title: HPV- HNSCC sample 32

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: DNA IP against 5-Methylcytosine

data_processing:
Basecalls performed using Bustard
The data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default paramters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package
Genome_build: GRCh37
Supplementary_files_format_and_content: Wig files generated in MEDIPS. Scores represent normalised (reads per million) read depth across the genome.

source_name: HNSCC

extract_protocol: DNA from these 3 HPV+ and 3 HPV- fresh-frozen HNSCC samples was subjected to AutoMeDIP-seq as previously described (Butcher and Beck 2010), using the NEBNext DNA Sample Prep Mastermix (New England Biolabs) for the library preparation and the MagMeDIP kit (Diagenode) for the immunoprecipitation. Adequate enrichment of the methylated DNA fraction (compared to input) was quality controlled using qPCR. Following adapter-mediated PCR, the library was subjected to size selection (300-350 bp) from low melting-point agarose gels. The excised fraction was quality controlled by qPCR.  Cluster generation and 36 base paired-end sequencing was performed by the UCL Genomics Core Facility according to the manufacturer’s recommendation, using an Illumina GAIIX platform.

tag: cell type

value: HNSCC

tag: hpv status

tag: medip antibody

tag: antibody vendor

value: Eurogentec, BI-MECY-0100

tag: antibody lot


title: HPV- HNSCC sample 96

status: Public on Nov 01 2012

type: SRA

description: DNA IP against 5-Methylcytosine

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: HPV+ HNSCC sample 125

description: DNA IP against 5-Methylcytosine


title: HPV+ HNSCC sample 39

description: DNA IP against 5-Methylcytosine


title: H111 bdsf complemented mutant

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: OD600 equal 2

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v4.9 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: CAFQ00000000.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

molecule: total RNA

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007). Ds cDNA was produced and Illumina librairies obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: rpfF mutant complemented with BDSF

value: planktonic cells

tag: medium

value: complex medium LB

tag: strain


title: HPV+ HNSCC sample 105

description: DNA IP against 5-Methylcytosine


title: Histone H3K27ac ChIP-Seq of CD56 Primary Cells; Histone.DS21716

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21716
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14503
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7027
****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM1027288_UW.CD56_Primary_Cells.H3K27ac.RO_01701.Histone.DS21716.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21716-Histone.DS21716.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD56 Primary Cells, Donor RO 01701, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16811
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,502,617
FINDPEAKS_SCORE: 0.4837
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4813
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9994
IROC_PERCENTILE: 89
POISSON_SCORE: 0.514
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027288_UW.CD56_Primary_Cells.H3K27ac.RO_01701.Histone.DS21716.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21716-Histone.DS21716.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD56 Primary Cells, Donor RO 01701, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16907
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD56 H3K27ac 01 16
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Histone H3K27ac Donor RO 01701 Library Histone.DS21716 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,502,617
FINDPEAKS_SCORE: 0.4837
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4813
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9994
IROC_PERCENTILE: 89
POISSON_SCORE: 0.514
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: flow sorted CD56+ Cells, year 37; Histone.DS21716

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD56 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: Histone H3K27ac

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Invitrogen Dynabeads

value: Active Motif


title: MG1655 + 20 ug/ml bicyclomycin 1

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

department: Biochemistry

institute: UW-Madison

description: RNA-Seq MG1655 cells treated with bicyclomycin

data_processing:
Base calling was performed by the DOE Joint Genome Institute using Illumina software.
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP.
Counts per million unique reads were calculated for each gene.
Genome_build: U00096.2
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

organism: Escherichia coli K-12

source_name: MG1655 + 20 ug/ml bicyclomycin

growth_protocol: Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4).

extract_protocol:
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents.
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs.

treatment_protocol: Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction.

value: wild-type

tag: molecule subtype

value: ribosome-depeleted RNA


title: MG1655 + 20 ug/ml bicyclomycin 2


title: H111 wt

description: OD600 equal 2

value: wt


title: IL15 1nM 24h RNASeq

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: treated IL-15

data_processing:
Basecalls performed using CASAVA version 1.8 (HiSeq 2000)
RNA-Seq reads were aligned to the mm8 genome assembly using Bowtie 0.12.4
Aligned reads are converted to BED format using unpublished python and perl scripts
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database
Genome_build: mm8
Supplementary_files_format_and_content: RPKM (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

organism: Mus musculus

source_name: CD8+ T Cells

growth_protocol: Splenic CD8+ T cells were isolated from 6 week-old female C57BL/6 mice and total RNA was isolated.

