title: Brain_rep1

description: One brain was collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

data_processing:
Illumina Casava1.7 software used for basecalling.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat/v2.0.0 with default parameters. The RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks/v2.0.2 with default parameters.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read counts, spretus-exon-SNP-read count.

source_name: Mouse adult hybrid brain

value: Adult whole brain


title: Brain_rep2

status: Public on Feb 20 2015

type: SRA

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

country: USA

institute: University of Washington

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus x Mus spretus

extract_protocol:
Mouse tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and then was subject to DNaseI digestion and purification using Qiagen RNAeasy Kit . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

tag: strain

tag: genotype

value: Xist+/-


title: Spleen_rep2

description: One spleen was collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

data_processing:
Illumina Casava1.7 software used for basecalling.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat/v2.0.0 with default parameters. The RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks/v2.0.2 with default parameters.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read count, spretus-exon-SNP-read count.

source_name: Mouse adult hybrid spleen

value: Adult whole spleen


title: SingleCellNo39

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

organism: Mus musculus

source_name: sscortex

growth_protocol: Wild type (CD1) and transgenic mice (5HT3-EGFP on a CD1 background) between postnatal 21 and 31 days of both sexes were used. In the transgenic mouse line, EGFP is expressed under the control of the Htr3a promoter.

extract_protocol:
Mice were deeply anesthetized with ketamine/xylazine (80mg/kg; 10mg/kg). The brain was quickly dissected and transferred to ice-cold oxygenated cutting solution (87 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM sucrose, 20 mM glucose, 1 mM CaCl2, and 2 mM MgSO4) and kept in the same solution during sectioning on a vibratome (VT1200 S, Leica) in 300 µm thick slices. The area of interest was dissected from each slice, and the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer's instructions. The cell suspension obtained was filtered with 20 µm filter (Partec) and kept in cold HBSS solution (SIGMA) with 0.2% BSA and 0.3% glucose. For FACS of EGFP cells, a BD FACSAria" III Cell Sorter B5/R3/V3 system was used. The cell suspension with 600-1000 cells/µL had C1 Suspension Reagent added (all 'C1' reagents were from Fluidigm, Inc.) in a ratio of 4 µL to every 7 µL cell suspension, and 11 µL of the cell suspension mix was immediately loaded on a C1 Single-Cell AutoPrep IFC microfluidic chip designed for 10- to 17-μm cells, and the chip was then processed on a Fluidigm C1 instrument using the 'mRNA Seq: Cell Load (1772x/1773x)' script (30 min at 4°C).
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

tag: Sex

value: female

tag: age


title: COPD lung tissue 815-COPD

city: Seoul

first: JaeHyun

last: Lim

address: Department of Biomedical Sciences, Seoul National University Graduate School, Biomedical Science Building 117, 103 Daehakro, Jongro-gu

country: South Korea

institute: Seoul National University

data_processing:
RNA-Seq reads were mapped to the human genome using TopHat (v 1.4.1)
Aligned reads were quantified using Cufflinks software (2.0.0)
Raw data were extracted as FPKM for each gene for each sample by cufflinks software. Data with zeroed FPKM values across all samples were excluded. Filtered data was normalized by upper quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files format is a simple table which each row indicates single gene and each column indicates single patients, and each cell indicates FPKM value.

organism: Homo sapiens

source_name: COPD lung tissue

extract_protocol:
Total RNA was isolated from normal fresh frozen tissue remote from lung cancer.
In order to construct cDNA libraries with the TruSeq RNA library kit, 1 ug of total RNA was used
The protocol consisted of poly A-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription

tag: disease state

value: COPD

value: lung


title: COPD lung tissue 743-COPD


title: COPD lung tissue 821-COPD


title: COPD lung tissue 852-COPD


title: COPD lung tissue 964-COPD


title: COPD lung tissue 648-COPD


title: COPD lung tissue 578-COPD


title: COPD lung tissue 634-COPD


title: COPD lung tissue 704-COPD


title: COPD lung tissue 5130-COPD


title: COPD lung tissue 565-COPD


title: COPD lung tissue 5215-COPD


title: SingleCellNo33


title: COPD lung tissue 984-COPD


title: SingleCellNo36


title: COPD lung tissue 5082-COPD


title: SingleCellNo37


title: SingleCellNo32


title: COPD lung tissue 5078-COPD


title: COPD lung tissue 5103-COPD


title: COPD lung tissue 4926-COPD


title: COPD lung tissue 4980-COPD


title: SingleCellNo31


title: COPD lung tissue 501-COPD


title: COPD lung tissue 465-COPD


title: COPD lung tissue 440-COPD


title: SingleCellNo35


title: SingleCellNo34


title: SingleCellNo30


title: COPD lung tissue 4169-COPD


title: COPD lung tissue 4136-COPD


title: COPD lung tissue 4066-COPD


title: SingleCellNo29


title: SingleCellNo28


title: COPD lung tissue 3907-COPD


title: SingleCellNo27


title: COPD lung tissue 3862-COPD


title: SingleCellNo38


title: SingleCellNo26


title: COPD lung tissue 3773-COPD


title: COPD lung tissue 376-COPD


title: COPD lung tissue 3722-COPD


title: SingleCellNo25


title: COPD lung tissue 3838-COPD


title: COPD lung tissue 3700-COPD


title: COPD lung tissue 367-COPD


title: COPD lung tissue 3430-COPD


title: COPD lung tissue 3387-COPD


title: COPD lung tissue 362-COPD


title: SingleCellNo23


title: COPD lung tissue 3333-COPD


title: SingleCellNo22


title: COPD lung tissue 3298-COPD


title: COPD lung tissue 4024-COPD


title: COPD lung tissue 3523-COPD


title: SingleCellNo21


title: COPD lung tissue 3147-COPD


title: COPD lung tissue 3103-COPD


title: COPD lung tissue 3264-COPD


title: SingleCellNo20


title: SingleCellNo19


title: COPD lung tissue 2981-COPD


title: COPD lung tissue 2966-COPD


title: COPD lung tissue 2846-COPD


title: SingleCellNo18


title: SingleCellNo24


title: COPD lung tissue 2821-COPD


title: COPD lung tissue 3652-COPD


title: SingleCellNo17


title: COPD lung tissue 2747-COPD


title: COPD lung tissue 2783-COPD


title: SingleCellNo16


title: COPD lung tissue 274-COPD


title: SingleCellNo15


title: COPD lung tissue 2702-COPD


title: COPD lung tissue 2700-COPD


title: COPD lung tissue 271-COPD


title: SingleCellNo14


title: COPD lung tissue 2673-COPD


title: SingleCellNo12


title: SingleCellNo13


title: COPD lung tissue 2616-COPD


title: COPD lung tissue 2625-COPD


title: COPD lung tissue 2578-COPD


title: SingleCellNo11


title: COPD lung tissue 2408-COPD


title: COPD lung tissue 2356-COPD


title: COPD lung tissue 2301-COPD


title: SingleCellNo9


title: COPD lung tissue 2269-COPD


title: COPD lung tissue 2216-COPD


title: SingleCellNo8


title: COPD lung tissue 2081-COPD


title: SingleCellNo6


title: SingleCellNo7


title: COPD lung tissue 2070-COPD


title: COPD lung tissue 206-COPD


title: COPD lung tissue 2618-COPD


title: COPD lung tissue 1890-COPD


title: COPD lung tissue 1845-COPD


title: COPD lung tissue 2134-COPD


title: COPD lung tissue 1809-COPD


title: SingleCellNo4


title: SingleCellNo3


title: SingleCellNo5


title: COPD lung tissue 1653-COPD


title: COPD lung tissue 1635-COPD


title: SingleCellNo10


title: SingleCellNo2


title: COPD lung tissue 2649-COPD


title: COPD lung tissue 1630-COPD


title: COPD lung tissue 157-COPD


title: COPD lung tissue 1506-COPD


title: COPD lung tissue 1566-COPD


title: COPD lung tissue 1494-COPD


title: COPD lung tissue 1516-COPD


title: Yap_ChIP_data

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

description: wild type

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9
peak is called by macs 1.4
Genome_build: ucsc mm9
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit. DNA was then A-tailed with Exo- Klenow (NEB), and adaptors were ligated using Quick T4 DNA Ligase (NEB).

treatment_protocol: Male mice (25-30 g) were anesthetized with isofluorane blended with oxygen. The chest was shaved and cleaned with alcohol. Prior to the incision, 0.1 ml of 0.1% lidocaine was introduced under the skin. The chest cavity was opened by an incision of the left second intercostal space. The pericardial sac was opened and dissected apart, the ascending portion of aorta was dissected from the surrounding tissues and a silk suture was passed underneath the aorta and ligated against a 25- gauge needle. The needle was then removed, resulting in a ligature with a fixed diameter tied around and constricting the aorta. The sham procedure was identical except that the aorta was not ligated.

tag: cell type

value: heart

value: Adult


title: COPD lung tissue 1493-COPD


title: COPD lung tissue 1480-COPD


title: PFC Pool4

city: Würzburg

first: Anna

last: Frey

address: Straubmühlweg 2a

department: Comprehensive Heart Failure Center (CHFC)

country: Germany

institute: University Hospital of Würzburg

description:
8 weeks after the operation
PFC Pool3 vs. PFC Pool4.xlsx

data_processing:
CLC-Bio Genomics Workbench software (CLC Bio, Denmark) was used to calculate gene expression levels based on Mortazavi et al. (Nat Methods. 2008;5:621-628) approach. The sensitivity of RNA-Seq is a function of both molar concentration and transcript length. We therefore quantified transcript levels in reads per kilobase of exon model per million mapped reads (RPKM). The RPKM measure of read density reflects the molar concentration of a transcript in the starting sample by normalizing for RNA length and for the total read number in the measurement. This facilitates transparent comparison of transcript levels both within and between samples.
The comparison within the both groups was performed using Excell 2010 (Microsoft, USA): hippocampal tissue after development of chronic heart failure vs. after sham operation, prefrontal cortical tissue after development of chronic heart failure vs. after sham operation and left myocardial tissue after development of chronic heart failure vs. after sham operation. Comparisons within the groups were based on the RPKM values of each singular gene and were performed logarithmically.
Genome_build: The reference genome used to align the reads was GRCm38 downloaded at the following ftp address: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38.p1/Primary_Assembly/assembled_chromosomes/FASTA/
Supplementary_files_format_and_content: Excel data files containing the Feature ID, Expression values, Transcripts annotated, Detected transcripts, Exon length, Unique gene reads, Total gene reads, Unique exon reads, Total exon reads, Ratio of unique to total (exon reads), Unique exon-exon reads, Total exon-exon reads, Unique intron-exon reads, Total intron-exon reads, Exons, RPKM, Median coverage, Chromosome, Chromosome region start, Chromosome region end.
Supplementary_files_format_and_content: Excel data files containing RPKM values of both groups (chronic heart failure vs. Sham-operation) and there comparison by logarithmic ratio of RPKM group-specific values.

source_name: prefrontal cortex

growth_protocol: Brain and heart tissue were recovered after the lethal anaesthesia with tribromoethanol (avertin). The brains were removed and snap frozen in isopentane. The hearts were  were weighed and stored in liquid nitrogen.

