title: C00111 Non-failing Left Ventricle

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
C00111
PolyA mRNA

data_processing:
Illumina Casava1.8 software used for basecalling.
The RNA-seq data were aligned to the hg19 reference genome using Tophat with default options.
Transcripts were assembled using Cufflinks. For differentially expressed genes, we carried out functional annotation analysis using DAVID; we further examined whether they were more likely to overlap with GWAS findings, the analysis was based on all GWAS signals summarized in the NHGRI GWAS catalogue.
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM_TRACKING file: Expression values as FPKMs were calculated using Cufflinks and RefSeq gene annotations. Columns are Official gene symbol, hg19 gene locus, FPKM expression value.
Supplementary_files_format_and_content: cuffdiff .txt file: Differential expression results from the cuffdiff program. Columns are Gene Symbol, gene locus, FPKM of group 1, FPKM of group 2 and an adjusted P value.

source_name: heart left ventricle, non-failing

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Illumina TruSeq® RNA Sample Preparation v2 with the final product size selected between 350 and 650 bp.

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

value: heart left ventricle

tag: heart failure

value: no

tag: disease status

value: non-failing

tag: gender

value: male

tag: age

tag: ethnicity

value: White/Caucasian


title: P01256 Non-failing Left Ventricle

status: Public on Jan 01 2015

type: SRA

country: USA

description:
P01256
PolyA mRNA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: P01207 Non-failing Left Ventricle

description:
P01207
PolyA mRNA

value: female


title: P00333 Idiopathic Dilated CMP Left Ventricle

description:
P00333
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

value: idiopathic dilated CMP


title: Donor1-Control-biological replicate 1

city: Cincinnati

first: Alexander

last: Lange

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Reseach Foundation

data_processing:
Sequences were aligned to the reference genome with TopHat
Sample were independently processed with Cufflinks to generate an initial transcriptome.
Cuffmerge was used to merge the transcriptomes into a single reference and annotate known genes and extend partial transcripts.  This common transcriptome was used in a second pass with Cufflinks to quantify transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tables include raw counts and FPKM values

source_name: Human airway tissue, control lentivirus

growth_protocol: A single cell suspension of passage 2 primary Human Bronchial Epithelial Cells (HBECs) that were transduced with hYAP(S127A) lentivirus or control lentivirus was grown in a 50-50 mixture of ALI medium-Cultrex BME reduced growth factor (RGF) (Trevigen Inc.) and cultures were maintained for 18-20 days.

extract_protocol:
Total RNA was isolated using a RNeasy Micro Kit (Qiagen)
Sequencing library was constructed using the Nextera XT DNA Sample Preparation Kit (Illumina)

tag: etiology

value: Smoker

tag: cell type

value: human bronchiolar epithelial cells


title: EZH1_rep1

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: ChIP DNA

library_source: genomic

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file.

molecule: genomic DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH1 ChIP

growth_protocol: Primary maturing fetal liver erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For ChIP-seq analysis using the Illumina HiSeq 2000, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer's protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC hg18) were retained for downstream data analysis.

value: fetal liver

value: CD34+ HSPC-derived proerythroblasts

tag: chip antibody

value: EZH1 (Homemade #738 by Dr. Vittorio Sartorelli)


title: C02182 Idiopathic Dilated CMP Left Ventricle

description:
C02182
PolyA mRNA


title: EZH1_shNT

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH1_shNT ChIP

value: EZH1_shNT (Homemade #738 by Dr. Vittorio Sartorelli)


title: EZH2_rep2

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH2 ChIP

value: EZH2 (Millipore 07-689)


title: EZH2_rep1

description: ChIP DNA

value: EZH2 (BD Biosciences 612666, lot 77337)


title: P00234 Ischemic Left Ventricle

description:
P00234
PolyA mRNA

source_name: heart left ventricle, ischemic

value: ischemic


title: EZH1_rep2

description: ChIP DNA

value: EZH1 (Abcam ab13665)


title: H3K4me3

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), H3K4me3 ChIP

value: H3K4me3 (Millipore 04-745, lot JBC1513701)


title: EED

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EED ChIP

value: EED (Millipore 17-10034)


title: H3K27me3

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), H3K27me3 ChIP


title: phyB mutant (targets)

city: Jinan

first: Xiao Hui

address: No. 202, Gongyebei Road

country: China

institute: Shandong Academy of Agricultural Sciences

description:
processed data file: Table2_targets.txt
miRNA-Seq and RNA-Seq (RACE)

data_processing:
Sequencing data was analyzed by ACGT101-miR pipeline script version 4.2 (LC Sciences, Houston, TX, USA). Raw reads resulted from sample preparation, with adaptors, low quality, without characteristics of miRNAs were removed. Clean reads were then mapped to rice genome to separate unique reads. Unique reads that has hits in rice mRNA database (http://rapdb.dna.affrc.go.jp/download/irgsp1.html), non-coding RNA sequences database (ftp://ftp.sanger.ac.uk/pub/databases/Rfam/10.1/), repeat-Repbase (http://www.girinst.org/repbase/update/index.html) were excluded from further analysis.
The remaining unique reads with length between 17 nt and 25 nt were used as queries to blast against the miRBase version 20.0 (http://www.mirbase.org/) to identify known miRNAs and novel 5p-/3p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignments. Unique sequences mapping to rice mature miRNAs in hairpin arms were identified as known miRNAs in group 1. The unique sequences mapping to the other arm of known rice precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p-/3p- derived miRNAs. The remaining sequences were mapped to other plant species precursors in miRBase 20.0 by blast search, and the mapped pre-miRNAs were further blasted against the rice genome to determine their genomic locations. Once small RNAs could not find their corresponding pre-miRNAs in miRBase, their flanking genome sequences were folded using MIREAP (http://sourceforge.net/projects/mireap/), and then Mfold program was used to predict their secondary structures.
Differentially expressed miRNAs between WT and phyB were identified by IDEG6 (http://telethon.bio.unipd.it/bioinfo/IDEG6_form). Fisher’s exact test and chi-squared 2 × 2 methods were used for the differential expression analysis, with fold change ≥ 2, and q value ≤ 0.01 as thresholds.
The CleaveLand 3.0 software package and the ACGT101-DEG program (LC Sciences, Houston, TX, USA) were adopted to identify the candidate targets of the known and novel miRNAs. In addition, a target prediction software TargetFinder (http://carringtonlab.org/resources/targetfinder) was also used to identify the potential target genes. A target that could be predicted both from degradome sequencing and TargetFinder analysis were retained as a candidate target. The GO analysis of the candidate target genes of known and novel miRNAs was carried out using AgriGO toolkit (http://bioinfo.cau.edu.cn/agriGO/).
Genome_build: miRbase20.0
Supplementary_files_format_and_content: The .txt files report known and novel miRNAs identified from WT and phyB libraries and targets predicted by targetfinder and validated by degradome sequencing

organism: Oryza sativa

source_name: the fourth leaf

growth_protocol: Seeds of WT rice (Oryza sativa L. cv. Nipponbare) and phyB mutant were surface-sterilized and cultured as previously described [60]. At the four-leaf stage, the fourth leaves were collected and immediately frozen in liquid nitrogen. To minimize biological variance, each sample was the mixture of leaves from four individual plants.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The quantity and purity of total RNAs were quantified by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Small RNA libraries were generated using the Illumina Trueseq Small RNA Sample Preparation kits (Illumina, San Diego, USA) according to the manufacturer’s guide.
Two degradome libraries were constructed using leaves of WT and phyB following the methods described recently [Ma Z, Coruh C, Axtell MJ: Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 2010, 22(4):1090-1103.]

tag: developmental stage

value: four-leaf stage

tag: genotype/variation

value: phyB mutant


title: WT wild type (targets)

tag: cultivar

value: Nipponbare

value: WT


title: EZH2_shNT

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH2_shNT ChIP

value: EZH2_shNT (BD Biosciences 612666, lot 77337)


title: phyB mutant (miRNA)

description:
processed data file: Table1_miRNA.txt
miRNA-Seq and RNA-Seq (RACE)


title: EZH1_shEZH2

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH1_shEZH2 ChIP

value: EZH1_shEZH2 (Homemade #738 by Dr. Vittorio Sartorelli)


title: NFE2

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), NFE2 ChIP

value: NFE2 (Santa Cruz Biotechnology sc-291)


title: H3K27me1

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), H3K27me1 ChIP

value: fetal liver


title: EZH2_shEZH2

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), EZH2_shEZH2 ChIP

value: CD34+ HSPC-derived proerythroblasts

value: EZH2_shEZH2 (BD Biosciences 612666, lot 77337)


title: TAL1

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), TAL1 ChIP

value: TAL1 (Santa Cruz Biotechnology sc-12984)


title: WT wild type (miRNA)


title: SW33K_rep3

city: College Station

first: James

middle: J

last: Cai

state: TX

address: TAMUS 4458

department: Veterinary Integrative Biosciences

institute: Texas A&M University

description: Marine threespine stickleback acclimated in full salinity (33 g/L) for 30 days

data_processing:
Clean reads were aligned by using TopHat v2.0.3,
Genes expression level was estimated by Cufflinks v2.0.2
Genome_build: gasAcu1 (http://genome.ucsc.edu/cgi-bin/hgGateway?db=gasAcu1)
Supplementary_files_format_and_content: Tab delimited txt file that includes FPKM values for all samples.

