title: CSB2_GFP

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

country: United Kingdom

institute: Cancer Research UK

description: Chip-Seq

data_processing:
ChipSeq: Alignments were performed using bwa (version 0.6.1) against the hg19 genome using a mismatch of 2 base pairs and a seed length of 36.
ChipSeq: Duplicates were removed and resulting bam files sorted and indexed using the Picard program (picard-tools package version 1.42; http://picard.sourceforge.net)
ChipSeq: Peak calling was performed using MACS (version 1.4.0rc2; Zhang et al., 2008) with default parameters: --gsize=2700000000 --tsize=36 --bw=300 --mfold=10,30 --pvalue=1e-05 --diag --keep-dup=all
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are those generated using MACS, showing the locations of peaks enriched in either GFP or N20 samples relative to input.

growth_protocol: CS1AN cells (CSB-null) were reconstituted by CSB-BAC, expression of CSB was assessed by western blot and UV-sensitivity defect rescue. Cells were cultured in DMEM + 10% FBS.

extract_protocol:
Cells were cross-linked with formaldehyde at 1% final concentration. Nuclei were extracted in low salt cnditions and burst in high salt before shearing the DNA to the reduced size of 300-500bp. ChIP was performed with antibodies against RNA Pol II (N20, santa cruz) or GFP/Flag-tagged CSB (GFP, abcam).
Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 36bp single end sequencing on the Illumina Genome Analyzer IIx.

tag: cell line background

value: CSB reconstituted by CSB-BAC

value: Transformed Skin fibroblasts

value: anti-GFP

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: MEF-4

status: Public on Sep 22 2014

type: SRA

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

description: RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

library_source: transcriptomic

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with mouse genome version mm9 and transcriptome defined by the mm9 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The mm9 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: single mouse embryonic fibroblast cell

extract_protocol:
Single cell were individually micromanipulated using an Eppendorf TransferMan NK 2 micromanipulator and ejected into PCR tubes containing RNA protective lysis buffer (10X PCR Buffer II, 25mM MgCl2, 10% NP40, 0.1 M DTT, SUPERase-In, Rnase Inhibitor, 0.5 uM UP1 Primer, 10mM dNTP and Nuclease-free water) and immediately flash frozen in liquid nitrogen. Single cells were then thawed for reverse transcription without further purification given they were individual single cells.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.

tag: tissue

value: single mouse embryonic fibroblast cell


title: CSB2_input

description: Chip-Seq

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: genotype/variation

tag: cell type


title: CS1AN2_N20

description: Chip-Seq

value: CSB-null

tag: chip antibody

value: anti-RNAP II (N20)

value: Santa Cruz


title: CSB2_N20

description: Chip-Seq


title: MEF-3


title: MEF-2


title: MEF-11


title: CS1AN2_input

description: Chip-Seq


title: CS1AN2_GFP

description: Chip-Seq


title: HP2_4

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: circulating pancreas tumor cell

extract_protocol:
Blood specimens from 3 patients with PDAC were subjected to microfluidic depletion of RBCs and CD45 and CD66b-positive WBCs, leaving single CTCs and small CTC-clusters in the final product (pubmed ID 23552373). The product containing enriched cells was collected in a 35mm petri dish and viewed using a Nikon Eclipse Ti inverted fluorescent microscope. Cells of interest were identified based on intact cellular morphology and lack of labeling with anti-CD45 magnetic beads. These target cells were individually micromanipulated with a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator and ejected into PCR tubes containing RNA protective lysis buffer and immediately flash frozen in liquid nitrogen.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

tag: patient

value: circulating pancreas tumor single cell in lysis buffer


title: CSB1_N20

description: Chip-Seq


title: MEF-12


title: HP2_5


title: MEF-10


title: CSB1_GFP

description: Chip-Seq


title: CSB1_input

description: Chip-Seq


title: GMP2-8-040513

source_name: single tumor cell circulating in mouse blood


title: MEF-1


title: GMP2-7-040513

value: single tumor cell circulating in mouse blood


title: GMP2-6-040513


title: CS1AN1_N20

description: Chip-Seq


title: CS1AN1_input

description: Chip-Seq


title: CS1AN1_GFP

description: Chip-Seq


title: GMP2-5-040513


title: GMP2-4-040513


title: GMP2-3-040513


title: GMP2-2-040513


title: GMP2-11-040513


title: GMP1-7-030413


title: GMP2-1-040513


title: GMP2-10-040513


title: GMP1-3-030413


title: GMP1-5-030413


title: GMP1-6-030413


title: GMP1-2-030413


title: GMP1-4-030413


title: GMP1-1-030413


title: at-seed-ler_wt_x_col_osd_met 2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana F1-seeds of Landsberg-erecta (female) crossed with Columbia-0  osd1-1 met1-3 (male)
seed_exp.txt

data_processing:
BS-seq: reads were mapped to the TAIR 10.0 version of the Arabidopsis reference genome with bowtie as implemented in Bismark version 0.7.8, allowing up to two mismatches per read. Alignments were deduplicated using perl scripts. Methylated cytosine-calls were performed using the methylation extractor in Bismark version 0.7.8.
RNA-seq: reads were mapped using TopHat. Only uniquely mapping reads were used for further analysis. Differentially expressed genes were identified using the DESeq package.
Genome_build: TAIR10
Supplementary_files_format_and_content: methylated cytosine calls and RNA abundance

organism: Arabidopsis thaliana

source_name: AT F1-Seed Landsberg x osd1 met1 Columbia

growth_protocol: All seed material was surface sterilized (5% sodium hypochlorite, 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on ½ MS (1% sucrose) in long day conditions (LD, 16h light / 8h darkness; 21°C). After 10 days in light conditions germination ratios were determined and/or plants were transferred to soil and grown under LD conditions.

extract_protocol: To obtain material for Bisulfite sequencing endosperm and embryo material from ca. 60 siliques of Ler x Col, Ler x osd1-1, Ler x osd1-1 met1-3 and Ler x met1-3 crosses was collected over several days and stored at -70°C before it was finally combined for DNA extraction. DNA was extracted using 2xCTAB.   To obtain material for RNA for sequencing seeds from 20 siliques of Ler x Col, Ler x osd1-1, Ler x osd1-1 met1-3 and Ler x met1-3 crosses were harvested into RNA later (Sigma) in triplicates and homogenized (Silamat S5 (IvoclarVivadent)) using glass beads. RNA was extracted following a modified protocol for the RNAqueous Kit (Ambion) and residual DNA was removed using 5 µl DNAseI (ThermoScientific), followed by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Ler plants were emasculated and after two days pollinated with Col, osd1-1, osd1-1 met1-3 or met1-3 pollen. 6-7 DAP seeds were dissected on a glass slide into endosperm and embryo samples in 0.3 M sorbitol / 3 M MES solution under a stereoscope using fine needles. Seed coat tissue was discarded and embryo/endosperm material was washed in sorbitol solution. Supernatant was removed and samples were frozen in liquid N and stored until all material was collected.

value: Seed

tag: genotype

value: Landsberg x osd1 met1 Columbia


title: at-seed-ler_wt_x_col_osd_met 1


title: at-seed-ler_wt_x_col_osd_met 3


title: GMP2-9-040513


title: at-seed-ler_wt_x_col_met 2

description:
Arabidopsis thaliana F1-seeds of Landsberg-erecta (female) crossed with Columbia-0  met1-3 (male)
seed_exp.txt

source_name: AT F1-Seed Landsberg x met1 Columbia

value: Landsberg x met1 Columbia


title: TetTKO.WGBS

first: Lan

last: Jiang

state: Massachusetts

address: 200 Longwood Ave

institute: Boston Children Hospital

data_processing:
for WGBS, Low quality bases and adapter containing reads were trimmed in raw data by trim_galore with default parameters. Bismark 0.7.9 was used to align bisulfite sequencing reads to reference genome mm9. Analyzing lamda DNA reads confirmed that more than 99.7% C was successfully bisulfite converted. Coverage depth and methylation level of each cytosine were extracted by bismark_methylation_extractor and samtools from sam files. DMR analysis was performed by methpipe-3.0.1. FDR was estimated by randomly shuffling the Tet TKO and E14 WT methylome to call DMR with same pipeline and parameters. For methylation level of a region, all the reads with 10 times coverage located in the region were pooled. Since bisulfite sequencing cannot distinguish 5mC and 5hmC, 5mC level in WT cells was corrected by subtracting 5hmC level obtained from TAB-seq (Yu et al., 2012). For both 100-bp tiles and DMR, methylation difference larger than 20% is considered as differentially methylated. K-mean clustering is done by heatmap R and R.
for RNA-seq , Sequence reads were mapped against the mouse genome (mm9) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation. All programs were performed with default setting (unless otherwise specified). The unique mapped reads (about 77% of total reads) were subsequently assembled into transcripts guided by reference annotation (UCSC gene models) with Cufflinks v2.0.2. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments). We identified the differentially expressed genes by requiring that the fold-change > 2 and the gene have a FPKM > 0.5 in at least one sample.
Genome_build: mm9
Supplementary_files_format_and_content: Results files include FPKM values for each RNA-seq (formatted as “ gene.name    chr     start   end     length  sample.name”)  and CpG methylation level for WGBS results (formatted as “chr pos methylation.level methylatedC.count all.read.count”).

source_name: ESC

extract_protocol:
The mouse ES cell line used in this study is E14Tg2a. Cells are cultured on 0.1% gelatin (Millipore) coated plates in DMEM (Life technologies) medium supplemented with 15% fetal bovine serum (Sigma), penicillin/streptomycin, non-essential amino acid, sodium pyruvate, GlutaMax, beta-mercaptoethanol (Life technologies) and 1000 units/ml LIF (ESGRO, Millipore) unless specified.
One microgram of DNA with 0.5% non-methylated lamda DNA spike-in was sheared by Covaris M220 instrument to average size of 350 bp in length. Then the DNA was end repaired, dA-tailed and methylated adaptors added. Bisulfite conversion was carried out using EpiTect fast bisulfite conversion kit (Qiagen) according to manufacturer’s instruction. To achieve best bisulfite conversion rate, 20 minutes were used in both conversion step. Then the bisulfite converted DNA was amplified with five PCR cycles to achieve the final library. The WGBS library was subjected to pair-end (2 x 110 bp) sequencing on Hiseq 2500 (Illumina).  for RNA-seq,  RNA samplers were prepared by RNeasy mini kit (Qiagen). Depleted of rRNA of carried out using ribo-zero kit (Epicentre). Barcoded RNA-seq libraries were constructed using NEBNext Ultra directional  RNA library prep kit for Illumina according to manufacturer’s instruction (New England Biolabs). WT.E14 was barcoded with Illumina standard indx6, GCCAAT while TetTKO sample was barcoded with index 12, CTTGTA.  Single end 50 bp sequencing was done on Hiseq 2500 (Illumina).