extract_protocol:
Total RNA both in the brain and in the heart tissue was extracted according to the Direct-Zol RNA Miniprep kit (https://www.zymoresearch.com/direct-zol; Zymo Research Corporation, Irvine). RNA of 3 ischemic chronic heart failure mice versus 6 sham operated mice was pooled and further subjected to RNA sequencing. To fabricate singular pools each probe of the group equally contributed with the final amount of 2 µg RNA per pool.
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA sequencing was performed by IGA Technology, Italy (http://www.igatechnology.com/). RNA samples were processed using TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat from Illumina (Illumina, Inc., CA, USA). Briefly, the total RNA was treated with Ribo-Zero to remove cytoplasmic rRNA, fragmented into small pieces using divalent cations under elevated temperature, cDNA was synthesized by reverse transcription and standard blunt-ending plus add ‘A’ was performed. Then, Illumina TruSeq adapters with indexes were ligated to the ends of the cDNA fragments. After ligation reaction and separation of not ligated adapters, samples were amplified by PCR to selectively enrich those cDNA fragments in the library having adapter molecules at both ends. A pool of the 4 samples was loaded on two lane of Illumina flowcell and clusters created by Illumina cBot. The clusters were sequenced at ultra-high throughput on the Illumina HiSeq2000 (Illumina Inc.).

value: prefrontal cortical brain tissue

tag: type of operation

value: sham operation as control

tag: group

value: sham control


title: COPD lung tissue 1380-COPD


title: COPD lung tissue 2350-COPD


title: PFC Pool3

value: myocardial infarction

value: chronic heart failure


title: COPD lung tissue 1141-COPD


title: Heart Pool3

description:
8 weeks after the operation
Heart Pool3 vs. Heart Pool4.xlsx

source_name: left ventricular myocardium

value: left myocardial tissue


title: COPD lung tissue 1423-COPD


title: HIPP Pool4

description:
8 weeks after the operation
HIPP Pool3 vs. HIPP Pool4.xlsx

source_name: hippocampus

value: hippocampal brain tissue


title: COPD lung tissue 1047-COPD


title: COPD lung tissue 1088-COPD


title: HIPP Pool3


title: COPD lung tissue 103907N-COPD


title: COPD lung tissue 090815N-COPD


title: COPD lung tissue 1444-COPD


title: Heart Pool4


title: COPD lung tissue 090743N-COPD


title: Normal lung tissue 935-NOR

source_name: Normal Lung Tissue

value: Normal


title: COPD lung tissue 1395-COPD


title: Normal lung tissue 987-NOR


title: COPD lung tissue 12-COPD


title: COPD lung tissue 1332-COPD


title: Normal lung tissue 899-NOR


title: Normal lung tissue 750-NOR


title: Normal lung tissue 841-NOR


title: Normal lung tissue 681-NOR


title: WT Input-2

city: Corvallis

first: Chrissa

last: Kioussi

state: OR

address: 1601 SW Jefferson Ave

institute: Oregon State University

data_processing:
Basecalls performed using thePrimary Illumina data image analysis, base calling, and filtering was preformed by the Casava pipline (version 1.8.2, Illumina)
Filtered reads from the ChIP and input control libraries were aligned to the mouse genome (NCBI37/mm9) reference assembly using BWA (version 0.6.2)
MACS (version 2.0.10), was used to identify genomic regions significantly enriched (q ≤ 0.05 ) in ChIP-seq samples over input controls, and the software “broad peaks” option was used to delineate the mapped extent of histone marks
Genome_build: mm9
Supplementary_files_format_and_content: bigWig - normalized abundance density (reads per million)
Supplementary_files_format_and_content: bigBed - peak calls

source_name: Forelimb

extract_protocol:
Limb biopsies from embryos were cross-linked for 20 min in freshly made fixation buffer (1% formaldehyde 100 mM NaCl, 0.5 mM EGTA, 50 mM HEPES, pH 8.0) and quenched by the addition of glycine (125 mM). Tissue was washed twice with ice cold phosphate-buffered saline and snap-frozen in liquid nitrogen prior to sonication (14 cycles of 10 sec at 20% output with 60 sec on ice between cycles, Branson 450 sonicator) in lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.0, protease inhibitors) to achieve an average sheared fragment size of 300 bp, with the primary smear between 200–450 bp. This sheared chromatin was used for immunoprecipitation.
Single-end libraries were generated using the Illumina TruSeq ChIP seq library prep kit, with the only protocol modification being size selection after fragment amplification. The library size selected was 200–300 bp in length, and after gel purification, Agilent Bioanalyzer was used to confirm size. Libraries were then loaded on Illumina HiSeq 2000 and sequenced to generate 51 bp reads.

value: ICR

tag: developmental stage

value: Forelimb

tag: chip antibody

value: none, input control


title: WT H3K27me3_ChIP-seq

value: rabbit anti-H3K27me3 (Millipore, 07-449)


title: WT Input-1


title: Normal lung tissue 640-NOR


title: Normal lung tissue 55-NOR


title: Normal lung tissue 572-NOR


title: Normal lung tissue 581-NOR


title: Normal lung tissue 5275-NOR


title: Normal lung tissue 507-NOR


title: Normal lung tissue 495-NOR


title: Normal lung tissue 5122-NOR


title: Normal lung tissue 4845-NOR


title: Normal lung tissue 4881-NOR


title: Normal lung tissue 4851-NOR


title: Normal lung tissue 4772-NOR


title: Normal lung tissue 4658-NOR


title: Normal lung tissue 4305-NOR


title: Normal lung tissue 4361-NOR


title: Normal lung tissue 4293-NOR


title: Normal lung tissue 4286-NOR


title: Normal lung tissue 4218-NOR


title: Normal lung tissue 4266-NOR


title: Normal lung tissue 4004-NOR


title: Normal lung tissue 522-NOR


title: Normal lung tissue 3965-NOR


title: Normal lung tissue 3917-NOR


title: Normal lung tissue 3883-NOR


title: Normal lung tissue 3813-NOR


title: Normal lung tissue 3725-NOR


title: Normal lung tissue 3699-NOR


title: COPD lung tissue 2178-COPD


title: Normal lung tissue 4208-NOR


title: Normal lung tissue 4172-NOR


title: Normal lung tissue 3327-NOR


title: Normal lung tissue 33-NOR


title: Normal lung tissue 3239-NOR


title: Normal lung tissue 3543-NOR


title: Normal lung tissue 3243-NOR


title: Yap_input_data

description: wild type


title: Normal lung tissue 3197-NOR


title: Normal lung tissue 3231-NOR


title: WT Pol2_ChIP-seq

value: mouse anti-Pol2 (Millipore, 17-672)


title: COPD lung tissue 1092-COPD

value: COPD


title: Normal lung tissue 3287-NOR

value: lung


title: Normal lung tissue 3732-NOR


title: Normal lung tissue 3161-NOR


title: Normal lung tissue 306-NOR


title: Normal lung tissue 3594-NOR


title: Normal lung tissue 3033-NOR


title: Normal lung tissue 3160-NOR


title: Normal lung tissue 2969-NOR


title: Normal lung tissue 300-NOR


title: Normal lung tissue 34-NOR


title: Normal lung tissue 2832-NOR


title: Normal lung tissue 2479-NOR


title: Normal lung tissue 201-NOR


title: Normal lung tissue 1907-NOR


title: Normal lung tissue 223-NOR


title: Normal lung tissue 252-NOR


title: Normal lung tissue 2367-NOR


title: Normal lung tissue 1901-NOR


title: Normal lung tissue 5202-NOR


title: Normal lung tissue 1787-NOR


title: Normal lung tissue 1770-NOR


title: Normal lung tissue 1617-NOR


title: SingleCellNo1

value: female


title: Normal lung tissue 155-NOR


title: Normal lung tissue 1503-NOR


title: Normal lung tissue 467-NOR


title: Normal lung tissue 1487-NOR


title: Normal lung tissue 1467-NOR


title: Normal lung tissue 1475-NOR


title: Normal lung tissue 1444-NOR


title: Normal lung tissue 2808-NOR


title: Normal lung tissue 2826-NOR


title: Normal lung tissue 1464-NOR


title: Normal lung tissue 2294-NOR


title: Normal lung tissue 2469-NOR


title: Normal lung tissue 1424-NOR


title: Normal lung tissue 1376-NOR


title: Normal lung tissue 1334-NOR


title: Normal lung tissue 1355-NOR


title: Normal lung tissue 1264-NOR


title: Normal lung tissue 1199-NOR


title: Normal lung tissue 110-NOR


title: Normal lung tissue 1079-NOR


title: PolIIS5p_Patski_ChIPSeq

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6

data_processing:
Basecalls performed using CASAVA version 1.7
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. Reads from single-end or paired-end sequencing were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using BWA (Burrows-Wheeler Aligner).
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
Peak regions were selected using all uniquely mapped reads by both CisGenome and MACS (Model-based Analysis of ChIP-Seq) (p=1e-5 as the cutoff).
The SNP-associated read counts were used to assess average allelic occupancy.
Genome_build: mm9

source_name: Patski cells

extract_protocol:
ChIP was performed using fixed chromatin from mouse brain or cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Genomic DNA was prepared from an aliquot of the same batch of nuclei from F1 brain
Sequencing libraries were prepared each from four pooled independent PolIIS5p or CTCF ChIP samples from Patski cells or from Xist mutant F1 brain, using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 300-600bp range. Control sequencing library was prepared from genomic DNA prepared from F1 brain.

value: Fibroblasts derived from hybrid embryonic kidney

value: PolII-S5p, Abcam ab5131


title: CTCF_brain_ChIPSeq

description: Brains were collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

value: Adult whole brain

value: CTCF, MillIpore 07-729


title: DNase-Seq 60 min Cort Constant Sample2

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: DNase-seq in cells treatment 600 nM Cort for 60 min

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%. Peaks with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV) text files include genomic locations (Chromosome, start, end ), z-score, p-value and the maximum density of hotspots. BedGraph is a file format that allows display of tag density profiles (signal maps) in a genome browser track

source_name: 3134 cells

growth_protocol: For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, and penicillin-streptomycin cocktail.

extract_protocol:
Lysates were clarified from sonicated nuclei.
Nuclei were isolated  and subjected to a limited DNase I digestion. Small DNA fragments where DNase I cut twice were isolated and prepared for sequencing according to the manufacturer (Illumina). ChIP-seq: Lysates were clarified from sonicated nuclei and p300-DNA complexes or BRG1-DNA complexes were isolated with antibody.

treatment_protocol: Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran treated serum 48 hours prior to conducting the experiment.  Cells were untreated or induced with 600nM Corticosterone, 100nM dexamethasone

tag: cell line

value: mouse mammary cells

tag: treatment

value: 600 nM Cort for 60 min

tag: replicate

value: replicate 1


title: DNase-Seq 60 min Cort Pulsed Sample2

description: DNase-seq in cells treatment 600 nM Cort for 20 min + 40 min in hormone-free medium


title: DNase-Seq 0 min Cort Sample 2

description: DNase-seq in untreated cells

value: none (untreated cells)


title: Normal lung tissue 1396-NOR

value: Normal


title: DNase-Seq 20 min Cort Sample 2

description: DNase-seq in cells treatment 600 nM Cort for 20 min

value: 600 nM Cort for 20 min


title: Normal lung tissue 1379-NOR


title: E82HA-1

first: Chuck

last: Murry

address: 850 Republican St., Box 358050

department: Institute for Stem Cell and Regenerative Medicine, Center for Cardiovascular Biology

description: isoform_fpkm.tsv, gene_fpkm.tsv

data_processing:
Reads were mapped to hg19 using tophat 1.3.3.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files with FPKM estimates at the gene (gene_fpkm.tsv) and isoform (isoform_fpkm.tsv) level, generated using Cufflinks.

source_name: Anterior hemogenic endothelial-derived cardiac myocytes

growth_protocol: Monolayer directed differentiation using Activin A and BMP4 for cardiac progenitor differentiation to cardiomyocytes. Monolayer directed differentiation with Activin A and BMP4 following by treatment with VEGF on day 2 for derivation of hemogenic endothelial cells. Hemogenic endothelial cells were then treated with 2 uM XAV to direct cardiac lineage development

extract_protocol:
RNA-isolation
pA enrichment

tag: developmental state

value: day 14

value: RUES2 hESCs


title: E84CVP-2

description: isoform_fpkm.tsv, gene_fpkm.tsv

source_name: Cardiac progenitor cell-derived cardiac myocytes


title: E84CVP-1

description: isoform_fpkm.tsv, gene_fpkm.tsv

value: Cardiac progenitor cell-derived cardiac myocytes


title: 3_fzt

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: maize AGPv2 genome
Supplementary_files_format_and_content: tag count file

organism: Zea mays

source_name: maize 2-week-old seedling

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).