organism: Gasterosteus aculeatus

growth_protocol: Synthetic sea salt (Instant Ocean) was mixed with aerated well water; tank salinities were monitored with a calibrated light refractometer (Vita Sine) and adjusted daily to within 1 g/L of the desired level. Water temperature was held at 11 ± 0.5°C, oxygen levels at >95% saturation, the photoperiod set to 12h day: 12h night, and all fish were fed daily to satiation with frozen brine shrimp.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All fish were treated in accordance with UC Davis Institutional Animal Care and Use Committee guidelines (protocol #16474).

value: Kidney

tag: Sex

value: adult female


title: SW33K_rep2

source_name: Marine threespine stickleback acclimated in full salinity (33 g/L) for 30 days


title: SW33K_rep1


title: FW33K_rep3

description: Freshwater threespine stickleback acclimated in full salinity (33 g/L) for 30 days


title: FW33K_rep2

source_name: Freshwater threespine stickleback acclimated in full salinity (33 g/L) for 30 days


title: SUZ12

description: ChIP DNA

source_name: Human primary fetal liver proerythroblasts (ProEs), SUZ12 ChIP

value: SUZ12 (Abcam ab12073; Active Motif 39357, lot 29111002)


title: FW33K_rep1


title: FW11K_rep3

description: Freshwater threespine stickleback acclimated in intermediate salinity (11 g/L) for 30 days


title: FW00K_rep3

description: Freshwater threespine stickleback acclimated in zero salinity (0 g/L) for 30 days


title: FW11K_rep1

source_name: Freshwater threespine stickleback acclimated in intermediate salinity (11 g/L) for 30 days


title: FW00K_rep1

source_name: Freshwater threespine stickleback acclimated in zero salinity (0 g/L) for 30 days


title: K716NA

city: Shenzhen

first: Gaille

last: Joo

address: Beishan Industrial Zone, Yantian District

institute: BGI

data_processing:
Adaptor sequences were removed from the raw sequencing data, and potentially erroneous tags that have only single copy and those contain unknown sequences were filtered out.
Tags were mapped to the constructed reference after filtration using SOAP2 allowing no more than one mismatch
Normalized TPM (transcripts per million clean tags) values and fold change (absolute value of log2ratio, cancer versus normal) were calculated using uniquely mapping tags
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include TPM values for each Sample

source_name: renal pelvis

extract_protocol:
Total RNA was extracted from UTUC and normal adjacent tissues using the TRIzol solution (Invitrogen, US) according to the manufacturer’s protocol, RNase-free DNase I was used to eliminate DNA contamination. The integrity RNA was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, US).
RNA libraries were prepared for sequencing using standard Illumina protocols
Digital gene expression tag profiling

value: renal pelvis

value: M

tag: tnm


title: K716CA


title: Bicalutamide, replicate 1

city: Stanford

first: Xun

last: Lan

state: CA

address: 318 Campus Dr. Room S240

department: Genetics

institute: Stanford University

description: ChIP-exo replicate 1

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.

source_name: Bicalutamide, replicate 1

growth_protocol: The androgen-dependent prostate cancer cell line LNCaP was obtained from the American Type Culture Collection, and cultured in the RPMI complete medium.

extract_protocol:
For LNCaP AR ChIP-exo, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-AR antibody.
For AR ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

treatment_protocol: For antagonist responsive experiments, LNCaP cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with Bicalutamide or Enzalutamide 10uM.

tag: cell line

value: LNCaP

tag: cancer

value: Prostate adenocarcinoma

tag: sample type

value: Androgen-sensitive

value: anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: Enzalutamide, replicate 1

description: ChIP-exo replicate 1

source_name: Enzalutamide, replicate 1


title: K507CA

value: F


title: Enzalutamide, replicate 2

description: ChIP-exo replicate 2

source_name: Enzalutamide, replicate 2


title: K331CA


title: K332NA


title: K331NA


title: K441NA


title: K441CA


title: K507NA


title: Bicalutamide, replicate 2

description: ChIP-exo replicate 2

source_name: Bicalutamide, replicate 2


title: K289NA


title: K508CA


title: K282NA


title: K282CA


title: K255NA


title: K332CA


title: FW11K_rep2


title: K255CA


title: K289CA


title: FW00K_rep2


title: K508NA


title: K100CA


title: K100NA


title: Hepatocyte

city: Leuven

first: Marc

last: Jacquemin

address: O&N I Herestraat 49 - bus 913

country: Belgium

institute: KU Leuven

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.6 with default settings
The abundance data was generated with cufflinks v.2.0.2 using the tool cuffcompare.
Genome_build: hg19 (NCBI Homo sapiens build 37.2)
Supplementary_files_format_and_content: the tmap files (output of cufflinks) with abundance measurements.

source_name: hepatocyte

growth_protocol: primary cells

extract_protocol:
To prepare cell extracts, the cells were pelleted by centrifugation and immediately lysed in variable amounts of CelLytic M cell lysis reagent (lysis buffer; Sigma-Aldrich) containing 1x protease inhibitor (Halt Protease inhibitor Single-use Cocktail; Thermo Scientific; Belgium) for 15 minutes on ice followed by 5 minutes centrifugation at 18,000g (13,000 rpm) at 4°C to remove the debris. The lysate was then used for further analysis.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kits v2  RS-122-2001

treatment_protocol: Human LSECs and hepatocytes were purified from normal liver cell suspension discarded during isolation of hepatocytes collected for transplantation. Briefly, liver cells were dispersed with collagenase and hepatocytes were isolated by filtration and low speed centrifugation.18 The cells remaining in the supernatant were collected and cryopreserved. In addition, LSECs at passage 1 were purchased from ScienCell (San Diego, CA) and human umbilical vein endothelial cells (HUVECs-passage 1) and hepatocytes from Promocell (Heidelberg, Germany). CHO cells transduced with an expression vector for FVIII were kindly provided by A. Benhida (University of Leuven, Belgium).19 The study was approved by the University of Louvain Ethics committee.

value: hepatocyte

tag: passages


title: HUVEC

source_name: HUVEC

value: Human umbilical vein endothelial cell


title: malignant prostate tumor 4 (M4) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
RNA-seq process: The RNA-seq data was aligned by RUM. Paired-end reads were mapped to the reference genome build (hg19). The RPKM (Reads Per Kilobase of exon model per Million mapped reads) count was calculated with RseQC. The reads count in exon regions was used to estimate the expression level of the genes. edgeR (empirical analysis of digital gene expression in R) was applied to conduct the differential expression analysis based on the count information. The differentially expressed genes were detected by a cut-off P-value < 0.01 between DHT treated and control data.
Genome_build: hg19
Supplementary_files_format_and_content: Bowtie alignment files and four column mapped reads information files for ChIP-exo data; edgeR differential expressed gene files for RNA-seq data.

source_name: Prostate cancer patient b

extract_protocol:
For LNCaP AR ChIP-exo, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-AR antibody. For tissue AR ChIP-exo, the frozen samples were trimmed and chopped into small pieces on ice, and then fixed immediately in 1% formaldehyde for 20 min at room temperature. After additional incubation with glycine for 10 min, the pellets were washed and homogenized in 1x PBS containing proteinase inhibitor. With sufficient lysis, the samples were then processed according to ChIP-exo procedures. For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, total RNA was mixed with the Ribo-Zero rRNA removal reagents (Epicentre Biotechnologies, Madison, WI) to remove all sizes of rRNA. After two rounds of removal processes, the rRNA-depleted RNA was recovered for library generation.
For AR ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, the ScriptSeq library preparation was performed with ScripSeq RNA-Seq Library Preparation kit following the manufacturer’s instructions. The di-tagged cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for pair-end using Illumina HiSeq 2000 at the OSUCCC sequencing core.

treatment_protocol: For hormone responsive experiments, LNCaP cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with 10 nM DHT.

tag: tisssue

value: malignant prostate tumors


title: malignant prostate tumor 4 (M4) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2


title: malignant prostate tumor 3 (M3) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2

source_name: Prostate cancer patient a


title: malignant prostate tumor 2 (M2) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2

source_name: Prostate cancer patient d


title: LNCaP DHT treated [RNA-seq replicate 2 ]

description:
LNCaP_RNAseq_edgeR_DHT_upRegulated_pvalue_0.01.xls
RNA-seq replicate 2 read1 and 2

source_name: LNCaP cells

tag: agent

value: 10 nm DHT

tag: type


title: non-malignant adjacent tissue 2 (N2) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2

value: non-malignant adjacent tissues


title: malignant prostate tumor 2 (M2) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2


title: non-malignant adjacent tissue 2 (N2) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2


title: non-malignant adjacent tissue 1 (N1) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2


title: LNCaP control [RNA-seq replicate 2 ]

description:
LNCaP_RNAseq_edgeR_DHT_downRegulated_pvalue_0.01.xls
RNA-seq replicate 2 read1 and 2

value: vehicle, control


title: malignant prostate tumor 1 (M1) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2

source_name: Prostate cancer patient c


title: malignant prostate tumor 1 (M1) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2


title: LNCaP DHT treated [RNA-seq replicate 1 ]


title: LNCaP DHT treated [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2


title: LNCaP DHT treated [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2


title: non-malignant adjacent tissue 1 (N1) [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2


title: LNCaP control [RNA-seq replicate 1 ]


title: LNCaP DHT treated FoxA1

description: ChIP-exo

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contains mapped reads information.