treatment_protocol: Generation of Tet TKO cells:   Tet TKO cells were generated using CRISPR method using the previously published guide-RNA sequence (REF). E14 cells cultured in 2i medium (DMEM/F12 supplemented with penicillin/streptomycin, GlutaMax, 1mM MEK inhibitor PD0325901 and 3mM GSK3 inhibitor CHIR99021) on Matrigel (BD biosciences) coated plates was transiently transfected with mixture of px330 vectors containing guide RNAs for Tet1, Tet2 and Tet3 along with one puromycin resistant gene containing empty vector using Fugene 6 transfection reagent (Promega). The cells were subcultured to a low density 24 hours later. Two days after transfection the cells were selected with 2 mg/ml puromycin for 48 hours. Viable clones were grown larger and picked up for mutation analysis. Mutations were first screened by PCR followed by restriction analysis as restriction sites were presented at CRISPR cutting sites. Then 5hmC level of DNA from mutant clones were analyzed by slot blot. DNA samples with significant lower level of 5hmC were digested to single nucleotide and analyzed by mass spectrometry to quantify the absolute 5hmC level. We found that in Tet1 Tet2 double knockout cells there were around 2% 5hmC left when compared to that of WT E14 cells, while in Tet TKO cells, no 5hmC was detectable. The Tet TKO cells along with WT E14 control cells were then adapted to serum containing culture condition for at least 17 days before further analysis.

tag: age

tag: cell line

value: ES cell line E14Tg2a

value: TetTKO


title: at-seed-ler_wt_x_col_met 3


title: TetTKO.RNA-seq


title: at-seed-ler_wt_x_col_met 1


title: WT.E14.WGBS

value: WT


title: at-seed-ler_wt_x_col_osd 1

description:
Arabidopsis thaliana F1-seeds of Landsberg-erecta (female) crossed with Columbia-0  osd1-1 (male)
seed_exp.txt

source_name: AT F1-Seed Landsberg x osd1 Columbia

value: Landsberg x osd1 Columbia


title: at-seed-ler_wt_x_col_wt 2

description:
Arabidopsis thaliana F1-seeds of Landsberg-erecta (female) crossed with Columbia-0  (male)
seed_exp.txt

source_name: AT F1-Seed Landsberg x Columbia

value: Landsberg x Columbia


title: at-seed-ler_wt_x_col_wt 3


title: MVth2_RNASeq

city: Cambridge

first: Stefano

last: Pluchino

address: Forvie Site, Robinson Way

department: Brain Repair Centre

institute: University of Cambridge

data_processing: Reads were mapped to the mouse genome (mm9) using Tophat. Transcripts were then assembled using Cufflinks using UCSC annotation as reference.

molecule: polyA RNA

source_name: Microvesicles derived from Neural Progenitor Cells cultured in Th2 conditions

growth_protocol: NPCs lines were prepared from the subventricular zone (SVZ) of 7-12 week old female SJL mice (18-20 gr. Charles River), as described (Pluchino et al., Nature, 2005).

extract_protocol: RNA purity and integrity was firstly confirmed by BioAnalyzer (Agilent,). Deep sequencing of the isolated polyA RNA was performed by Eastern Sequence and Informatics Hub (EASIH; University of Cambridge, UK) on the Illumina GAIIx platform (Illumina, CA) according to the Illumina RNA-Seq protocol.

treatment_protocol: NPCs were plated in complete growth medium (CGM) with or without either Th1 (500 IU/ml recombinant mouse IFN-γ, BD Biosciences; 200 UI/ml recombinant mouse TNF-α, Pepro Tech Inc.; 100 UI/ml recombinant mouse IL-1β, Euroclone) or Th2 (10 ng/ml recombinant murine IL-4, R&D; 10 ng/ml recombinant mouse IL-5, R&D; 10 ng/ml recombinant mouse IL-13, R&D) cytokine mixes for 16 hours in vitro, as described (Pluchino et al., 2008). At the end of the conditioning, NPCs were harvested and the supernatants processed for the collection of either MVs or EXOs.

value: Microvesicles

tag: strain

value: SJL

tag: culturing conditions

value: Th2 cytokines supplemented medium (10 ng/ml recombinant murine IL-4, R&D; 10 ng/ml recombinant mouse IL-5, R&D; 10 ng/ml recombinant mouse IL-13, R&D)


title: MVth1_RNASeq

source_name: Microvesicles derived from Neural Progenitor Cells cultured in Th1 conditions

value: Th1 cytokines supplemented medium (500 IU/ml recombinant mouse IFN-γ, BD Biosciences; 200 UI/ml recombinant mouse TNF-α, Pepro Tech Inc.; 100 UI/ml recombinant mouse IL-1β, Euroclone)


title: EXOth1_RNASeq

source_name: Exosomes derived from Neural Progenitor Cells cultured in Th1 conditions

value: Exosomes


title: MVbasal_RNASeq

source_name: Microvesicles derived from Neural Progenitor Cells cultured in basal conditions

value: Basal medium


title: EXObasal_RNASeq

source_name: Exosomes derived from Neural Progenitor Cells cultured in basal conditions


title: at-seed-ler_wt_x_col_wt 1


title: EXOth2_RNASeq

source_name: Exosomes derived from Neural Progenitor Cells cultured in Th2 conditions


title: at-sperm-col_jas_1n

description: Arabidopsis thaliana 1n sperm  of Columbia-0 jason-3

source_name: AT 1n-Sperm jas3 Columbia

value: Sperm

value: jas3 Columbia


title: at-sperm-col_jas_2n

description: Arabidopsis thaliana 2n sperm  of Columbia-0 jason-3

source_name: AT 2n-Sperm jas3 Columbia


title: at-endosperm-ler_wt_x_col_met

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta (female) crossed with Columbia0  met1-3  (male)

source_name: AT F1-Endosperm Landsberg x met1 Columbia

value: Endosperm


title: NPCth2_RNASeq

source_name: SVZ derived Neural Progenitor Cells cultured in Th2 conditions

value: Neural Progenitor Cells


title: NPCth1_RNASeq

source_name: SVZ derived Neural Progenitor Cells cultured in Th1 conditions


title: NPCbasal_RNASeq

source_name: SVZ derived Neural Progenitor Cells cultured in basal conditions


title: WT.E14.RNA-seq


title: at-seed-ler_wt_x_col_osd 2

value: Seed


title: at-endosperm-ler_wt_x_col_wt

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta (female) crossed with Columbia-0  (male)

source_name: AT F1-Endosperm Landsberg x Columbia


title: at-seed-ler_wt_x_col_osd 3


title: at-endosperm-ler_wt_x_col_osd

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta (female) crossed with Columbia-osd1-1  (male)

source_name: AT F1-Endosperm Landsberg x  osd1 Columbia

value: Landsberg x  osd1 Columbia


title: at-embryo-ler_wt_x_col_osd_met

description: Arabidopsis thaliana F1-embryo of Landsberg-erecta (female) crossed with Columbia-0 osd1-1 met1-3 (male)

source_name: AT F1-Embryo Landsberg x osd1 met Columbia

value: Embryo

value: Landsberg x osd1 met Columbia


title: at-endosperm-ler_wt_x_col_osd_met

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta (female) crossed with Columbia 0 osd1-1 met1-3  (male)

source_name: AT F1-Endosperm Landsberg x osd1 met Columbia


title: at-embryo-ler_wt_x_col_osd

description: Arabidopsis thaliana F1-embryo of Landsberg-erecta (female) crossed with Columbia-0 osd1-1 (male)

source_name: AT F1-Embryo Landsberg x  osd1 Columbia


title: at-embryo-ler_wt_x_col_wt

description: Arabidopsis thaliana F1-embryo of Landsberg-erecta (female) crossed with Columbia-0  (male)

source_name: AT F1-Embryo Landsberg x Columbia


title: 2383 piglet with GG genotype of FUT1 gene

status: Public on Sep 21 2014

city: Yangzhou

last: Ye

state: Jiangsu

address: Daxue Road  NO 88

department: animal science and technology

country: China

institute: Yangzhou university

description: 2385 piglet and 2383 piglet were a pair of full-sib with AA and GG genotype at M307 positionof FUT1 gene, respectively.

data_processing: Sequenced sequences (sequ-seqs) were pro-cessed using Illumina's Genome Analyzer Pipeline software.The sequ-seqs were then subjected to a series of additional filters with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 15.0: (1) not sequencing adapters;(2) containing no more than two N (ambiguious bases); (3) being longer than 15 nt or shorter than 55 nt.The sequ-seqs that satisfy the acceptance criteria were used for further study.

organism: Sus scrofa

growth_protocol: The pig resource populations of the Sutai breed, either resistant or sensitive to the ETEC F18 strain, were housed under the same conditions.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Gaithersburg, MD, USA) according to the manufacturer's protocol.

treatment_protocol: The animals were sacrificed to collect duodenal tissues, which were immediately preserved in liquid nitrogen and subsequently stored in a -70Cfreezer.

value: duodenal

tag: subject

value: 2383 piglet

value: GG genotype at M307 of FUT1 gene

tag: breed

value: Sutai


title: 2134 piglet with GG genotype of FUT1 gene

description: 2129 piglet and 2134 piglet were a pair of full-sib with AA and GG genotype at M307 position of FUT1 gene, respectively.