value: seedling

tag: genotype/variation

value: fzt mutation


title: Normal lung tissue 3157-NOR

value: lung


title: 3_A619

value: control


title: 1Tm_fzt

source_name: maize tassel primordia

value: tassel primordia


title: 1Tm_Nsib


title: 2Tm_fzt


title: Normal lung tissue 1017-NOR


title: fzt_mRNA_5


title: 2Tm_Nsib


title: 3Tm_Nsib


title: COPD lung tissue 190-COPD

value: COPD


title: COPD lung tissue 1785-COPD


title: fzt_mRNA_2


title: E82HA-2

description: isoform_fpkm.tsv, gene_fpkm.tsv

value: Anterior hemogenic endothelial-derived cardiac myocytes


title: fzt_mRNA_1


title: A619_mRNA_5


title: A619_mRNA_4


title: 3Tm_fzt


title: A619_mRNA_2


title: 2T_fzt


title: A619_mRNA_1


title: 3T_fzt


title: 3T_A619


title: 2T_A619


title: 1_fzt


title: 1T_A619


title: 1T_fzt


title: 2_fzt


title: fzt_mRNA_4


title: 1_A619


title: ppk1 knock-in 3

city: New Haven

first: Yu-Min

last: Chuang

state: CT

address: 1 Gilbert St TAC S410

department: Infectious disease

institute: Yale University

description: mid log growth stage (OD 0.5)

data_processing:
The sequence quality of the datasets was checked by fastQC software
The RNA-seq data were aligned with the CDC1551 genome obtained from Ensembl (bacteria, http://bacteria.ensembl.org) using bowtie2
HTSeq-count script written in python was used to obtain the read counts of each CDC1551 gene from the SAM alignment file.
The GTF annotation file from the bacterial Ensembl website was used during read counting for gene annotation. Since the library was strand-specific, HTSeq was employed with appropriate configurations (default). Normalization and analysis of differential expression were performed using DEseq2 package of bioconductor.
Genome_build: n/a
Supplementary_files_format_and_content: genes and counts

organism: Mycobacterium tuberculosis CDC1551

source_name: bacteria

growth_protocol: The logarithmically growing cultures (O.D.= 0.5) of the Rv1026 knock-down, ppk1 knock-in, and empty vector control strains

extract_protocol:
RNA was harvested using Trizol-based methods
RNA libraries were prepared by standard Illumina protocols

value: ppk1 knock-in


title: ppk1 knock-in 2

description: mid log growth stage (OD 0.5)


title: ppk1 knock-in 1

description: mid log growth stage (OD 0.5)


title: mouse neuron MRE

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Raw reads were aligned to mouse genome mm9 using Bowtie
For MeDIP-seq, redandunt reads were discard
For MRE-seq, reads were filtered by MRE recognization site in genome.
in house scripts were used to generated reads density for MeDIP and CpG density for MRE
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, read density for MeDIP and CpG density for MRE

source_name: cultured mouse neuron

growth_protocol: Cortical neurons from E15 CD-1 mice (Charles River Laboratories, Cambridge, MA) were plated and cultured in neurobasal medium (Invitrogen #21103-049) with B27 serum-free supplement (Invitrogen #17504-044), glutamine (5mM) and penicillin/streptomycin. Cells were typically seeded at a density of “one forebrain per 24-well plate”. Neurons were stimulated with KCl (55 mM) at 5DIV for 4 h.

extract_protocol:
For MeDIP, 5–15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA), than DNA was sonicated to ~100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml−1, Eurogentec. Catalog No. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml−1, Jackson Immunoresearch. Catalog No. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology. Catalog No. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml−1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.
For MRE:  DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100–300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 µl used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 μl used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

treatment_protocol: FK866 was obtained from National Institute of Mental Health Chemical Synthesis and Drug Supply Program (MH number F-901). 10nM of FK866 (diluted from 0.1M DMSO stock) was added to the culture medium 24 h prior to stimulation with KCl. Nicotinamide mononucleotide (NMN; Sigma #N3501) was added at the same time as FK866. 5’-aza-cytidine (5AzaC; Sigma #A2385) (10 µM) freshly prepared in DMSO was added 48 h prior to KCl stimulation (which was 24 h prior to FK866 addition). Medium containing 5AzaC was replenished every 24 h to ensure maintenance of adequate levels.

value: cultured mouse neuron

tag: antibody

tag: genetic background


title: 25mM, rep. 2

first: Luis

last: Sayavedra-Soto

address: Cordley Hall 2082

department: Botany and Plant Pathology

data_processing:
Aligned reads using Bowtie version 2.1.0 with options "--no-mixed --no-discordant -k 3 --gbar 100 --trim5 10 --trim3 10 -1 $sample/mate_1.fastq -2 $sample/mate_2.fastq -S $sample/alignments.sam"
Custom Python script matched alignments to gene annotations. Gene expression counts were aggregated from reads aligning unambiguously to each gene. A small list of homologs was used to resolve reads aligning ambiguously between the homologous genes to a single gene count.
NBPSeq version 0.1.8 was used to calculate differential gene expression by pairwise comparison.
Genome_build: N.winogradskyi: NC_007406.1, Contig6  [organism=Nitrobacter winogradskyi] [strain=Nb-255]
Supplementary_files_format_and_content: differential gene expression is tab-separated text output from NBPSeq

organism: Nitrobacter winogradskyi

source_name: cultures

growth_protocol: Chemostat cultures at D=0.008 h-1 with 60 mM NO2-; Samples were 0 mM NH4+; 1 mM NH4+; and 25 mmNH4+

extract_protocol:
Three biological replicates. Total RNA obtained using FastRNA kit (MP Biomedical). rRNA  removed with MICROBExpress (Ambion).
Standard illumina protocol; high-throughput; mRNASeq

treatment_protocol: Transcriptome comparisons among treatments

tag: phenotype

value: Nitritre oxidizer

value: 25 mM NH4+


title: 25mM, rep. 1


title: mouse neuron MeDIP

value: Methylcytidine


title: 25mM, rep. 3


title: Cabut ChIPSeq

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: chromatin IP against Cabut

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.PeakSeq was used to create the signal maps as wig files.
Peak-calling: Peak detection was performed with the PeakSeq program (http://www.gersteinlab.org/proj/PeakSeq/), using the Input DNA published in GEO GSE24115 record as a control. The final peak files are provided in BED format.
Genome_build: dm3
Supplementary_files_format_and_content: Cabut_aligned.wig(WIG, genome wide ChIP profile)
Supplementary_files_format_and_content: Cabut.peaks.txt (BED, signal enriched regions)

organism: Drosophila melanogaster

source_name: Wing imaginal discs

growth_protocol: Flies were grown in standard medium.

extract_protocol:
Chromatin from Drosophila third instar larvae wing discs was immunoprecipitated with 2 ug of antibody using standard protocols.
Libraries were prepared according to Illumina instructions.

tag: genotype

value: wt

value: third instar larvae

tag: tissue

value: wing imaginal disc

value: Cabut

tag: chip antibody manufacturer

value: Generated in N. Paricio's lab (Belacortu et al. 2011)

value: Canton S


title: 1mM, rep. 3

value: 1 mM NH4+


title: RV1026 knock-down 3

description: mid log growth stage (OD 0.5)

tag: strain

value: RV1026 knock-down


title: 1mM, rep. 2


title: RV1026 knock-down 2

description: mid log growth stage (OD 0.5)


title: 1mM, rep. 1


title: RV1026 knock-down 1

description: mid log growth stage (OD 0.5)


title: Empty vector 3

description: mid log growth stage (OD 0.5)

value: Empty vector


title: Empty vector 2

description: mid log growth stage (OD 0.5)


title: 0mM, rep. 3

value: 0 mM NH4+


title: 0mM, rep. 2


title: 2_A619

value: seedling

value: control


title: Empty vector 1

description: mid log growth stage (OD 0.5)


title: 0mM, rep. 1


title: WT H3K4me3_ChIP-seq

value: ICR

value: Forelimb

value: rabbit anti-H3K4me3 (Abcam, ab1342)


title: Normal lung tissue 421-NOR

tag: disease state

value: Normal

value: lung


title: wild type

status: Public on Feb 19 2015

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

description: Immunoprecipitated DNA

data_processing:
Mapping was performed using BWA tool (version 0.5.9) against the reference genome
Reference genome used: Escherichia coli K12 MG1655, version: iGenome
Peak detection and count of coverage were done using SEQMONK version 0.21.0 by Fasteris SA
Genome_build: Reference genome used: Escherichia coli K12 MG1655, version: iGenome
Supplementary_files_format_and_content: .txt file file with raw and normalized counts of coverage

organism: Escherichia coli

source_name: bacterial cell culture

growth_protocol: The ΔbolA and wt 3xflag strains were used to perform ChIP-seq experiments. Overnight cultures were diluted 1/100 in fresh LB medium and grown until OD600 0.6

extract_protocol:
Cross-linked cells were harvested and washed two times with ice-cold PBS. Cells were resuspended in 450μl of TES buffer (50mM Tris-HCl pH 7.5, 150mM NaCl) and 20μl of lysis solution (13.6mg/ml lysozyme, 50% glycerol, 50mM Tris-HCl pH7.5, 100mM NaCl, 1mM DTT, 0.1% Triton X-100) followed of a 5min incubation at room temperature. 10μl of cOmplete EDTA free protease inhibitor (Roche) were added and incubated 10min at room temperature. 550μl of ChIP buffer (1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, 167mM NaCl, 20μl/ml of cOmplete EDTA free protease inhibitor (Roche) were added followed of 10min incubation at 37ºC. The lysate was then sonicated (UP200S-Hielscher) to an average size between 300bp and 700bp with 5 cycles of and amplitude of 55%, 0.45sec pulse during 10sec and 50sec in ice. Insoluble cell debris were removed by centrifugation at 20000g for 3min at 4ºC and the supernatant collected. The supernatant was added to α-Flag-agarose beads (Sigma) and incubated at 4ºC under rotation. The samples were then washed once with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 150mM NaCl), once with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1), and twice with TE buffer (10mM Tris-HCl pH 8.1, 1mM EDTA). Two washes with 250μl of freshly prepared elution buffer (1% SDS, 100mM NaHCO3) were done followed by vortexing and incubation under rotation at room temperature for 15min. To reverse the cross-link 30μl of 5M NaCl were added to the elute and incubated over night at 65ºC. Finally, 4μl of 0.5M EDTA, 20μl of 1M Tris-HCl pH 6.5 and 2μl of 10mg/ml Proteinase-K (Sigma) were added and the suspension incubated at 45ºC for 2h. DNA was purified and recovered by standard phenol-chloroform extraction and ethanol precipitation with 20μg of glycogen.
Library construction was performed by processing in vitro samples to generate a library of short inserts (the DNA Colonies Template Library) by Fasteris SA, Switzerland

treatment_protocol: 10 mM of sodium phosphate and formaldehyde to a final concentration of 1% were then added. After 10min of incubation at room temperature, the samples were incubated 30 min in ice

value: wt 3xflag strain

value: wild type

value: anti-Flag (Sigma)


title: ΔbolA

description: Immunoprecipitated DNA

value: no tag

value: ΔbolA


title: Hdac1_ChIP

city: shanghai

first: Naihe

last: Jing

address: 320 Yue Yang Road

country: China

institute: institute of biochemistry and cell biology

data_processing:
Reads was uniquely mapped to mm10 using bowtie (version 0.12.8) with two mismatches allowed
Peaks were called using MACS (macs14 1.4.2) with default parameter
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using  MACS (macs14 1.4.2); Scores represent tags per 10 bp. Comma-delimited bed files include genomic locations (Chromosome, start, end ), peak id and -10*log10(p value).

