title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Liver Tissue; renlab.H3K4me3.STL011LI.01.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY307
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17521
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Caucasian

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: HFSC_Sox9 Het_RNA-Seq_2

status: Public on Jan 28 2014

type: SRA

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

country: USA

institute: aecom

description:
processed data file: FPKM_RNA_seq_KO_experiments_mm9.txt
Control replicate 2

library_source: transcriptomic

data_processing:
ChiP Seq: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification using software MACS. ChIP-Seq Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm;
RNA-seq:Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the tophat program using tophat2 with default parameters. Transcripts abundance was estimated by cufflinks 1.0.3.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from RNAseq experiement. Bed files lists coordinates of peaks called from ChiP-seq experiment

molecule: total RNA

organism: Mus musculus

source_name: HFSC_Sox9 Het_RNA-Seq

growth_protocol: HFSCs were FACS-purifed from the telogen back skins of indicated ages of mice

extract_protocol: ChIP-Seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). RNA-Seq: Illumina TruSeq™ RNA kit (Catalog # RS-930-20 01)

treatment_protocol: ChIP-Seq: No treatment;  RNA-Seq: RU486-treatment to activate CrePGR, males P48-P61, females P53-P66

tag: strain background

value: C57BL6, mixed

tag: genotype/variation

value: wild type (control)

tag: gender

value: female

tag: age

tag: tissue

value: back skins

tag: sorting markers

value: integrin α6hi and CD34+  and ScaI- and YFP+

tag: cell type

value: hair follicle stem cells (HFSCs)


title: HFSC_Sox9_ChIPSeq_2

description:
processed data file: HFSC_Sox9_ChIPSeq_2_peaks.bed
Chromatin IP against Sox9

library_source: genomic

molecule: genomic DNA

value: integrin α6hi and CD34+  and ScaI-

tag: chip antibody

value: Sox9 Ab

tag: chip antibody vendor

tag: chip antibody cat. #


title: IFE_input DNA_ChIP-Seq_1

description: input DNA

source_name: IFE_input DNA_ChIP-Seq

value: integrin α6hi and CD34-  and ScaI-

value: intefollicular epidermal cells (IFE)


title: Input DNA

city: Los Angeles

first: Peggy

middle: J

last: Farnham

state: CA

address: 1450 Biggy Street 6514 NRT

department: Molecular Biology and Biochemistry

institute: University of Southern California

data_processing:
Illumina Casava 1.8.2 software used for basecalling
ChIP-seq sequence reads were alligned to the UCSC human genome assembly HG19 using bowtie 2 (H3K27Ac), Illumina eland pipeline (TCF7L2), BWA Input DNA
ChIP-seq peaks were called using Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) with the following settings for H3K27Ac: 250bp fragments, alpha-value=0.0001, FDR=0.001, histone modification analysis.  For TCF7L2: 150 bp fragments, alpha-value=0.001, FDR=0.001
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peak files in gff format

organism: Homo sapiens

source_name: prostate cancer cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: LNCaP

tag: passage

tag: growth protocol

value: Cells were grown in RPMI with 10% FBS (not charcoal-stripped) and collected when 80% confluent


title: TCF7L2 ChIP-seq

value: TCF7L2 (Cell Signaling Technology  C48H11, 2569)


title: Digital Genomic Footprinting assay of Small Bowel Mucosa; DGF.DS20770

status: Public on Jan 29 2014

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20770
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15514
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: Small Intestine tissue; DGF.DS20770

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Small Intestine

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: Digital Genomic Footprinting

value: Qiagen minElut


title: HFSC_input DNA_ChIP-Seq_2

description: input DNA

source_name: HFSC_input DNA_ChIP-Seq

tag: strain background

value: female

value: back skins

value: integrin α6hi and CD34+  and ScaI-

value: hair follicle stem cells (HFSCs)


title: HFSC_Sox9_ChIP-Seq_1

description:
processed data file: HFSC_Sox9_ChIP-Seq_1_peaks.bed
Chromatin IP against Sox9

value: Sox9 Ab

value: Millipore


title: H3K27Ac -DHT ChIP-seq

value: LNCaP

value: Cells were grown in RPMI with charcoal-stripped serum and collected when 80% confluent


title: H3K27Ac +DHT ChIP-seq

value: Cells were grown in RPMI with charcoal-stripped serum, and stimulated with 10nM DHT for 4hr before collection (collected when 80% confluent)


title: Input sample

city: Sevilla

first: Silvia

last: Picossi

address: Avda. Americo Vespucio 49

department: Instituto de Bioquímica Vegetal y Fotosíntesis

country: Spain

institute: CSIC

description: Total DNA

data_processing:
Libraries were loaded at 8pM concentration into the flow cell using the Cluster Station running recipe v7 with the Single-Read Cluster Generation Kit v4 (all Illumina).
The flow cell was loaded into the Genome Analyzer II and samples were sequenced for 120 nucleotides from a single end using the Sequencing Kit v5 and recipe v8 (all Illumina). Manufacturer’s recommendations were strictly followed.
Illumina sequencing data were pre-processed with the standard Illumina pipeline version 1.5 and sequences were aligned to the Anabaena sp. PCC 7120 genome with the Bowtie software 0.12.5. (Langmead et al., 2009)
The Triform algorithm method (Kornacker et al., 2012) was used to the identify peak regions found in the ChIP sample with respect to the control.
The processed data files include 3 files per genome location (chromosome, plasmid alpha, beta, delta, epsilon and gamma) where the peaks have been found. They can be visualized using the Integrative Genome Viewer (Broad Institute) (Thorvaldsdotti et al., 2012)
Genome_build: Anabaena sp. PCC 7120 genome (http://wiki.annotation.jp/Kazusa:CyanoBase:Anabaena_sp._PCC_7120)
Supplementary_files_format_and_content: There are 3 files per chromosome/plasmid to be visualized with the Integrative Genome Viewer (Broad Institute). First, the genome sequence (.seq) is imported along with the .bed file. Then, the .igv file is the one containing the information of the obtained peaks.

organism: Anabaena

source_name: Cells of Anabaena

growth_protocol: Cells of Anabaena sp. PCC 7120 growing in ammonium-containing medium were filtered, washed, and resuspended in the same medium without ammonium and incubated for 3 h with aeration.

extract_protocol:
DNA was purified using phenol:chloroform extraction followed by ethanol precipitation with ammonium acetate and glycogen. DNA was dissolved in DNAse-free purified water.
ChIP DNA Sample Prep Kit (Illumina)

treatment_protocol: Cells were treated with formaldehyde (1 %, 15 min) and glycine (125 mM, 5 min), and collected. The cells were broken, the DNA was sheared by sonication, and a sample was taken for the control (Input). The extract was incubated with affinity-purified anti-NtcA, and the immunoprecipitated material was pulled down using Protein G. The immunoprecipitated material was eluted at 65 ºC. Crosslinking reversion was carried out at 65ºC for 5h and proteins were eliminated using Proteinase K at 55ºC for 2h.

tag: type of sample

value: Total DNA control (Input)

tag: strain


title: Digital Genomic Footprinting assay of Psoas Muscle; DGF.DS20325

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15563
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; DGF.DS20325

value: Psoas Muscle

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American


title: ChIP sample

description: Immunoprecipitated DNA

value: ChIP sample

value: anti-NtcA


title: rfx1_32h

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

description: mRNAs from Fusarium graminearum Z-3639 Δrfx1 strains 32 h after inoculation

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
RFXI_CM_processed.txt: FGDB_v32

organism: Fusarium graminearum

source_name: Fusarium graminearum Δrfx1 deletion mutant

growth_protocol: Conidia of the fungal strains were inoculated in complete media and incubated with shaking at 200 rpm, 25°C,

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

tag: genotype/variation

value: Δrfx1 deletion mutant


title: Dre_155_6hpf_PAL

city: Cambridge

first: Stephen

last: Eichhorn

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_155_6hpf.txt
processed data file: Dre_155_6hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_155_6hpf_PAL_raw_intensities.txt.gz

data_processing:
Raw read files were stripped of adaptor and mapped to the appropriate species' genome and/or transcriptome.
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. Poly(A)-tail length measurements were generated using PAL-seq tags that mapped within the 3' UTR of an annotated gene.
Genome_build: Human: hg18; Mouse: mm9; Zebrafish: danRer7; Drosophila: dm3; Arabidopsis: tair10; S. cerevisiae: sacCer3; S. pombe: Spombe1; Xenopus: Unigene
Supplementary_files_format_and_content: One set of processed data files contains abundance and poly(A)-tail length measurements for each gene. Another set contains raw fluorescence intensities for each base for each cycle of sequencing-by-synthesis and streptavidin flow-in for each sequencing cluster. Another set contains normalized streptavidin fluorescence intensities for each sequencing cluster.

molecule: cytoplasmic RNA

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Each sample was grown or maintained in accordance with standard protocols.

extract_protocol: Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)

treatment_protocol: RNA-seq: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Subtelny et al., 2014 (GSE52809).                                 PAL-seq: Polyadenylated ends in total RNA were ligated to a biotinylated adaptor, then partially digested with RNase T1. The resulting fragments were size-selected (104-750 nt), captured on streptavidin beads, and used for library preparation.

