SID [B7941]


title: SID [B8697]


title: SID [B7144]


title: SID [B8489]


title: SID [B8269]


title: SID [B8240]


title: SID [B8453]


title: SID [B7858]


title: SID [B8158]


title: SID [B7326]


title: SID [B7005]


title: SID [B6033]


title: SRB Globular stage suspensor-biological replicate 2

status: Public on May 10 2014

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: The suspensor region was captured from six-micron paraffin sections using the Leica LMD6000 system

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Sequenced reads were quality-filtered. Reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to the Phaseolus vulgaris genome (v1.0) using bowtie v0.12.7 with parameters -v 3 -5 9 -3 1 --best --strata.
Read counts to the Phaseolus vulgaris gene models (v1.0) were computed using BedTools. Only uniquely mapped reads were used.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008).
Genome_build: Phaseolus vulgaris v1.0 (Phytozome)
Supplementary_files_format_and_content: tab-delimited text file including gene model of Phaseolus vulgaris and normalized RPKM value.

organism: Phaseolus coccineus

source_name: Laser-captured  suspensor region from globular-stage embryo

growth_protocol: Scarlet runner bean plants (Hammond's Dwarf Red Flower) were grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22C. Flowers were hand-pollinated and tagged.

extract_protocol: Six days after hand pollination, seeds with length between 1.6mm and 2.5mm and containing globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)). Embryo regions were captured from six-micron sections using a Leica DM6000 system. Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA). Five nanograms of total RNA was converted to complementary DNA (cDNAs) and amplified using the Nugen Ovation RNA-Seq kit. Approximately 500 nanograms of cDNA was used as template for blunt end repair, 3' A Tailing and adapter ligation following the Illumina mRNA-Seq protocol. Purified cDNAs were amplified by PCR for 10 cycles. PCR-amplified cDNA fragments were size selected using the AMpure XP beads (Beckman). Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Hammond's Dwarf Red Flower

value: globular stage embryo

tag: embryonic region

value: suspensor


title: SID [B8722]


title: SID [B6828]


title: SID [B5965]


title: SRB Globular stage suspensor-biological replicate 1


title: SRB Globular stage embryo proper-biological replicate 2

description: The embryo proper region was captured from six-micron paraffin sections using the Leica LMD6000 system

source_name: Laser-captured  embryo proper region from globular-stage embryo

value: embryo proper


title: SID [B7683]


title: Common Bean Globular stage embryo proper-biological replicate 2

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Sequenced reads were quality-filtered. Reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to the Phaseolus vulgaris genome (v1.0) using bowtie v0.12.7 with parameters -v 2 --best --strata. The bases with more than 1% error rate at the 5’ and 3’ end were trimmed during the alignment.
Read counts to the Phaseolus vulgaris gene models (v1.0) were computed using BedTools. Only uniquely mapped reads were used.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008).
Genome_build: Phaseolus vulgaris v1.0 (Phytozome)
Supplementary_files_format_and_content: tab-delimited text file including gene model of Phaseolus vulgaris and normalized RPKM value.

organism: Phaseolus vulgaris

growth_protocol: Common bean plants (G19833) were grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22C. One month after sowing, the plants were moved into a short-day growth chamber with a 8:16 light-dark cycle at 22C for two weeks to initiate flowering. After two weeks of short-day treatment, the plants were moved back to 16:8 light-dark cycle at 22C. The flowers, that were about to open and had not released pollen, were tagged as zero-day after pollination.

extract_protocol: Six days after pollination, seeds with length between 1.6mm and 2.0mm  and containing globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al., Plant Physiol.132. 27-35 (2003)). Embryo regions were captured from six-micron sections using a Leica DM6000 system. Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA). Five nanograms of total RNA was converted to complementary DNA (cDNAs) and amplified using the Nugen Ovation RNA-Seq kit. Approximately 500 nanograms of cDNA was used as a template for blunt end repairs, 3' A Tailing and adapter ligation following the Illumina mRNA-Seq protocol. Purified cDNAs were amplified by PCR for 10 cycles. PCR-amplified cDNA fragments were size selected using the AMpure XP beads (Beckman). Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: globular-stage embryo


title: Common Bean Globular stage suspensor-biological replicate 2


title: SRB Globular stage embryo proper-biological replicate 1


title: SID [B10175]


title: SID [B7811]


title: SID [B7862]


title: SID [B6111]


title: SID [B10585]


title: SID [B8073]


title: SID [B10132]


title: Common Bean Globular stage embryo proper-biological replicate 1


title: SID [B10388]


title: SID [B10072]


title: SID [B7759]


title: SID [B5996]


title: SID [B8710]


title: SID [B7228]


title: SID [B10073]


title: SID [B10307]


title: SID [B10284]


title: Common Bean Globular stage suspensor-biological replicate 1