source_name: ESC differentiated day 2 cells

growth_protocol: ESCs were plated onto gelatin coated dish and differentiated in serum-free N2B27 medium at the density of 0.5-1×10^4 cells/cm2.

extract_protocol:
Cells were cross-linked, lysed and sonicated to generate DNA fragments with an average size of 200 bp
10-15 ng IP DNA and input DNA measured by Qubit Fluorometer (Invitrogen) were used to construct DNA library by using ChIP-Seq Sample Prep Kit (Illumina) according to Illumina's instructions. Adapter-modified DNA between 200 and 350 bp were isolated by agarose gel electrophoresis and purified. Then, DNA was enriched by 18 cycles of linker-mediated-PCR using primers from Illumina.

tag: cell type

value: ESC differentiated cells

tag: differentiated days

value: 2 days

value: HDAC1 (3 FLAG-HDAC1)

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #


title: Hdac1_Input

tag: chip antibody


title: RRBS in cell type dME_shGATA4_1 RRBS_061314_mesoD2

city: Cambridge

first: Alexander

last: Tsankov

address: 7 Divinity Drive

institute: Harvard University

description: RRBS in cell type dME_shGATA4_1

data_processing:
Reads were aligned to the hg19 reference assembly using bwa version 0.5.7 (Li et al., Bioinformatics 2009) with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp. For the bigWig files, extended reads were summed at each base and normalized for sequencing depth by scaling the y-axis to represent cumulative reads per 1 million reads sequenced. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing the normalized occupancy (extended read count) across all genomic coordinates for each MNChIP-seq profile.
Supplementary_files_format_and_content: BED format file which contains the peak locations.
Supplementary_files_format_and_content: bigBed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column

growth_protocol: When human ES cells reached 60-70% confluency on MEFs, the cells were plated as clumps on 6-well plates coated with Matrigel (Life Technologies) in mTeSR1 basal medium (Stem Cell Technologies). We maintained the cells for three days in feeder-free culture and then induced directed differentiation towards mesendoderm (dMS), endoderm (dEN), mesoderm (dME), and ectoderm (dEC) using different media conditions. For mesendoderm and endoderm differentiation cells were cultured for 12 and 120 hours, respectively, in Roswell Park Memorial Institute (RPMI) medium (Life Technologies) supplemented with 100ng/ml Activin A (R&D Systems), 50nM/ml WNT3A (R&D Systems), 0.5% FBS (Hyclone), 200mM GlutaMax (Life Technologies), .2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. For the first 24 hours of mesoderm differentiation, cells were cultured in DMEM/F12 medium supplemented with 100ng/ml Activin A (R&D Systems), 10 ng/ml bFGF (Millipore), 100ng/ml BMP4 (R&D Systems), 100ng/ml VEGF (R&D Systems), 0.5% FBS (Hyclone), 200mM GlutaMax (Life Technologies), 0.2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. From 24 to 120 hours of mesoderm differentiation, Activin A was removed from the culture. For ectoderm differentiation cells were cultured in DMEM/F12 medium supplemented with 2µM TGFb inhibitor (Tocris, A83-01), 2µM WNT3A inhibitor (Tocris, PNU-74654), 2uM Dorsomorphin BMP inhibitor (Tocris), 15% KOSR (Life Technologies), .2X MEM Non-Essental Amino Acids Solution (Life Technologies), and 55µM b-mercaptoethanol. Media was changed daily.

extract_protocol:
Cells were grown to a final count of 10 million, resuspended in PBS, and crosslinked in 10% formaldehyde solution for 10 minutes at room temperature.  Following quenching with 0.125M glycine and two PBS washes, we isolated nuclei using cell lysis buffer (20 mM Tris-HCl ph8, 85mM KCl, 0.5% NP40). Nuclei were then digested using MNase (Worthington, LS004797) as done in (Henikoff et al., PNAS 2011). Digestion was stopped with 0.05M EGTA and chromatin was aliquoted into 1-2 million cells per ChIP. Antibodies were added and immunoprecipitation was carried out overnight at 4°C as done in1. The next day, protein G beads (Life Technology, 10009D) were added for 2 hours at 4°C to isolate the protein bound DNA and washed twice using Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1,), and TE Buffer pH 8 (10mM Tris-HCl, pH 8, 1mM EDTA pH 8). DNA was eluted twice using 100µL of ChIP Elution Buffer (1% SDS, 0.1M NaHCO3) at 65°C for 15 minutes. Crosslinking was reversed by addition of 32µl reverse crosslinking salt mixture (250 mM Tris-HCl pH 6.5, 62.5 mM EDTA pH 8, 1.25 M NaCl, 5mg/ml Proteinase K) for 5-18 hours at 65°C. DNA was isolated using phenol/chloroform extraction and treated with DNase-free RNase for 30 minutes at 37°C. The whole cell extract (WCE) control was generated using MNase treated material that was then reverse crosslinked and phenol chloroform extracted, skipping the immunoprecipitation and washing steps.
MNChIP-seq library construction was performed as in (Henikoff et al., PNAS 2011) with gel size selection from 140bp to 720bp as described in (Gu et al., 2010). RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010).

tag: cell line

value: dME shGATA4


title: CD4+ T-cells

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description: PRO-seq

data_processing:
library strategy: PRO-seq
Existing PRO-seq or GRO-seq data was combined from the indicated GEO repositories.
dREG (v. 1.0) was used to identify TREs using the indicated dataset.
We used a cutoff threshold of 0.77 to identify dREG 'peaks' and merged neighboring peaks within 500 bp.
Genome_build: hg19
Supplementary_files_format_and_content: Raw dREG scores, peak calls, and PRO-seq or GRO-seq data are provided in standard bigWig or BED file formats.

source_name: Primary Pan-CD4+ cells isolated by positive selection of the CD4 antigen

extract_protocol:
Both primary and Jurkat CD4+ T-cells were maintained in RPMI-1640 media supplemented with 10% FBS, and treated for 30 minutes with low amounts of DMSO and ethanol (as they are controls for a separate experiment, manuscript in preparation).  To isolate nuclei, cells were resuspended in 1mL lysis buffer (10mM Tris-Cl pH 8, 300mM sucrose, 10mM NaCl, 2mM MgAc2, 3mM CaCl2, and 0.1% NP-40).  Nuclei were washed in 10mL of wash buffer (10mM Tris-Cl pH 8, 300mM sucrose, 10mM NaCl, and 2mM MgAc2) to dilute free NTPs.  Nuclei were washed in 1mL, and subsequently resuspended in 50uL, of storage buffer (50mL Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, and 0.1mM EDTA), snap frozen in liquid nitrogen, and kept for up to 6 months before preforming PRO-seq.
PRO-seq was run exactly as described in Kwak et. al. (2008) Science.  Briefly, nuclei were added to equal volume Nuclear Run-On(NRO) reaction mixture (10 mM Tris-HCl pH 8.0, 300 mM KCl, 1% Sarkosyl, 5 mM MgCl2, 1mM DTT, 500μM biotin-11-A/C/G/UTP (Perkin-Elmer), 0.8 u/μl RNase inhibitor) and incubated for 5 min at 30̊C. Nascent RNA was extracted using Trizol and precipitated in ethanol. Extracted nascent RNA was fragmented by base hydrolysis in 0.1 N NaOH on ice for 8-10 min, and neutralized by adding equal volume of 1 M Tris-HCl pH 6.8.  Excessive salt and residual NTPs were removed by using P-30 column (Bio-rad). Fragmented nascent RNA was bound to 30 μl of Streptavidin M-280 magnetic beads (Invitrogen) following the manufacturer’s instructions. The beads were washed once in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.4, 0.5% Triton X-100), once in medium salt (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100), and once in low salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). Bound RNA was extracted from the bead using Trizol (Invitrogen) in two consecutive extractions.  RNA from each extraction was ethanol precipitated, re-suspended in depc H2O and pooled. Fragmented nascent RNA was re-suspended in depc H2O and ligated to a reverse 3' Illumina Hi-Seq adapter using T4 RNA ligase I (NEB) following the manufacturer's recommendations for 6 hours at 20C.  Ligated RNA was enriched with another round of purification on Streptavidin beads and Trizol extracted, as described above.  RNA products were treated with Tobacco Acid Pyrophosphatase (TAP, Epicentre) and Polynucleotide Kinase (PNK, NEB) to repair 5’ ends, and ligated to the reverse 5’ RNA adaptor for 6 hours at 20C.  The labeled RNA was purified a third time on Streptavidin beads.  Adaptor ligated nascent RNA was reverse transcribed using 25 pmol RT primer and amplified using Illumina TRU-seq barcodes.  Amplified product was PAGE purified and sequenced using Illumina HiSeq 2000 at Cornell University.

value: CD4+ T-cells

tag: treated with

value: none (untreated)

tag: molecule subtype

value: nascent RNA


title: Jurkat T-cells

description: PRO-seq

source_name: Jurkat T-cell leukemia cell line

value: Jurkat T-cells

value: Jurkat T-cell leukemia cell line


title: RRBS in cell type dME RRBS_061314_mesoC1

description: RRBS in cell type dME

source_name: dME

value: dME


title: RRBS in cell type dEN_shGATA4_1 RRBS_061314_endoD2

description: RRBS in cell type dEN_shGATA4_1

value: dEN shGATA4


title: RRBS in cell type dEN RRBS_061314_endoC1

description: RRBS in cell type dEN

source_name: dEN

value: dEN


title: HAND1 MNChIP-seq in cell type dMS eHand_071013_mesendo

description: HAND1 MNChIP-seq in cell type dMS

source_name: dMS

value: dMS

value: HAND1(Santa Cruz,sc-22817 X,F2304)


title: CMYC MNChIP-seq in cell type HUES64 cMyc_110812_h64

description: CMYC MNChIP-seq in cell type HUES64

value: CMYC(Santa Cruz,sc-764x,A2111)


title: CMYC MNChIP-seq in cell type dMS cMyc_111512_mesendo

description: CMYC MNChIP-seq in cell type dMS


title: CMYC MNChIP-seq in cell type dEC cMyc_022813_ecto

description: CMYC MNChIP-seq in cell type dEC

source_name: dEC

value: dEC


title: HAND1 MNChIP-seq in cell type dME eHand_022113_meso

description: HAND1 MNChIP-seq in cell type dME


title: CMYC MNChIP-seq in cell type dME cMyc_022113_meso

description: CMYC MNChIP-seq in cell type dME


title: CMYC MNChIP-seq in cell type dEN cMyc_022113_endo

description: CMYC MNChIP-seq in cell type dEN


title: HAND2 MNChIP-seq in cell type dME dHand_070213_meso

description: HAND2 MNChIP-seq in cell type dME

value: HAND2(Santa Cruz,sc-22818 X,I2804)