value: AB

tag: developmental stage

value: 6 hours post-fertilization


title: Hyphae transcriptome_0

city: Beijing

first: Keke

last: Liu

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institude of microbiology,Chinese academy of sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drechslerella stenobrocha 248 whole genome using tophat
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using cufflink
Genome_build: Drechslerella stenobrocha 248

organism: Drechslerella stenobrocha

source_name: Hyphal cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Drechslerella stenobrocha 248

value: Hyphae

value: Hyphal cells


title: Hyphae with constricting rings transcriptome_22

source_name: Hyphal cells and constricting ring cells

value: Hyphae with constricting rings


title: IFE_Sox9_ChIPSeq_1

description:
processed data file: IFE_Sox9_ChIPSeq_1_peaks.bed
Chromatin IP against Sox9

tag: gender

value: female

tag: age

tag: tissue

value: back skins

tag: sorting markers

value: integrin α6hi and CD34-  and ScaI-

value: intefollicular epidermal cells (IFE)

value: Sox9 Ab

value: Millipore


title: R0P2

status: Public on Jan 27 2014

city: East Lansing

first: Yuwares

last: Malila

state: Michigan

address: 3340 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

description: Sample 6

data_processing:
1. Paired end reads from 8 libraries (2 conditions, 4 bio-replicates each) of M. gallopavo mRNA were generated with the Illumina GAIIx.
2. Filter passing read pairs were aligned to the M. gallopavo reference genome (Turkey_2.01, UMD, Ensemble release 61) using the spliced RNA aware aligner, TopHat.  Reads from each library were aligned separately.  The reference gene annotation (same version as above) was provided to TopHat to provided information about predicted splice junctions.
3. Novel splice junctions predicted from each of the 8 libraries were combined with the splice annotations from the reference to create a single, non-redundant set of predicted splice sites.  TopHat is better able to map spliced reads if a list of potential junctions is provided as input.
4. Each library was aligned to the reference a second time, providing the non-redundant set of potential splice sites as input.
5. The alignments produced from each library were used as input to Cufflinks.  Cufflinks examines RNA-Seq alignments and generates a set of predicted transcripts based on assembly of overlapping reads.
6. The transcript models generated by Cufflinks for each library were combined into a single, non-redundant set of transcript/gene models with Cuffcompare.  The reference annotation is also provided to Cuffcompare to associate the predicted gene models with their most likely reference model.
7. The models generated by Cuffcompare are filtered to remove those models with little support from the underlying read alignments.  If aligned reads are observed in only one of the six libraries, that model is removed from the final set. The models generated by Cuffcompare were removed and replaced with the reference annotation for the mitochondrial genome.
8. The alignments for each library produced during by the second round of TopHat (step 4) and the set of gene models (step 7) were used as input to htseq-count.  This program compares a set of alignments to an annotation file and reports the number of fragments uniquely aligned to each gene in the annotation.
9. Differential expression testing was performed using the Bioconductor R package, DESeq.  The read counts per locus generated by htseq-count were used as input for DESeq. DESeq makes adjustments for the number of counts in each sample (RON1, RON2,...etc.), calculates sample variance from the biological replicates, tests for differential expression producing a p-value (probability that the observed difference occurred by chance) and then adjusts the p-value to correct for multiple testing.
Genome_build: Turkey_2.01, UMD, Ensemble release 61
Supplementary_files_format_and_content: Strasburg_201011.curated.gtf is are the gene models built by cuffcomare and curated to remove poorly support models (output of data processing step 7)
Supplementary_files_format_and_content: CountsPerLocus.txt is a tab delimited text file. First row is a header row. Column 1 containes the gene_ids as defined in Strasburg_201011.curated.gtf. The remaining columns are the read counts assigned from each sample to each gene by htseq-count (processing step 8).

organism: Meleagris gallopavo

source_name: Turkey breast meat_PSE

growth_protocol: Growth protocol was described in Chiang et al, 2008. Briefly, 43 birds of RBC2 turkeys were obtained from The Ohio State University. Birds were raised using conventional husbandry practices for commercial turkeys at MSU Poultry farm. Turkeys were harvested at 22 week of age using standard industry practices in the MSU Meat Laboratory.

extract_protocol: Breast meat was collected and snap frozen in liquid nitrogen and stored at -80C until RNA isolation. Total RNA was isolated from frozen breast meat using TRIReagent® Solution (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s instructions. Integrity of total RNA was determined using Agilent 2100 Bioanalyzer (Santa Clara, CA).  For libraries construction, 10 μg of samples with an RNA Integrity Number (RIN) equal or exceeding 8.0 (RIN = 10 is the best) was utilized in library construction.

treatment_protocol: Breast meat samples were classified as “normal” or “PSE” based on percent marinade uptake at 24h post-slaughter. Normal meat referred to sample with high marinade uptake; conversely, PSE samples were grouped with low marinade uptake.

tag: genetic line

value: Random-bred (RBC2)

value: 22 weeks

value: Pectoralis major muscle

tag: meat quality

value: pale, soft and exudative (PSE)

value: low

tag: replicate

value: replicate 2


title: R0P3

description: Sample 7

tag: percent marinade uptake at 24h post-slaughter

value: replicate 3


title: R0P4

description: Sample 8

value: replicate 4


title: R0P1

description: Sample 5

value: replicate 1


title: R0N4

description: Sample 4

source_name: Turkey breast meat_normal

value: normal

value: high


title: R0N2

description: Sample 2


title: mES_shLuc_ctrl

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: RNA-Seq

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
Genome_build: mm8
Supplementary_files_format_and_content: The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.

molecule: polyA RNA

source_name: shLuc ES cells

growth_protocol: ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For differentiation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.

extract_protocol:
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell line

value: R1 ES cell

tag: antibody


title: shKdm5b_H3K27ac_mESC

description: Chromatin IP against H3K27ac

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7).Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm8
Supplementary_files_format_and_content: BED

source_name: shKdm5b ES cells

extract_protocol:
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: shLuc_nLIF_d4_Input_mESC

description: Direct sequencing following sonication of x-linked chromatin

source_name: shLuc noLIF day4 ES cells


title: shKdm5b_nLIF_d4_Input_mESC

source_name: shKdm5b noLIF day4 ES cells


title: shLuc_H3K27ac_mESC

description: Chromatin IP against H3K27ac


title: shLuc_nLIF_d4_H3K4me1_mESC

description: Chromatin IP against H3K4me1

value: Anti-H3K4me1 antibody (Abcam; ab8895)


title: shKdm5b_nLIF_d4_H3K4me2_mESC

description: Chromatin IP against H3K4me2

value: Anti-H3K4me2 antibody (Abcam; ab32356)


title: WT_24h

description: mRNAs from Fusarium graminearum Z-3639 wild-type strains 24 h after inoculation

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
WT_CM_processed.txt: FGDB_v32

source_name: Fusarium graminearum wild-type strains

value: wild-type


title: HFSC_input DNA_ChIP-Seq_1

description: input DNA

value: female

value: back skins

value: integrin α6hi and CD34+  and ScaI-

tag: cell type

value: hair follicle stem cells (HFSCs)

tag: chip antibody


title: shLuc_nLIF_d4_H3K4me2_mESC

description: Chromatin IP against H3K4me2


title: Hyphae with constricting rings transcriptome_28

value: Drechslerella stenobrocha 248

value: Hyphae with constricting rings

value: Hyphal cells and constricting ring cells


title: shLuc_nLIF_d3_Input_mESC

source_name: shLuc noLIF day3 ES cells


title: shKdm5b_nLIF_d4_H3K4me3_mESC

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; CS200580)


title: shKdm5b_nLIF_d3_Input_mESC

source_name: shKdm5b noLIF day3 ES cells


title: shKdm5b_nLIF_d3_H3K4me1_mESC

description: Chromatin IP against H3K4me1


title: shKdm5b_nLIF_d3_H3K4me2_mESC

description: Chromatin IP against H3K4me2


title: shKdm5b_nLIF_d3_H3K4me3_mESC

description: Chromatin IP against H3K4me3


title: R0N3

description: Sample 3

value: Random-bred (RBC2)

value: 22 weeks

value: Pectoralis major muscle

value: replicate 3


title: R0N1

description: Sample 1

value: normal

value: high

value: replicate 1


title: mES_shKdm5b

description: RNA-Seq

value: R1 ES cell


title: shLuc_nLIF_d3_H3K4me1_mESC

description: Chromatin IP against H3K4me1

value: Anti-H3K4me1 antibody (Abcam; ab8895)


title: W. dermatitidis in pH2.5 minimal media replicate 3

first: Christina

middle: A

last: Cuomo

address: 7 Cambridge Center

institute: Broad Institute

description: pH 2.5 replicate 3

data_processing:
Base caller: GAPipeline RTA1.12.4.2 Sequencer Application 1.4.8
Aligner: Trinity (version r2013-02-25) alignReads.pl (parameters --aligner bowtie (version 1) and --SS_lib_type RF)
Estimate counts: Trinity run_RSEM.pl (RSEM version 1.2.3) on properly mapped paired reads (parameters --paired --no_group_by_component --SS_lib_type RF)
Normalized counts: Trinity summarize_RSEM_fpkm.pl on RSEM output
Differential expression: edgeR (version 3.2.4) with TMM normalization
Genome_build: AFPA01000000
Supplementary_files_format_and_content: Wangiella_pH_GEOsubmission_processeddata.txt reports FPKM counts, and FC/FDR from Edge R.

organism: Exophiala dermatitidis

source_name: W. dermatitidis cells, pH 2.5

growth_protocol: W. dermatitidis cells were cultured in defined minimal medium adjusted at pH6 and pH2.5, respectively, with shaking at 25 oC for 24 hours

extract_protocol:
RiboPureYM-Yeast Kit (Invitrogen)
dUTP second strand marking method (Parkhomchuck 2009 NAR 37:e123) with modifications previously described (Cuomo 2012 Genome Research 22: 2478-2488)

tag: stress


title: W. dermatitidis in pH2.5 minimal media replicate 2

description: pH 2.5 replicate 2


title: shLuc_nLIF_d3_H3K4me2_mESC

description: Chromatin IP against H3K4me2

value: Anti-H3K4me2 antibody (Abcam; ab32356)