extract_protocol:
After treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-FoxA1 antibody.
T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

value: anti-FoxA1 from Santa Cruz Biotechnology (Santa Cruz, CA)


title: LNCaP control [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2


title: H3K9me3_ChIP_prg1_0414

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: ~ 200 bp

data_processing:
Demultiplexing based on the inline barcode and index assignment. Remove 3' linker sequence for small RNA-seq and pre-mRNA-seq libraries. For small RNA-seq, mRNA-seq and pre-mRNA-seq, identical reads in each library were collapsed and counted as one read.
ChIP-seq reads were aligned to the C. elegans genome (version WS190/ce6) using Bowtie (version 0.12.7) with a command "bowtie C_elegans_genome -q -t -v 0 -a --strata --best -p 2 -5 3 -3 8 fastqFile bowtieOutput".  RNA-seq reads were simliarly aligned to the C. elegans genome after collapsing identical reads in each library.
1kb-coverage values were calculated by counting the number of sequenced reads aligned to each 1kb window in the C. elegans genome. The numbers were then normalized by sequencing depth (in millions). A segment of 12-kb sequence at the end of chromosome I encodes C. elegans ribosomal RNAs. The actual copy numbers of the rRNA genes are larger than the copy numbers indicated by the annotated genome. This region was excluded for this analysis.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: Sample 1-10, 20, and 21: matrix listing the whole-genome ChIP-seq coverage at 1-kb resolution. Column 1: chromosome; column 2: start position of the 1kb segment (zero-based) column 3 and subsequent columnes: RPKM values for different samples. Sample IDs were indicated in the first row.
Supplementary_files_format_and_content: Sample 11- 19: fasta files for RNA-seq reads with identical reads in each library collapsed to one read. The number of identical reads for each sequence was indicated as the last number in the sequence name. The inline barcodes in the 5' ends and the 3' linker sequence were removed.

organism: Caenorhabditis elegans

source_name: whole adult animals

growth_protocol: Synchronized populations of C. elegans (wild type strain N2 or mutant strains ) were cultured on NGM plates at 19°C with E.coli OP50 as food (Brenner, 1974).

extract_protocol:
ChIP-seq experiments (sample 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21): 100-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment,  2 μg of anti-H3K9me3 (ab8898, Abcam), anti-Pol II-8WG16 (ab817, Abcam), anti-Pol II-S2 (ab5095, Abcam), or anti-Pol II-S5 (ab5131, Abcam) antibody was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg /ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate were treated similarly to reverse crosslink) and then subject to organic extraction and DNA precipitation.
small RNA-seq experiments (sample 18 and 19):  Small RNA was extracted from frozen synchronized adult worm pellets (100-200 μl) using mirVana miRNA isolation kit (Life technologies).
pre-mRNA-seq experiments (sample 11 and 12): Worm grinds were resuspended in 1ml of pre-chilled RIPA buffer (1xPBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To cross-link, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4 °C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate were spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode],  output level: high, interval: 0.5, three times of 8-minute sonication).  For each immumoprecipiation experiment,  2 μg anti-Pol II-S2 (ab5095, Abcam) antibody was added to 400 μl of the lysate (approximately 50 μg DNA). The IP mix was rotated overnight at 4 °C .  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse corss-links, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg /ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate were treated similarly to reverse cross-link samples) and then subject to phenol/Chloroform extraction, RNA/DNA precipitation, DNase I treatment, phenol/Chloroform extraction, and RNA precipitation. RNA was then fragmentated using Fragmentation Reagents (Ambion).
mRNA-seq experiments (sample 13, 14, 15, 16, and 17): Total RNA was extracted from frozen synchronized adult worm pellets (100-200 μl) using Trizol (Life Technologies). mRNA was selected from total RNA using Poly(A)Purist MAG kit (Life Technologies). mRNA was then fragmentated using Fragmentation Reagents (Ambion). 0.5-1 μg of mRNA was used for each mRNA-seq library.
ChIP-seq (sample 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21): Same as described in Gu SG et. al. 2012 (PMID: 22231482).
pre-mRNA-seq (sample 11 and  12):  The fragmented RNA was treated with T4 polynucleotide kinase (New England Biolabs).  The 3’ end of RNA was ligated to an adenylated DNA oligo  (IDT linker-1: 5’-rAppCTGTAGGCACCATCAATC-3’) using T4 RNA ligase 1 (New England Biolabs) without ATP. ~15-35 nt RNA captured by the 3’ linker oligo was purified using 8 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by a 5’ end ligation reaction using a DNA-RNA hybrid oligo (5’-ACGCTCTTCCGATCTrNrNrNrN-3’, rNrNrNrN as 4-nt barcode) using T4 RNA ligase 1 (New England Biolabs) with ATP.  cDNA was synthesized by using SuperScript III Reverse transcriptase (Life Technologies) and primer SG460 (5‘-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’), followed by  PCR amplification with primers SG-465 (5‘-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and SG-46X (5’-CAAGCAGAAGACGGCATACGAGAT[6-nt index]GTGACTGGAGTTCAGACGTGTGCTCTTCC-3’). To ensure that amplified DNA are still annealed to a true complement and avoid reannealing-distortion in the resulting libraries ( referenceParameswaran et al., 2007), PCR reactions were titrated with increasing cycle numbers; cycle numbers for which product levels have not saturated (i.e. product levels still able to increase substantially with additional cycles) were selected. After separating PCR products on 3 % agarose gels, DNA bands of the expected size were extracted (QIAchange® Gel Extraction Kit [Invitrogen]; omitting the 50°C heating step), followed by massive parallel DNA sequencing (Illumina HiSeq2000).
small RNA-seq (sample 18 and 19): Same as described in Gu SG et. al. 2012 (PMID: 22231482).
mRNA-seq (sample 13, 14, 15, 16, 17): 0.5-1 μg fragmented oligo(dT)-selected mRNA was used to construct each mRNA-seq library. The fragmented RNA was treated with T4 polynucleotide kinase (New England Biolabs).  The 3’ end of RNA was ligated to an adenylated DNA oligo  (IDT linker-1: 5’-rAppCTGTAGGCACCATCAATC-3’) using T4 RNA ligase 1 (New England Biolabs) without ATP. ~35-60 nt RNA captured by the 3’ linker oligo was purified using 8 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by a 5’ end ligation reaction using a DNA-RNA hybrid oligo (5’-ACGCTCTTCCGATCTrNrNrNrN-3’, rNrNrNrN as 4-nt barcode) using T4 RNA ligase 1 (New England Biolabs) with ATP.  cDNA was synthesized by using SuperScript III Reverse transcriptase (Life Technologies) and primer SG460 (5‘-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’), followed by  PCR amplification with primers SG-465 (5‘-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and SG-46X (5’-CAAGCAGAAGACGGCATACGAGAT[6-nt index]GTGACTGGAGTTCAGACGTGTGCTCTTCC-3’). To ensure that amplified DNA are still annealed to a true complement and avoid reannealing-distortion in the resulting libraries ( referenceParameswaran et al., 2007), PCR reactions were titrated with increasing cycle numbers; cycle numbers for which product levels have not saturated (i.e. product levels still able to increase substantially with additional cycles) were selected. After separating PCR products on 3 % agarose gels, DNA bands of the expected size were extracted (QIAchange® Gel Extraction Kit [Invitrogen]; omitting the 50°C heating step), followed by massive parallel DNA sequencing (Illumina HiSeq2000).
ChIP-seq for sample 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21.
small RNA-seq (5' monophosphate-independent) for sample 11,12,18 and 19.
mRNA-seq for sample 13, 14, 15, 16,

treatment_protocol: Fore all samples, young adult worms were flash frozen and ground to fine powder in liquid nitrogen using mortar and pestle.