value: 2134 piglet sib of 2129


title: 512 piglet with GG genotype of FUT1 gene rep2

description: A repetition of sepuencing for 512 piglet

value: 512 piglet sib of 524


title: 524 piglet with AA genotype of FUT1 gene

description: 524 piglet and 512 piglet were a pair of full-sib with AA and GG genotype at M307 positionof FUT1 gene, respectively.

value: 524 piglet sib of 512

value: AA genotype at M307 of FUT1 gene


title: 512 piglet with GG genotype of FUT1 gene rep1


title: 2129 piglet with AA genotype of FUT1 gene

value: 2129 piglet sib of 2134


title: Midgut_m12-13

status: Public on Sep 20 2014

city: Canberra

first: Stephen

middle: Leslie

last: Pearce

state: ACT

address: Clunies Ross St, Black Mountain

department: Ecosystem Sciences

country: Australia

institute: CSIRO

data_processing:
Data filtering was performed with PRINSEQ 0.20.3 to remove q<3 reads
Read alignments were performed with TopHat 2.0.6 using default parameters
Expression quantification and tests for differential expression were carried out by cuffdiff 2.0.2 using the -N -u -b -T parameters
Genome_build: Flybase release r5.47
Supplementary_files_format_and_content: cuffData.db file containing FPKM estimations for genes in each sample and the results of DE testing. Suitable for analysis with the cummeRbund R package (http://compbio.mit.edu/cummeRbund)

organism: Drosophila melanogaster

source_name: third-instar larval midgut

extract_protocol:
Regions of the third instar larval midgut were identified with a GFP expressing line and dissected into RNAlater. Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit.
Library construction carried out at Macrogen

value: midgut

tag: midgut region


title: at-embryo-ler_wt_x_col_met

description: Arabidopsis thaliana F1-embryo of Landsberg-erecta (female) crossed with Columbia 0 met1-3 (male)

source_name: AT F1-Embryo Landsberg x met1 Columbia

value: Landsberg x met1 Columbia


title: Midgut_m10-11


title: Midgut_m2


title: Midgut_m3-4-5


title: 72h

city: Nashville

first: James

middle: G

last: Patton

state: TN

address: 1161 21st avenue south

department: Biological Sciences

institute: Vanderbilt University

description: light-damaged 72h

data_processing:
Sequencing reads were processed to remove adapter sequences and mapped to the ZV9 zebrafish genome.
Bowtie (Langmead et al., 2009) was used to map the resulting reads to miRNA hairpin sequences from miRbase (www.miRbase.org)
Reads were further filtered to remove reads derived from precursor miRNA loop regions or passenger strands
Genome_build: Zv9
Supplementary_files_format_and_content: text files showing miRNA abundance; located on the series level

organism: Danio rerio

source_name: Retina

extract_protocol:
Retinas were collected in TRIzol reagent and total RNA was extracted and size fractionated on 15% urea acrylamide gels. 15-30 nt small RNAs were size selected, ligated to 3’ and 5’ end adapters and amplified by RT-PCR to generate small RNA libraries as described (Wei et al., 2012).
Libraries were constructed following the protocol published by Wei et al., 2012

value: albino (alb-/-)

value: adult

value: wildtype

value: retina


title: Midgut_m6


title: Midgut_m1


title: Midgut_m9


title: Midgut_m7-8


title: 0h


title: RNA-seq nsc repeat

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
ChIP-Seq reads were aligned to the human genome (hg19) using the Bowtie (Langmead et al. 2009) software using the preset parameters. Only uniquely mapping reads were used for the further analysis. RNA-Seq reads from NSC, SF7761 and SF8628 were aligned to the human genome hg19 and to gene annotations from Refseq gene using TopHat v2.05 (Trapnell et al. 2009).
For the ChIP-Seq, the average coverage in each base pair was computed across the genome and rendered in the Integrative Genomics Viewer. For the RNA-Seq, Cufflinks v2.0.2 (Trapnell et al. 2010) was used to quantify FPKM values.
Peak detection was done using MACS (Feng et al. 2012) for H3K4me3 and using SICER (Zang et al. 2009) for H3K27me3 and EZH2. For the H3K4me3 peak, we used P-value < 1 × 10-6. For the H3K27me3 and EZH2 peak, we used P-value < 1 × 10-6 and FDR <0.01, window size of 200, and gap size of 600.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-Seq, peaks are reported in bed files; bigwig files have scores that represent the normalization reads density. The excel file is the FPKM values (caculated by cufflinks) for the RNA-seq samples.

source_name: whole cell

growth_protocol: SF7761 and SF8628 cell lines from patients harboring the histone H3.3 K27M mutation were obtained from Hashizume et al. (2012). NSCs (N7800-100) were purchased from Invitrogen and cultured and maintained in NSC medium (A10509-01, StemPro NSC SFM, Invitrogen).

extract_protocol:
ChIP was performed the same way as ChIP assay, except that DNA was recovered from the protein G complex using elution buffer (10 mM Tris at pH 8.0, 10 mM EDTA at pH 8.0, 1% SDS, 150 mM NaCL, 5 mM DTT). DNA was subsequently purified using Qiagen Mini Elute PCR purification kit. Total RNA was extracted using the miRNeasy Mini Kit (Qiagen #217004).
The ChIP DNA libraries were prepared with the Ovation Ultralow DR Multiplex system (NuGEN). RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN).

value: neural stem cell (NSC)

tag: cell cycle stage

value: asynchronization


title: RNA-seq nsc


title: RNA-seq sf8628

value: SF8628 cell line


title: sf7761 H3K27me3

value: SF7761 cell line


title: sf7761 igg

value: igg


title: nsc H3K27me3


title: sf7761 EZH2


title: sf7761 input

value: input


title: sf7761 H3K4me3


title: nsc EZH2


title: nsc input


title: nsc igg


title: 28d

description: light-damaged 28d


title: DEN treated WT replicate 2

status: Public on Sep 19 2014

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

data_processing:
Base calling was performed using software provided with the Ion Proton sequencer.
Sequenced reads were trimmed for adaptor sequence and mapped to mm9 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html)
Tags overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized using EDASeq and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing normalized read counts for each gene.

source_name: Liver

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum

extract_protocol:
Approximately 20 µg of total RNAs were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, Carlsbad, CA, USA)
The isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.

value: 8 months

value: WT

value: liver

tag: agent

value: 25ml per kg DEN (diethyl nitrosamine)


title: RNA-seq sf8628 repeat


title: RNA-seq sf7761 repeat


title: Col-0 ctrl rep2

city: Beijing

first: Yuxin

last: Hu

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology

institute: Institute of Botany, CAS

data_processing:
RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 15 reads were trimmed Fastx package, then mapped to wild type Col-0 whole genome using bowtie2 with default settings, allowing 2 nucleotide mismatches
Generated BAM files were sorted and indexed with SAMtools package
Number of Reads of each gene was counted and calculated with HTSeq package
Genome_build: Col-0 TAIR10.22
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromsomes, start, end, length and RPKM values for each Sample

source_name: whole rosette

growth_protocol: Seeds were sown on 1:1 peat: vermiculite, stratified for three days, and then grown at 22°C/19°C for a week. Subsequently the geminated seedlings were transplanted into new 1:1 peat: vermiculite mixture, one plants per pot (6cm x 6cm), and eight plants per genotype. All plants were randomly placed, grown in controlled chamber (Weiss Bio1300; Weiss Gallenkamp), at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.

extract_protocol:
Ten to 15 rosettes per genotype (Col-0, C24, Te, CT101) from control and ozone treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with GeneJet Plant RNA purification Mini Kit (Fermentas, now part of Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: Plants were exposed with 350 nL L-1 ozone for two hours.

value: whole rosette

tag: genotypes

tag: developmental stage

value: 3 weeks old plants

tag: treatment

value: control


title: Col-0 O3 rep1

tag: tissue

value: 350 ppb ozone exposure for 2hr


title: Col-0 ctrl rep3


title: DEN treated WT replicate 1


title: Col-0 ctrl rep1


title: CT101 ctrl rep3


title: Col-0 O3 rep2


title: CT101 O3 rep3


title: RNA-seq sf7761

tag: cell type


title: CT101 O3 rep2


title: CT101 O3 rep1


title: Te O3 rep3

value: Te


title: Te O3 rep2


title: CT101 ctrl rep1


title: Te O3 rep1


title: Te ctrl rep3


title: Te ctrl rep1


title: C24 O3 rep3


title: C24 O3 rep2


title: C24 O3 rep1


title: nsc H3K4me3

tag: chip antibody


title: C24 ctrl rep3


title: C24 ctrl rep1


title: C24 ctrl rep2


title: Col-0 O3 rep3


title: mel90.07

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using TopHat version 2.0.9 with the NCBI Build 37 reference genome
Read counts per gene were quantified using HTSeq version 0.5.4
Genome_build: HG19
Supplementary_files_format_and_content: txt file with raw read count data