title: W. dermatitidis in pH2.5 minimal media replicate 1

description: pH 2.5 replicate 1


title: shLuc_nLIF_d3_H3K4me3_mESC

description: Chromatin IP against H3K4me3


title: shLuc_nLIF_d2_Input_mESC

source_name: shLuc noLIF day2 ES cells


title: shKdm5b_nLIF_d4_H3K4me1_mESC

description: Chromatin IP against H3K4me1


title: shKdm5b_nLIF_d2_Input_mESC

source_name: shKdm5b noLIF day2 ES cells


title: shKdm5b_nLIF_d2_H3K4me1_mESC

description: Chromatin IP against H3K4me1


title: shLuc_nLIF_d4_H3K4me3_mESC

description: Chromatin IP against H3K4me3


title: shKdm5b_nLIF_d2_H3K4me3_mESC

description: Chromatin IP against H3K4me3


title: shKdm5b_nLIF_d2_H3K4me2_mESC

description: Chromatin IP against H3K4me2


title: W. dermatitidis in pH6 minimal media replicate 2

description: pH 6 replicate 2

source_name: W. dermatitidis cells, pH 6

value: pH 6


title: shLuc_nLIF_d2_H3K4me1_mESC

description: Chromatin IP against H3K4me1


title: W. dermatitidis in pH6 minimal media replicate 1

description: pH 6 replicate 1


title: SC_shGNMT_MDM_2_RRBS

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm9 (Mus musculus) reference genome using the BSMAP (http://rrbsmap.computational-epigenetics.org/) with  the following parameters -s 12 -D C-CGG .
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 5X coverage. We use methylKit  to compute methylation ratios  and  differential methylation analysis  (http://code.google.com/p/methylkit/)
Genome_build: mm9
Supplementary_files_format_and_content: [Sample].call files contain location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs
Supplementary_files_format_and_content: (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for
Supplementary_files_format_and_content: methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Supplementary_files_format_and_content: Format:
Supplementary_files_format_and_content: <chrBase>
Supplementary_files_format_and_content: <chr (mm9)>
Supplementary_files_format_and_content: <Base>
Supplementary_files_format_and_content: <directon of read/alignment>
Supplementary_files_format_and_content: <coverage>
Supplementary_files_format_and_content: <freqC>
Supplementary_files_format_and_content: <freqT
Supplementary_files_format_and_content: <quality scores for each base in read>

source_name: Sciatic nerves

extract_protocol:
(1) After isolation, cultured Schwann cells were scraped, flash-frozen in liquid nitrogen, before pooling together for genomic DNA extraction using PureLINK Genomic Extraction kit from Invitrogen.
RRBS/MspI followed by a modified TruSeq DNA sample preparation kit (Illumina Inc.). Samples were multiplexed according to Illumina's recommendations and experimental design.

treatment_protocol: Schwann cells were isolated from scitaic nerves from C57Bl6J mice, and then either treated with SAMe or GNMT silenced by lentiviral vectors.

value: Post natal day 5-8

value: Schwann cells

tag: medium

value: Schwann cell medium (Low methionine)

tag: treatment

value: no treatment


title: shKdm5b_LSD1i_Input_mESC_rep2

source_name: shKdm5b LSD1i ES cells


title: SC_shGNMT_2_RRBS

tag: strain

value: Schwann cell medium


title: shLuc_nLIF_d2_H3K4me3_mESC

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; CS200580)


title: shLuc_LSD1i_Input_mESC_rep2

source_name: shLuc LSD1i ES cells


title: SC_shGNMT_MDM_1_RRBS


title: SC_shGNMT_1_RRBS


title: shLuc_nLIF_d2_H3K4me2_mESC

description: Chromatin IP against H3K4me2


title: SC_shControl_1_RRBS


title: shKdm5b_LSD1i_H3K4me3_mESC_rep2

description: Chromatin IP against H3K4me3


title: SC_shControl_2_RRBS


title: SC_SAMe_1_RRBS

value: SAMe supplementation


title: SC_SAMe_2_RRBS


title: shLuc_LSD1i_H3K4me1_mESC_rep2

description: Chromatin IP against H3K4me1


title: shLuc_LSD1i_H3K4me2_mESC_rep2

description: Chromatin IP against H3K4me2


title: shKdm5b_LSD1i_H3K4me2_mESC_rep2

description: Chromatin IP against H3K4me2


title: SC_Control_1_RRBS


title: SC_Control_2_RRBS


title: W. dermatitidis in pH6 minimal media replicate 3

description: pH 6 replicate 3


title: shKdm5b_LSD1i_Input_mESC_rep1


title: db_db_2_B_RRBS

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were filtered from the adapter sequences and  their quality score using trim_galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those  with at least 20 phred quality score.
Reads were mapped to mm9 (Mus musculus) reference genome using the BSMAP (http://rrbsmap.computational-epigenetics.org/) with  the following parameters -s 12 -D C-CGG .
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 5X coverage. We use methylKit  to compute methylation ratios and differential methylation analysis  (http://code.google.com/p/methylkit/)
[Sample].call files contain location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs   (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for   methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Genome_build: mm9
Supplementary_files_format_and_content: Format:   <chrBase>  <chr (mm9)>  <Base>  <directon of read/alignment>  <coverage>  <freqC>  <freqT>

growth_protocol: Sciatic nerves from C57Bl6J, GNMT (wt and KO) and (db/+ or db/db) mice of either sex, were dissected and pooled together at different developmental stages.

extract_protocol:
After isolation, nerves were desheathed and flash-frozen in liquid nitrogen, before pooling together for genomic DNA extraction using PureLINK Genomic Extraction kit from Invitrogen.
RRBS/MspI followed by a modified TruSeq DNA sample preparation kit (Illumina Inc.). Samples were multiplexed according to Illumina's recommendations and experimental design.

tag: genotype

value: db/db

value: Post natal day 180


title: shLuc_LSD1i_Input_mESC_rep1


title: db_db_1_A_RRBS


title: db_db_2_A_RRBS


title: db_db_1_B_RRBS


title: shKdm5b_LSD1i_H3K4me2_mESC_rep1

description: Chromatin IP against H3K4me2


title: shKdm5b_LSD1i_H3K4me1_mESC_rep1

description: Chromatin IP against H3K4me1


title: db_plus_2_A_RRBS

value: db/+


title: db_plus_2_B_RRBS


title: db_plus_1_B_RRBS


title: shLuc_LSD1i_H3K4me3_mESC_rep1

description: Chromatin IP against H3K4me3


title: shLuc_LSD1i_H3K4me2_mESC_rep1

description: Chromatin IP against H3K4me2


title: shKdm5b_LSD1i_H3K4me1_mESC_rep2

description: Chromatin IP against H3K4me1


title: db_plus_1_A_RRBS


title: shLuc_LSD1i_H3K4me3_mESC_rep2

description: Chromatin IP against H3K4me3


title: shKdm5b_Input_mESC_rep2


title: GNMT_WT2_B_RRBS

value: GNMT WT

value: Post natal day 90


title: shLuc_Input_mESC_rep2


title: GNMT_WT1_B_RRBS


title: shKdm5b_H3K4me3_mESC_rep2

description: Chromatin IP against H3K4me3


title: GNMT_WT1_A_RRBS


title: GNMT_WT2_A_RRBS


title: shLuc_H3K4me2_mESC_rep2

description: Chromatin IP against H3K4me2


title: shKdm5b_H3K4me2_mESC_rep2

description: Chromatin IP against H3K4me2


title: GNMT_KO2_A_RRBS

value: GNMT KO


title: GNMT_KO2_B_RRBS


title: shLuc_H3K4me3_mESC_rep2

description: Chromatin IP against H3K4me3

value: R1 ES cell


title: GNMT_KO1_A_RRBS


title: GNMT_KO1_B_RRBS


title: P60_2_RRBS

value: WT

value: Post natal day 60


title: shKdm5b_Input_for_K4me1_mESC


title: shLuc_LSD1i_H3K4me1_mESC_rep1

description: Chromatin IP against H3K4me1

value: Anti-H3K4me1 antibody (Abcam; ab8895)


title: P60_1_RRBS


title: shLuc_Input_for_K4me1_mESC


title: shLuc_H3K4me1_mESC

description: Chromatin IP against H3K4me3


title: shKdm5b_H3K4me1_mESC

description: Chromatin IP against H3K4me2


title: shKdm5b_Input_mESC_rep1


title: shKdm5b_LSD1i_H3K4me3_mESC_rep1

description: Chromatin IP against H3K4me3


title: P10_3_RRBS

value: Post natal day 10


title: shLuc_Input_mESC_rep1


title: P10_2_RRBS


title: At_INPUT-ChIP_rep1

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description: ChIP-seq and RNA-seq were performed in two and one biological replicates, respectively.

data_processing:
Basecalls performed using SHORE v0.7alpha3.
Quality filtering included trimming of low quality nucleotides.
ChIP-seq and RNA-seq reads were mapped against the Arabidopsis thaliana reference (TAIR10) using Bowtie choosing one match in case of multiple ones and allowing one mismatch.
For the ChIP-seq libraries, since average read coverage was highly correlated between the two Chip-seq biological replicates, they were pooled for subsequent analysis. In order to reduce biases introduced by PCR amplification, a maximum of 5 reads mapping at exactly the same positions were taken into account.
Peak detection was done using SICER normalising the ChIP-seq coverage by the INPUT coverage. Window size was adjusted according to the distribution of the mark over the genes: 150 bp for H3K4me3 and 300 bp for H3K27me3. Effective genome size was estimated as 85% of the total genome and FDR set at 10−3 .
mRNA abundance for each gene was estimated as the average number of positions mapped to its transcribed region over the total number of positions covered.
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: bedGraph = scores represent the ChIP-seq coverage ; bed = scores represent number of reads per domain ; covexonsByGene.txt = mRNA abundance per gene

organism: Arabidopsis thaliana

source_name: young leaves

growth_protocol: Plants of Arabidopsis thaliana accession Columbia-0 were grown in soil under short day conditions (8h light/16h dark) at 22.5C.

extract_protocol:
Chromatin extraction and immunoprecipitation was performed essentially as described in (Gendrel et al., 2005). Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
20 ng of immunoprecipitated (IP) and genomic (INPUT) DNA and 1 ug of total RNA were used to prepare libraries with the ChIP-Seq DNA Sample Prep Kit IP-102-1001 and TruSeq RNA Sample Prep Kit v2 RS-122-2002 (Illumina), respectively. Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Libraries were sequenced with Illumina Genome Analyzer IIx according to manufacturers instructions.


title: shKdm5b_H3K4me2_mESC_rep1

description: Chromatin IP against H3K4me2

value: Anti-H3K4me2 antibody (Abcam; ab32356)


title: At_H3K27me3_rep2


title: At_H3K27me3_rep1


title: NB_3_RRBS

value: New born


title: At_H3K4me3_rep2


title: P10_1_RRBS


title: shKdm5b_H3K4me3_mESC_rep1

description: Chromatin IP against H3K4me3


title: shLuc_H3K4me2_mESC_rep1

description: Chromatin IP against H3K4me2


title: KDM5B_mESC

description: Chromatin IP against KDM5B

source_name: ES cells

value: Anti-KDM5B antibody (Abcam; ab50958)


title: NB_1_RRBS


title: qHFSC_TCF4_ChIPSeq

status: Public on Jan 26 2014

city: New York

first: Wen-Hui

last: Lien

state: NY

address: 1230 York Ave Box#300

department: Mammalian cell biology and development

institute: The Rockefeller Unoversity

description: Chromatin IP against TCF4

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification using software MACS.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm
wig files created using IGVtools with 25bp windows
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: Mouse back skins