extract_protocol: Three identically treated samples were pooled and cDNAs were synthesized using 2.5 ng of the pooled RNA and amplified by a two step PCR process (12 cycles with UP1 and UP2 primers followed by 9 cycles with AUP1* and AUP2* primers. After fragmentation using Bioraptor (Diagenode, Delville, NJ), 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen), ends were repaired, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs). The PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Not treated or treated with 1 nM or 500 nM of IL-2 or IL-15 for the indicated times (4hr and 24hr)

value: CD8+ T

tag: treatment

value: IL15 1nM 24h

tag: tissue

value: Spleen


title: H111 bdsf mutant

description: OD600 equal 2

value: rpfF mutant

value: planktonic cells

value: complex medium LB


title: IL2 500nM 24h RNASeq

description: treated IL-2


title: IL15 1nM 4h RNASeq

description: treated IL-15

value: IL15 1nM 4h


title: IL15 500nM 4h RNASeq

description: treated IL-15


title: IL2 1nM 4h RNASeq

description: treated IL-2

value: IL2 1nM 4h


title: IL15 500nM 24h RNASeq

description: treated IL-15


title: Cont RNASeq

description: non-treated


title: Chromatin accessibility assay of fetal ovary; DNase.DS17445

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS17445
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14479
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14478
****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM1027306_UW.Fetal_Ovary.ChromatinAccessibility.H23758_H23604.DNase.DS17445.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS17445.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Ovary Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Ovary, Donor H23758_H23604, Library DNase.DS17445 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17608
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,805,468
FINDPEAKS_SCORE: 0.3057
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3032
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3781
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027306_UW.Fetal_Ovary.ChromatinAccessibility.H23758_H23604.DNase.DS17445.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS17445.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Ovary Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Ovary, Donor H23758_H23604, Library DNase.DS17445 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17562
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FO DNase 04 45
BROWSER_TRACK_DESCRIPTION: UW Fetal Ovary DNase Hypersensitivity Donor H23758_H23604 Library DNase.DS17445 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,805,468
FINDPEAKS_SCORE: 0.3057
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3032
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3781
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Fetal Ovary primary tissue, pool; DNase.DS17445

value: Fetal Ovary

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: pool

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: IL2 1nM 24h RNASeq

description: treated IL-2

value: CD8+ T

value: IL2 1nM 24h


title: IL2 500nM 4h RNASeq

description: treated IL-2

value: IL2 500nM 4h

value: Spleen


title: WT rep1

status: Public on Oct 31 2012

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

description: sequencing barcode id: Indx6

data_processing:
mRNA-seq reads generated from each sample were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie/Tophat v1.3.1 (http://tophat.cbcb.umd.edu) which allows mapping across splice sites by reads segmentation. All programs were used with default setting unless otherwise specified.
Mapped reads (83-84% of total reads) were subsequently assembled into transcripts guided by reference annotation (mm9, USCS gene annotation) with Cufflinks v1.0.3 (http://cufflinks.cbcb.umd.edu).
Expression level of each transcript was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).  Two or three biological replicates were used in each genotype to identify transcripts that showed significant differences at a FDR cutoff <0.05 between wild type and Tet1Gt/Gt by Cuffdiff v1.0.3.
Functional annotation of significantly different transcripts and enrichment analysis was performed with DAVID (http://david.abcc.ncifcrf.gov).
Genome_build: mm9
Supplementary_files_format_and_content: Text file include average FPKM for wildtype and average FPKM for Tet1-knockout, and statistics generated by CuffLinks (cuffdiff)

source_name: Primordial germ cells

extract_protocol: Total RNA was purified from 500-2,000 PGCs using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra low input RNA kit (Clontech, US). The amplified cDNA (2-70 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illumina’s construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in three lanes of Illumina Hiseq 2000 instrument.