source_name: Melanoma

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

tag: braf/nras mutation

value: NRAS

value: Melanoma cell line


title: WM1366


title: M016X1


title: BLM

value: BLM


title: MZ2-mel


title: CT101 ctrl rep2


title: 518.A2

value: BRAF


title: mel95.23


title: A875


title: ahr-1(ju145) mutant

city: Kuopio

first: Vuokko

last: Aarnio

department: A. I. Virtanen Institute, Department of Neurobiology

country: Finland

institute: University of Eastern Finland

data_processing:
The quality of the reads was checked with FastQC. Reads were not filtered based on quality. The mean quality score was above 32 at each read position and the overall quality score was between 32 and 40 for the vast majority of the reads (data not shown). There were few undetermined “N” bases and all reads were of the same length (100 nt). The average GC content matched the theoretical distribution in all of the samples. No over-represented sequences were listed in the quality check with FastQC. Some bases were enriched in a particular position of the reads.
Reads containing full adapter or primer sequences used in the sample preparation step were searched with a script created by the authors. No reads were removed since only 0.13 % to 0.18 % of the reads contained an adapter sequence.
To find possible reads arising from dietary Escherichia coli (E. coli), the reads were mapped to E. coli OP50 strain draft genome (NCBI, ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT/Escherichia_coli_OP50_uid49051) with Bowtie 2.0.2 ( Langmead et al., 2009) allowing only exact matches. The parameters were set as follows: -k 1, --score-min L, 0, 0, --minins 100, --maxins 300. Only 0.001% to 0.002% of the read pairs concordantly matched the E. coli genome. The aligning reads were not removed from further steps of the analysis.
The reads were aligned to C. elegans genome (version WS220, Release 62, Ensembl) with TopHat 1.3.1 that used Bowtie 2.0.2 and SAMtools 0.1.16. Novel splice sites were not searched but the reads that did not directly align to the genome were compared against known splice sites obtained from the gene annotation file Caenorhabditis_elegans.WS220.62.gtf (Ensembl, ftp://ftp.ensembl.org/pub/release-62/gtf/caenorhabditis_elegans/). Parameter values were set as follows: --mate-inner-dist 0, --mate-std-dev 50, --no-novel-juncs, --transcriptome-max-hits 10, --max-multihits 10, --b2-N 1, --no-novelindels, -G Caenorhabditis_elegans.WS220.62.gtf.
Differential gene expression analyses ahr-1(ia03) vs. wild-type and ahr-1(ju145) vs. wild-type were performed using the Cuffdiff program of Cufflinks 1.3.0 and the file Caenorhabditis_elegans.WS220.62.gtf that contains annotations for 45,343 predicted transcripts. Transcripts with false discovery rate-corrected p-values (q values) < 0.05 and fold change > 2 (or < 0.5), and FPKM value of > 0 in both samples, were defined as differentially expressed.
Genome_build: Caenorhabditis elegans genome (version WS220, Release 62, Ensembl, ftp://ftp.ensembl.org/pub/release-62/fasta/caenorhabditis_elegans/dna/)
Supplementary_files_format_and_content: The processed data files are .xls files modified from Cufflinks (Cuffdiff) output. They are matrices that state the following information to all of the tested genes: ID (Wormbase sequence name) Wormbase locus name if available, genomic coodinates (locus), test status (see Cufflinks manual), FPKM value in the wild-type N2 sample, FPKM value in the ahr-1 mutant sample, value of test statistic used in the determination of differential expression, p-value, false discovery rate -corrected p-value a.k.a. q-value, whether q-value is <0.05 (yes/no), fold change FPKM(ahr-1 mutant)/FPKM(wild-type), whether the gene was determined to be differentially expressed in the experiment (yes/no) and whether the gene was differentially expressed in both ahr-1 mutants used in the study (yes/no).

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: The nematodes were grown in standard laboratory conditions. To make synchronized L4 stage cultures, eggs were harvested from gravid adults with hypochlorite treatment and grown to the L4 larval stage. The nematodes were harvested with sterile water, washed once and stored in RNAlater reagent and frozen at -20 C.

extract_protocol:
Total RNA was isolated from L4 larval stage wild-type and ahr-1 mutant animals with TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Briefly, 1 ml of Trizol Reagent was added to 100 ul of nematode pellet and the sample was shaken manually for 5 minutes. 200 ul of chloroform was added and the sample was shaken again for 3 minutes. The sample was centrifuged and the aquous upper layer was taken  to new tubes. An equal volume of isopropanol was added and the sample was incubated for 10 min in room temperature and centrifuged. The RNA debris was washed with 1 ml of 75 % ethanol and let dry. The isolated RNA was dissolved in water. Contaminating DNA was removed with Ambion TURBO DNA-free kit (Applied Biosystems, Austin, TX, USA) as described in the manual supplied by the manufacturer. Briefly, 10xTURBO DNAse Buffer and DNAse were added and the sample was incubated at +37 C and centrifuged to remove DNA.  Supernatant was taken into new tubes.
mRNA libraries were made using the RNA-seq Sample Preparation Kit according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA).

tag: strain name

tag: genotype/variation

value: ahr-1(ju145) mutant


title: mel1.12

tag: cell line


title: ahr-1(ia03) mutant

value: ahr-1(ia03) mutant


title: mel0.08


title: mel99.08


title: mel888


title: Wild-type N2

value: Wild-type


title: D10


title: Te ctrl rep2


title: F172 GJ

status: Public on Sep 18 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: Pyrosequencing

data_processing:
Pyrosequencing analysis was conducted according to the methods described in the previous studies (Hur M, Kim Y, Song HR, et al. Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl Environ Microbiol 2011;77:7611-9.).
Any reads containing two or more ambiguous nucleotides, reads with low quality score (average score < 25), or reads shorter than 300 base pairs, were discarded. Potential chimeric sequences were detected by the Bellerophon method, which compares the BLASTN search results between the forward half and reverse half sequences.
The taxonomic classification of each read was assigned against the EzTaxon-e database (http://eztaxon-e.ezbiocloud.net), which contains the 16S rRNA gene sequence of type strains that have valid published names and representative species level phylotypes of either cultured or uncultured entries in GenBank public database with complete hierarchical taxonomic classification from the phylum to the species.
The species richness of samples was determined by the abundance-based coverage estimator (ACE), Chao1 estimator and Jackknife estimator. In addition, Simpson diversity index, Shannon diversity index, and Good's library coverage were calculated in the CLcommunity program (Chunlab Inc., Seoul, Korea).
Random subsampling was conducted to equalize the read size of samples for comparing different read sizes among samples. To compare the operational taxonomic units (OTUs) between samples, shared OTUs were obtained with the XOR analysis of the CLcommunity program.
Genome_build: EzTaxon-e database (http://eztaxon-e.ezbiocloud.net)
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample

organism: human gut metagenome

extract_protocol:
Two pieces of gastric mucosa and gastric juice (500 ul) were excised and subjected to bacterial genomic DNA (gDNA) extraction using a commercial kit (iNtRON Biotechnology, Gyeonggi, Korea). Briefly, the tissues were treated with lysozyme at 37°C for 15 min and lysed with a buffer containing proteinase K and RNase A at 65°C for 15 min. The lysates were subsequently mixed with binding buffer and the gDNA was purified using resin columns.
PCR amplification was performed using primers targeting the V1 to V3 regions of the 16S rRNA gene with extracted DNA. For bacterial amplification, barcoded primer of 9F (5’-CCTATCCCCTGTGTGCCTTGGCAGTC-TCAG-AC-AGAGTTTGATCMTGGCTCAG-3’; underlined sequence indicates the target region primer) and 541R (5’-CCATCTCATCCCTGCGTGTCTCCGAC-TCAG-X-AC-ATTACCGCGGCTGCTGG-3’; ‘X’ indicates the unique barcode for each subject). Pyrosequencing was performed on GS Junior Sequencing system; Chunlab, Inc., Seoul, Korea.

tag: host organism

value: Human

tag: host tissue

value: stomach

tag: host tissue subsection

value: gastric juice

tag: biopsy type

tag: helicobacter pylori status

value: HP positive control


title: S881 GJ

description: Pyrosequencing

value: HP positive cancer


title: S957 GJ

description: Pyrosequencing


title: C334 GJ

description: Pyrosequencing

value: HP negative control


title: S870_b

description: Pyrosequencing

value: gastric body

value: gastric mucosal biopsy


title: S700_b

description: Pyrosequencing


title: S692_b

description: Pyrosequencing

value: HP negative cancer


title: S701_b

description: Pyrosequencing


title: S673_b

description: Pyrosequencing


title: S639_b

description: Pyrosequencing


title: S881_b

description: Pyrosequencing


title: S616_b

description: Pyrosequencing


title: SK-MEL-147


title: F21_b

description: Pyrosequencing


title: F39_b

description: Pyrosequencing


title: F195_b

description: Pyrosequencing


title: S512_b

description: Pyrosequencing


title: F196_b

description: Pyrosequencing


title: C352_b

description: Pyrosequencing


title: F168_b

description: Pyrosequencing


title: FU2869(Ds259)

description: Pyrosequencing

value: gastric antrum, follow-up sample


title: C116_b

description: Pyrosequencing


title: C1_b

description: Pyrosequencing


title: FU2634(f196)

description: Pyrosequencing


title: FU2475(Ds71)

description: Pyrosequencing


title: FU2180(F182)

description: Pyrosequencing


title: FU2548(S253)

description: Pyrosequencing


title: FU2591(f21)

description: Pyrosequencing


title: FU2089(S675)

description: Pyrosequencing


title: FU1447(S228)

description: Pyrosequencing


title: FU2097(DS64)

description: Pyrosequencing


title: FU1723(C4)

description: Pyrosequencing


title: FU2060(F30)

description: Pyrosequencing


title: FU159(f39)

description: Pyrosequencing


title: f_u2379(S260)

description: Pyrosequencing


title: f_u290(B68)

description: Pyrosequencing


title: f_u1198(DS110)

description: Pyrosequencing


title: S957

description: Pyrosequencing

value: gastric antrum


title: s97

description: Pyrosequencing


title: f_u1956(s135)