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

tag: gender

value: female

value: telogen back skin

value: integrin α6 and CD34

value: Telogen quiescent hair follicle stem cells (HFSCs)

value: TCF-4 Antibody (N-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: NB_2_RRBS

tag: age


title: qHFSC_TCF3_ChIPSeq

description: Chromatin IP against TCF3

tag: tissue

tag: sorting markers

tag: chip antibody reference

value: Fuchs lab; Nguyen et al, 2006


title: shLuc_H3K4me3_mESC_rep1

description: Chromatin IP against H3K4me3

source_name: shLuc ES cells

value: Anti-H3K4me3 antibody (Millipore; CS200580)


title: qHFSC_TLE_ChIPSeq

description: Chromatin IP against TLE

value: TLE Antibody (C-19)


title: β-cat cKO

data_processing:
RNA-Seq reads (51bp, single-ended) were aligned to the mouse genome (NCBI37/mm9) using the software TopHat (version 2.0.4)
The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 2.1.1) to assemble aligned RNA-Seq reads into transcripts.
These transcripts were compared to the gene model for annotated transcripts obtained from the Ensembl database (72/GRCm38).
The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
Transcript abundances were measured in FPKM (fragments per kilobase of exon per million fragments mapped). Expression profiles were quantile-normalized across samples for comparison.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: β-cat cKO

extract_protocol:
RNAs from FACS-sorted populations were purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions.  Quality of the RNA for sequencing was determined using Agilent 2100 Bioanalyzer, all samples used had RNA integrity numbers (RIN) > 8.
Library preparation using Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility, and RNAs were sequenced on Illumina HiSeq 2000 machines.

value: back skin

tag: Sex

value: Female

value: Ctnnb1 cKO (K15CrePGR;Ctnnb1fl/fl; Rosa-YFPfl/stop/fl)


title: LacZ(-) Bu-HFSC

description:
Sample 2
processed data file: axin_M_FPKM.txt

data_processing:
RNA-Seq reads (51bp, single-ended) were aligned to the mouse genome (NCBI37/mm9) using the software TopHat (version 2.0.4)
The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 2.1.1) to assemble aligned RNA-Seq reads into transcripts.
These transcripts were compared to the gene model for annotated transcripts obtained from the Ensembl database (72/GRCm38).
The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
Transcript abundances were measured in FPKM (fragments per kilobase of exon per million fragments mapped). Expression profiles were quantile-normalized across samples for comparison.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing FPKM values for each sample

growth_protocol: Bu-HFSCs were FACS-purifed from the telogen>anagen back skins of Axin2LacZ/+ mice using FASC-Gal method

value: male

tag: genotype/variation

value: Mouse back skins

value: bulge hair follicle stem cells (Bu-HFSCs)


title: β-cat Het

source_name: β-cat Het

value: Ctnnb1 Het (K15CrePGR;Ctnnb1+/fl; Rosa-YFPfl/stop/fl)


title: 231-oct4A

status: Public on Jan 25 2014

city: Tianjin

first: Long

last: Shen

address: 22 Qixiangtai Road

institute: School of Basic Medical Sciences, Tianjin Medical University

data_processing:
Base-calling: OLB-1.9.4
Data filtering: R&D Perl Remove reads with adapters; Remove reads in which unknown bases are more than 5%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Read alignment: SOAP2.20 -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 3
DEGs detection: R&D Perl FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1
Cluster Analysis: Cluster 3.0  -e 7 -g 7 -m a
Genome_build: Build Genome: hg19
Supplementary_files_format_and_content: RPKM

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 derived cells were cultured in DMEM media supplemented with 10% fetal bovine serum and 1%  NEAA

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 231-mcsA was a stable cell line while MDA-MB-231 cells transfected with a blank control plasmid, 231-oct4A was a stable cell line while MDA-MB-231 cells transfected with an oct4 overexpression plasmid.

tag: transfection

value: oct4 plasmid

tag: cell line

value: epithelial cell

tag: disease

value: adenocarcinoma

tag: ethnicity

value: caucasian


title: GM02555

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

country: Canada

institute: McGill University and Génome Québec Innovation Centre

data_processing:
100 bp paired-end sequencing was carried out on the Illumina HiSeq 2000 system. Reads were mapped to the bisulfite converted reference genome using BWA and further processed according to a protocol from Johnson et al, PMID: 22870857, Curr Protoc Mol Biol.
For further analyses we kept only sites covered ≥ 2-fold on each strand and with a methylation level difference of ≤ 40% between F- and R-strand. We further discarded sites not mapping to uniquely referenced locations on autosomes, chromosome X, Y, or M.
Genome_build: HG19
Supplementary_files_format_and_content: Tab separated, with columns representing: Chr, CG start, CG end, methC fwd, totalC fwd, meth fwd [%], methC rev, totalC rev, meth rev [%], methC fdw+rev, totalC fwd+rev, meth fwd+rev [%]

source_name: Skin fibroblast

growth_protocol: The Fibroblast primary cell lines were grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, the cells were harvested.

extract_protocol:
Genomic DNA was extracted from cell pellets using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer’s protocol.
We constructed genomic DNA libraries using the TruSeq Sample Preparation kit (Illumina Inc.) following the Illumina standard protocol: the ends of the fragments were repaired, an adenine was added at the 3′ extremities of the fragments and Illumina TruSeq adapters were ligated at each extremity.  After adaptor ligation, we treated DNA with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s protocol.

value: female


title: Twin pair T Control MeDIP-seq

city: Herston

first: Lutz

last: Krause

state: QLD

address: 300 Herston Rd

department: Genetics and Computational Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
From the raw fastq files, Illumina quality scores were converted into Sanger Phred quality scores using MAQ
Alignment to hg19 was performed using the Burrows-Wheeler algorithm
MEDIPS package was used to calculate RPM (reads per millions scores) by defining bin sizes of 500bp with an overlap of 250bp across the genome
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated file containing RPM (reads per million) scores for each 500bp window and each sample; only windows with at least one aligned read are included.

source_name: Human blood

extract_protocol:
DNA was extracted from whole blood using a salt extraction method
MeDIP-Sequencing was performed by BGI at its Shenzhan laboratory. Extracted DNA was fragmented using a Covaris sonication system and sequencing libraries were prepared from 5µg fragmented gDNA. End repair, <A> base addition and adaptor ligation steps were performed using Illumina's Single-End DNA Sample Prep kit. Adaptor-ligated DNA was immunoprecipitated by anti-5mC using a commercial antibody (Diagenode). MeDIP DNA was purified with ZYMO DNA Clean & Concentrator-5 columns, and amplified using adaptor-mediated PCR. DNA fragments between 220 and 320 bp in size were gel-excised.

tag: diagnosis

value: Healthy (Control)

value: Male

value: blood


title: Twin pair U Control MeDIP-seq


title: GM02316


title: GM02456


title: Twin pair W Control MeDIP-seq


title: Twin pair U Case MeDIP-seq

value: Major Depressive Disorder (MDD)


title: GM02317


title: At_H3K4me3_rep1

tag: chip antibody


title: Twin pair S Control MeDIP-seq


title: 231-mcsA

value: control

tag: cell type


title: At_mRNA_rep1

tag: strain


title: Twin pair S Case MeDIP-seq

tag: gender


title: Twin pair V Case MeDIP-seq


title: Twin pair R Control MeDIP-seq


title: Twin pair V Control MeDIP-seq


title: LacZ(+) Bu-HFSC

description:
Sample 1
processed data file: axin_M_FPKM.txt


title: Twin pair T Case MeDIP-seq


title: Twin pair P Control MeDIP-seq


title: Twin pair O Case MeDIP-seq


title: Twin pair N Case MeDIP-seq


title: Twin pair P Case MeDIP-seq


title: Twin pair N Control MeDIP-seq


title: Twin pair Q Case MeDIP-seq


title: Twin pair Q Control MeDIP-seq


title: Twin pair M Control MeDIP-seq


title: Twin pair I Control MeDIP-seq


title: Twin pair H Control MeDIP-seq


title: Twin pair M Case MeDIP-seq


title: Twin pair K Case MeDIP-seq


title: Twin pair R Case MeDIP-seq


title: Twin pair L Case MeDIP-seq


title: Twin pair F Case MeDIP-seq


title: Twin pair F Control MeDIP-seq


title: Twin pair K Control MeDIP-seq


title: Twin pair J Control MeDIP-seq


title: Twin pair O Control MeDIP-seq


title: Twin pair D Case MeDIP-seq


title: Twin pair E Control MeDIP-seq


title: Twin pair I Case MeDIP-seq


title: Twin pair J Case MeDIP-seq


title: Twin pair C Control MeDIP-seq


title: Twin pair B Case MeDIP-seq


title: Twin pair B Control MeDIP-seq


title: Twin pair H Case MeDIP-seq


title: Twin pair L Control MeDIP-seq


title: Twin pair G Case MeDIP-seq


title: Twin pair D Control MeDIP-seq


title: Twin pair W Case MeDIP-seq


title: Twin pair C Case MeDIP-seq


title: Twin pair A Case MeDIP-seq


title: Sample 99 Cleavage

status: Public on Jan 24 2014

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (minimum quality of 20, max 1 exception. trimming not required).
RNA-seq, CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against A. queenslandica genome  Aqu1(bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on Aqu1 exon annotation (union of overlapping reads).
Genome_build: Aqu1 (Ensembl)
Supplementary_files_format_and_content: read counts

organism: Amphimedon queenslandica

source_name: Sample 99

growth_protocol: Embryos, larvae and post-larvae were collected individually at Heron Island, the Great Barrier Reef, Australia.

extract_protocol:
RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

treatment_protocol: samples staged by morphology and imaged before being stored in 20 μl RNA later.