tag: genotype

tag: antibody

value: anti-Pol II H3K9me3 antibody (ab8898, Abcam)

value: young adult

tag: barcode

value: TAG


title: sRNA_hrde1

description:
small RNA
~15-35 nt

value: CTGG

tag: linker

value: CTGTAGGCACCATCAATC


title: PolII_S2_ChIP_prg1_0414

description: ~ 200 bp

value: anti-Pol II S2 antibody (ab5095, Abcam)

value: GCT


title: LNCaP control [ChIP-exo replicate 1 ]

description: ChIP-exo replicate 1 read1 and 2

value: LNCaP

tag: tissue

value: Prostate adenocarcinoma

value: Androgen-sensitive

tag: chip antibody


title: mRNA_nrde4

description:
oligo-dT-selected mRNA
~35-60 nt

tag: developmental stage


title: LNCaP control FoxA1

description: ChIP-exo


title: malignant prostate tumor 3 (M3) [ChIP-exo replicate 2 ]

description: ChIP-exo replicate 2 read1 and 2

value: anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: mRNA_hrde1

description:
oligo-dT-selected mRNA
~35-60 nt

value: TATG, TCGC


title: mRNA_nrde2

description:
oligo-dT-selected mRNA
~35-60 nt

value: CGTC


title: pre_mRNA_hrde1

description:
Pol II (S2) co-IP RNA
~15-35 nt

value: ACTT


title: mRNA_WT

description:
oligo-dT-selected mRNA
~35-60 nt

value: wild type (N2)

value: GGGT, GTTA


title: pre_mRNA_WT

description:
Pol II (S2) co-IP RNA
~15-35 nt

value: GGGT


title: sRNA_WT

description:
small RNA
~15-35 nt


title: H3K9me3_ChIP_hrde1

description: ~ 200 bp

value: anti-Pol II H3K9me3 antibody (ab8898, Abcam)


title: PolII_8wg16_ChIP_hrde1

description: ~ 200 bp

value: anti-Pol II 8WG16 antibody (ab817, Abcam)

value: young adult


title: PolII_S5_ChIP_hrde1

description: ~ 200 bp

value: anti-Pol II S5 antibody (ab5131, Abcam)


title: PolII_S2_ChIP_hrde1

description: ~ 200 bp

value: CTA


title: mRNA_nrde3

description:
oligo-dT-selected mRNA
~35-60 nt

value: GTTA

value: CTGTAGGCACCATCAATC


title: PolII_S5_ChIP_WT

description: ~ 200 bp


title: PolII_S2_ChIP_WT

description: ~ 200 bp

value: anti-Pol II S2 antibody (ab5095, Abcam)


title: ChIP_input_hrde1

description: ~ 200 bp

value: GCT


title: ChIP_input_WT

description: ~ 200 bp


title: PolII_8wg16_ChIP_WT

description: ~ 200 bp

value: AGC


title: SSv2_mECx_rep2_SR_RUN

city: Ann Arbor

first: Saurabh

last: Agarwal

state: Michigan

address: 1241 E. Catherine St. 5815 Medical Science II

department: Human Genetics

institute: University of Michigan

data_processing:
Bad quality reads and adaptor sequences were filtered out.
Mapped to mm9 build using TOPHAT v2.0.9
Either the coverage by the whole read (read1 or read2) or the first base of read1 (Read_Start) is calculated. Data is shown in a strand-specific manner on either the positive or negative strand of the genome.
Wig files were normalized to 10 million non-rRNA reads and converted to bigwig using wigtobigwig utility
Genome_build: mm9
Supplementary_files_format_and_content: bigwig format

organism: Mus musculus

source_name: E16.5 mouse embryonic cortex

growth_protocol: mES cells were grown on gelatined plates in DMEM (high glucose) with 15% FBS, 1X NEAA, 1X Glutamax, 0.1mM beta-mercaptoethanol, 1X Penicillin/Streptomycin and 1000U/ml LIF. E16.5 pregnant female mouse was dissected and the cortices from embryos were isolated and homogenized in Trizol.

extract_protocol:
Cells or Tissues were harvested in Trizol. After phase separation, RNA was purified using Qiagen RNeasy Kit.
ScriptSeq v2

tag: growth

value: embryo


title: miRNA_small_RNA_WT_mES_read1_no_barcode

source_name: mouse embryonic stem cells

extract_protocol:
Cells or Tissues were harvested in Trizol. After phase separation, RNA was purified using Qiagen RNeasy Kit. Small RNA isolated using Ambion's mirVana kit.
Illumina Small RNA TruSeq kit

value: cultured in vitro


title: DLAF_mECx_rep1_SR_RUN

extract_protocol:
Cells or Tissues were harvested in Trizol. After phase separation, RNA was purified using Qiagen RNeasy Kit.
DLAF


title: SSv2_mECx_rep3_SR_RUN


title: DLAF_mECx_Klenow_low_rep1_SR_RUN

extract_protocol:
Cells or Tissues were harvested in Trizol. After phase separation, RNA was purified using Qiagen RNeasy Kit.
DLAF+Klenow


title: DLAF_mECx_Klenow_high_rep2_SR_RUN


title: dUTP_KDM1A_KD_mES_03_rep2_PE_RUN

description: Reads OK but read1 not analyzed

extract_protocol:
Cells or Tissues were harvested in Trizol. After phase separation, RNA was purified using Qiagen RNeasy Kit.
dUTP


title: DLAF_mECx_Klenow_high_rep1_SR_RUN


title: DLAF_mECx_Klenow_low_rep2_SR_RUN


title: DLAF_mECx_rep3_SR_RUN


title: DLAF_KDM1A_KD_mES_03_rep2_PE_RUN_small

description: Reads OK but not analyzed due to low #


title: dUTP_KDM1A_KD_mES_03_rep1_PE_RUN

description: Reads OK but read1 not analyzed


title: H3K9me3_ChIP_WT

description: ~ 200 bp


title: DLAF_KDM1A_KD_mES_03_rep1_PE_RUN

description: 'read1' file could not be analyzed due to a technical difficulty (3rd base had a lower read quality)


title: dUTP_KDM1A_KD_mES_03_rep2_SR_RUN


title: DLAF_KDM1A_KD_mES_03_rep1_SR_RUN


title: DLAF_KDM1A_KD_mES_03_rep2_PE_RUN


title: DLAF_KDM1A_KD_mES_03_rep2_SR_RUN


title: dUTP_KDM1A_KD_mES_03_rep1_SR_RUN


title: dUTP_WT_mES_17_rep2_PE_RUN

description: Reads OK but read1 not analyzed


title: dUTP_WT_mES_17_rep2_SR_RUN


title: SSv2_mECx_rep1_SR_RUN


title: DLAF_mECx_rep2_SR_RUN


title: dUTP_WT_mES_17_rep1_PE_RUN

description: Reads OK but read1 not analyzed


title: DLAF_WT_mES_17_rep2_PE_RUN_small

description: Reads OK but not analyzed due to low #


title: dUTP_WT_mES_17_rep1_SR_RUN


title: DLAF_WT_mES_17_rep1_PE_RUN_small

description: Reads OK but not analyzed due to low #


title: DLAF_WT_mES_17_rep2_SR_RUN


title: DLAF_WT_mCN_rep1_SR_RUN

value: 10 Days in vitro


title: DLAF_WT_mES_17_rep1_PE_RUN


title: SclKO-iScl_ES_Scl_INP

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

data_processing:
Debarcoding of the multiplex runs was performed using Unix shell scripts.
Tags were mapped to the mouse genome (mm9) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks
Scl peaks were mapped to nearby genes within 200kb range from TSS using Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010). Peak intersections and overlaps with differentially expressed genes were performed using Galaxy (Blankenberg et al., 2010) and in house Ubix shell scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks

source_name: ES cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain SclKO-iScl ES cells.

extract_protocol:
Cells were trypsinized, washed with PBS and crosslinked with 1% formaldehyde in PBS for 10 min at RT. After PBS washing, cells were resuspended in 400 μl of lysis buffer (1% SDS, 20 mM EDTA and 50 mM Tris-HCl (pH 8.0)) containing protease inhibitors (Roche, Indianapolis, IN), incubated for 10 min on ice and sonicated using Misonix cup-horn sonicator to achieve, on average, 200bp fragments. The lysate was diluted 10 times with ChIP dilution buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 16.7 mM Tris-HCl (pH 8.1) and immunoprecipitatied with 4 ug of corresponding  antibody overnight at 4 degrees. 20 μl of the lysates were used as input. The complexes were captured using protein A Dynabeads (Invitrogen, Grand Island, NY) and washed twice with the following buffers: low-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1); high-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl); LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE (10 mM Tris-HCl and 1 mM EDTA (pH 8.0)). After elution with 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 1% SDS, crosslinks were reversed by overnight incubation at 65°C. Samples were then treated with RNase A for 30 min at 37°C and proteinase K for 2 h at 56°C. DNA was subsequently purified using Qiagen MinElute Columns according to manufacturers instructions. DNA concentration was measured using a Qubit (Invitrogen, Grand Island, NY).
The library for sequencing was constructed using Ovation Ultralow DR Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: ES cells were treated 48h with 1ug/ml doxycycline. ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days. At day 2 of EB culture the cells were treated for 48h with 1ug/ml doxycycline.

tag: cell type

value: ES cells

tag: cell-line

value: SclKO-iScl mESC

tag: treatment

value: 48h 1ug/ml doxycycline


title: DLAF_WT_mES_17_rep1_SR_RUN


title: SclKO-iScl_MES_Scl

value: SclKO-iScl ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

value: EB formation, 48h 1ug/ml doxycycline from day2 of EB formation, enrichment for Flk1+ cells at day 4

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: SclKO-iScl_ES_Scl_rep2


title: MLL preGM rep2

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Data were processed using the standard GTAC RNA-seq analysis pipeline (https://gtac.wustl.edu/services/sequencing/index.php?section=analysis)
Reads were mapped to the mouse genome Ensemble version R72 using Tophat v2.0.8 with Bowtie2 v2.1.0.
Reads within exons were counted using HTSeq
Differentially expressed genes were identified using edgeR using the protocol described in the edgeR vignette
Genome_build: Ensembl R72

source_name: PreGM progenitor cells

growth_protocol: OptiMEM supplemented with 10% FCS in the presence of SCF (10-50 ng/ml), IL3 (5 ng/ml), and G-CSF (5 ng/ml) and 1 microg/ml Doxycycline

extract_protocol:
Rneasy micro kit
SMARTer universal low input RNA kit for sequencing

value: FACS sorted as Lin-Sca1-ckit+CD150-CD105-CD41-CD16/32-

tag: strain

value: Cultured for 48h with Doxycycline


title: WT_MES_Hand1

source_name: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain  ES cells.