value: Primordial germ cells

tag: age

value: embryonic 13.5 day

tag: genotype

value: wild type


title: HPV- HNSCC sample 29

description: DNA IP against 5-Methylcytosine

tag: cell type

value: HNSCC

tag: hpv status

value: Eurogentec, BI-MECY-0100


title: Tet1-KO rep2

description: sequencing barcode id: Indx15


title: WT rep2

description: sequencing barcode id: Indx11


title: WT rep3

description: sequencing barcode id: Indx12


title: Tet1-KO rep1

description: sequencing barcode id: Indx14


title: MG1655 2

description: RNA-Seq MG1655 cells

value: wild-type

value: ribosome-depeleted RNA


title: MG1655 1

description: RNA-Seq MG1655 cells


title: Metafemale

city: Columbia

first: Lin

last: Sun

state: MO

address: 311 Tucker Hall

department: Biological Sciences

institute: University of Missouri

description: three biological repeats

data_processing:
We used TopHat to map the RNA-Seq reads of each replicate of each sample to the Drosophila melanogaster genome (dm3) in the UCSC genome browser  in conjunction with the RefSeq genome reference annotation (RefSeq Assembly ID: GCF_000001215.2; GenBank Assembly ID: GCA_000001215.2)
The threshold of mismatch was set to 2. Overall, ~80% of reads of each replicate were mapped to the genome
The reads that were mapped to a unique location on the genome were used to calculate the RNA counts of the genes. We used both our in-house tool (MULTICOM) and a public tool (HTseq)to calculate read counts of the genes in a replicate according to the genome mapping outputs and the RefSeq genome reference annotation.
The counts of the genes in a replicate calculated by MULTICOM or HTseq were normalized by dividing them by the total number of uniquely mapped reads in the replicate
Genome_build: Release 5
Supplementary_files_format_and_content: .txt files with the averaged normalized reads for each genes of three biological repeats

organism: Drosophila melanogaster

source_name: Third instar larvae

growth_protocol: All the stocks are incubated at 20 degree

extract_protocol:
Total RNA was isolated using TRIZOL Reagent (Invitrogen) and  High-throughput sequencing services were performed at the University of Missouri DNA Core Facility
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq RNA sample preparation kit (#RS-930-2001).

tag: gender type

value: Metafemale

tag: biological replicates

value: HMF1, HMF2, HMF3


title: Male

description: three biological repeats

tag: gender

value: Male

value: CM1, CM2, CM3


title: Female

description: three biological repeats

value: Female

value: CF1,CF2, CF3


title: psq_INPUT_1

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  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 15 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.

treatment_protocol: No Treatment

value: iso1 (y; bw cn sp)

tag: developmental stage


title: Kr_INPUT_1

tag: strain


title: RNA S1123-03, i8

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: ILLUMINA HiSeq sequencing reads

data_processing:
Base calling: Illumina CASAVA
Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data]
Conversion from BAM to SAM: SAMtools 0.1.11
Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011)
RPKM computation: mrfQuantifier (part of RSEQtools, same note about version)
Genome_build: hGRC37 (hg19)

molecule: polyA RNA

source_name: iPS

growth_protocol: Fibroblast were growth under standar condition in DMEM high Glucose media containing 10% FBS. iPSCs were mantained on matrigel coated plates in DMEM/F12 media containing 1% N2 supplement, 2% B27 supplement, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1% penicillin/ streptomycin, 0.5 mg/mL BSA Fraction V, 0.12 mM monothioglycerol. Colonies were passed using dispase.

extract_protocol:
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).
Fibroblast  RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA.   Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for  members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.

tag: passage number

value: iPS


title: RNA S1123-03, i9

description: ILLUMINA HiSeq sequencing reads


title: A2h

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

state: NY

address: 1 Bungtown Rd.

institute: CSHL

data_processing:
5'-end of the sequenced reads starts with "T" and needs to be trimmed bioinformatically before analysis. 3'-adapter (TGGAATTCTCGGGTGCCAAGGC) was removed. The resulting reads were used to select Penelope-derived small RNAs. NOTE: the Penelope-small RNAs do not map to the D. melanogaster genome. Reads mapping to the release5 genome of D. melanogaster were the basis for normalization.
Genome_build: release5 genome
Supplementary_files_format_and_content: "T_at_1" is a characteristic of small RNAs, whether at 5'-end position 1 there is "T"   "A_at_10" is for position 10, if it has "A"  "match" is amount of mismatches after mapping small RNAs to a consensus sequence. in this case after mapping to Penelope transposon

source_name: ovaries

growth_protocol: Flies were grown at 25 degrees on standart media

extract_protocol:
RNA was isolated from 3-5 days old flies using Trizol reagent
Small RNAs were size selected (23-29 nt) on 15% PAGE and ligated consistently to 3-' and 5'-adapters (Tru-seq protocol) using T4 RNA ligase2trunc and T4 ligase1, respectively. The resulting sequences were PCR amplified and gel purified. Libraries were multiplexed using TruSeq approach.