tag: developmental stage

value: Cleavage


title: Sample 98 Late ring (cylinder)

source_name: Sample 98

value: Late ring (cylinder)


title: Sample 97 Late spot

source_name: Sample 97

value: Late spot


title: Twin pair E Case MeDIP-seq

value: Female


title: Sample 95 Late spot

source_name: Sample 95


title: Sample 94 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 94


title: Endogenous small RNAs from A. thaliana col-0_WT_rosette leaves_2

city: Poznan

first: Wojciech

middle: M.

last: Karlowski

address: Umultowska 89

country: Poland

institute: Adam Mickiewicz University

description: one RNA isolation, two independent small RNA seq

data_processing:
data processing step included quality filtering, adaptor trimming and size selection for 18-24 nt fragments (in-house developed Python and Perl scripts)
42c7faaxx.txt

source_name: 35-day-old plant rosette leaves

growth_protocol: Plants were grown under 16 h day (150–200 µmol m-2s-1), constant temperature 22°C and humidity of 70% in ‘Jiffy soil' (Jiffy International AS, Kristiansand, Norway) in a growth chamber.

extract_protocol: RNA (35 µg per sample) was sent to BC Cancer Agency (Canada)  under 96% EtOH and Na-acetate (final concentration = 0.3M). cDNA library was constructed at BC Cancer Agency according to their protocol.

tag: ecotype

value: wild type

value: rosette leaves

value: 35-day-old (fully developed)


title: Sample 96 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 96


title: Sample 81 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 81


title: Sample 87 Spot

source_name: Sample 87

value: Spot


title: Sample 88 Late spot

source_name: Sample 88


title: Sample 86 Ring (round)

source_name: Sample 86

value: Ring (round)


title: Twin pair A Control MeDIP-seq


title: Sample 79 Late spot

source_name: Sample 79


title: Sample 78 Spot

source_name: Sample 78


title: Sample 84 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 84


title: Sample 85 Ring (round)

source_name: Sample 85


title: Small RNA deep sequencing of KMB17 cells infected with human hepatitis A virus 21 days post-infection

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

description:
Small RNA Illumina HiSeq 2000 deep sequencing.
Small RNAs isolated from KMB17 cells infected by hepatitis A virus genotype IA (isolate H2) were used to prepare cDNA library and Illumina HiSeq 2000 deep sequencing.
Synonym name: Human hepatitis A virus Hu/China/H2/1982. A cell-adapted vaccine strain, GenBank: EF406357.1.

data_processing:
Illumina's Genome Analyzer Pipeline software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the viral (GenBank: EF406359.1) and human whole genome using SOAP2 v2.04. with default parameters and  bowtie v1.0.0 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Genome_build: Human NCBI whole genome
Genome_build: Hepatitis A virus strain H2K20 (GenBank: EF406359.1)
Supplementary_files_format_and_content: Fasta files generated using bowtie v1.0.0. Small RNA sequences with abundance measurements. Description line: [sample name]_[sequence number]_[normalized counts]_[normalized depth].

organism:
Homo sapiens
Hepatovirus A

source_name: human diploid fibroblast cells (KMB17), human hepatitis A virus genotype IA (isolate H2) infected, 21 days post-infection

growth_protocol: The human embryonic lung diploid fibroblast cell line KMB17 (Institute of Medical Biology, CAMS) was grown in Minimum Essential Medium (MEM) supplemented with 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and newborn calf serum (Minhai Biotechnology, Beijing, China) (10% in growth and 2% in maintenance medium) in 5% CO2 at 37℃. Human hepatitis A virus genotype IA (isolate H2), which is an attenuated strain (Institute of Medical Biology, CAMS), was derived from the fecal specimen of a patient with hepatitis A that was collected anonymously from Hanzhou, China. After isolation and passage in a culture of newborn monkey (Macaca Mulatta) kidney cells, adaptation to growth and serial passages at a low temperature (32℃) in KMB17 cells, the strain became attenuated.

extract_protocol:
Twenty-one days after infection, total RNA was extracted from the HAV-infected cells and the corresponding mock-infected cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to manufacturer's instructions.
Subsequently, the isolated RNA was treated with DNase I (TaKaRa, Dalian, China) to remove DNA contaminants. Total RNA was electrophoresed by 15% denaturing polyacrylamide gel electrophoresis (PAGE) with 8 M urea, and small RNAs, of 15～30 nt, were excised out of the gel and purified. Subsequently, 5' RNA adaptors and 3' RNA adapters were ligated to the sRNA ends. The sRNAs with adapters were amplified by RT-PCR using the Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, and the generated cDNA libraries were sequenced using Illumina HiSeqTM 2000 sequencing technology (Berry Genomics Biotechnology, Beijing, China).

treatment_protocol: KMB17 cells were grown in a T25 flask (Nunc, Weisbaden, Germany) using complete MEM medium with 10% newborn calf serum. When KMB17 cells were grown to approximately 80-90% confluence (approximately 1×10^7 cells), the cells were infected with the human hepatitis A virus genotype IA (isolate H2) at a multiplicity of infection (MOI) of 0.5 50% tissue culture infective dose (TCID50) /cell. Mock-infected cells were used as a negative control in parallel. After 37℃ absorption for 2 hours, maintenance medium with 2% newborn calf serum was added, and infected cells were cultured at 35℃ for 21 days.

tag: human cell line

tag: human cell type

value: embryonic lung-derived diploid fibroblast cell line

tag: infection

value: hepatitis A virus genotype IA (isolate H2) (GenBank:EF406357.1)

tag: time point

value: 21 days post-infection

tag: cell passages


title: Sample 74 Spot

source_name: Sample 74


title: Sample 70 Ring (round)

source_name: Sample 70


title: Sample 66 Spot

source_name: Sample 66


title: Sample 62 Late spot

source_name: Sample 62


title: Sample 60 Brown

source_name: Sample 60

value: Brown


title: Sample 68 Cloud

source_name: Sample 68

value: Cloud


title: Sample 64 Cloud

source_name: Sample 64


title: Sample 65 Cleavage

source_name: Sample 65


title: Sample 63 Brown

source_name: Sample 63


title: Sample 59 Brown

source_name: Sample 59


title: Sample 57 Late ring (cylinder)

source_name: Sample 57


title: Sample 51 Cloud

source_name: Sample 51


title: Sample 50 Cleavage

source_name: Sample 50


title: Sample 48 Spot

source_name: Sample 48


title: Sample 100 Cleavage

source_name: Sample 100


title: Sample 46 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 46


title: Sample 41 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 41


title: Sample 38 Late ring (cylinder)

source_name: Sample 38


title: Sample 43 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 43


title: Sample 42 Ring (round)

source_name: Sample 42


title: Sample 39 Cleavage

source_name: Sample 39


title: Sample 40 Spot

source_name: Sample 40


title: Twin pair G Control MeDIP-seq

source_name: Human blood

value: Healthy (Control)

value: Male

tag: tissue

value: blood


title: acetyl H3K9

city: Beltsville

first: Congjun

last: Li

state: MD

address: 10300 Baltimore Ave

department: BFGL

institute: ARS, USDA

data_processing:
For enriched-region (peaks) identification, we used the MACS (Model-based Analysis of ChIP-seq) algorithm for peak detection
Using MACS version 1.4 (Orc2, 20110214) and ARGUMENTS settings as band width =200; model fold = 10, 30; P value cutoff = 1.00e-05 range for calculating regional lambda is 10,000 bps.
Genome_build: bosTau4

organism: Bos taurus

source_name: MDBK cells, butyrate-treated, acetyl H3K9

extract_protocol: Cells were treated with 10 mM butyrate for 24 hr, The cells were scraped from the flask and homogenized with ice-cold Dounce homogenizer to release the nuclei.  The collected nuclei were resuspended in digestion buffer and enzymatic shearing was performed. ChIP with anti H3, H4 and acetyl-H3 and H4.

value: MDBK


title: acetyl-H3K27

source_name: MDBK cells, butyrate-treated, acetyl-H3K27


title: Sample 35 Cleavage

source_name: Sample 35

value: Cleavage


title: tetra-acetyl-H4 ChIP-seq

source_name: MDBK cells, butyrate-treated, tetra-acetyl-H4 ChIP-seq


title: acetyl-H4K16 ChIP-seq

source_name: MDBK cells, butyrate-treated, acetyl-H4K16 ChIP-seq


title: Histone H3

source_name: MDBK cell, normal, Histone H3


title: Sample 32 Late ring (cylinder)

source_name: Sample 32

value: Late ring (cylinder)


title: Sample 34 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 34


title: Sample 30 Spot

source_name: Sample 30


title: acetyl-H4K12 ChIP-seq

source_name: MDBK cells, butyrate-treated, acetyl-H4K12 ChIP-seq


title: acetyl-H4K5 ChIP-seq

source_name: MDBK cells, butyrate-treated, acetyl-H4K5 ChIP-seq


title: Histone H4 ChIP-seq

source_name: MDBK cells, normal, Histone H4 ChIP-seq


title: acetyl-H3K18-ChIP-seq

source_name: MDBK cells, butyrate-treated, acetyl-H3K18-ChIP-seq


title: Sample 29 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 29


title: trimethyl-H3K9-ChIP-seq

source_name: MDBK cells, butyrate-treated, trimethyl-H3K9-ChIP-seq


title: Sample 28 Brown

source_name: Sample 28


title: Sample 27 Late ring (cylinder)

source_name: Sample 27


title: Sample 26 Ring (round)

source_name: Sample 26


title: Sample 7 Late spot

source_name: Sample 7

value: Late spot


title: Sample 9 Brown

source_name: Sample 9


title: Sample 6 Cloud

source_name: Sample 6


title: Sample 5 Brown

source_name: Sample 5


title: Sample 3 Cleavage

source_name: Sample 3


title: Sample 25 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 25


title: Sample 22 Free-swimming larvae (released in a two-hour period between 12-2pm)

source_name: Sample 22


title: Sample 19 Late ring (cylinder)

source_name: Sample 19


title: Sample 2 Ring (round)

source_name: Sample 2


title: Sample 13 Ring (round)

source_name: Sample 13


title: Cdk9_MM1S_DMSO_forCdk9i_ChipSeq

first: Richard

last: Young

description:
Chromatin IP against Cdk9_MM1S_DMSO_forCdk9i
barcode (already removed): GTGAAA