title: WCE (sonicated) in cell type dME WCE_072712_meso

description: WCE (sonicated) in cell type dME


title: HAND1 MNChIP-seq in cell type HUES64 eHand_070213_h64

description: HAND1 MNChIP-seq in cell type HUES64


title: WCE (Mnase treated) in cell type HUES64 WCE-M15_070512_h64

description: WCE (Mnase treated) in cell type HUES64


title: WCE (Mnase treated) in cell type HUES64 WCE-M19_070912_h64

description: WCE (Mnase treated) in cell type HUES64


title: TRIM28 MNChIP-seq in cell type HUES64 Trim28_ab_031313_h64

description: TRIM28 MNChIP-seq in cell type HUES64


title: TRIM28 MNChIP-seq in cell type dMS Trim28_071013_mesendo

description: TRIM28 MNChIP-seq in cell type dMS


title: TRIM28 MNChIP-seq in cell type dME Trim28_070213_meso

description: TRIM28 MNChIP-seq in cell type dME


title: TRIM28 MNChIP-seq in cell type dEN Trim28_070213_endo

description: TRIM28 MNChIP-seq in cell type dEN


title: TRIM28 MNChIP-seq in cell type dEC Trim28_062613_ecto

description: TRIM28 MNChIP-seq in cell type dEC


title: THAP11 MNChIP-seq in cell type HUES64 Thap11_ab_031313_h64

description: THAP11 MNChIP-seq in cell type HUES64


title: THAP11 MNChIP-seq in cell type dMS Thap11_071013_mesendo

description: THAP11 MNChIP-seq in cell type dMS


title: THAP11 MNChIP-seq in cell type dME Thap11_070213_meso

description: THAP11 MNChIP-seq in cell type dME


title: THAP11 MNChIP-seq in cell type dEN Thap11_070213_endo

description: THAP11 MNChIP-seq in cell type dEN


title: THAP11 MNChIP-seq in cell type dEC Thap11_062613_ecto

description: THAP11 MNChIP-seq in cell type dEC


title: TCF4 MNChIP-seq in cell type dEC Tcf4_022813_ecto

description: TCF4 MNChIP-seq in cell type dEC

value: TCF4(Cell Signaling,2569BF,3)


title: TCF4 MNChIP-seq in cell type HUES64 Tcf4_110812_h64

description: TCF4 MNChIP-seq in cell type HUES64


title: TCF4 MNChIP-seq in cell type dME Tcf4_022113_meso

description: TCF4 MNChIP-seq in cell type dME


title: TCF4 MNChIP-seq in cell type dMS Tcf4_022113_mesendo

description: TCF4 MNChIP-seq in cell type dMS


title: TAL1 MNChIP-seq in cell type dME Tal1_ab_070213_meso

description: TAL1 MNChIP-seq in cell type dME


title: WCE (sonicated) in cell type HUES64 WCE_072712_h64

description: WCE (sonicated) in cell type HUES64


title: TAL1 MNChIP-seq in cell type HUES64 Tal1_062613_h64

description: TAL1 MNChIP-seq in cell type HUES64


title: TCF4 MNChIP-seq in cell type dEN Tcf4_022113_endo

description: TCF4 MNChIP-seq in cell type dEN


title: T MNChIP-seq in cell type dMS T_022813_mesendo

description: T MNChIP-seq in cell type dMS


title: fst2

city: West Lafayette

middle: Peter

last: Woloshuk

state: IN

address: 915 West State St

institute: Purdue University

data_processing:
RNA sequence data from each sample were mapped to the reference genome of Gibberella moniliformis, which was downloaded (June 2014) from the Broad Institute Fusarium Comparative Database (http://www.broadinstitute.org).
Sequence data were mapped to the reference genome was done with CLC Genomics Workbench (version 7.0.4, CLC Bio, Boston), and gene expression was quantified as reads per kilobase per million mapped reads (RPKM)
Statistical analysis (pairwise t-testing) was also conducted with the CLC Genomics software
Genome_build: Gibberella moniliformis
Supplementary_files_format_and_content: Excel files include RPKM values for each sample and mean value for each strain

organism: Fusarium verticillioides

source_name: 6dpi infected maize kernel

growth_protocol: Kernels of maize inbred B73 were submerged in deionized water and autoclaved for 15 min.  Afterwards, the kernels were crushed slightly to disrupt the pericarp, and approximately 7 g of kernels (10-12 kernels) were placed in glass vials (20 ml) and autoclaved for 30 min.  Four replicate vials of the WT and ∆fst1 were inoculated with 100 µl of 10^6 conidia/ml.  Vials were incubated at 28°C for 6 days, then flash frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was isolated from the content of each vial and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).  Further purification was achieved by treatment with the DNA-Free RNA kit (Zymo Research, Irvine, CA, USA).
The Purdue Genetic Core Facility conducted quality assessment, processing, and sequencing of the RNA.  The RNA samples had a RIN (RNA Integrity Number) over 7.0 as determined with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).  Paired-end sequences were obtained with an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA).  Sequence data were trimmed of adapters and filtered to remove low quality sequence and reads less than 30 nt.

value: fst1 mutant strian


title: fst3


title: fst1


title: T MNChIP-seq in cell type HUES64 T_021113_h64

description: T MNChIP-seq in cell type HUES64


title: WT4

value: wild type


title: WT3


title: T MNChIP-seq in cell type dMS T_111212_mesendo

description: T MNChIP-seq in cell type dMS


title: STAT3 MNChIP-seq in cell type dME Stat3_070213_meso

description: STAT3 MNChIP-seq in cell type dME

value: STAT3(Cell Signaling,4904BF,4)


title: STAT3 MNChIP-seq in cell type HUES64 Stat3_cs_070213_h64

description: STAT3 MNChIP-seq in cell type HUES64


title: WT2


title: SRF MNChIP-seq in cell type dMS Srf_111212_mesendo

description: SRF MNChIP-seq in cell type dMS

value: SRF(Santa Cruz,sc-335 X,H0511)


title: Normal lung tissue 3702-NOR

data_processing:
RNA-Seq reads were mapped to the human genome using TopHat (v 1.4.1)
Aligned reads were quantified using Cufflinks software (2.0.0)
Raw data were extracted as FPKM for each gene for each sample by cufflinks software. Data with zeroed FPKM values across all samples were excluded. Filtered data was normalized by upper quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files format is a simple table which each row indicates single gene and each column indicates single patients, and each cell indicates FPKM value.

source_name: Normal Lung Tissue

extract_protocol:
Total RNA was isolated from normal fresh frozen tissue remote from lung cancer.
In order to construct cDNA libraries with the TruSeq RNA library kit, 1 ug of total RNA was used
The protocol consisted of poly A-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription

value: Normal

value: lung


title: WT1


title: SRF MNChIP-seq in cell type HUES64 Srf_110812_h64

description: SRF MNChIP-seq in cell type HUES64


title: fst4


title: SRF MNChIP-seq in cell type dME Srf_111312_meso

description: SRF MNChIP-seq in cell type dME


title: SRF MNChIP-seq in cell type HUES64 Srf_110512_h64

description: SRF MNChIP-seq in cell type HUES64


title: SRF MNChIP-seq in cell type dEN Srf_022113_endo

description: SRF MNChIP-seq in cell type dEN


title: SP1 MNChIP-seq in cell type HUES64 Sp1_cs_070213_h64

description: SP1 MNChIP-seq in cell type HUES64

value: SP1(Cell Signaling,9389BF,2)


title: SP1 MNChIP-seq in cell type dEN Sp1_cs_041914_endo

description: SP1 MNChIP-seq in cell type dEN


title: SP1 MNChIP-seq in cell type HUES64 Sp1_cs_021113_h64

description: SP1 MNChIP-seq in cell type HUES64


title: SOX2 MNChIP-seq in cell type HUES64 Sox2_122811_h64

description: SOX2 MNChIP-seq in cell type HUES64

value: SOX2(Santa Cruz,sc-17320 X,L3011)


title: SOX2 MNChIP-seq in cell type HUES64 Sox2_110812_h64

description: SOX2 MNChIP-seq in cell type HUES64


title: SOX2 MNChIP-seq in cell type dMS Sox2_111212_mesendo

description: SOX2 MNChIP-seq in cell type dMS


title: SOX17 MNChIP-seq in cell type dME Sox17_071013_meso

description: SOX17 MNChIP-seq in cell type dME

value: dME


title: SOX17 MNChIP-seq in cell type dEN Sox17_120312_endo

description: SOX17 MNChIP-seq in cell type dEN


title: SOX2 MNChIP-seq in cell type dME Sox2_031313_meso

description: SOX2 MNChIP-seq in cell type dME


title: SOX17 MNChIP-seq in cell type dMS Sox17_022113_mesendo

description: SOX17 MNChIP-seq in cell type dMS


title: STAT3 MNChIP-seq in cell type dEN Stat3_070213_endo

description: STAT3 MNChIP-seq in cell type dEN


title: SNAI2 MNChIP-seq in cell type HUES64 Snai2_021113_h64

description: SNAI2 MNChIP-seq in cell type HUES64

value: SNAI2(Santa Cruz,sc-15391 X,I2409)


title: SOX17 MNChIP-seq in cell type HUES64 Sox17_021113_h64

description: SOX17 MNChIP-seq in cell type HUES64


title: SMAD4 MNChIP-seq in cell type HUES64 Smad4_070213_h64

description: SMAD4 MNChIP-seq in cell type HUES64

value: SMAD4(Cell Signaling,9515BF,3)


title: SMAD4 MNChIP-seq in cell type dME Smad4_052214_meso

description: SMAD4 MNChIP-seq in cell type dME


title: SNAI2 MNChIP-seq in cell type dME Snai2_022113_meso

description: SNAI2 MNChIP-seq in cell type dME


title: SMAD4 MNChIP-seq in cell type dME Smad4_022113_meso

description: SMAD4 MNChIP-seq in cell type dME


title: SMAD4 MNChIP-seq in cell type dEC Smad4_022813_ecto

description: SMAD4 MNChIP-seq in cell type dEC


title: SMAD4 MNChIP-seq in cell type dMS Smad4_022113_mesendo

description: SMAD4 MNChIP-seq in cell type dMS

value: dMS


title: SRF MNChIP-seq in cell type dEC Srf_120312_ecto

description: SRF MNChIP-seq in cell type dEC


title: SRF MNChIP-seq in cell type HUES64 Srf_010212_h64

description: SRF MNChIP-seq in cell type HUES64


title: SMAD4 MNChIP-seq in cell type dEN Smad4_022113_endo

description: SMAD4 MNChIP-seq in cell type dEN

value: dEN


title: SMAD4 MNChIP-seq in cell type HUES64 Smad4_021113_h64

description: SMAD4 MNChIP-seq in cell type HUES64


title: SMAD23 MNChIP-seq in cell type dMS Smad23_022813_mesendo

description: SMAD23 MNChIP-seq in cell type dMS

value: SMAD23(Cell Signaling,8685P,1)


title: SMAD23 MNChIP-seq in cell type dEN Smad23_022813_endo

description: SMAD23 MNChIP-seq in cell type dEN


title: SMAD1 MNChIP-seq in cell type dMS Smad1_111512_mesendo

description: SMAD1 MNChIP-seq in cell type dMS

value: SMAD1(Cell Signaling,9743BF,3)


title: SMAD23 MNChIP-seq in cell type dEC Smad23_022813_ecto

description: SMAD23 MNChIP-seq in cell type dEC

value: dEC


title: SMAD23 MNChIP-seq in cell type HUES64 Smad23_021113_h64

description: SMAD23 MNChIP-seq in cell type HUES64


title: SMAD1 MNChIP-seq in cell type dME_shGATA4_3 Smad1_062914_mesoD3

value: dME shGATA4


title: SMAD1 MNChIP-seq in cell type HUES64 Smad1_110812_h64

description: SMAD1 MNChIP-seq in cell type HUES64


title: SMAD1 MNChIP-seq in cell type dME_shGATA4_2 Smad1_062914_mesoD22


title: SMAD1 MNChIP-seq in cell type dME Smad1_062914_mesoC1

description: SMAD1 MNChIP-seq in cell type dME


title: SOX2 MNChIP-seq in cell type dEN Sox2_022813_endo

description: SOX2 MNChIP-seq in cell type dEN


title: SMAD1 MNChIP-seq in cell type dEN_shGATA4_2 Smad1_062914_endoD22

value: dEN shGATA4


title: SMAD1 MNChIP-seq in cell type dME_shGATA4_1 Smad1_062914_mesoD2


title: SMAD1 MNChIP-seq in cell type dEN_shGATA4_3 Smad1_062914_endoD3


title: SMAD1 MNChIP-seq in cell type dEN_shGATA4_1 Smad1_062914_endoD2


title: SMAD1 MNChIP-seq in cell type dEN Smad1_062914_endoC1

description: SMAD1 MNChIP-seq in cell type dEN


title: SALL4 MNChIP-seq in cell type dMS Sall4_111512_mesendo

description: SALL4 MNChIP-seq in cell type dMS

value: SALL4(Santa Cruz,sc-101147,G1811)