description: Pyrosequencing


title: S871

description: Pyrosequencing


title: s870

description: Pyrosequencing


title: C29_b

description: Pyrosequencing


title: s700

description: Pyrosequencing


title: S692

description: Pyrosequencing


title: s673

description: Pyrosequencing


title: S559

description: Pyrosequencing


title: s616

description: Pyrosequencing


title: s512

description: Pyrosequencing


title: S490

description: Pyrosequencing


title: s390

description: Pyrosequencing


title: S488

description: Pyrosequencing


title: S318

description: Pyrosequencing


title: S260

description: Pyrosequencing


title: S243

description: Pyrosequencing


title: S227

description: Pyrosequencing


title: S253

description: Pyrosequencing


title: S170

description: Pyrosequencing


title: S135

description: Pyrosequencing


title: S228

description: Pyrosequencing


title: F96

description: Pyrosequencing


title: FU2240

description: Pyrosequencing


title: F56

description: Pyrosequencing


title: S675

description: Pyrosequencing


title: f39

description: Pyrosequencing


title: f196

description: Pyrosequencing


title: s639

description: Pyrosequencing


title: f21

description: Pyrosequencing


title: F30

description: Pyrosequencing


title: S740

description: Pyrosequencing


title: F195

description: Pyrosequencing


title: F182

description: Pyrosequencing


title: S613

description: Pyrosequencing


title: F172

description: Pyrosequencing


title: s701

description: Pyrosequencing


title: F106

description: Pyrosequencing


title: Ds71

description: Pyrosequencing


title: Ds64

description: Pyrosequencing


title: DS7

description: Pyrosequencing


title: Ds262

description: Pyrosequencing


title: Ds259

description: Pyrosequencing


title: Ds272

description: Pyrosequencing


title: Ds271

description: Pyrosequencing


title: Ds100

description: Pyrosequencing


title: Ds211

description: Pyrosequencing


title: S13

description: Pyrosequencing


title: Ds110

description: Pyrosequencing


title: C45

description: Pyrosequencing


title: C4

description: Pyrosequencing


title: C47

description: Pyrosequencing


title: C334

description: Pyrosequencing


title: c352

description: Pyrosequencing


title: C61

description: Pyrosequencing


title: C132

description: Pyrosequencing


title: c291

description: Pyrosequencing


title: c116

description: Pyrosequencing


title: c29

description: Pyrosequencing


title: C106

description: Pyrosequencing


title: c1

description: Pyrosequencing


title: Input DNA

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: total DNA

data_processing:
Libraries were sequenced on the Illumina Genome Analyzer IIx using the Single-Read Cluster Generation Kit v4 and 38 Cycle Sequencing Kit v4.
Data were processed using the Illumina Pipeline Software v1.60. The aligned sequences were generated using the ELAND module within the Illumina Genome Analyzer Pipeline Software, v1.3 (Illumina, Inc.) and mapped to the assembly 18 of human genome.
Transcription factor binding sites were identified using SISSRs peak-finder v1.4  (Site Identification from Short Sequence Reads) (Jothi et al., 2008). To reduce false positive calls, DNA input was used as a background channel in SISSRs.
Genome_build: hg18
Supplementary_files_format_and_content: PROX1vsInput_hg18.bed was generated using SISSRS peak-finder, default parameters, input DNA used as background. The file contains thelist of identified binding sites. The columns correspond to: 1) Chromosome, 2) Binding site start-position, 3) Binding site end-position, 4) Number of tags/reads supporting the identified binding site, 5) Fold enrichment, i.e. ratio of number of tags in the ChIP sample versus number of tags in the background sample, 6) P-value, i.e. probability that one would expect to see such fold enrichment between the ChIP and the background sample just by chance.

growth_protocol: SW480 cells (CCL-228) were purchased from ATCC. SW480R cells were sub-populated as described (Petrova et al., 2008). The cells were cultured as described by the manufacturers (ATCC), in RPMI medium (1640+GlutaMAXTM-I, Gibco) 10%FBS and 1%p/s at 37°C in 5%CO2.

extract_protocol:
0.5x107 SW480R cells were cross-linked with formaldehyde, chromatin was fragmented using Simple ChIP Enzymatic Chromatin IP Kits (Cell Signaling) and immunoprecipitated using 5µg goat anti–human PROX1 antibody (R&D Systems) complexed with protein G Sepharose (GE Healthcare).
10 ng of ChIP sample was quantified using the Qubit fluorometer (Invitrogen) and DNA were prepared using the ChIP-Seq Sample Preparation Kit (Illumina) according to the manufacturer’s protocol.

value: Epithelial tumor cells isolated from human colorectal adenocarcinoma


title: PROX1_ChIPSEQ

description: total DNA

value: goat anti–human PROX1 antibody (R&D Systems)


title: B148

description: Pyrosequencing


title: C197

description: Pyrosequencing


title: B68

description: Pyrosequencing


title: Heat-12h_nonpolyA

first: Zhi

middle: John

last: Lu

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
For the mixed-tissue total RNA-seq, the first four and the last five nucleotides of raw reads were trimmed, for poly(A)- RNA-seq data, the first three nucleotides of raw reads were trimmed due to bad quality using the FASTX-toolkit.
Reads were then mapped to TAIR10 rRNA sequences by Bowtie (v 0.12.9) with 1 mismatch, and retained reads were further mapped to TAIR10 genome using TopHat (v 2.0.8) with 2 mismatches.
Transcriptome was re-assembled using the Cufflinks and Cuffcompare program following the pipeline (Trapnell et al. 2012). Novel transcripts were not overlapped with any of the gold-standard genomic elements.
Genome_build: TAIR10
Supplementary_files_format_and_content: 1. Excel file includes all lncRNAs predicted in Arabidopsis (Appendix_1_Full_matrix_of_lncRNAs_in_Arabidopsis.xlsx); 2. Excel file includes differentially expressed lncRNAs under stress conditions (Appendix_2_List_of_differentially_expressed_lncRNAs_under_stress_conditions.xlsx); 3. Excel file includes functional annotation of co-expressed lncRNAs (Appendix_3_Functional_annotation_of_co-expressed_lncRNAs.xlsx).

source_name: Seedling

growth_protocol: Wild-type Arabidopsis thaliana (Col-0) seeds were sterilized in a 0.1% Triton X-100 and 20 % sodium hypochlorite solution for 10 min and then rinsed in sterilized water 10 times. Seeds were then grown on 1/2 strength Murashige & Skoog (MS) media supplemented with 1% sucrose, 0.1% MES, pH 5.7, and 1.2% agar. Agar plates were cultured at 22-24 ºC, 16:8h day/night, and a light intensity of 100 μmol m-2 s-1. Twelve-day-old seedlings were exposed the the stress environments. Seedlings were also planted in soil and allowed to flower. After which inflorescences, rosette leaves, cauline leaves, and stems were collected.

extract_protocol:
Tissues and seedlings were frozen in liquid nitrogen and immediately used to isolate total RNA (QIAGEN RNeasy Plant Mini Kit), which was then quantified using NanoDrop 1000. The same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. The poly(A)- RNAs of seedling samples were collected by removing poly(A)+ RNAs four times using Oligotex mRNA Mini Kit (QIAGEN). Then rRNAs were removed from poly(A)- RNAs three times as the mixed tissue sample.
For the mixed tissue sample, RNA was fragmented and enriched by agarose gel at ~330 nt. Strand-specific cDNA library was constructed by ligating different adapters according to the SMART library construction method (Levin et al. 2010), and then sequenced by Illumina Hisequation 2000 using the 100nt paired-end sequencing protocol. For seedling samples, fragmentation and enrichment of RNAs after poly(A)+ RNAs and rRNAs removal were the same as described for the mixed tissue RNA sequencing. Fragments (200~500nt) were excised from the gel and purified for sequencing. We used the SMART™ cDNA Library Construction Kit for strand-specific cDNA library construction. The 100nt single-end sequencing protocol of Illumina Hisequation 2000 was selected.

treatment_protocol: 300mM mannitol (drought), 200mM NaCl (salinity), 4 ºC (cold), 37 ºC (heat).

value: seedling

tag: age

value: 12 days

tag: ecotype

value: 37 ºC

tag: time point

value: 12 hours


title: Drought-12h_nonpolyA

value: 300mM mannitol


title: Heat-3h_nonpolyA

value: 3 hours


title: Salt-3h_nonpolyA

value: 200mM NaCl


title: Drought-3h_nonpolyA


title: Salt-12h_nonpolyA


title: Cold-12h_nonpolyA

value: 4 ºC


title: Control-3h_nonpolyA

value: No treatment


title: Tissue_mix_total

source_name: Mixed tissues

value: inflorescences, rosette leaves, cauline leaves, and stems

value: 5 weeks


title: WY6

city: Chapel Hill

first: Zefeng

state: NC

address: 4113 Genetic Medicine

department: Pharmacology

institute: UNC

data_processing:
Sequenced reads were mapped to hg18 and hg19 whole genome using MapSplice v2.1.2 with default parameters
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks (hg19 alignment were used)
The changes of splicing isoforms were analyzed by MISO pipeline (hg18 alignment were used)
Genome_build: hg18/hg19
Supplementary_files_format_and_content: RPKM values are included in the cufflink output files for each sample

source_name: cell line

growth_protocol: Cells were grown on RPMI-1640 complete medium (GIBCO, BRL) supplemented with 10%FBS and without antibiotics upto 80% confluency at standard cell culture conditions.

extract_protocol:
The cells dislodged form plates using PBS  and total RNA was purified using Qiagen RnaEasy Minikit
The polyadenylated RNA were purified to construct sequencing library using Illumina TruSeq Total RNA Sample Prep kits (conducted by UNC High Throughput Sequencing Facility)

treatment_protocol: The samples described are stable lines expressing RBM4 (pCDH) or control vector and are selected on puromycin

value: RBM4 overexpression


title: WY5

value: Wild type


title: tax-Post-R6

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

description: Post treatment sample from patient 6

data_processing:
Basecalling was preformed using standard Illumina pipeline
Reads were mapped to the genome using TopHat v1.4.1, allow upto 2 mismatches and using a custom junctions library derived from Ensembl version 68
Reads falling in each gene model from Ensembl 68 were counted using HTSeq verion 0.5.3
Genes with fewer than two none zero counts were removed. Read counts were normalized using the TMM method via the edgeR bioconductor package  and differentially expressed genes identified using a paired negative bionomial generalized linear model with the same package
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited table containing the read counts for each sample for each gene, and tab-delimited table of fitted expression changes with statistcal significance for each gene

source_name: TRUSS-guided prostatic biopsy of clinically advanced/metastatic prostate cancer tissue

extract_protocol:
Total RNA was extracted from pre- and post-AAT samples using the RNeasy Mini Kit (QIAgen, 74104) according to manufacturer's instructions.  RNA quantity and quality was evaluated by spectrophotometry using the NanoDrop 2000 spectrophotometer (Thermo Scientific) and 2100 Bioanalyzer (Agilent) RNA electropherograms, with calculation of RNA integrity number (RIN) (35).  Samples were included for RNA sequencing if RIN > 6 and total RNA > 500 ng
Samples were processed using the Illumina RNA-Seq protocol (Illumina) according to manufacturer's instructions without poly(A) mRNA selection.  The cDNA sample library was subsequently normalized using the Illumina DSN (Duplex-specific Nuclease) protocol according to manufacturer's instructions.