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Treated with DMSO (for 6 hours), use with Cdk9 inhibitor studies

tag: antibody catalog number

value: Santa Cruz SC-484

tag: duration

tag: drug

value: DMSO


title: Sample 10 Cloud

source_name: Sample 10


title: Small RNA deep sequencing of mock-infected KMB17 cells 21 days post-infection

description:
Small RNA Illumina HiSeq 2000 deep sequencing.
Small RNAs isolated from mock-infected KMB17 cells were used to prepare cDNA library and Illumina HiSeq 2000 deep sequencing.

source_name: human diploid fibroblast cells (KMB17), mock infected, 21 days post-infection

growth_protocol: The human embryonic lung diploid fibroblast cell line KMB17 (Institute of Medical Biology, CAMS) was grown in Minimum Essential Medium (MEM) supplemented with 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and newborn calf serum (Minhai Biotechnology, Beijing, China) (10% in growth and 2% in maintenance medium) in 5% CO2 at 37℃. Human hepatitis A virus genotype IA (isolate H2), which is an attenuated strain (Institute of Medical Biology, CAMS), was derived from the fecal specimen of a patient with hepatitis A that was collected anonymously from Hanzhou, China. After isolation and passage in a culture of newborn monkey (Macaca Mulatta) kidney cells (Zhejiang Academy of Medical Science, China), adaptation to growth and serial passages at a low temperature (32℃) in KMB17 cells, the strain became attenuated.

extract_protocol:
Twenty-one days after infection, total RNA was extracted from the HAV-infected cells and the corresponding mock-infected cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to manufacturer's instructions.
Subsequently, the isolated RNA was treated with DNase I (TaKaRa, Dalian, China) to remove DNA contaminants. Total RNA was electrophoresed by 15% denaturing polyacrylamide gel electrophoresis (PAGE) with 8 M urea, and small RNAs, of 15～30 nt, were excised out of the gel and purified. Subsequently, 5' RNA adaptors and 3' RNA adapters were ligated to the sRNA ends. The sRNAs with adapters were amplified by RT-PCR using the Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, and the generated cDNA libraries were sequenced using Illumina HiSeqTM 2000 sequencing technology (BerryGenomics Biotechnology, Beijing, China).

value: mock


title: RNAPol2_MM1S_DMSO_forCdk7i_ChipSeq

description:
Chromatin IP against RNAPol2_MM1S_DMSO_forCdk7i
barcode (already removed): CAGATC

treatment_protocol: Treated with DMSO (for 6 hours), used as the vehicle control for Cdk7 inhibitor experiments

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

tag: cell line


title: Sample 1 Late ring (cylinder)

source_name: Sample 1


title: Cdk7_MM1S_DMSO_forCdk7i_ChipSeq

description:
Chromatin IP against Cdk7_MM1S_DMSO_forCdk7i
barcode (already removed): TAGCTT

treatment_protocol: Treated with DMSO (for 6 hours), for Cdk7 inhibitor

value: Bethyl A300-405A


title: Sample 8 Cloud

source_name: Sample 8


title: ACR IP_adult_testis_rep1_smallRNA

city: Cold Spring Harbor

first: Semir

last: Beyaz

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

description:
19-33 nt size fractionated RNA
processed data file: ACRIP_vs_Lysate_exp.txt

data_processing:
clip 3' end adaptor GATCGGTACAGTTGCAGTAAGAGC, keep reads with min length 15nt
reads mapped to mm9 mouse genome release using Tophat (Trapnell C, et al. 2009 Bioinformatics )  with up to 2 mis-matches and a maximum of 100 multiple alignments otherwise suppressed)
Cuffdiff (Trapnell C, et al. 2010 Nature Biotechnology) was used for differential analsyis.
Genome_build: mm9
Supplementary_files_format_and_content: txt files with all mappers, their reads number and genomic annotation and comparison to long RNA

source_name: ACR IP_adult_testis_small RNA

growth_protocol: mice were maintained according to the guidelines of the Cold Spring Harbor Laboratory Institutional Animal Care and Use Committee.

extract_protocol:
Chromatoid body was purified according (Meikar et al. 2010 Exp Cell Res). Briefly after dissection seminiferouse tubels were dissociated with collagenese to the cell suspension.  The cells were crosslinked with formaledehyed, resuspend in RIPA buffer and sonicated.  The resulting lysates were centrifuged and supernatant or pellet1 were collected. The pellet1 was resuspended in RIPA buffer, sonicated again and filtrated through 5ul filters.  After centrifugation pellet2 was resuspended in RIPA buffer and incubated with Dynabeads-IgG (lnvitrogen) bounded either with rabbit MVH, IgG or ACR antibodies. After washes the IP complexes were reversed cross-links in RIPA and RNA was extracted with Trizol reagent (Invitrogen).
Total RNA prepared with Trizol reagent (Invitrogen) was size selected (19-33nt) on 15% vertical polyacrylamide/urea gel.
small RNA libraries were prepared according (Malone et al. Cold Spring Harb Protoc. 2012 ). Size selected RNA was ligated with 3' adaptor Modban oligonucleotide with mutant T4 RNA ligase 2, truncated (home made). The ligated products were sized fractionated on 15% vertical polyacrylamide/urea gel and ligated with 5’ adaptor with T4 RNA ligase (Ambion). Then ligated products were separated on 15% vertical polyacrylamide/urea gel and used for reverse transcription with random hexamers and Superscript lll reverse transcriptase (Invitrogen). cDNA was amplified using Illimina primers and used for following sequencing on IIllimina platphorms.

tag: age

value: at least 6 weeks old

tag: sample type

value: control  ACR IP from lysate of  adult testes

tag: rip antibody

value: Acrosin

tag: rip antibody vendor

value: Santa Cruz

tag: rip antibody cat. #

tag: molecule subtype

value: 19-33 nt size fractionated RNA


title: MVH IP_adult_testis_rep2_smallRNA

description:
19-33 nt size fractionated RNA
processed data file: MVHIP_RNAseq_vs_smRNAsq_Exp.txt

source_name: MVH IP_adult_testis_small RNA

tag: strain

value: MVH IP from lysate of  adult testes

value: MVH antibody

tag: rip ref.

value: Kotaja et al., 2006 PNAS


title: pellet1_adult_testis_rep1_smallRNA

description:
19-33 nt size fractionated RNA
processed data file: Pellet_vs_Lysate_exp.txt

source_name: pellet1_adult_testis_small RNA

value: first pellet from  adult testis lysate during chromatoid body purification


title: hetMIWI_round_spermatids_adult_testis_rep1_smallRNA

description:
19-33 nt size fractionated RNA
processed data file: hetMIWI_round_spermatids_exp.txt

value: round spermatid sorted from adult testes


title: pellet2_adult_testis_rep1_smallRNA

source_name: pellet2_adult_testis_small RNA

value: second pellet from adult testis lysate during chromatoid body purification


title: MVH IP_adult_testis_rep1_ smallRNA

source_name: MVH IP_adult_testis_ small RNA


title: ACR IP_adult_testis_rep2_RNAseq

description: processed data file(s): IgG_ACR_IP_mapping_summary.xlsx

data_processing:
first 8 nucleotides from 5 'end  of paired-end read1 and paired-end read2 were trimmed and PE reads 1 were reverse-complemented before genomic mapping
mapped to mm9 mouse genome release with Tophat with 2 mismatches and maximum of 100 multiple alignments.
Cuffdiff  was used according to (Anders and Huber 2010, Genome Biol 11: R106.)
Genome_build: mm9
Supplementary_files_format_and_content: Results of cuffdiff for refseq genes, piRNAs, TE, and other non-coding RNAs (cutoff FPKM >=5 was used), both total estimated expression and differentially expressed between MVH IP and RS, MVH IP and lysate adult testes (p-value < 1e-5).

source_name: ACR IP_adult_testis

extract_protocol:
Chromatoid body was purified according (Meikar et al. 2010 Exp Cell Res). Briefly after dissection seminiferouse tubels were dissociated with collagenese to the cell suspension.  The cells were crosslinked with formaledehyed, resuspend in RIPA buffer and sonicated.  The resulting lysates were centrifuged and supernatant or pellet1 were collected. The pellet1 was resuspended in RIPA buffer, sonicated again and filtrated through 5ul filters.  After centrifugation pellet2 was resuspended in RIPA buffer and incubated with Dynabeads-IgG (lnvitrogen) bounded either with rabbit MVH, IgG or ACR antibodies. After washes the IP complexes were reversed cross-links in RIPA and RNA was extracted with Trizol reagent (Invitrogen).
total RNA was prepared with Trizol reagent (Invitrogen)
Transcriptome libraries were prepared according  (Armour et al. 2009, Nat Methods) using not-so-random priming (NSR). 1 ug total RNA was revere transcribed using SuperScript III enzyme with first-strand NSR primer. RNA template was removed with RNase H (Invitrogen) Then cDNA was mixed with exo− Klenow fragment (NEB) second-strand NSR primer to synthesize the second strand. For PCR amplification, purified second-strand synthesis reaction were mixed with ExpandPLUS enzyme (Roche) and PE-P5-SBS3 and PE-P7-SBS8 primers. Products were run on a 2% low-melt agarose gel, and the 350–500 bp. range were purified.