title: SMAD1 MNChIP-seq in cell type dEN Smad1_022113_endo

description: SMAD1 MNChIP-seq in cell type dEN


title: SMAD1 MNChIP-seq in cell type dME Smad1_022113_meso

description: SMAD1 MNChIP-seq in cell type dME


title: REX1 MNChIP-seq in cell type HUES64 Rex1_110812_h64

description: REX1 MNChIP-seq in cell type HUES64


title: SALL4 MNChIP-seq in cell type HUES64 Sall4_010212_h64

description: SALL4 MNChIP-seq in cell type HUES64


title: REX1 MNChIP-seq in cell type dEN Rex1_070213_endo

description: REX1 MNChIP-seq in cell type dEN


title: POU5F1 MNChIP-seq in cell type HUES64 Pou5f1_122811_h64

description: POU5F1 MNChIP-seq in cell type HUES64


title: POU5F1 MNChIP-seq in cell type dMS Pou5f1_111212_mesendo

description: POU5F1 MNChIP-seq in cell type dMS


title: POU5F1 MNChIP-seq in cell type HUES64 Pou5f1_110812_h64

description: POU5F1 MNChIP-seq in cell type HUES64


title: POU5F1 MNChIP-seq in cell type dEC Pou5f1_120312_ecto

description: POU5F1 MNChIP-seq in cell type dEC


title: POU5F1 MNChIP-seq in cell type HUES64 Pou5f1_110512_h64

description: POU5F1 MNChIP-seq in cell type HUES64


title: POU5F1 MNChIP-seq in cell type dEN Pou5f1_022813_endo

description: POU5F1 MNChIP-seq in cell type dEN


title: POU5F1 MNChIP-seq in cell type dME Pou5f1_031313_meso

description: POU5F1 MNChIP-seq in cell type dME


title: POL2 MNChIP-seq in cell type dEC Pol2_120312_ecto

description: POL2 MNChIP-seq in cell type dEC


title: POL2 MNChIP-seq in cell type dME Pol2_111312_meso

description: POL2 MNChIP-seq in cell type dME


title: POL2 MNChIP-seq in cell type dEN Pol2_111912_endo

description: POL2 MNChIP-seq in cell type dEN


title: POL2 MNChIP-seq in cell type dMS Pol2_111512_mesendo

description: POL2 MNChIP-seq in cell type dMS


title: POL2 MNChIP-seq in cell type HUES64 Pol2_110512_h64

description: POL2 MNChIP-seq in cell type HUES64


title: POL2 MNChIP-seq in cell type HUES64 Pol2_110812_h64

description: POL2 MNChIP-seq in cell type HUES64


title: SMAD1 MNChIP-seq in cell type dEC Smad1_022813_ecto

description: SMAD1 MNChIP-seq in cell type dEC


title: PAX6 MNChIP-seq in cell type dEN Pax6_010812_endo3d

description: PAX6 MNChIP-seq in cell type dEN


title: PAX6 MNChIP-seq in cell type dEC Pax6_022813_ecto

description: PAX6 MNChIP-seq in cell type dEC


title: OTX2 MNChIP-seq in cell type HUES64 Otx2_110512_h64

description: OTX2 MNChIP-seq in cell type HUES64


title: OTX2 MNChIP-seq in cell type dME Otx2_111312_meso

description: OTX2 MNChIP-seq in cell type dME


title: OTX2 MNChIP-seq in cell type HUES64 Otx2_110812_h64

description: OTX2 MNChIP-seq in cell type HUES64


title: OTX2 MNChIP-seq in cell type dEC Otx2_062613_ecto

description: OTX2 MNChIP-seq in cell type dEC


title: REX1 MNChIP-seq in cell type dME Rex1_022113_meso

description: REX1 MNChIP-seq in cell type dME


title: OTX2 MNChIP-seq in cell type dEN Otx2_042214_endo

description: OTX2 MNChIP-seq in cell type dEN


title: OTX2 MNChIP-seq in cell type HUES64 Otx2_050114_h64

description: OTX2 MNChIP-seq in cell type HUES64


title: OTX2 MNChIP-seq in cell type dEC Otx2_022813_ecto

description: OTX2 MNChIP-seq in cell type dEC


title: OTX2 MNChIP-seq in cell type dEN Otx2_022113_endo

description: OTX2 MNChIP-seq in cell type dEN


title: OTX2 MNChIP-seq in cell type dMS Otx2_022113_mesendo

description: OTX2 MNChIP-seq in cell type dMS


title: NANOG MNChIP-seq in cell type dME Nanog_031313_meso

description: NANOG MNChIP-seq in cell type dME

value: NANOG(R&D Systems,AF1997,KKJ0512051)


title: NANOG MNChIP-seq in cell type HUES64 Nanog_110112_h64

description: NANOG MNChIP-seq in cell type HUES64


title: NANOG MNChIP-seq in cell type HUES64 Nanog_010212_h64

description: NANOG MNChIP-seq in cell type HUES64


title: NANOG MNChIP-seq in cell type dEN Nanog_022813_endo

description: NANOG MNChIP-seq in cell type dEN


title: NANOG MNChIP-seq in cell type dMS Nanog_111212_mesendo

description: NANOG MNChIP-seq in cell type dMS


title: OTX2 MNChIP-seq in cell type HUES64 Otx2_020912_h64

description: OTX2 MNChIP-seq in cell type HUES64


title: NANOG MNChIP-seq in cell type HUES64 Nanog_110812_h64

description: NANOG MNChIP-seq in cell type HUES64


title: NANOG MNChIP-seq in cell type HUES64 Nanog_110512_h64

description: NANOG MNChIP-seq in cell type HUES64


title: NANOG MNChIP-seq in cell type dEN Nanog_111312_endo

description: NANOG MNChIP-seq in cell type dEN


title: NR5A2 MNChIP-seq in cell type dMS NR5A2_111212_mesendo

description: NR5A2 MNChIP-seq in cell type dMS


title: NR5A2 MNChIP-seq in cell type HUES64 NR5A2_021113_h64

description: NR5A2 MNChIP-seq in cell type HUES64


title: LEF1 MNChIP-seq in cell type dMS Lef1_111512_mesendo

description: LEF1 MNChIP-seq in cell type dMS

value: LEF1(Santa Cruz,sc-8591 X,J0510)


title: LEF1 MNChIP-seq in cell type dME Lef1_022113_meso

description: LEF1 MNChIP-seq in cell type dME


title: KLF5 MNChIP-seq in cell type HUES64 Klf5_062613_h64

description: KLF5 MNChIP-seq in cell type HUES64

value: KLF5(Santa Cruz,sc-22797 X,I2804)


title: KLF5 MNChIP-seq in cell type dEN Klf5_022813_endo

description: KLF5 MNChIP-seq in cell type dEN


title: HNF4A MNChIP-seq in cell type HUES64 Hnf4a_070213_h64

description: HNF4A MNChIP-seq in cell type HUES64

value: HNF4A(Santa Cruz,sc-8987 X,L1709)


title: HNF4A MNChIP-seq in cell type dEN Hnf4a_070213_endo

description: HNF4A MNChIP-seq in cell type dEN


title: HNF4A MNChIP-seq in cell type dMS Hnf4a_022813_mesendo

description: HNF4A MNChIP-seq in cell type dMS


title: HNF1B MNChIP-seq in cell type dEN Hnf1b_070213_endo

description: HNF1B MNChIP-seq in cell type dEN

value: HNF1B(Santa Cruz,sc-22840 X,E2108)


title: HNF4A MNChIP-seq in cell type dEN Hnf4a_022813_endo

description: HNF4A MNChIP-seq in cell type dEN


title: HNF1B MNChIP-seq in cell type dMS Hnf1b_022113_mesendo

description: HNF1B MNChIP-seq in cell type dMS


title: HNF1B MNChIP-seq in cell type dEN Hnf1b_010812_endo3d

description: HNF1B MNChIP-seq in cell type dEN


title: HNF1B MNChIP-seq in cell type HUES64 Hnf1b_021113_h64

description: HNF1B MNChIP-seq in cell type HUES64


title: H3K9me3 MNChIP-seq in cell type dMS H3K9me3_041914_mesendo

description: H3K9me3 MNChIP-seq in cell type dMS


title: H3K4me1 MNChIP-seq in cell type dMS H3K4me1_041914_mesendo

description: H3K4me1 MNChIP-seq in cell type dMS


title: H3K4me3 MNChIP-seq in cell type dMS H3K4me3_041914_mesendo

description: H3K4me3 MNChIP-seq in cell type dMS


title: H3K27me3 MNChIP-seq in cell type dMS H3K27me3_041914_mesendo

description: H3K27me3 MNChIP-seq in cell type dMS


title: H3K27Ac MNChIP-seq in cell type dME_shGATA4_3 H3K27ac_062914_mesoD3


title: H3K27Ac MNChIP-seq in cell type dMS H3K27ac_ab_041914_mesendo

description: H3K27Ac MNChIP-seq in cell type dMS


title: H3K27Ac MNChIP-seq in cell type dME_shGATA4_1 H3K27ac_062914_mesoD2


title: H3K27Ac MNChIP-seq in cell type dME H3K27ac_062914_mesoC1

description: H3K27Ac MNChIP-seq in cell type dME


title: H3K27Ac MNChIP-seq in cell type dME_shGATA4_2 H3K27ac_062914_mesoD22


title: H3K27Ac MNChIP-seq in cell type dEN_shGATA4_2 H3K27ac_062914_endoD22


title: KLF5 MNChIP-seq in cell type dMS Klf5_022813_mesendo

description: KLF5 MNChIP-seq in cell type dMS


title: H3K27Ac MNChIP-seq in cell type dEN_shGATA4_3 H3K27ac_062914_endoD3


title: H3K27Ac MNChIP-seq in cell type dEN_shGATA4_1 H3K27ac_062914_endoD2


title: GATA6 MNChIP-seq in cell type dMS Gata6_111512_mesendo

description: GATA6 MNChIP-seq in cell type dMS

value: GATA6(Santa Cruz,sc-7244 X,H0911)


title: GATA6 MNChIP-seq in cell type dEN Gata6_rd_042214_endo

description: GATA6 MNChIP-seq in cell type dEN


title: HEY1 MNChIP-seq in cell type dME Hey1_031313_meso

description: HEY1 MNChIP-seq in cell type dME

value: dME

value: HEY1(Santa Cruz,sc-16424 X,F2411)


title: GATA6 MNChIP-seq in cell type dME Gata6_111312_meso

description: GATA6 MNChIP-seq in cell type dME


title: GATA4 MNChIP-seq in cell type dME Gata4_sort_050114_meso

description: GATA4 MNChIP-seq in cell type dME

value: GATA4(R&D Systems,AF2606,VAZ0312041)