treatment_protocol: ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.

value: mESC

value: EB formation, enrichment for Flk1+ cells at day 4

tag: genotype/variation

value: wildtype

tag: chip antibody cat.#

tag: chip antibody lot


title: MLL preGM rep3


title: SclKO-iScl_ES_Scl_rep1


title: DLAF_KDM1A_KD_mES_03_rep1_PE_RUN_small

description: Reads OK but not analyzed due to low #


title: WT preGM rep3

value: C57bl/6 WT


title: MLL HSC rep2

source_name: Hematopoietic stem cells

value: FACS sorted as Lin-Sca1+ckit+CD48-CD150+


title: WT HSC rep3


title: MLL HSC rep1


title: WT HSC rep1


title: WT HSC rep2


title: DLAF_WT_mES_17_rep2_PE_RUN


title: Col4a3 KO AntimiR-21 rep4

city: San Diego

first: Vivek

last: Kaimal

address: 10614 Science Center Dr.

department: Bioinformatics

institute: Regulus Therapeutics

description: treated with antimiR-21

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), a quality control tool for high throughput sequence data, was used for checking q-scores and reads were not trimmed prior to alignments.
The data were aligned against UCSC mouse genome version mm10 using STAR aligner (Dobin, A. et al., Bioinformatics, 2013).
From BAM files, gene-level counts of uniquely mapped reads were computed using SAMTools (Li H. et al, Bioinformatics, 2009) and HTSeq v0.5.4p5 (Anders S. et al, bioRxiv preprint, 2014).
Gene level counts were then normalized with the R/Bioconductor package limma (Smyth, G. K., Springer, 2005) using the voom (Law CW, et al. Genome Biology, 2014) /variance stabilization method
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with gene counts for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized Log2 transformed data matrix

source_name: Kidney

extract_protocol:
Total RNA from tissue was extracted as per manufacturer’s instructions (miREASY kit, Qiagen). RNA quality was assessed using BioAnalyzer (Agilent). Illumina’s TruSeq RNA Sample Preparation v2 kit was used to construct libraries. Briefly, 150ng of total RNA input was used. The libraries were quantified using KAPA library quantification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Kidney

tag: age

value: 5.5 weeks


title: Col4a3 KO AntimiR-21 rep2

description: treated with antimiR-21


title: Col4a3 KO AntimiR-21 rep3

description: treated with antimiR-21


title: WT preGM rep1


title: MLL preGM rep1


title: WT preGM rep2


title: Col4a3 KO PBS rep4

description: treated with PBS


title: Col4a3 KO PBS rep3

description: treated with PBS


title: Col4a3 KO AntimiR-21 rep1

description: treated with antimiR-21


title: Col4a3 KO PBS rep1

description: treated with PBS


title: Col4a3 KO PBS rep2

description: treated with PBS


title: Col4a3 HET rep3

description: treated with PBS


title: Col4a3 HET rep2

description: treated with PBS


title: Col4a3 HET rep1

description: treated with PBS


title: Col4a3 KO AntimiR-21 rep3

description: treated with antimiR-21

data_processing:
FastqMcf (https://code.google.com/p/ea-utils/wiki/FastqMcf), a clipping tool was used. Briefly, it scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.
The data were aligned against UCSC mouse genome version mm9 using RSEM (Li, B. and Dewey, CN., BMC Bioinformatics, 2011)/Bowtie (Langmead B. et al., Genome Biology, 2009) tools for alignment and abundance quantificaton.
Gene level counts were then normalized with the R/Bioconductor package limma (Smyth, G. K., Springer, 2005) using the voom (Law CW, et al. Genome Biology, 2014) /variance stabilization method
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with gene counts for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized Log2 transformed data matrix

value: 9 weeks


title: Col4a3 KO AntimiR-21 rep2

description: treated with antimiR-21


title: MLL HSC rep3


title: Col4a3 KO AntimiR-21 rep1

description: treated with antimiR-21


title: WT rep3

description: no treatment

value: wild type


title: Col4a3 KO PBS rep3

description: treated with PBS


title: Col4a3 KO PBS rep2

description: treated with PBS


title: Mst1/2 CKO_pooled

description: pooled RNA from 4 independent mice

data_processing:
Sequences were aligned to the reference genome with TopHat
Sample were independently processed with Cufflinks to generate an initial transcriptome.
Cuffmerge was used to merge the transcriptomes into a single reference and annotate known genes and extend partial transcripts.  This common transcriptome was used in a second pass with Cufflinks to quantify transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tables include raw counts and FPKM values

source_name: pooled Mst1/2 D/D

extract_protocol:
Lin-/CD326+/CD24-intermediate cells were isolated by fluorescence cell sorting to enrich for non-ciliated, secretory airway epithelial cells.  Total RNA from Lin-/CD326+/CD24-intermediate cells of control (n=4) and Mst1/2 D/D (n=4) mice was extraced using a RNeasy Micro kit (Qiagen).  Genotype matched samples were pooled and analyzed by RNA-seq to identify transcriptional changes following deletion of Mst1 and Mst2 from mature lung.
Sequencing library was constructed using the Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: Adult mice were maintained on doxycycline food (625 mg/kg; Harlan Teklad) for 16 days

value: lung

value: adult

tag: cell sorting

value: Lin-/CD326+/CD24-intermediate cells


title: Control_pooled

description: pooled RNA from 4 independent mice

source_name: pooled Control

tag: tissue


title: WT rep2

description: no treatment


title: RNA-seq rep3

city: Parkville

first: Marnie

last: Blewitt

state: VIC

address: 1G Royal Parade

department: Molecular Medicine Division

country: Australia

institute: WEHI

description: RNA-seq

data_processing:
aligned by tophat version 2.0.8 with --b2-very-senisitve (RNA-seq).
RNA-seq was counted over exomes with featureCounts from Rsubread.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values, providing counts over gene body and promoter for the ChIP-seq and WCE data, and counts over exons for RNA-seq data.

source_name: hematopoietic stem and progenitor cell population isolated from the bone marrow of adult mice that had received foetal liver cell transplants

extract_protocol:
The mouse hematopoietic stem and progenitor cell population for ChIP was isolated from E14.5 foetal livers from C57BL/6 mice by fluorescence-activated cell sorting based on the following cell surface marker profile: lineage (Ter119, B220, CD5, CD3, Gr1) negative, c-Kit+ and Sca1+. Similarly, adult bone marrow hematopoietic stem and progenitor cells for RNA-seq were sorted based on lineage (Ter119, B220, CD19, Mac1, Gr1, CD2, CD3, CD8) negative, c-Kit+ and Sca1+ cell surface marker expression. Approximately 250,000 cells were used for each ChIP, whereas 30,000 to 100,000 cells were used to prepare RNA for the RNA-seq.
For chromatin immunoprecipitation, formaldehyde cross-linked cells were sonicated in a Covaris sonicator.  A small fraction of sonicated material was retained as the WCE sample and the remainder was incubated with either an antibody against H3 (AbCam) or H3K27me3 (Millipore) overnight at 4°C. Immune complexes were purified by incubation with protein G beads (Life Technologies) at 4°C for an hour.  Cross-links were reversed by incubation at 65°C for 4 hours before DNA fragments were purified with the ChIP Clean and Concentrator kit (Zymo). Sequencing libraries were prepared using the TruSeq DNA Sample Prep Kit (Illumina) and sequencing was performed on a HiSeq2000 (Illumina).

tag: background strain

tag: cell population

value: hematopoietic stem and progenitor cells


title: RNA-seq rep1

description: RNA-seq


title: H3K27me3 rep2

description: Histone H3K27me3 ChIP-seq

data_processing:
aligned by bowtie2 version 2.2.3 with --very-sensitive-local (ChIP-seq and WCE).
ChIP-seq counts over genes and promoters (defined as -2kbp to +2kp after TSS) were calculated in R.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values, providing counts over gene body and promoter for the ChIP-seq and WCE data, and counts over exons for RNA-seq data.