value: control ACR IP from lysate of adult testes


title: hetMIWI_round_spermatids_adult_testis_rep1_RNAseq

description: processed data file(s): hetMIWI_round_spermatids_adult_testis_rep1_geneExp.txt


title: ACR IP_adult_testis_rep1_RNAseq


title: Sample 4 Brown

source_name: Sample 4

tag: developmental stage

value: Brown


title: MVH IP_adult_testis_rep3_RNAseq

description: processed data file(s): MVHIP_refGene_Exp.txt, MVHIP_TE_Exp.txt, MVHIP_piRNA_Exp.tx, MVHIP_potherNA_Exp.txt, MVHIPvsLys_RSvsLys_RNAseq_DiffEnrich_summary.xls, MVHIP_RNAseq_vs_smRNAsq_Exp.txt, MVHIPvsRs_RNAseq_DiffEnrich_summary.xls, Lys_sup_pelle_rs_mvhip_Exp.txt

source_name: MVH IP_adult_testis

value: MVH IP from lysate of adult testes


title: MVH IP_adult_testis_rep2_RNAseq


title: Sample 17 Cloud

source_name: Sample 17

value: Cloud


title: MVH IP_adult_testis_rep1_RNAseq

description: processed data file(s): MVHIP_refGene_Exp.txt, MVHIP_TE_Exp.txt, MVHIP_piRNA_Exp.tx, MVHIP_potherNA_Exp.txt, MVHIPvsLys_RSvsLys_RNAseq_DiffEnrich_summary.xls, Lys_sup_pelle_rs_mvhip_Exp.txt, MVHIP_RNAseq_vs_smRNAsq_Exp.txt, MVHIPvsRs_RNAseq_DiffEnrich_summary.xls, Lys_sup_pelle_rs_mvhip_Exp.txt


title: IgG IP_adult_testis_rep1_RNAseq

source_name: IgG IP_adult_testis

value: control IgG IP from lysate of adult testes

value: rabbit IgG

value: Neomarkers


title: round spermatids adult_testis_above_500bp_rep1_RNAseq

description: processed data file(s): RS_refGene_Exp.txt, RS_TE_Exp.txt, RS_piRNA_Exp.txt, RS_otherRNA_Exp.txt, MVHIPvsLys_RSvsLys_RNAseq_DiffEnrich_summary.xls, Lys_sup_pelle_rs_mvhip_Exp.txt, MVHIPvsRs_RNAseq_DiffEnrich_summary.xls

value: at least 6 weeks old


title: round spermatids adult_testis_rep1_RNAseq

source_name: round spermatids adult_testis


title: lysate_adult_testis_rep1_RNAseq

description: processed data file(s): lys_refGene_Exp.txt, lys_TE_Exp.txt, MVHIPvsLys_RSvsLys_RNAseq_DiffEnrich_summary.xls, Lys_sup_pelle_rs_mvhip_Exp.txt

value: adult testes lysate


title: supernatant_adult_testis_rep1_RNAseq

description: processed data file(s): Lys_sup_pelle_rs_mvhip_Exp.txt

value: suprenatant prepared from adult testis lysate


title: pellet2_adult_testis_rep1_RNAseq


title: supernatant_adult_testis_rep1_smallRNA

description:
19-33 nt size fractionated RNA
processed data file: Supernatant_vs_Lysate_exp.txt

source_name: supernatant_adult_testis_small RNA

value: 19-33 nt size fractionated RNA


title: C. briggsae young adults (sample A)

status: Public on Jan 23 2014

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequencing reads for each sample and stage were seperately mapped to the transcriptome using bwa (version 0.5.7) with default parameters.
Reads were aggregated across all isoforms of a given gene.
Aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
Genome_build: WS190
Supplementary_files_format_and_content: data_rpkm.txt: Tab separated data file listing all genes (rows) and expression data in RPKM for all samples and stages. Column name indicates species (cel: C. elegan; cbr: C. briggsae), stage and sample name, separated by an underscore.

organism: Caenorhabditis briggsae

source_name: poly(A)-extracted mRNA library

growth_protocol: Gravid adult worms were treated with bleach to isolate embryos  Part of the embryos were used for RNA extraction and further analysis, while the remaining embryos were incubated in M9 buffer without food at room temperature for 12h to hatch and arrest at the L1 stage. The starved, synchronized L1 larvae were set out in S-medium (S-Basal supplemented with 3 mM MgCl2, 3 mM CaCl, 10 mM potassium citrate, supplemented with a mix of antibiotics and antimycotics. Worms were fed with the E. coli strain AT713 and cultivated at 20°C.  Staging was determined by examining a subset of animals under an inverted microscope at intervals for size determination and vulval development. Animals were collected at the L1, L2, L3, early L4, late L4 and young adult (pre-gravid) stages and washed several times in M9 buffer.  Exact times for growth after addition of food to starved L1s for wildtype C. elegans N2 were as follows:  L1 larvae were grown for 7h, L2 for 20h, L3 for 29h, early L4 for 41h, late L4 for 52h and young Adults for 57 h. For wild type C. briggsae AF16 the harvesting time points were: 6h for L1, 20h for L2, 28h for L3, 41h for early L4, 53h for late L4 and young adult after 63h. This timeline was repeated once to obtain biological replicate samples, the initial samples are referred to as biological replicate samples A, the samples from the second time course as biological replicate samples B.

extract_protocol:
All samples were cleaned from bacteria and debris by either several M9 buffer washing steps or sucrose gradient centrifugation, pelleted by centrifugation at 3000 rpm, 3 min, 4°C and stored in TRIzol Reagent, 1 ml per 100 µL worm pellet, at -80°C for RNA and protein isolation.
Poly(A)+ RNA libraries were prepared from total RNA.

tag: temperature

value: young adults


title: C. briggsae mixed stages reference (sample A, replicate 1)

value: mixed stages reference


title: ACR IP_adult_testis_rep3_RNAseq

value: Acrosin

value: Santa Cruz


title: C. briggsae late L4 larvae (sample A)

value: late L4 larvae


title: C. briggsae L4 larvae (sample A)

value: L4 larvae


title: lysate_adult_testis_rep1_smallRNA

description:
19-33 nt size fractionated RNA
processed data file: Supernatant_vs_Lysate_exp.txt, Pellet_vs_Lysate_exp.txt

source_name: lysate_adult_testis_small RNA


title: C. briggsae mixed stages reference (sample A, replicate 2)


title: pellet1_adult_testis_rep1_RNAseq

value: first pellet from adult testis lysate during chromatoid body purification


title: C. briggsae L3 larvae (sample A)

value: L3 larvae


title: C. briggsae L2 larvae (sample A)

value: L2 larvae


title: C. briggsae L1 larvae (sample A, replicate 1)

value: L1 larvae


title: C. briggsae mixed embryos (sample B)

value: mixed embryos


title: C. briggsae L1 larvae (sample A, replicate 2)


title: C. briggsae mixed embryos (sample A, replicate 1)


title: C. briggsae mixed embryos (sample A, replicate 2)


title: C. briggsae L1 larvae (sample B)


title: H3K27Me3_CST_sh3_ChIPSeq

city: Atlanta

first: Meng

last: Zhao

state: GA

address: 1518 Clifton Rd, #369

department: BIOS

institute: Emory University

description: stable EED knockdown cells

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with up to 3 mismatches
peaks were called using HPeak version 3 with the following setting: 25 bp window, 1e-3 significant level, using pair-end setting with dynamic fragment length
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files were generated using HPeak ver. 3, which provided peak loci, height, width, summit location and log(p-value)

source_name: DU145 prostate cancer cells

growth_protocol: Du145 cells were growth following ATCC instruction

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode)
ChIP-Seq libraries were prepared using standard Illumina protocol. ChIP-enriched DNA samples (10-20 ng) were converted to blunt-ended fragments using a combination of T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina PE1.0/PE2.0 primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified using the Bioanalyzer 2100 (Agilent) and each sample was sequenced in a single lane on the Illumina HiSeq 2000 (40 nucleotide read length).

treatment_protocol: stable cells were selected with puromycin

value: DU145 prostate cancer cells

tag: genotype/variation

value: EED knockdown

tag: chip antibody

value: Anti-H3K27me3 [rabbit, Cell Signaling, cat# 9733, lot# 5]


title: H3K27Me3_CST_Scr_ChIPSeq

description: Scramble

value: control


title: BMI1_CST_sh3_ChIPSeq

description: stable EED knockdown cells

value: Anti-BMI1 [rabbit, Cell Signaling, cat# 6964, lot# 1]


title: RING1B_CST_sh3_ChIPSeq

description: stable EED knockdown cells

value: Anti-RING1B [rabbit, Cell Signaling, cat# 5694, lot# 1]


title: RING1A_CST_sh3_ChIPSeq

description: stable EED knockdown cells

value: Anti-RING1A [rabbit, Cell Signaling, cat# 2820, lot# 1]


title: BMI1_CST_Scr_ChIPSeq

description: Scramble


title: RING1B_CST_Scr_ChIPSeq

description: Scramble


title: RING1A_CST_Scr_ChIPSeq

description: Scramble


title: WT-11 y iPSC-mDA + GFP-progerin p 3

first: Jeffrey

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were mapped to the human genome (Hg19) using STAR 2.3.0e with default mapping parameters
Read counts were generated from mapped reads using HT-Seq count
Genome_build: Hg19
Supplementary_files_format_and_content: Txt files containing total read counts per gene from HT-Seq counts using mode = "union"

source_name: iPSC-derived midbrain dopamine (mDA) neurons

growth_protocol: mDA neuron differentiation: A modified version of the dual-SMAD inhibition protocol was used to direct cells towards floor plate-based mDA neurons as described previously6 and schematized in Supplementary Figure 6a.  iPSC-derived mDA neurons were replated on day 30 of differentiation at 260,000 cells per cm2 on dishes pre-coated with polyornithine (PO; 15 μg/ml)/ Laminin (1 μg/ml)/ Fibronectin (2 μg/ml) in Neurobasal/B27/L-glutamine-containing medium(NB/B27; Life Technologies) supplemented with 10 μM Y-27632 (until day 32) and with BDNF (brain-derived neurotrophic factor, 20 ng/ml; R&D), ascorbic acid (AA; 0.2 mM, Sigma), GDNF (glial cell line-derived neurotrophic factor, 20 ng/ml; R&D), TGFβ3 (transforming growth factor type β3, 1 ng/ml; R&D), dibutyryl cAMP (0.5 mM; Sigma), and DAPT (10 nM; Tocris,).  One to two days after plating, cells were treated with 1 μg/ml mitomycin C (Tocris) for 1 hour to kill any remaining proliferating contaminants.  iPSC-derived mDA neurons were fed every 2 to 3 days and maintained without passaging until the desired timepoint for a given experiment.

extract_protocol:
Cells were lysed directly in Trizol (Life Technologies).   RNA was extracted using chloroform and ethanol precipitation and further cleaned using the miRNeasy kit (Qiagen).
After ribogreen quantification and quality control of Agilent BioAnalyzer, 500ng of total underwent polyA selection and Truseq library preparation according to instruction provided by Illumina (TruSeq™ RNA Sample Prep Kit v2), with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2000 in a 75bp/75bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 74 million paired reads were generated per sample. At the most the ribosomal reads represented 0.3% and the percent of mRNA bases was closed to 55% on average.