treatment_protocol: standard AAT consisting Luteinising hormone-releasing hormone (LHRH) agonists with anti-androgen "flare" protection. Repeat TRUSS biopsy was performed at ~22 weeks following initiation of AAT, specifically targeting tumour-rich areas

value: Prostate Tumour

value: Post-treatment


title: tax-Post-R3

description: Post treatment sample from patient 3 (removed from final analysis)


title: tax-Post-R5

description: Post treatment sample from patient 5


title: tax-Pre-R6

description: Pre treatment sample from patient 6

value: Pre-treatment


title: tax-Post-R4

description: Post treatment sample from patient 4


title: tax-Post-R1

description: Post treatment sample from patient 1


title: tax-Pre-R2

description: Pre treatment sample from patient 2 (removed from final analysis)


title: YTHDC1-PAR-CLIP-rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E. 57th. Street

department: Chemistry

institute: The University of Chicago

description:
Sample2
small RNA fragments crosslinked with YTHDC1

data_processing:
General: Illumina Casava 1.8.2 software were used for basecalling.
General: Reads were aligned to the hg19 genome assembly using bowtie version 1.0 with at most 2 mismatch allowed -n 2 -g 1.
PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: The PeakInGene results were organized in the Microsoft Excel format

source_name: HeLa cell

extract_protocol:
fed with 4SU, UV crosslink, partial digested by RNase T1, anti-flag-beads IP, recovered by Zymo RNA clean and concentrator
NEBNext small RNA library prepration kit for illumina (NEB)

value: HeLa

value: C-terminal flag-tagged YTHDC1 was transfected and expressed for 24h (0.75ug plasmid/mL)

tag: immunoprecipitation reagent

value: anti-flag magnetic beads (Sigma-Aldrich, catalog# M8823, lot# SLBH6865V)


title: tax-Pre-R5

description: Pre treatment sample from patient 5


title: YTHDC1-PAR-CLIP-rep1

description:
Sample1
small RNA fragments crosslinked with YTHDC1

extract_protocol:
fed with 4SU, UV crosslink, partial digested by RNase T1, anti-flag-beads IP, recovered by Zymo RNA clean and concentrator
Truseq small RNA sample prepration kit (illumina)

tag: treatment


title: tax-Pre-R1

description: Pre treatment sample from patient 1

tag: tissue


title: tax-Pre-R4

description: Pre treatment sample from patient 4


title: tax-Pre-R3

description: Pre treatment sample from patient 3 (removed from final analysis)


title: Tropicalis_H3K27Me3_stage10.5

status: Public on Sep 17 2014

city: Stanford

first: Julie

last: Baker

state: CA

address: 300 Pastuer Drive

department: Genetics

institute: Stanford University

data_processing:
ChIP-Seq reads are mapped to xenTro2 genome using the bwa-sw tool. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
Genome_build:  UCSC xenTro2
Supplementary_files_format_and_content: ChIP-seq homer-output as a .txt file contains annotated peaks for Samples

organism: Xenopus tropicalis

source_name: ChIP DNA

growth_protocol: X. tropicalis embryos were generated by in vitro fertilization and were staged according to Nieuwkoop and Faber morphological criteria.

extract_protocol:
Chromatin immunoprecipitation from whole embryo lysates was performed  using pools of 250 embryos. ChIP DNA was used for library construction.
Illumina multiplex adopter were used for these samples and  libaries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx or HiSeq2000 following the manufacturer's protocols.

value: whole embryo

value: wild type

tag: developmental stage

value: H3K27me3 (ActiveMotif, 39535)

tag: multiplex adapters

value: CTTGTA


title: Tropicalis_H3K27Ac-nodal-inhibited_stage9

data_processing:
ChIP-Seq reads are mapped to xenTro2 genome using the bowtie tool using the following settings: bowtie --best --strata -m 1 –chunkmbs 200. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
Genome_build:  UCSC xenTro2
Supplementary_files_format_and_content: ChIP-seq homer-output as a .txt file contains annotated peaks for Samples

extract_protocol:
Chromatin immunoprecipitation from whole embryo lysates was performed  using pools of 250 embryos. ChIP DNA was used for library construction.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.

treatment_protocol: For Nodal inhibition, embryos were cultured in SB431542 (Tocris) beginning at the 4 cell stage.  For each cohort of treated embryos, a few embryos were raised to stage 10.5 and to stage 20, to confirm loss of blastopore and of dorsal anterior development.

value: SB treated nodal inhibited

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: Tropicalis_H3K27Me3_stage9

value: GGCTAC


title: Cold-3h_nonpolyA

value: seedling

value: 12 days

value: 4 ºC

value: 3 hours


title: Tropicalis_H3K27Ac_stage9

value: CGATGT


title: Tropicalis_H3K27Me3_stage8

value: TAGCTT


title: Tropicalis_H3K27Ac_stage8

value: ATCACG


title: Tropicalis_H3K27Ac_stage10.5

value: TTAGGC


title: tax-Post-R2

description: Post treatment sample from patient 2 (removed from final analysis)

value: Prostate Tumour

value: Post-treatment


title: Tropicalis_H3K4Me3_stage8

value: whole embryo

value: H3K4me3 (ActiveMotif, 39159)


title: Tropicalis_H3K4Me1_stage8

value: wild type

value: H3K4me1 (Abcam, ab8895)

value: TGACCA


title: Tropicalis_H3K4Me3_stage9


title: Tropicalis_H3K4Me3_stage10.5


title: Tropicalis_Smad2/3_stage9

value: Smad2/3 (FL-425) (Santa Cruz Biotechnology, sc-8332)


title: Tropicalis_H3K4Me1_stage9 (repeated in RG-pool3 )

value: ACAGTG


title: Tropicalis_Input_stage9

source_name: Input chromatin


title: Tropicalis_Input_stage8

extract_protocol:
Chromatin immunoprecipitation from whole embryo lysates was performed  using pools of 250 embryos. ChIP DNA was used for library construction.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx or HiSeq2000 following the manufacturer's protocols.


title: Tropicalis_H3K4Me1-nodal-inhibited_stage9

value: SB treated nodal inhibited


title: Tropicalis_3seq_stage9-Nodal-Inhibited-R1

description:
processed data file: 3seq_annotated_called_regions.txt
library strategy: RNA-3seq

data_processing:
Raw counts from 3-SEQ datasets are calculated and annotated to the closest genes using the Unipeak software.
Genome_build:  UCSC xenTro2
Supplementary_files_format_and_content: 3seq_annotated_called_regions.txt

source_name: mRNA

extract_protocol:
Total RNA was extracted with Trizol reagent, followed by mRNA preparation using oligo-DT Dynabeads (Invitrogen, cat #610.06).
400 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.


title: siE3-1

city: LYON

first: Jean-Marc

last: Vanacker

address: 28 rue A Fleming

country: France

institute: IGFL

data_processing:
RTA software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome Hg19 with TopHat 1.3.3
Sequences reads were counted with HTSeq-count with the union option
Differential expression was analyzed with DESeq
Genome_build: Hg19
Supplementary_files_format_and_content: this file contains count data for each sample and differential expression (siERRalpha vs siC) with fold change and padj

source_name: MDA-MB231 cells

growth_protocol: MDA-MB231 cells were grown in DMEM, supplemented with 10% FCS

extract_protocol:
RNA were extracted using RNeasy Qiagen kit
RNA libraries were prepared using standard Illumina procedures

treatment_protocol: siRNA were transfected using interferin under conditions recommended by the supplier (Ozyme)

value: MDA-MB231 cells

tag: sirna


title: siC-1

value: siC


title: siE1-2


title: siE2-1


title: siE3-2


title: siE1-1


title: siC-2


title: siE2-2


title: Tropicalis_3seq_stage9-R1

tag: genotype/variation


title: Tropicalis_3seq_stage8-R1


title: Tropicalis_Smad2/3_stage10.5


title: Tropicalis_3seq_stage10.5-R1


title: Tropicalis_H3K4Me1_stage10.5

value: GCCAAT


title: Myf5(GFP+);Pdgfra-;Itga7+, replicate 1

status: Public on Sep 16 2014

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Hight-throught sequencing was performed using an Illumina HiSeq 2000 by the Functional Genomics Core at the University of Pennsylvania.
FastQ files were aligned to mouse genome mm9 using TopHat, then differentially expressed genes were identifed by CuffDiff.
Genome_build: mm9
Supplementary_files_format_and_content: Plain text file containing cuffdiff results

source_name: E14.5 Embryonic fibroblasts

growth_protocol: E14.5 embryos harvested from Myf5-cre;mTmG mice housed at 20°C with a 12-hour light/12-hour dark cycle

extract_protocol:
Total RNA was extracted from freshly sorted cells using the TRIzol method (Invitrogen) combined with QIAGEN RNeasy Micro Column.
RNA-seq libraries were generated by Illumina Truseq RNA Sample Preparation Kit.

treatment_protocol: Embryos were digested in 6.1 mg ml-1 collagenase and 2.4 mg ml-1 dispase in DMEM for 40 min at 37 °C in a shaking water bath.Digested tissue was successively filtered through 100 µm and 40 µm cell strainers. Cells were then suspended in DMEM with 5% FBS, and stained with antibodies for 30 min at 4 °C in the dark. Stained cells were sorted with BD FACS Aria.

tag: strain

tag: cell type

value: embryo; dorsal body wall


title: Myf5(GFP+);Pdgfra-;Itga7+, replicate 2


title: Tropicalis_Smad2/3_stage8


title: Myf5(GFP+);Pdgfra+, replicate 1


title: Myf5(GFP+);Pdgfra+, replicate 2


title: HiGlu_Rep2

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

data_processing:
reads were mapped to mm9 (NCBI build 37) using STAR
Bedtools was used to create count tables of the sorted bam files using reads aligning to RefSeq defined exons.
DESeq was used for statistical comparison.
Genome_build: mm9 (NCBI build 37)

source_name: isolated islets

growth_protocol: Isolated were isolated by collagenase injection through the common bile duct per common protocols, cultured and stimulated as described and collected in Trizol.