source_name: hematopoietic stem and progenitor cells from E14.5 foetal liver


title: H3K27me3 rep1

description: Histone H3K27me3 ChIP-seq


title: H3K27me3 rep3

description: Histone H3K27me3 ChIP-seq


title: WCE

description: Whole cell extract


title: H3 rep2

description: Histone H3 ChIP-seq


title: H3 rep1

description: Histone H3 ChIP-seq


title: Hpc7_H3K27ac

source_name: Hematopoietic progenitors

growth_protocol: HPC7 cells were grown in  Iscove´s modified Dulbecco´s media (IMDM) (Gibco), supplemented with NaHCO3, 1.5 x 10-4 M MTG (Sigma),1% of penicillin and streptomycine, 10% of FBS and mouse Stem cell factor (SCF) at 100ng/mL (R&D systems)

extract_protocol:
Cells werewashed with PBS and crosslinked with 1% formaldehyde in PBS for 10 min at RT. After PBS washing, cells were resuspended in 400 μl of lysis buffer (1% SDS, 20 mM EDTA and 50 mM Tris-HCl (pH 8.0)) containing protease inhibitors (Roche, Indianapolis, IN), incubated for 10 min on ice and sonicated using Misonix cup-horn sonicator to achieve, on average, 200bp fragments. The lysate was diluted 10 times with ChIP dilution buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 16.7 mM Tris-HCl (pH 8.1) and immunoprecipitatied with 4 ug of corresponding  antibody overnight at 4 degrees. 20 μl of the lysates were used as input. The complexes were captured using protein A Dynabeads (Invitrogen, Grand Island, NY) and washed twice with the following buffers: low-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1); high-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl); LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE (10 mM Tris-HCl and 1 mM EDTA (pH 8.0)). After elution with 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 1% SDS, crosslinks were reversed by overnight incubation at 65°C. Samples were then treated with RNase A for 30 min at 37°C and proteinase K for 2 h at 56°C. DNA was subsequently purified using Qiagen MinElute Columns according to manufacturers instructions. DNA concentration was measured using a Qubit (Invitrogen, Grand Island, NY).
The library for sequencing was constructed using Ovation Ultralow DR Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: non-treated

tag: cell line

value: Hematopoietic progenitors

value: no treatment

tag: chip antibody

tag: vendor

value: abcam


title: Wild-type control

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

description:
Wild-type control, Animal 1 [Wt1-RPE]
Wild-type control, Animal 2 [Wt2-RPE]
Wild-type control, Animal 3 [Wt3-RPE]

data_processing:
Basecalling and quality scoring on Cassava 1.8.2
Alignment to mouse mm10 genome using Bowtie with settings tophat -p 4 --keep-tmp mm10UCSC *input_file*.fastq; where "mm10USCS" points to Bowtie genome index files
HTseq  summary of counts across genes, python -m HTSeq.scripts.count -s no -m intersection-strict <path to .sam file> <path to genome annotation .gtf file> > <path to output file>
EdgeR - caclulation of differential expression using HTSeq counts merged.txt as input, removing all genes that have less than 1 count in 2 or more sample, and using ExactTest to define differntial expression.
Genome_build: mm10
Supplementary_files_format_and_content: HTseq_counts_merged.txt contains read counts per gene produced by HTseq, where each data column corresponds to a sample. EdgeR genes prefiltered.txt contains output from EdgeR,  and includes fold change between AhR KO and WT, average CPM across all samples, and metrics of statistical testing of differential expression per gene. Both .txt files are flat tab delimited files.

source_name: RPE-choroid tissue, WT

growth_protocol: 11-13 month old mice

extract_protocol:
Eyes were enucleated, anterior segment and retina removed, RPE/choroid was isolated in Trizol and RNA extracted with Qiagen Rneasy mini kit with DNase1 digestion
RPE-choroid from two eyes was pooled and libraries prepared with the Illumina TruSeq kit with polyA enrichment

treatment_protocol: No treatment

value: AhR +/+

value: retinal pigment epithelium (RPE)-choroid

value: 11-13 months


title: AhR knockout

description:
AhR knockout, Animal 1 [AhR4-RPE]
AhR knockout, Animal 2 [AhR5-RPE]
AhR knockout, Animal 3 [AhR6-RPE]

source_name: RPE-choroid tissue, AhR KO

value: AhR -/-


title: Col4a3 KO PBS rep1

description: treated with PBS


title: WT rep1

description: no treatment


title: ESC_RRBS

data_processing:
Debarcoding of the multiplex runs was performed using in house shell script
RRBS data was aligned with bs-seeker2 (Guo et al., 2013).
Differentially methylated cytosines were calculated with methyl-kit (Akalin et al., 2012).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: WT mES cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain WT and SclKO (Porcher et al., 1996) ES cells. MEL cells were grown in RPMI 1640 with L-Glutamine plus10% of FBS,1% of penicillin and streptomycine.

extract_protocol:
Genomic DNA was extracted using Allprep DNA/RNA Mini Kit (Quiagen) and quanitated with QUBIT (Life technology). RRBS libraries were generated starting from 240-450 ng of genomic DNA as previously described (Meissner et al., 2005) with minor modifications. Briefly, MspI- generated fragments were end-repaired and adenylated before ligation with Illumina TruSeq adapters. DNA purifications of each enzymatic reaction as well as size-selection of adapter-ligated fragments ranging from 200-350bp were carried out using AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed twice with EpiTect kit (QIAGEN) in order to optimize the efficiency. Bisulfite-converted libraries were amplified using MyTaq Mix (Bioline) with the following program: 98°C for 2min, (98°C for 15sec, 60°C for 30sec, 72°C for 30sec) 12 cycles, 72°C for 5 min, 4°C indefinitely.
The library for sequencing was constructed using Ovation Ultralow DR Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

tag: cell-line

value: WT J1 mESC

tag: cell type

value: WT mES cells


title: WT_MES_RRBS

treatment_protocol:
EB formation, enrichment for Flk1+ cells at day 4
ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.

value: WT ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells


title: Sample 16

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-30nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

tag: developmental stage

value: Embryo

tag: sample type

value: progeny of unc-22 RNAi animals


title: SclKO_MES_INP_Lsd1

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain WT and Gata1&2KO ES cells. MEL cells were grown in RPMI 1640 with L-Glutamine plus10% of FBS,1% of penicillin and streptomycine. HL1 cells were grown in Claycomb Medium with L-Glutamine plus 10% of FBS,1% of penicillin and streptomycine and 0.1mM Norephinephrine.

treatment_protocol:
EB formation, enrichment for Flk1+ cells at day 4
ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.
ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.

value: SclKO J1 mESC

value: SclKO ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells


title: HL1_H3K27ac

source_name: Cardiomyocytes

treatment_protocol:
none
ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.

value: Cardiomyocytes

tag: chip antibody vendor

tag: chip antibody cat. #

value: Abcam

tag: chip antibody lot #


title: SclKO_MES_Lsd1


title: Gata12KO_MES_Scl_rep2

value: Gata1&2KO J1 mESC

value: Gata12KO ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells


title: RNA-seq rep2

description: RNA-seq

value: hematopoietic stem and progenitor cells


title: Gata12KO_MES_H3K27ac


title: HL1_INP


title: WT_MES_Lsd1


title: MEL_RRBS

source_name: Mouse erythroleukemic cells

value: MEL

value: Mouse erythroleukemic cells


title: Gata12KO_MES_H3K4me1


title: SclKO_MES_RRBS


title: Sample 14

description: 5' polyphosphatase treated

value: progeny of dpy-11 RNAI animals


title: Sample 13

description: 5' polyphosphatase treated

value: Adult

value: Progeny of unc-22 RNAi animals


title: HL1_H3K4me1


title: WT_MES_Ezh2

value: WT J1 mESC

value: Active Motif


title: WT_MES_INP

value: WT ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells


title: SclKO_MES_INP


title: Sample 10

description: 5' polyphosphatase treated

value: Progeny of dpy-11 RNAi animals


title: Sample 9

description: 5' polyphosphatase treated

value: Progeny of Orsay infected animals


title: SclKO_MES_H3K27ac

value: SclKO J1 mESC


title: Sample 8

description: 5' polyphosphatase treated

value: unc-22 RNAi


title: WT_MES_H3K27ac


title: SclKO_MES_H3K4me1

value: SclKO ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells


title: WT_MES_INP_Lsd1


title: Sample 15

description: 5' polyphosphatase treated

value: Embryo


title: Sample 6

description: 5' polyphosphatase treated

value: Orsay virus infection


title: Sample 7

description: 5' polyphosphatase treated

value: dpy-11 RNAi


title: E1-4_degradome_seq

city: Wuhan

first: Xiaomeng

last: Wu

state: Hubei

address: Shizishan No.1

department: College of Horticulture & Forestry Sciences

institute: HuaZhong Agricultural University

description: PolyA RNA

data_processing:
For sequencing data of sRNA and degradome, low-quality tags were first filtered, leaving the remanent high-quality tags with no more than four positions with quality score lower than ten and no more than six positions with quality score lower than 13 between the 1st and the 30th nucleotide. Contaminants were further eliminated, including 5’ or 3’ adaptors, tags with no inserted sequence, tags with polyA sequence, tags shorter than 18 nt. Clean sRNA reads were finally obtained after the adaptors having been trimmed.  For degradome sequencing result, the same procedure was used to filter out the contaminants. After ncRNAs and polyN sequences (polyA/T/C/G) eliminated, the reminant clean reads were regarded as clean degradome reads.
sRNAs perfectly matched to Rfam10.0 (http://rfam.sanger.ac.uk/) were identified as non-coding RNAs (ncRNA)
Raw count of the read was normalized into standardized (STD) count RPM (reads per million) by the equation STD = (raw count/total count)*1,000,000
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each read

organism: Citrus sinensis

source_name: mixed embryogenic callus exposed to  somatic embryo induction for 1, 2, 3, 4 weeks

growth_protocol: Nonembryogenic callus of Valencia sweet orange (Citrus sinensis L. Osb.) was newly induced from epicotyl segment and cultured in darkness on MT medium supplemented with 1.5 mg/L 2, 4- ichlorophenoxyacetic acid (2, 4-D), 1 mg/L 1-naphthaleneacetic acid (NAA), 0.15 mg/L kinetin, 1 mg/L zeatin and 5% sucrose, as depicted by Deng, PhD dissertation of Huazhong Agricultural University, 1987. Nonembryogenic callus preservation medium was similar to the induction medium except that 2, 4-D and sucrose concentration were 1 mg/L and 4% respectively. Embryogenic callus of Valencia sweet orange was induced from immature ovule 28 years ago and preserved on MT medium (Murashige and Tucke,In: Chapman HD (ed) Proceedings of the international citrus symposium, Riverside, California, 1969).