title: GATA4 MNChIP-seq in cell type dME Gata4_unsort_050114_meso

description: GATA4 MNChIP-seq in cell type dME


title: GATA6 MNChIP-seq in cell type dEN Gata6_010812_endo3d

description: GATA6 MNChIP-seq in cell type dEN


title: GATA4 MNChIP-seq in cell type dEN Gata4_111312_endo

description: GATA4 MNChIP-seq in cell type dEN


title: GATA4 MNChIP-seq in cell type dME_shGATA4_3 Gata4_062914_mesoD3


title: GATA4 MNChIP-seq in cell type dME_shGATA4_2 Gata4_062914_mesoD22


title: GATA4 MNChIP-seq in cell type dME_shGATA4_1 Gata4_062914_mesoD2


title: H3K27Ac MNChIP-seq in cell type dMS H3K27ac_am_041914_mesendo

description: H3K27Ac MNChIP-seq in cell type dMS

value: dMS


title: GATA4 MNChIP-seq in cell type dME Gata4_062914_mesoC1

description: GATA4 MNChIP-seq in cell type dME


title: GATA4 MNChIP-seq in cell type dEN_shGATA4_3 Gata4_062914_endoD3


title: GATA4 MNChIP-seq in cell type dEN Gata4_062914_endoC1

description: GATA4 MNChIP-seq in cell type dEN

value: dEN


title: GATA4 MNChIP-seq in cell type dEN_shGATA4_1 Gata4_062914_endoD2


title: GATA4 MNChIP-seq in cell type dEN_shGATA4_2 Gata4_062914_endoD22


title: GATA4 MNChIP-seq in cell type dME Gata4_041914_meso

description: GATA4 MNChIP-seq in cell type dME


title: GATA4 MNChIP-seq in cell type dEN Gata4_042214_endo

description: GATA4 MNChIP-seq in cell type dEN


title: GATA4 MNChIP-seq in cell type dME Gata4_022113_meso

description: GATA4 MNChIP-seq in cell type dME


title: H3K27Ac MNChIP-seq in cell type dEN H3K27ac_062914_endoC1

description: H3K27Ac MNChIP-seq in cell type dEN


title: GATA4 MNChIP-seq in cell type dMS Gata4_022113_mesendo

description: GATA4 MNChIP-seq in cell type dMS


title: GATA4 MNChIP-seq in cell type HUES64 Gata4_021113_h64

description: GATA4 MNChIP-seq in cell type HUES64


title: GATA6 MNChIP-seq in cell type dEN Gata6_111312_endo

description: GATA6 MNChIP-seq in cell type dEN


title: GATA6 MNChIP-seq in cell type dME Gata6_rd_041914_meso

description: GATA6 MNChIP-seq in cell type dME


title: FOXA2 MNChIP-seq in cell type HUES64 FoxA2_070213_h64

description: FOXA2 MNChIP-seq in cell type HUES64

value: FOXA2(Santa Cruz,sc-6554 X,C1810)


title: GATA6 MNChIP-seq in cell type HUES64 Gata6_062613_h64

description: GATA6 MNChIP-seq in cell type HUES64


title: FOXA2 MNChIP-seq in cell type dMS FoxA2_022113_mesendo

description: FOXA2 MNChIP-seq in cell type dMS


title: FOXA2 MNChIP-seq in cell type dEN FoxA2_rd_041914_endo

description: FOXA2 MNChIP-seq in cell type dEN


title: FOXA2 MNChIP-seq in cell type dEN FoxA2_010812_endo3d

description: FOXA2 MNChIP-seq in cell type dEN


title: FOXA1 MNChIP-seq in cell type dEN FoxA1_111312_endo

description: FOXA1 MNChIP-seq in cell type dEN

value: FOXA1(Santa Cruz,sc-101058,H1111)


title: FOXA1 MNChIP-seq in cell type dEN FoxA1_041914_endo

description: FOXA1 MNChIP-seq in cell type dEN


title: FOXA1 MNChIP-seq in cell type HUES64 FoxA1_021113_h64

description: FOXA1 MNChIP-seq in cell type HUES64


title: FOXA1 MNChIP-seq in cell type dEN FoxA1_010812_endo3d

description: FOXA1 MNChIP-seq in cell type dEN


title: FOXA1 MNChIP-seq in cell type dMS FoxA1_022813_mesendo

description: FOXA1 MNChIP-seq in cell type dMS


title: EOMES MNChIP-seq in cell type dEN Eomes_041914_endo

description: EOMES MNChIP-seq in cell type dEN


title: EOMES MNChIP-seq in cell type dEN Eomes_022113_endo

description: EOMES MNChIP-seq in cell type dEN


title: EOMES MNChIP-seq in cell type dMS Eomes_071212_mesendo

description: EOMES MNChIP-seq in cell type dMS


title: CTCF MNChIP-seq in cell type dMS Ctcf_111512_mesendo

description: CTCF MNChIP-seq in cell type dMS


title: CTCF MNChIP-seq in cell type dME Ctcf_111312_meso

description: CTCF MNChIP-seq in cell type dME


title: CTCF MNChIP-seq in cell type dEC Ctcf_120312_ecto

description: CTCF MNChIP-seq in cell type dEC

value: dEC


title: CTCF MNChIP-seq in cell type HUES64 Ctcf_110812_h64

description: CTCF MNChIP-seq in cell type HUES64


title: CDX2 MNChIP-seq in cell type dME Cdx2_031313_meso

description: CDX2 MNChIP-seq in cell type dME


title: PRDM1 MNChIP-seq in cell type dEN Blimp1_111312_endo

description: PRDM1 MNChIP-seq in cell type dEN

value: PRDM1(Cell Signaling,9115BF,5)


title: PRDM1 MNChIP-seq in cell type HUES64 Blimp1_070213_h64

description: PRDM1 MNChIP-seq in cell type HUES64


title: CTCF MNChIP-seq in cell type dEN Ctcf_111912_endo

description: CTCF MNChIP-seq in cell type dEN


title: PRDM1 MNChIP-seq in cell type dMS Blimp1_022813_mesendo

description: PRDM1 MNChIP-seq in cell type dMS


title: D6-H3AC_Input

source_name: ESC differentiated day 6 cells

value: ESC differentiated cells

value: 6 days

value: H3AC (acetylated histone H3)

value: Millipore


title: D6-H3AC_ChIP


title: FOXA2 MNChIP-seq in cell type dEN FoxA2_041914_endo

description: FOXA2 MNChIP-seq in cell type dEN


title: D4-H3AC_Input

source_name: ESC differentiated day 4 cells

value: 4 days


title: D4-H3AC_ChIP


title: PRDM1 MNChIP-seq in cell type dEN Blimp1_061112_endo

description: PRDM1 MNChIP-seq in cell type dEN


title: D2-H3AC_ChIP

value: 2 days


title: D2-H3AC_Input


title: EOMES MNChIP-seq in cell type dMS Eomes_111212_mesendo

description: EOMES MNChIP-seq in cell type dMS


title: EOMES MNChIP-seq in cell type HUES64 Eomes_021113_h64

description: EOMES MNChIP-seq in cell type HUES64


title: CTCF MNChIP-seq in cell type HUES64 Ctcf_052212_h64

description: CTCF MNChIP-seq in cell type HUES64


title: CTCF MNChIP-seq in cell type HUES64 Ctcf_110512_h64

description: CTCF MNChIP-seq in cell type HUES64


title: MNase-seq_PS_WT_ubH2A

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
genomic DNA, Mnase
wardrobe number: 414

data_processing:
Data analysis was performed in Wardrobe Experiment Management System (https://code.google.com/p/genome-tools/).
Reads were aligned to the mouse genome (mm10) with bowtie (version 1.0.0(8)) and displayed on a local mirror of UCSC genome browser as coverage.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq data, reads were mapped to the mm10 genome using tophat (version 2.0.9 (10)) and assigned to the refseq genes using Wardrobe algorithm. For-ChIP-seq, Islands enrichment were identified using MACS2

source_name: Isolated pachytene spermatocytes

growth_protocol: GS cells were cultured in normal condition.PS and RS were isolated from adult wild-type or Scml2-KO mice with BSA gradient methods

extract_protocol:
For ChIP-seq of crosslink samples, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. For ChIP-seq of MNase samples, lysate was digested with Mnase and Histone-DNA complexes were isolated with antibodies. For RNA-seq, RNA was purified using RNeasy mini kit.
DNA library for ChIP-seq (both crosslink and MNase samples) was prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (NEB) and Agencourt AMPure XP (Beckman Coulter). For RNA-seq, TruSeq™ RNA Sample Prep Kit v2 -Set A was used for library construction.

tag: genotype/variation

value: Wild-type

value: Isolated pachytene spermatocytes

value: Rabbit anti-ubH2A (Cell Signaling, catalog#8240, lot#1)


title: MNase-seq_PS_KO_ubH2A

description:
genomic DNA, Mnase
wardrobe number: 415


title: ChIPseq_GS_WT_Bmi1

description:
genomic DNA, Cross link
wardrobe number: 208

source_name: Cultured germline stem cells

value: CD1 x C57BL/6

value: Cultured germline stem cells

value: Mouse anti-Bmi1 (Millipore, catalog#05-637, lot#2019726)


title: ChIPseq_GS_WT_Input_CL

description:
genomic DNA, Cross link
wardrobe number: 210

value: none (input)


title: MNase-seq_PS_WT_ubH2A_Input_Mnase

description:
genomic DNA, Mnase
wardrobe number: 271


title: MNase-seq_GS_WT_Input_Mnase

description:
genomic DNA, Mnase
wardrobe number: 270


title: RNAseq_RS_KO_2

description: wardrobe number: 386

source_name: Isolated round spermatids

value: Isolated round spermatids


title: ChIPseq_GS_WT_Scml2

description:
genomic DNA, Cross link
wardrobe number: 209

value: Rabbit anti-Scml2 (produced in-house; Hasegawa et al.)


title: ChIPseq_GS_WT_Rnf2

description:
genomic DNA, Cross link
wardrobe number: 207

value: Mouse anti-Rnf2 (MBL, catalog#D139-3, lot#014)


title: RNAseq_RS_KO_1

description: wardrobe number: 385


title: RNAseq_PS_KO2

description: wardrobe number: 384


title: RNAseq_RS_WT_2

description: wardrobe number: 100


title: RNAseq_PS_KO1

description: wardrobe number: 383


title: RNAseq_PS_WT_2

description: wardrobe number: 363


title: RNAseq_PS_WT_1

description: wardrobe number: 343


title: RNAseq_GS_WT_1

description: wardrobe number: 296


title: RNAseq_GS_WT_2

description: wardrobe number: 351


title: D1PO

status: Public on Feb 18 2015

city: Morgantown

first: Hao

last: Ma

state: WV

address: Agriculture Science Building, Evansdale Drive

department: Animal & Nutritional Sciences

institute: West Virginia University

data_processing:
A software package, ACGT101-miR V3.5 (LC Sciences) was used for analyzing dequencing data generated
‘‘Impurity’’ sequences including sequences with low resolution, copy number less than 3 and length less than 15 nts or larger than 26 nts, adapter sequences, junk sequences (such as .= 80% of A,C, G or T; .= 3 Ns; only A, C, or only G, T), and simple sequence were filtered.
The sequences mapping to the databases of mRNA, RFam and Repbase were also removed.
The remaining sequences were used to BLAST against all miRNAs in the miRbase database (release 21) to identify known miRNAs. The sequences that did not match known miRNAs were mapped to rainbow trout genome to identify potentially novel miRNAs.
Genome_build: miRbase database (release 21)
Supplementary_files_format_and_content: Excel files containing known or predicted miRNA name, sequence, number of reads, chromosome, strand, hairpin start, and hairpin end.

organism: Oncorhynchus mykiss

source_name: day 1 post-ovulation

growth_protocol: Samples from commercial populations of Troutlodge Inc., were reared for at least two generations using commercial trout feed under the temperature of 12.0-12.5°C in treated spring water recirculating partially in  the National Center for Cool and Cold Water Aquaculture (NCCCWA).