extract_protocol:
Islets were collected in Trizol and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: islets

value: mixed

tag: Stage

value: adult, 3 months

value: 16.8 mM glucose for 12 hours


title: Tropicalis_Input_stage10.5


title: LoGlu_Rep1

value: 2.8 mM glucose for 2 hours


title: p2malpha

data_processing:
reads were mapped to mm9 (NCBI build 37) using STAR
Bedtools was used to create count tables of the sorted bam files using reads aligning to RefSeq defined exons.
DESeq was used for statistical comparison.
Genome_build: mm9 (NCBI build 37)
Supplementary_files_format_and_content: normalized abundance measurements

source_name: FACS-purified alpha cells

growth_protocol: Isolated were isolated by collagenase injection through the common bile duct per common protocols. Isolated islets were cultured overnight in RPMI supplemented with 11 mM glucose and 10% FBS and pen/strep and dissociated the following morning by trypsin (0.25%) EDTA and gentle titturation for FACS purification.

extract_protocol:
Cells were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: FACS-purified alpha cells

value: adult


title: p2falpha


title: p3fbeta

source_name: FACS-purified beta cells

value: FACS-purified beta cells


title: p3mbeta


title: BY_RM_42min_R3

city: Seattle

first: Joshua

last: Akey

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
We used the "aln" and "sampe" commands in BWA version 0.5.9 (Li and Durbin 2009) to map both the RNA sequence reads to the BY genome and, separately, the RM genome.
After mapping reads, we sorted BAM files and marked duplicate reads using Picard version 1.43 (http://picard.sourceforge.net) and the Sort_Sam tool with the "SORT_ORDER=coordinate" option, the BuildBamIndex tool, and the MarkDuplicates tool. For all tools, we set "VERBOSITY=ERROR" and "VALIDATION_STRINGENCY=LENIENT".
To obtain a set of variants for allele-specific read calling in the BYxRM diploid, we used LASTZ (http://www.bx.psu.edu/ miller_lab) to infer alignment scoring parameters appropriate for aligning the BY and RM genomes and to generate pairwise alignments between all chromosomes of the two strains. We then used Threaded Blockset Aligner (TBA) (Blanchette et al. 2004) to compute a whole-genome alignment that is not biased in favor of a particular reference genome. We performed assignment of individual RNA-seq reads as originating from either the BY or the RM allele of each gene as described in Skelly et al. 2011, with the following two changes. First, any read with an alignment to one genome that scores higher had to overlap one of the SNVs between BY and RM that were identified. Second, we did not perform a correction for GC content.
Genome_build: sacCer3
Genome_build: S. cerevisiae RM11_1a (http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/MultiDownloads.html)
Supplementary_files_format_and_content: A text file containing four columns: featureName (a yeast gene), snpIndex (a number denoting the snp; each snp in the file has a unique snpIndex identifier), BY (the count of reads mapping to that snp that match the BY allele better), RM (the count of reads mapping to that snp that match the RM allele better).

organism: Saccharomyces cerevisiae

growth_protocol: The BYxRM hybrid diploid was grown at 24°C to mid-log phase (OD600 0.8–1.0) in 60 mL of yeast extract peptone dextrose (YEPD).

extract_protocol:
The collected yeast cells from each time point were stored at -80°C for no more than 2 days before we extracted total RNA from the cells using a standard phenol-chloroform preparation.
We used a TruSeq RNA Sample Prep v2 Kit (Illumina) to create a sequencing library from the total RNA collected for each decay rate time course time point from each replicate. Per the protocol for the kit, we isolated mRNA from the total RNA using two rounds of poly(A) selection, then fragmented the isolated mRNA into approximately 150 base pair fragments, and finally, used random hexamer primers to produce cDNA. We created barcoded sequencing libraries from the cDNA from each sample and, in an effort to minimize technical variation between the data acquired from different decay rate time points, all samples from all replicates were sequenced in the same lane on an Illumina HiSeq 2000 (50 bp paired-end reads).

treatment_protocol: We abruptly shifted the culture to 37°C via addition of 60 mL of 50°C YEPD. Immediately following, and at 6, 12, 18, 24, and 42 min after addition of the 50°C medium, we collected 20 mL aliquots of the culture using vacuum filtration. To maintain the increased temperature of the culture, we housed it in a 37°C shaking incubator between collection time points. The collected yeast cells from each time point were flash frozen in liquid nitrogen and then stored at -80°C for no more than 2 days.

value: BY4716 x RM11_1a diploid

tag: time point (after addition of the 50°c medium)

value: 42 min

tag: sample type

value: YEPD liquid culture


title: BY_RM_18min_R3

value: 18 min


title: BY_RM_6min_R3

value: 6 min


title: BY_RM_12min_R3

value: 12 min


title: PACT1_a

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

description:
a, b and c are biological replicates.
small RNA-seq

data_processing:
The base calling was done by Illumina Pipeline (CASAVA) v1.8.2.
The 3′ adaptor sequences starting with “TGGAATTC” were removed, and the sequence reads with short length (<16 nt) or artifacts (e.g. long homopolymer) or low quality (Phred quality <20 in >15% of nucleotides) were filtered out using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered sequence reads were aligned to hg19 reference genomes from UCSC, respectively. The BWA short-read aligner (Li and Durbin, 2009) version 0.7.5a-r405 was used for the alignment, with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region.
Each aligned read was classified using intersectBed in Bedtools (Quinlan and Hall, 2010) with annotations retrieved from RefSeq, GtRNAdb, FlyBase, RepeatMasker, Rfam, and miRBase.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include miRNA, strand, read #, and RPM score

source_name: PACT1 KO

growth_protocol: Wild-type and KO HeLa cells were grown in DMEM media supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol reagent. 10 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq small RNA sample preparation kit.

value: PACT1 KO

tag: cell line

value: HeLa


title: TRBP1_b

source_name: TRBP1 KO

value: TRBP1 KO


title: BY_RM_0min_R3

value: 0 min


title: BY_RM_24min_R2

value: 24 min


title: BY_RM_24min_R3


title: DKO1_a

source_name: TRBP1 & PACT1 double KO

value: TRBP1 & PACT1 double KO


title: BY_RM_42min_R2


title: BY_RM_18min_R2


title: BY_RM_12min_R2


title: TRBP1_c


title: TRBP1_a


title: HiGlu_Rep1

value: islets

value: mixed

value: adult, 3 months

value: 16.8 mM glucose for 12 hours


title: WT_c

source_name: WT

value: WT


title: U1-RAP-RNA-FA-140503

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

description: RAP-RNA using probes targeting U1 in cells crosslinked with formaldehyde

data_processing:
Align to repetitive mm9 RNA sequences from RefSeq and RepeatMasker (RNA only)
Align to mm9 genome with Bowtie2-2.1.0 (DNA) or with Tophat-2.0.8 (RNA)
Remove duplicate reads with Picard (DNA only)
Remove reads with MAPQ < 30
Connect paired-end reads to fragments (DNA only)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig: Coverage at 5bp resolution across genome

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol:
RNA Antisense Purification (RAP) followed by DNA or RNA sequencing was performed as described in Engreitz et al. 2014
custom strand-specific RNA-Sequencing (see Engreitz et al 2013)

value: embryonic stem cell

tag: experiment type

value: RAP-RNA

tag: drug

tag: crosslinking

value: Formaldehyde

tag: gender

value: male


title: LoGlu_Rep2

tag: treatment

value: 2.8 mM glucose for 2 hours


title: BY_RM_6min_R2

value: BY4716 x RM11_1a diploid

value: 6 min

value: YEPD liquid culture


title: BY_RM_0min_R2


title: WT_a

value: HeLa


title: BY_RM_42min_R1

value: 42 min


title: WT_b


title: BY_RM_12min_R1

value: 12 min


title: BY_RM_24min_R1

value: 24 min


title: BY_RM_6min_R1


title: BY_RM_18min_R1

value: 18 min


title: BY_RM_0min_R1

value: 0 min


title: Skud

status: Public on Sep 15 2014

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

institute: Univ. Bordeaux

data_processing:
Raw reads were filtered to obtain only reads with an average quality > 20 using the approach described by Sasson and Michael (2010) then mapped to whole genomes using bowtie v0.12.7 with parameters -v 2 -m 1, splice junctions were found by TopHat with default parameters and defined intron size -i 49 -I 1050.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in each intron were counted and normalized by the size of intron and by the size of the library. For genes reads falling in the exons only were counted and normalized as above.
Genome_build: sacCer3
Supplementary_files_format_and_content: *_comp.txt: tab-delimited text files include intron RPKM values for each Sample; *_introns.bed: TopHat junction output for each Sample

organism: Saccharomyces kudriavzevii

source_name: whole cells

growth_protocol: YPD media, 30 ºC, 200 rpm

extract_protocol:
Cells were collected at absorbance of 0.5 at 600 nm. RNA was extraced using Qiagen RNA extraction kit according to manufacurer's instructions. Ten μg of total RNA was processed with the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA.
cDNA libraries were constructed using the SOLiD 4.0 System from Life Technologies according to the standard manufacturer's protocol.