extract_protocol:
Total RNA was extracted from citrus callus using Trizol reagent, with a improved protocal from Liu et al., J Huazhong Agric Univ, 2006.
For each sample, small RNA of 16-28 nt in length was fractionated from total RNA, before adaptors were ligated to the 5' and 3' end. RT-PCR product of the ligated RNA was sequenced on Illumina sequencing platform (Lu et al.,Science, 2005). For degradome library construction, messenger RNA (mRNA) with polyA tail was enriched from total RNA, before adaptors were ligated to the 5’ end of the uncapped mRNA. RT-PCR product of the ligated mRNA was sliced by the restriction endonuclease MmeI, producing short tags with the uncapped end, which was sequenced on Illumina sequencing platform (German et al., Nat. Biotech., 2008).

treatment_protocol: EC was moved from MT growth medium with 4% sucrose as to MT medium with 2% glycerol  to induce somatic embryo

value: mixed embryogenic callus

tag: treatment


title: Sample 12

description: 5' polyphosphatase treated

tag: genotype


title: SclKO_MES_Ezh2


title: EC_degradome_seq

description: PolyA RNA

source_name: embryogenic callus

value: embryogenic callus


title: EC_sRNAseq

description: Low Molecular Weight RNA


title: NEC_degradome_seq

description: PolyA RNA

source_name: nonembryogenic callus

value: nonembryogenic callus


title: NEC_sRNAseq

description: Low Molecular Weight RNA


title: E1-4_sRNAseq

description: Low Molecular Weight RNA

value: exposed to  somatic embryo induction for 1, 2, 3, 4 weeks


title: Quiescence; exp. #2

city: Montpellier Cedex 5

first: Laurent

last: Journot

address: 141 rue de la cardonille

department: Institut de Genomique Fonctionnelle

country: France

institute: Centre National de la Recherche Scientifique

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 1.4.8) and Real-Time Analysis component (RTA 1.12.4.0).
Reads were mapped to the full mm9 mouse reference genome using the eland_rna module of CASAVA 1.8.2 (Illumina).
Counting was performed with CASAVA's variant detection and counting module. UCSC annotation file (refFlat.txt.gz; 2012-01-15) was used to retrieve annotations on genes and exons. GeneIDs are from the NCBI (gene2refseq.gz; 2012-01-19).
Counts were normalized using the Relative Log Expression (RLE) method as implemented in edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Text file with 5 columns for gene description. The next columns correspond to the normalized abundance measurements (RLE normalization using edgeR statistical package) for each sample

source_name: 3T3-L1 cell line

growth_protocol: 3T3-L1 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C. The medium was renewed every 2 days.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer's instructions.
RNA-Seq libraries were prepared the 'TruSeq RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.
Unstranded RNA-Seq libraries were sequenced using the 'Single Read 100 nt' mode on a HiSeq2000 sequencer.

treatment_protocol: To induce adipogenic differentiation, cells were treated with 5 µg/µl insulin, 1 µM dexamethasone, and 0.25 mM isobutylmethylxanthine for 48 hours. Cells were subsequently treated with  5 µg/µl insulin.

tag: strain

value: Swiss albino

tag: culture stage

value: 48 hours confluence


title: Differentiation; exp. #2

value: 6 days after IDX addition


title: Sample 11

description: 5' polyphosphatase treated

value: Progeny of unc-22 RNAi animals


title: Differentiation; exp. #1


title: Clonal expansion; exp. #2

value: 10 hours after IDX addition


title: Clonal expansion; exp. #1


title: R14

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

description: Sample 4

data_processing:
The original image data was transferred into sequence data by base calling (using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
A comparison of “clean reads” by SOAPaligner/soap2 (parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling
Genome_build: Reference_assembled_isotig_seq.fna downloaded from PMID:22428017 (also available on Series records)
Supplementary_files_format_and_content: text file containing RPKM values

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
Total RNA from regenerative (from animals at 3 dpe, 7 dpe, 14 dpe, 21 dpe) and normal intestines was extracted and DNase-treated using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Germany), following the manufacturer’ s instructions.
The quality and concentration of RNA were measured by NanoDrop 1000 (Thermo) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

tag: tissue

value: intestine at 14dpe


title: Quiescence; exp. #1


title: Proliferation; exp. #2

value: exponential proliferation


title: WT_MES_H3K4me1

value: WT J1 mESC

value: WT ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

value: Abcam


title: Proliferation; exp. #1


title: R3

description: Sample 2

value: intestine at 3dpe


title: R7

description: Sample 3

value: intestine at 7dpe


title: WT_d475EB

data_processing:
Debarcoding of the multiplex runs was performed using in house shell script
Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.
The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate FPKM values. Assemblies  were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value less than 0.01 where considered as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and Excel table wiith differential expression analysis results

source_name: WT mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain SclhCD4 knock-in (Chung et al., 2002), SclKO (Porcher et al., 1996), WT, Gata2KO and Gata1&2KO ES cells. MEL cells were grown in RPMI 1640 with L-Glutamine plus10% of FBS,1% of penicillin and streptomycine. HPC7 cells were grown in  Iscove´s modified Dulbecco´s media (IMDM) (Gibco), supplemented with NaHCO3, 1.5 x 10-4 M MTG (Sigma),1% of penicillin and streptomycine, 10% of FBS and mouse Stem cell factor (SCF) at 100ng/mL (R&D systems)

extract_protocol:
Cells were digested by collagenase-dispase treatment, stained with CD31, Tie2 and CD41 antibodies and FACS sorted for Tie2+CD31+CD41- endothelial cell population.
The library for sequencing was constructed using Encore Complete RNA-Seq DR Multiplex System 1-8 (Nugen). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: ES cells were differentiated into endothelial cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4.75 days.

value: endothelial cells

tag: genotype/variation

value: Wild type

value: EB formation, FACS sorting for Tie2+CD31+CD41- endothelial cells at day 4.75


title: Gata12KO_d475EB

source_name: Gata1&2KO mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells


title: R0

description: Sample 1

value: normal intestine


title: SclKO_d475EB

source_name: SclKO mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

value: SclKO


title: R21

description: Sample 5

value: intestine at 21dpe


title: Hpc7_H3K4me1

data_processing:
Debarcoding of the multiplex runs was performed using Fastx toolkit or Unix shell scripts.
Tags were mapped to the mouse genome (mm9) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks
Scl peaks were mapped to nearby genes within 200kb range from TSS using Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010). Peak intersections and overlaps with differentially expressed genes were performed using Galaxy (Blankenberg et al., 2010) and in house Ubix shell scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain WT and Gata1&2KO ES cells. MEL cells were grown in RPMI 1640 with L-Glutamine plus10% of FBS,1% of penicillin and streptomycine. HPC7 cells were grown in  Iscove´s modified Dulbecco´s media (IMDM) (Gibco), supplemented with NaHCO3, 1.5 x 10-4 M MTG (Sigma),1% of penicillin and streptomycine, 10% of FBS and mouse Stem cell factor (SCF) at 100ng/mL (R&D systems).

extract_protocol:
Cells were trypsinized, washed with PBS and crosslinked with 1% formaldehyde in PBS for 10 min at RT. After PBS washing, cells were resuspended in 400 μl of lysis buffer (1% SDS, 20 mM EDTA and 50 mM Tris-HCl (pH 8.0)) containing protease inhibitors (Roche, Indianapolis, IN), incubated for 10 min on ice and sonicated using Misonix cup-horn sonicator to achieve, on average, 200bp fragments for ChIP-seq and 500bp fragments for ChIP-PCR. The lysate was diluted 10 times with ChIP dilution buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 16.7 mM Tris-HCl (pH 8.1) and immunoprecipitatied with 4 ug of corresponding antibody overnight at 4 degrees. 20 μl of the lysates were used as input. The complexes were captured using protein A Dynabeads (Invitrogen, Grand Island, NY) and washed twice with the following buffers: low-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1); high-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl); LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE (10 mM Tris-HCl and 1 mM EDTA (pH 8.0)). After elution with 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 1% SDS, crosslinks were reversed by overnight incubation at 65°C. Samples were then treated with RNase A for 30 min at 37°C and proteinase K for 2 h at 56°C. DNA was subsequently purified using Qiagen MinElute Columns according to manufacturers instructions. DNA concentration was measured using a Qubit (Invitrogen, Grand Island, NY).
The library for sequencing was constructed using Ovation Ultralow IL Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

value: Hematopoietic progenitors

value: no treatment


title: MEL_Scl

value: MEL

value: Mouse erythroleukemic cells

value: Santa Cruz


title: Hpc7_INP

value: N/A (input sample)


title: Rosa chinensis 'Pallida'  RNA-seq

city: Kunming

first: huijun

last: yan

address: Kunming, Yunnan, P. R. China

institute: Flower Research Institute of Yunnan Academy of Agricultural Sciences

description: high-throughput profiling of transcriptome in Rosa chinensis 'Pallida'

data_processing:
The Paired-end reads RNA-seq reads were aligned to Rosa chinensis 'Pallida' sequence using bowtie (Langmead and Salzberg, 2012). The gene expression levels were measured in reads per kilobase of exon model per million mapped reads (RPKM), (Mortazavi et al., 2008). The script of pysam (http://code.google.com/p/pysam/) and wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) were required to produce BigWig files.
The script of pysam (http://code.google.com/p/pysam/) and wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) were required to produce BigWig files.
Genome_build: RosaV1
Supplementary_files_format_and_content: The Bigwig file presents RNA-seq coverage and transcript abundance on a per base-pair level.