treatment_protocol: mDA neurons were transfected with modified-RNA expressing either nuclear-GFP or GFP-progerin on 5 consecutive days prior to analysis on day 6.

tag: cell type

tag: donor age (years)

tag: expression construct

value: Progerin GFP


title: WT-82 y iPSC-mDA + GFP-progerin p 3

value: iPSC-derived midbrain dopamine (mDA) neurons


title: WT-11 y iPSC-mDA + Nuclear GFP n 1

value: Nuclear GFP


title: WT-11 y iPSC-mDA + Nuclear GFP n 3


title: WT-82 y iPSC-mDA + Nuclear GFP n 1


title: siSRA_BiolRep2

city: Boulder

first: Linghe

last: Xi

state: CO

address: 3415 Colorado Avenue

institute: CU Boulder

description:
sample_2
MCF-7 cells, 32 h after treatment with siSRA siRNA

data_processing:
Primary data evaluation was performed using the FastX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).  RNA-seq reads were aligned to the human genome (hg19 build) using tophat2.0.4 (http://tophat.cbcb.umd.edu), in conjunction with bowtie2.0.0 (http://bowtie-bio.sourceforge.net). Regulated genes were called by cuffdiff with either "-g" or "-G" option, using three biological replicates for knockdown and three biological replicates for control treatments.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt files include output information produced by cuffdiff, including fold change and significance for RefSeq genes. The "siCtrl_VS_siSRA_assemblenewgenes" file was generated by cuffdiff with the "-g" option. The "siCtrl_VS_siSRA_notassemblenewgenes" was generated by cuffdiff with the "-G" option.

source_name: MCF-7 cell culture

growth_protocol: MCF-7 cells were cultured in high glucose DMEM with 10% fetal bovine serum, 2 mM Glutamax-1, 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: mRNA was extracted by Trizol™ (Ambion)

treatment_protocol: Cells were transfected using siCtrl or siSRA siRNAs with Lipofectamine™ RNAiMAX Reagent (invitrogen) using a reverse transfection strategy.

value: SRA knockdown

tag: biological replicates


title: WT-82 y iPSC-mDA + GFP-progerin p 1


title: siSRA_BiolRep3

tag: cell line


title: WT-82 y iPSC-mDA + Nuclear GFP n 3


title: siCtrl_BiolRep3

description:
sample_1
MCF-7 cells, 32 h after treatment with siCtrl siRNA


title: C. elegans mixed stages reference (sample A, replicate 2)

organism: Caenorhabditis elegans

value: mixed stages reference


title: uH2A_CST_sh3_ChIPSeq

description: stable EED knockdown cells

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with up to 3 mismatches
peaks were called using HPeak version 3 with the following setting: 25 bp window, 1e-3 significant level, using pair-end setting with dynamic fragment length
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files were generated using Hpeak-pairend, which provided peak loci, height, width, summit location and log(p-value)

growth_protocol: Cells were grown in RPMI 1640 containing 10% FBS and selection antibiotics

value: Anti-uH2A (rabbit)[Cell Signaling, cat# 8240S, Lot# 1]


title: uH2A_CST_Scr_ChIPSeq

description: Scramble


title: EED_Scr_ChIPSeq

description: Scramble

value: Anti-EED [Millipore, cat# 05-1320, Lot# NG1841057]


title: uH2A_Millipore_sh3_ChIPSeq

description: stable EED knockdown cells

value: Anti-uH2A (mouse) [Millipore, cat# 05-678, Lot# 1970374]


title: EED_sh3_ChIPSeq

description: stable EED knockdown cells


title: C. elegans mixed stages reference (sample A, replicate 1)


title: uH2A_Millipore_Scr_ChIPSeq

description: Scramble


title: C. elegans late L4 larvae (sample A)

value: late L4 larvae


title: C. elegans L4 larvae (sample A)

value: L4 larvae


title: C. elegans young adults (sample A)

value: young adults


title: WT-11 y iPSC-mDA + GFP-progerin p 1


title: C. elegans L2 larvae (sample A)

value: L2 larvae


title: C. elegans L3 larvae (sample A)

value: L3 larvae


title: C. elegans L1 larvae (sample B)

value: L1 larvae


title: siSRA_BiolRep1


title: C. elegans mixed embryos (sample B)

value: mixed embryos


title: C. elegans L1 larvae (sample A, replicate 2)


title: siCtrl_BiolRep2

value: control


title: C. elegans mixed embryos (sample A, replicate 2)


title: siCtrl_BiolRep1


title: Set D mut-15

city: Fort Collins

first: Taiowa

last: Montgomery

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
18-30 nt small RNAs
TAP Treated RNA

data_processing:
Base calling and fastq files were generated using Illumina software.
Small RNA sequences were parsed from the 3' adapter sequence (TGGAATTCTCGGGTGCCAAGG) and aligned to the C. elegans reference genome WS204 using CASHX v. 2.0.
Genome_build: WS204
Supplementary_files_format_and_content: Tab-separated (TSV) files containing each sequence, regardless of whether or not they aligned to the genome, and total number of reads were generated using custom perl scripts.

source_name: Whole worms

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol:
Total RNA was isolated from stage-matched animals by Trizol extraction followed by two rounds of chloroform extractions and precipitated using isopropanol.
Small RNAs were size selected, tobacco acid pyrophosphatase (TAP) treated to remove 5’ di- and triphosphate groups, ligated to 5’ and 3’ adapters, subjected to reverse transcription, amplified by PCR, and gel purified in preparation for sequencing.

value: Gravid Adults

tag: complete genotype


title: Set D mut-2

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set D rde-2

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set D mut-7

description:
18-30 nt small RNAs
TAP Treated RNA

value: mut-7(pk204) III


title: Set C wild type

description:
18-30 nt small RNAs
TAP Treated RNA

value: wild type


title: Set C mut-16

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set B mut-14(pk738) smut-1 rep1

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV; mut-14(pk738) smut-1(tm1301) V


title: C. elegans L1 larvae (sample A, replicate 1)


title: Set B mut-14(pk738) smut-1 rep2

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set B mut-14(pk738) rep2

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV; mut-14(pk738) V


title: Set B smut-1 rep2

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV; smut-1(tm1301) V


title: Set B mut-14(pk738) rep1

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set B control rep1

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV


title: Set A mut-14 smut-1

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV; mut-14(mg464) smut-1(tm1301) V


title: Set B control rep2

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set A smut-1

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set A control

description:
18-30 nt small RNAs
TAP Treated RNA


title: C. elegans mixed embryos (sample A, replicate 1)


title: wt_sRNA

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: small RNA from wild type S. pombe cells

data_processing:
The data were processed by searching the raw reads for adapter sequence and trimming it off, leaving only small RNA sequences (using custom written scripts).
The reads were mapped to S. pombe genome and mRNA sequences using WU-BLAST (Gish, W. 1996-2003).
The aligned reads were processed using custom written scripts, using genome feature annotation version 09-05-2011 (Sanger)
Genome_build: release 23-8-2007 (Sanger)
Supplementary_files_format_and_content: Spo_wt_sRNA.txt (Tab-delimited list of read sequence and count); RNAprofiling_sRNA_summary.txt (Tab-delimited list of genes and sRNA read counts per gene as well as log2 of strand specific mutant to wt ratio of RNA profiling values)

organism: Schizosaccharomyces pombe 972h-

source_name: sRNA from wild type S. pombe

growth_protocol: Yeast cultures were grown in YES media at 30°C.

extract_protocol:
Cells were disrupted and total RNA was isolated by grinding frozen cell pellet using mortar and pestle in liquid nitrogen in the presence of Trizol (Invitrogen). The RNA was extracted using Trizol according to manufacturer's directions. 10-40 nt fraction was enriched using flashPAGE (Ambion).
The adapters (Small RNA Oligo Only, Illumina) were ligated sequentially using T4 RNA Ligase (Promega); each step was followed by purification by denaturing PAGE. The library was reverse-transcribed using Superscript II (Invitrogen) and amplified using Phusion Hot Start DNA Polymerase (Finnzymes).

treatment_protocol: Liquid yeast cultures were grown in YES media at 30°C until mid-logarithmic phase.


title: RARa binding in the control group

city: Sacramento

first: Yuqi

last: He

state: California

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie
Peaks were called by using MACS
Genome_build: mm10
Supplementary_files_format_and_content: Peaks called by MACS were included in BED files

source_name: Liver

extract_protocol:
Grand in liquid nitrogen, then fixed, sonication, pull down by antibody
Illumina True-Seq Kit

treatment_protocol: Wild type C57/BL mice were treated with normal diet (control) or retinoic acid diet (RA) for 1 day by feeding

tag: gender

value: Male

tag: age

value: 3 Month

tag: tissue

value: Liver


title: RXRa binding in the control group


title: RARb binding in the control group


title: RARb binding in the RA-treatment group


title: vehicle-1

first: Susan

middle: K.

last: Logan

state: New York

address: 522 1st Ave, Smilow Research Building, Rm # 1211

department: NYU Cancer Institute, Mol Pharm and Biochem

institute: NYU School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
The 3' adaptor was removed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned against human genome using Bowtie v1.0.0.
Abundance estimation and differential expression analysis are done using Cufflinks v2.0.2.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: summary_isoforms_fpkm_tracking.xls: summary of read number and the isoform-level abundance of each sample
Supplementary_files_format_and_content: isoform_exp_diff.xls: pairwise comparison and statistical test results

source_name: prostate cancer cells

extract_protocol:
QIAGEN RNA Extraction Kit
Directional mRNA-Seq Sample Preparation

tag: sample type

value: vehicle control


title: si-control-1


title: RXRa binding in the RA-treatment group


title: si-control-2


title: vehicle-2


title: Input for control and RA-treatment groups


title: si-bcat-2

value: β-catenin knockdown


title: Set B smut-1 rep1

description:
18-30 nt small RNAs
TAP Treated RNA


title: Set D wild type

description:
18-30 nt small RNAs
TAP Treated RNA


title: si-bcat-1


title: Set A mut-14

description:
18-30 nt small RNAs
TAP Treated RNA

value: unc-119 III; mgSi4[ubl-1p::GFP::siR-1-sensor-ubl-13'UTR] IV; mut-14(mg464) V