value: NCYC 2889

tag: genotype


title: Suva

organism: Saccharomyces uvarum

growth_protocol: YPD media, 28 ºC, 200 rpm

value: NCYC 2669


title: WT_CR_A

city: Philadelphia

first: Shelley

middle: L

last: Berger

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Departments of Cell & Developmental Biology; Biology; Genetics

institute: University of Pennsylvania

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to sacCer2 using bowtie with default settings
FPKM values were generated using cufflinks v. 2.0.2 with default settings
Genome_build: sacCer2
Supplementary_files_format_and_content: FPKM values were generated using cufflinks v. 2.0.2 with default settings and combining the replicates for statistical power

source_name: WT Saccharomyces cerevisiae

growth_protocol: 30 degrees celcius; synthetic complete media; NR - 2% glucose, CR - 0.05% glucose

extract_protocol:
QIAGEN miRNeasy mini Kit
Ambion RNA fragmentation reagent and Illumina Small RNA Sequencing library preparation kit

value: WT

tag: growth protocol

value: Calorie-restricted

tag: biological replicate

value: A


title: WT_NR_B

value: non-restricted

value: B


title: WT_NR_A


title: WT_CR_B


title: Bp35

city: Singapore

first: Tannistha

last: Nandi

address: 60 Biopolis Street, Genome, #02-01

department: Cancer Therapeutics & Stratified Oncology

country: Singapore

institute: Genome Institute of Singapore

description: SMRTbell™ sequencing

data_processing:
PacBio Genome Assembly
Genomes were assembled using HGAP(Chin, Alexander, Marks, Klammer, Drake, Heiner, Clum, Copeland, Huddleston, Eichler et al. 2013) with default parameters in the SMRT Analysis Suite version 2.1 (Pacific Biosciences, Menlo Park, CA, USA).  Additional manual assembly of contigs was carried out in cases of unique overlapping sequence.  Consensus sequence polishing was done with the Quiver algorithm in GenomicConsensus version 0.7.0.
Base modification analysis
Base modification analysis was carried out by mapping SMRT sequencing reads to the respective assemblies using the BLASR mapper and the Pacific Biosciences' SMRT Analysis Suite version 2.1 using the standard mapping protocol.  To identify modified positions, the pipeline uses kinetic signals acquired during SMRT sequencing compared to an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions as described in http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf.  The clustering of the sequence motifs was done using PacBio's Motif Finder (https://github.com/PacificBiosciences/DevNet/wiki/Motiffinder).
Genome_build: Not Applicable
Supplementary_files_format_and_content: comma separated value format and base modifications

organism: Burkholderia pseudomallei

source_name: Clinical

growth_protocol: Each Bp strain is grown on Tryptone-Soy Agar (Oxoid)

extract_protocol:
Genomic DNA was extracted using the QIAGEN Genomic Tip 500/G kit (QIAGEN, Valencia, CA), as per manufacturer’s instructions. Manipulations of live bacteria were performed in a BioSafety Level 3 facility in DSO National Laboratories.
To perform construction of a 17 kb SMRTbell™ library, genomic DNA (gDNA) was first analyzed on Field Inversion Gel Electrophoresis (FIGE) to ensure presence of high molecular weight gDNA.  Twenty micrograms of gDNA was sheared using g-TUBEs (Covaris, Inc).  Of the 20 ug sheared DNA, 10 ug were treated to repair apurinic/apyrimidinic sites, thymine dimers, nicks and gaps. Following this DNA damage repair, the ends of the double stranded fragments were polished to fill in any 5’ overhangs while removing any 3’ overhangs.  The ends were then phosphorylated suitable for ligation with hairpin adapters supplied in the DNA Template Prep Kit 2.0 (3kb-10kb) (Pacific Biosciences, Menlo Park, CA. USA). The library was run on a BluePippin™ system (Sage Science, Inc., Beverly, MA., USA) to select for SMRTbell templates greater than 10 kb.  The resulting average insert size was 17 kb based on 2100 Bioanalyzer (Agilent Technologies Genomics, Santa Clara, CA., USA).  After size selection, sequencing primers were annealed to the hairpins of the SMRTbell templates followed by binding with the P4 sequencing polymerase (Pacific Biosciences, Menlo Park, CA. USA). To sequence the 17 kb SMRTbell library, the polymerase-bound templates were bound to MagBeads for zmw- loading in the PacBio RSII System at an on-plate concentration of 150 pM. They were subsequently sequenced using the DNA Sequencing Kit 2.0, with data collection of 180 mins (Pacific Biosciences, Menlo Park, CA. USA).


title: ISW2K215R_CR

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to sacCer3 using bowtie2 -t --phred33-quals -k1 -N 1 --n-ceil 0,0.15 -p 20 -x -U -S
Aligned reads normalized by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalized by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.

source_name: ISW2K215R Saccharomyces cerevisiae - calorie restricted

extract_protocol:
QIAGEN Blood and Cell Culture DNA Kit
NEBNext DNA Library Prep Master Mix Set for Illumina

treatment_protocol: Cell walls were digested with zymolyase followed by digestion of chromatin with MNase and ExoIII

value: Mnase-treated DNA


title: ISW2DEL_NR

source_name: ISW2DEL Saccharomyces cerevisiae

value: Non-restricted


title: ISW2DEL_CR

source_name: ISW2DEL Saccharomyces cerevisiae - calorie restricted


title: ISW2K215R_NR

source_name: ISW2K215R Saccharomyces cerevisiae


title: Bp33

description: SMRTbell™ sequencing


title: Luc KD replicate 3

city: Bronx

first: Matthew

middle: Jon

last: Gamble

address: 1300 Morris Park Ave / Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Sample 3

data_processing:
Base calls performed using CASAVA version 1.7
The sequencing reads were trimmed of barcodes and aligned to the human genome (hg19) using GSNAP version 2012-07-12
The reads were then binned into genes (Ensemble ens67) using HTSeq version v0.5.3p3 (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html).
Identification of differential gene expression for protein coding genes with at least 20 reads across all replicates was performed with DESeq (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include uniquely mapping read counts for each gene
Supplementary_files_format_and_content: DESeq output consists of tab separated values for baseMean, baseMeanA(Luc KD), baseMeanB(macroH2A1 KD), foldChange, log2FoldChange, pval, padj.

source_name: IMR90_Luc KD

growth_protocol: IMR90 (ATCC, CCL-186) primary human fetal lung fibroblast cells were cultured in MEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche).
RNA samples were treated with RNase-free DNaseI and purified by using the RNeasy Mini Kit (QIAGEN). The resulting RNA was depleted of ribosomal RNA by using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre). The rRNA-depleted RNA was used to synthesize the first strand cDNA using SuperScript® III First-Strand Synthesis System (Invitrogen) according to the manufacturers instructions. Subsequently, the second strand was generated by using E. coli DNA ligase (Invitrogen), E. coli DNA polymerase (Invitrogen), and dUTP, dCTP, dATP, and dGTP set (10 µmol each, Promega), in the Second Strand Buffer (Invitrogen). Then the cDNA were sheared with Covaris to roughly 300bp. After fragmentation, samples were purified with MinElute columns (Qiagen).  And the protruding 3’ and 5’ ends of the fragments were repaired using T4 DNA Polymerase (NEB) and T4 DNA Polynucleotide kinase (NEB) in T4 DNA ligase buffer (NEB). Next, dA ends were generated by employing Klenow Fragment (3’->5’ exo-, NEB), in Buffer 2 (NEB). Adapter ligation reactions were then set up using indexed adapters and Quick Ligase (NEB). The products were used as the template for UNG (Fermentas) treatment and PCR amplification using Phusion High-Fidelity DNA Polymerase (NEB). The libraries were visualized on 2% E-Gel® General Purpose Agarose Gels (Invitrogen). The barcoded libraries were sequenced on a single lane of a HiSeq2500 (Illumina).

value: human primary lung fibroblasts

value: expressing shRNA directed against luciferase as a control


title: macroH2A1 KD replicate 3

description: Sample 6

source_name: IMR90_macroH2A1 KD

value: expressing shRNA directed against macroH2A1


title: macroH2A1 KD replicate 2

description: Sample 5


title: Luc KD replicate 2

description: Sample 2


title: input replicate2

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using ELAND  version 1.7.0
significant genomic regions were identified by comparing matched ChIP and input samples with ISOR version 0.4 with the following settings: segmentation_pval(0.01), gap_length(1000)
Genome_build: hg19
Supplementary_files_format_and_content: gappedPeak files are as described (http://genome.ucsc.edu/FAQ/FAQformat.html#format13) the signalValues represent the log2 odds ratio of a segment and the pValue (-log10) represents the significance of the enrichment or depletion. The gaps are regions of at least 1kb with no mapped reads from either the input or ChIP samples
Supplementary_files_format_and_content: bedGraph files for segments where gaps have been subtracted. The scores represent the log2 odds ratio of each segment.

extract_protocol:
Cells were grown to 80 to 90% confluence in 15cm dishes, cross-linked with 1% formaldehyde in PBS at room temperature for 10 min, then quenched in 125 mM glycine in PBS at room temperature for 5 min.  The cells were washed by cold PBS once and were collected by centrifugation and sonication in lysis buffer (50mM Tris pH 7.9, 10 mM EDTA, 1% SDS, 1x protease inhibitor cocktail and 1mM DTT) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation 14,000rpm for 10min at 4 °C, and 20 µl supernatant was used as input for quantitation, the remaining supernatant was diluted 10-fold in dilution buffer (20 mM Tris pH 7.9, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 1X protease inhibitor cocktail and 1mM DTT), and pre-cleared by incubation with protein A-agarose beads at 4°C for 3hr. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions at 4°C overnight with an antibody against macroH2A1, then incubated with protein A-agarose beads at 4°C for 2hr. No antibody negative controls were included for every ChIP experiment. The immuneprecipitated DNA was cleared of protein by digestion with 0.4mg/ml glycogen and proteinase K (2.5U/ml, Roche) in Txn stop buffer (20 mM EDTA, 0.2 M Nacl and 1% SDS) at 37°C for 1 hour. The DNA was then extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and ethanol precipitated.
DNA fragments from ChIP reactions were repaired using T4 DNA Polymerase (NEB) and T4 DNA Polynucleotide kinase (NEB) in T4 DNA ligase buffer (NEB). Next, dA ends were generated by employing Klenow Fragment (3’->5’ exo-, NEB), in Buffer 2 (NEB). Adapter ligation reactions were then set up using indexed adapters and Quick Ligase (NEB). Ligation-mediated PCR was then performed using Phusion High-Fidelity DNA Polymerase (NEB). The libraries were visualized on 2% E-Gel® General Purpose Agarose Gels (Invitrogen). Sequencing for the macroH2A1 ChIPs were performed on an Illumina HiSeq 2500 at the Einstein Epigenomics Core Facility. Sequences reads were mapped to the human genome version hg19 using ELAND version 1.7.0 (Illumina).

tag: chip antibody


title: Ncas

organism: Naumovozyma castellii


title: WT_CR

source_name: WT Saccharomyces cerevisiae - calorie restricted


title: macroH2A1 ChIP replicate 2

source_name: IMR90_macroH2A1 ChIP

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat.#


title: input replicate 1


title: Luc KD replicate 1

description: Sample 1

tag: genotype/variation


title: macroH2A1 ChIP replicate 1

tag: cell type