organism: Rosa chinensis

growth_protocol: All of Rosa chinensis 'Pallida' used in this study were grown under controlled conditions in a greenhouse of  Flower Research Intitute of Yunnan Academy of Agricultural Sciences.

extract_protocol:
Total RNAs were extracted from Flower bud, open flower and senescent flower with CTAB reagent method (Invitrogen).
Equal volumes of RNA from flower buds, open flowers and senescent flowers were pooled. RNA quality and quantity were verified using a NanoDrop 1000 spectrophotometer and an Agilent 2100 Bioanalyzer prior to further processing. Total RNA was treated with DNase I prior to library construction, and poly-(A) mRNA was purified with Magnetic Oligo (dT) Beads. Double-stranded cDNA was further subjected to end-repair using T4 DNA polymerase, the Klenow fragment, and T4 polynucleotide kinase followed by a single A dNTP base addition using Klenow 3’ to 5’ exo-polymerase, then ligated with an adapter or index adapter using T4 DNA ligase.

tag: cultivar

value: Pallida


title: WT_MES_INP_rep2

source_name: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

tag: cell line

value: WT J1 mESC

value: Flk1+ mesodermal cells

value: EB formation, enrichment for Flk1+ cells at day 4


title: Gata12KO_MES_Scl_rep1

value: Gata1&2KO mESC

tag: chip antibody


title: WT_MES_IgG

value: normal goat IgG


title: WT_MES_Scl_rep2


title: WT_MES_Scl_rep1


title: Vehicle Rep #4

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The sequenced reads from fastq files were mapped to mm9 using STAR version 2.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffdiff from the Cufflinks suite (Trapnell Nature biotechnology), using upper quartile normalization.
RPKM of all 8 samples were combined into a single file.
Genome_build: mm9

source_name: Cecal GIST tumor

extract_protocol:
GIST tumors from the cecums of mice were explanted and grounded in 1000 μl Trizol (Invitrogen) using a PowerGen homogenizer (Fisher Scientific), followed by addition of 200 μl chloroform. The samples were then centrifuged at 10,000g for 15 min. The upper phase was mixed with an equal volume of 70% ethanol, and the RNA was further purified using E.Z.N.A total RNA kit (Omega).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cecal GIST tumor

value: Kit V558Delta/+; Etv1 flox/flox; Rosa26 CreERT2/CreERT2


title: Vehicle Rep #3


title: Tamoxifen Rep #3


title: Tamoxifen Rep #4


title: WT_MES_INP_rep1


title: activatedT_input_H3K4me3

city: La Jolla

first: Carol

last: Katayama

address: 9500 Gilman Dr.

department: BIO/CMM

institute: UC San Diego

data_processing:
For ChIP-Seq (single end reads), reads were aligned to the mm9 genome using Bowtie (v0.12.7), keeping only reads that mapped to a single, unique location.  Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/).
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include bedgraph files (Chipseq fragment density files which were analyzed using  the UCSC Genome Browser) and a bed file (peak position file used for motif analysis using HOMER)

source_name: spleen

growth_protocol: CD4+ T cells were isolated from spleens from C57bl/6 mice by magnetic bead selection.Cells were treated with biotinylated antibodies allowing a negative selection on the Automacs separation system (Miltenyi Biotech). Cells were fixed in formahdehyde and frozen. Purity of CD4 T cells was greater than 90%.

extract_protocol: Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers with the respective indexes for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size- selected from a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq 2000 (Illumina) following the manufacturer's protocols.

treatment_protocol: For purification of activated cells, naïve CD4+ T cells were prepared as described. Plates were coated with goat-anti-hamster antibodies followed by anti-CD3e (2C11) and the naïve T cells plated in complete RPMI including anti-CD28. 72 hours later cells were harvested, fixed with formaldehyde and frozen.

tag: genetic background


title: naiveT-input_H3K4me3


title: naiveT_input_foxo1


title: activatedT-H3K4me3_ChIPseq


title: naiveT-H3K4me3_ChIPseq


title: Tamoxifen Rep #2


title: Tamoxifen Rep #1


title: Vehicle Rep #1


title: naiveT_foxo1_ChIPseq

value: FKHR (H-128)X (sc-11350X, Santa Cruz Biotechnology), lot# F0310


title: Gata12KO_MES_INP


title: Ngn3-neg

city: Boston

first: Gustavo

last: Mostoslavsky

state: MA

address: 670 Albany, Suite 209

department: Medicine

institute: Boston University School of Medicine

data_processing:
Base quality control and trimming were performed with FastQC and FASTQ Groomer
Sequence reads were then mapped to mm10 genome using TopHat (version 1.5.0)
Transcripts were assembled using Cufflinks. Transcript abundances were determined using Cufflinks and are reported as FPKM
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by Cufflinks include tracking ID, locus, coverage and FPKM values

molecule: polyA RNA

source_name: Non-enteroendocrine cells

extract_protocol:
Mice were euthanized by CO2 inhalation and the upper small intestine was removed, opened longitudinally, and rinsed several times in cold PBS. The tissue was chopped and incubated in cold PBS supplemented with 2mM EDTA. The villous fraction was recovered and digested to single cells with 1 mg/ml collagenase. Single cell suspensions were separated immediately by flow cytometry using a BD FACSAria flow cytometer. RNA extraction was performed using the RNeasy Micro kit and RNA quality was assessed using a 2100 Bioanalyzer. For each of the three libraries, total RNA samples were pooled in equal amounts and nonamplified polyadenylated mRNA was purified for the synthesis of complementary DNA (cDNA).
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced with an Illumina Genome Analyzer II

value: Non-enteroendocrine small intestine epithelial cells


title: Ngn3-TOMATO

source_name: Enteroendocrine cells

value: Small intestine epithelial cells derived from Ngn3-expressing progenitors


title: 5hmC_C

city: Beijing

first: Zechen

last: Chong

address: NO. 7 Beitucheng West Road

institute: Beijing Institute of Genomics

description: Sample 2

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9-r16
Peaks were called using MACS version 1.4.2 with default parameter
Genome_build: mm9
Supplementary_files_format_and_content: The files are generated by MACS version 1.4.2, including chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment

source_name: ES cells

extract_protocol:
After incubation with 100µM AA for 24 h, the cells were washed by PBS, and trypsinized and collected for AA extraction. The cell pellets were washed by PBS, and then resuspended in 200µL of a PBS/5 mM EDTA solution. After pipetting the cells up and down several times, samples were frozen (by liquid nitrogen) and thawed (37 °C) repeatedly three times. The supernatants were obtained by centrifugation at 12, 000 g for 10 minutes at 4 °C and then filtered by ultra-filtration tubes (MW cutoff: 10 KDa, Pall, Port Washington, NY) to remove proteins and nuclear acid. Before UHPLC-MS/MS detection of AA, 10µM [13C6]-AA (Torto Research Chemicals, Toronto, Ontario, Canada) was added to the filtrates as internal isotope standard.
Genomic DNA from mouse ES cells treated with AA or not was purified by using Wizard genomic DNA purification kit (Promega) with additional Proteinase K treatment and rehydrated in 10 mM Tris (pH 8.0). Genomic DNA samples were further sonicated into short fragments (about 300bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to manufacturer’s instructions. Sonicated DNA was then purified with phenol/chloroform/isoamyl alcohol (25:24:1) precipitation. The 5hmC containing DNA was pulled down by using a chemical labeling method using The Hydroxymethyl Collector™ Kit (Active Motif).

value: mouse ES cells

tag: enrichment method

value: The Hydroxymethyl Collector™ Kit (biotin-based enrichment of 5-hydroxymethylcytosine)


title: 5hmC_V

description: Sample 1

tag: cell type

tag: incubated with

value: 100µM ascorbic acid (AA, vitamin C (Vc)) for 24 h


title: HeK4me1 ChIP-Seq

data_processing:
The sequenced reads from fastq files were mapped to hg18 using Bowtie v1.
Duplicate reads were discarded
Peaks were called against input DNA (sequencing deposited in GSE22441) using MACS 1.4
Genome_build: hg18

source_name: GIST48 Cells

growth_protocol: Cells were grown in log phase using standard tissue culture media.

extract_protocol:
GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with antibody, washed, eluted, reverse cross-linked, and purified.
Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer.

value: H3K4me1, Abcam, ab8895

value: GIST cell line


title: GIP-GFP

source_name: GIP-expressing enteroendocrine cells

value: GIP-expressing small intestine epithelial cells