extract_protocol:
Total RNA from the eggs was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions followed by additional purification steps with lithium chloride precipitation.
Small RNA libraries were generated according to Illumina's sample preparation instruction.

tag: developmental stage

value: day 1 post-ovulation

tag: survival rate

value: eggs


title: MNase-seq_GS_WT_ubH2A

description:
genomic DNA, Mnase
wardrobe number: 211


title: D14PO

source_name: day 14 post-ovulation

value: day 14 post-ovulation

value: less than 50.0%


title: GPA-85_HumanDC_smallRNA_RNAseq

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were trimmed to remove 3' adaptor
Read quality was assessed and reads were filtered using the R bioconductor package ShortRead. We removed reads (i) reads containing a mononucleotide repeat longer than 10nt, (ii) reads containing >75% mono, di or tri-nucleotide repeat, (iii) reads containing >20% "N" bases, (iv) reads shorter than 16nt or longer than 26nt
Reads were mapped to the human genome using bowtie (version 0.12.7) with parameters -v 2 -m 50 -a --best --strata
Cross-mapping correction (de Hoon et al., 2010) was applied to handle reads that mapped to multiple genomic locations
Reads aligning to mature miRNAs (miRBase v20, minimum overlap 75%) were extracted using BEDTools.
miRNA expression levels were calculated as the sum of the read counts of all sequences aligning to the mature miRNA
miRNA expression levels were normalised across samples by scaling counts of all miRNAs by a sizeFactor calculated using the function calculateSizeFactor from the bioconductor package DESeq (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of scaled, unfiltered expression levels for all detected mature miRNAs (miRBase v20) in all 116 samples (txt)

source_name: monocyte-derived Dendritic Cells

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation. Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Monocytes were then cultured for 5 days in RPMI-1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen).
Indexed sequencing libraries were prepared using the Illumina TruSeq protocol following isolation of low molecular weight (small) RNA fragments. Once prepared, indexed cDNA libraries were pooled (8 or 12 libraries per pool) in equimolar amounts and sequenced with single-end 50-bp reads on the Illumina HiSeq2000.

treatment_protocol: Monocyte-derived DCs were infected (~2x10^6 cells per condition) at an MOI of 1:1 with one of a panel of bacteria (Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis Beijing strain GC1237, Mycobacterium bovis BCG, Salmonella typhimurium strain Keller, Staphloccocus epidermidis and Yersinia pseudotuberculosis), or left uninfected, for 1h at 37c. Next the cells were washed and cultured for a further hour with 50ug/ml gentamycin. The cells were then washed a second time and cultured in complete medium with 5ug/ml gentamycin for an additional 4h, 18h and 48h.

value: monocyte-derived Dendritic Cells

tag: donor

tag: infection agent

value: Yersinia pseudotuberculosis

tag: time point


title: GPA-131_HumanDC_smallRNA_RNAseq


title: GPA-172_HumanDC_smallRNA_RNAseq


title: GPA-152_HumanDC_smallRNA_RNAseq


title: GPA-109_HumanDC_smallRNA_RNAseq


title: GPA-89_HumanDC_smallRNA_RNAseq


title: GPA-174_HumanDC_smallRNA_RNAseq


title: GPA-179_HumanDC_smallRNA_RNAseq


title: GPA-111_HumanDC_smallRNA_RNAseq


title: GPA-133_HumanDC_smallRNA_RNAseq


title: RNAseq_RS_WT_1

description: wardrobe number: 99


title: GPA-156_HumanDC_smallRNA_RNAseq


title: GPA-135_HumanDC_smallRNA_RNAseq


title: GPA-71_HumanDC_smallRNA_RNAseq


title: GPA-159_HumanDC_smallRNA_RNAseq


title: GPA-140_HumanDC_smallRNA_RNAseq

value: Staphloccocus epidermidis


title: D7PO

source_name: day 7 post-ovulation

value: day 7 post-ovulation

tag: tissue


title: GPA-176_HumanDC_smallRNA_RNAseq


title: GPA-92_HumanDC_smallRNA_RNAseq


title: GPA-158_HumanDC_smallRNA_RNAseq


title: GPA-103_HumanDC_smallRNA_RNAseq


title: GPA-184_HumanDC_smallRNA_RNAseq


title: GPA-104_HumanDC_smallRNA_RNAseq


title: GPA-86_HumanDC_smallRNA_RNAseq


title: GPA-175_HumanDC_smallRNA_RNAseq

value: Salmonella typhimurium strain Keller


title: GPA-122_HumanDC_smallRNA_RNAseq


title: GPA-134_HumanDC_smallRNA_RNAseq


title: GPA-154_HumanDC_smallRNA_RNAseq


title: GPA-113_HumanDC_smallRNA_RNAseq


title: GPA-69_HumanDC_smallRNA_RNAseq


title: GPA-70_HumanDC_smallRNA_RNAseq


title: GPA-155_HumanDC_smallRNA_RNAseq


title: GPA-157_HumanDC_smallRNA_RNAseq


title: GPA-182_HumanDC_smallRNA_RNAseq


title: GPA-112_HumanDC_smallRNA_RNAseq


title: GPA-72_HumanDC_smallRNA_RNAseq


title: GPA-93_HumanDC_smallRNA_RNAseq


title: GPA-91_HumanDC_smallRNA_RNAseq


title: GPA-181_HumanDC_smallRNA_RNAseq


title: GPA-114_HumanDC_smallRNA_RNAseq


title: GPA-116_HumanDC_smallRNA_RNAseq


title: GPA-162_HumanDC_smallRNA_RNAseq


title: GPA-160_HumanDC_smallRNA_RNAseq


title: GPA-121_HumanDC_smallRNA_RNAseq

value: Mycobacterium tuberculosis Beijing strain GC1237


title: GPA-141_HumanDC_smallRNA_RNAseq


title: GPA-79_HumanDC_smallRNA_RNAseq


title: GPA-180_HumanDC_smallRNA_RNAseq


title: GPA-99_HumanDC_smallRNA_RNAseq


title: GPA-146_HumanDC_smallRNA_RNAseq


title: GPA-125_HumanDC_smallRNA_RNAseq


title: GPA-101_HumanDC_smallRNA_RNAseq


title: GPA-81_HumanDC_smallRNA_RNAseq


title: GPA-148_HumanDC_smallRNA_RNAseq


title: GPA-168_HumanDC_smallRNA_RNAseq


title: GPA-127_HumanDC_smallRNA_RNAseq


title: GPA-137_HumanDC_smallRNA_RNAseq


title: GPA-83_HumanDC_smallRNA_RNAseq


title: GPA-106_HumanDC_smallRNA_RNAseq


title: GPA-150_HumanDC_smallRNA_RNAseq


title: GPA-170_HumanDC_smallRNA_RNAseq


title: GPA-178_HumanDC_smallRNA_RNAseq


title: GPA-129_HumanDC_smallRNA_RNAseq


title: GPA-136_HumanDC_smallRNA_RNAseq

value: Mycobacterium tuberculosis H37Rv


title: GPA-74_HumanDC_smallRNA_RNAseq


title: GPA-94_HumanDC_smallRNA_RNAseq


title: GPA-183_HumanDC_smallRNA_RNAseq


title: GPA-87_HumanDC_smallRNA_RNAseq


title: GPA-73_HumanDC_smallRNA_RNAseq


title: GPA-161_HumanDC_smallRNA_RNAseq


title: GPA-138_HumanDC_smallRNA_RNAseq


title: GPA-115_HumanDC_smallRNA_RNAseq


title: GPA-117_HumanDC_smallRNA_RNAseq


title: GPA-95_HumanDC_smallRNA_RNAseq


title: GPA-163_HumanDC_smallRNA_RNAseq


title: GPA-75_HumanDC_smallRNA_RNAseq


title: GPA-142_HumanDC_smallRNA_RNAseq


title: GPA-119_HumanDC_smallRNA_RNAseq


title: GPA-77_HumanDC_smallRNA_RNAseq


title: GPA-97_HumanDC_smallRNA_RNAseq


title: Normal lung tissue 1207-NOR

city: Seoul

first: JaeHyun

last: Lim

address: Department of Biomedical Sciences, Seoul National University Graduate School, Biomedical Science Building 117, 103 Daehakro, Jongro-gu

institute: Seoul National University

value: Normal

value: lung


title: GPA-144_HumanDC_smallRNA_RNAseq


title: GPA-123_HumanDC_smallRNA_RNAseq


title: GPA-165_HumanDC_smallRNA_RNAseq


title: GPA-102_HumanDC_smallRNA_RNAseq

value: Mycobacterium bovis BCG


title: GPA-149_HumanDC_smallRNA_RNAseq


title: GPA-169_HumanDC_smallRNA_RNAseq


title: GPA-82_HumanDC_smallRNA_RNAseq


title: GPA-153_HumanDC_smallRNA_RNAseq


title: GPA-108_HumanDC_smallRNA_RNAseq


title: GPA-107_HumanDC_smallRNA_RNAseq


title: GPA-132_HumanDC_smallRNA_RNAseq


title: GPA-171_HumanDC_smallRNA_RNAseq


title: GPA-84_HumanDC_smallRNA_RNAseq


title: GPA-88_HumanDC_smallRNA_RNAseq


title: GPA-173_HumanDC_smallRNA_RNAseq


title: GPA-130_HumanDC_smallRNA_RNAseq


title: GPA-151_HumanDC_smallRNA_RNAseq


title: GPA-90_HumanDC_smallRNA_RNAseq


title: GPA-110_HumanDC_smallRNA_RNAseq


title: GPA-139_HumanDC_smallRNA_RNAseq

value: Non-infected


title: GPA-177_HumanDC_smallRNA_RNAseq


title: GPA-118_HumanDC_smallRNA_RNAseq


title: GPA-96_HumanDC_smallRNA_RNAseq


title: GPA-120_HumanDC_smallRNA_RNAseq


title: GPA-164_HumanDC_smallRNA_RNAseq


title: GPA-143_HumanDC_smallRNA_RNAseq


title: GPA-128_HumanDC_smallRNA_RNAseq


title: GPA-166_HumanDC_smallRNA_RNAseq


title: GPA-98_HumanDC_smallRNA_RNAseq


title: GPA-145_HumanDC_smallRNA_RNAseq


title: GPA-78_HumanDC_smallRNA_RNAseq


title: GPA-124_HumanDC_smallRNA_RNAseq


title: GPA-167_HumanDC_smallRNA_RNAseq


title: GPA-80_HumanDC_smallRNA_RNAseq


title: GPA-100_HumanDC_smallRNA_RNAseq


title: CUTLL1_T4_T3AGAROSE_24HR_R1

city: New York

first: Tharu

middle: M

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Reads that passed filter were aligned to hg19 using TopHat (Trapnell et al., 2009).
Gene expression expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially expressed genes were identified with the edgeR package (Robinson et al., 2010).  Genes with a p-value < 0.01 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count is provided as a .txt file.

source_name: CUTLL1 cells

growth_protocol: Cells were grown in RPMI 1640 medium with 10% FBS, 2mM glutamine, and pen/strep.

extract_protocol:
Total RNA was harvested with Trizol reagent (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

treatment_protocol: Cells were treated with agarose alone or T3- and T4-bound agarose (Sigma) for 24 hours.

tag: treatment

value: T3- and T4-bound agarose, 24hrs


title: GPA-126_HumanDC_smallRNA_RNAseq


title: GPA-105_HumanDC_smallRNA_RNAseq


title: CUTLL1_T4_T3AGAROSE_24HR_R2


title: CUTLL1_CON_24HR_R1

value: Agarose alone, 24hrs


title: CUTLL1_CON_24HR_R3


title: CUTLL1_T4_T3AGAROSE_24HR_R3