value: ovaries


title: A1a


title: RNA S1123-01, F

description: ILLUMINA HiSeq sequencing reads

source_name: fibroblast

value: fibroblast


title: RNA 03-04, i6

description: ILLUMINA HiSeq sequencing reads


title: A2d


title: RNA 03-04, i1

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-04, i5

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-02, i11

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-02, F

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-02, i17

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-03, F

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-01, i3

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-02, i2

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-01, i1

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-04, F

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-03, i3

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-03, F

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-02, i9

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-02, i8

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-02, i5

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-02, F

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-03, i1

description: ILLUMINA HiSeq sequencing reads


title: RNA S1123-01, i4

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-01, i3

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-01, i9

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-03, i2

description: ILLUMINA HiSeq sequencing reads


title: RNA 03-01, F

description: ILLUMINA HiSeq sequencing reads


title: LSECs 2

status: Public on Oct 30 2012

city: New York

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were aligned to hg18 using TopHat with default parameters
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript

source_name: LSEC

extract_protocol: Illumina TruSeq, PE 51x2

value: LSEC


title: BMS 1

source_name: BMS

value: BMS (bone marrow stroma)


title: HUVECs 2

source_name: HUVEC

value: HUVEC


title: CD34+


title: BMS 2


title: LSECs 1


title: rAC-VECs 2

source_name: rAC-VEC

value: rAC-VEC


title: rAC-VEC clone 3


title: A-seq siRNA CF Im68 2

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

institute: University of Basel

description: 3' adapter sequence: AAAAAATGGAATTCTCGGGTGCCAAGG

data_processing:
A-seq reads were pre-processed to remove the six diagnostic adenosines derived from the poly(A) tail as well as the 3' adaptor sequence and then were mapped to the human genome (hg19) and annotated using the CLIPZ server. For the construction of the set of 3' end cleavage sites, we only used reads that had the adaptor removed, mapped uniquely to genomic regions and whose annotation was "mRNA", "repeat", "miscRNA", or "unknown". Based on the precise mapping of the 3' ends of these reads we computed putative cleavage sites with their associated abundance. To minimize the frequency of internal priming sites in our data set, we discarded those that in the eight-nucleotide-region immediately downstream of the putative cleavage site had at least seven A nucleotides.
The raw reads were processed on the CLIPZ server (http://http://www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245).
Genome_build: hg19, GRCh37 Genome Reference Consortium Human Reference 37
Supplementary_files_format_and_content: BED file containing inferred 3' ends

growth_protocol: HEK293 cells were routinely grown in DMEM supplemented with 10% FCS in the presence of antibiotics.

extract_protocol: A-seq protocol: A-seq starts with selection of the poly(A)-containing RNAs on oligo-(dT)25 Dynabeads, followed by partial digestion with RNase I that cleaves after any nucleotide or alkaline hydrolysis. The 5' ends are then phosphorylated, the 3' ends blocked by 3'dATP and an RNA primer is ligated to the 5' end of the RNA fragments. Our reverse transcription (RT) primer features an anchor nucleotide (A, C or G) designed to align to the first nucleotide upstream of the poly(A) tail, followed by six dTs that anneal to the first six nucleotides (nt) of the poly(A) tail. Following are a stem-loop containing the 3' adaptor sense strand (needed for priming the subsequent PCR reaction), its complement, and finally a stretch of 18 dTs, which together with the 6 dTs after the anchor nucleotide form a 24 nucleotide(nt)-long contiguous oligo dT stretch that aligns to the poly(A) tail. The products of RT and PCR are therefore expected to have 6 As preceding the 3' adaptor (AAAAAATGGAATTCTCGGGTGCCAAGG).

treatment_protocol: For RNAi, HEK293 cells were seeded at a density of 20% in six well plates and all subsequent steps were done according to the "forward method" from the RNAiMAX protocol (Invitrogen). The next day, double stranded siRNAs were incubated with Lipofectamine RNAiMAX (Invitrogen) and added to the wells. After 3 days, cells were harvested and used for confirmation of the siRNA treatment by Western blot and for A-seq.

tag: cell line

tag: sirna

value: 5'-NNGACCGAGA UUACAUGGAUA-3' dsRNA oligo from Dharmacon

tag: fragmentation

value: RNase I digestion


title: rAC-VECs 1


title: A-seq siRNA Ctrl for CF Im68 KD

value: scrambled-A


title: A-seq siRNA CF Im59

value: Ambion S21772

value: alkaline hydrolysis


title: A-seq siRNA CF Im25

value: Ambion S224836


title: RNA 03-01, i2

description: ILLUMINA HiSeq sequencing reads


title: A-seq siRNA Control


title: C2_T0

city: San Francisco

first: Peter

middle: James

last: Turnbaugh

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

data_processing:
Pre-processing of raw reads: trimmed ends to min score = 20 and minimum length = 20, required both pairs, concatenated each trimmed pair
Mapped reads to 539 human-associated genomes (http://www.hmpdacc.org/) using SSAHA (version 2; parameters: -best 1 -score 20 -solexa)
The number of transcripts assigned to each gene was then tallied.
Supplementary_files_format_and_content: Counts files were generated. Values are total reads assigned and fraction reads assigned (#reads/total reads) [columns 2 and 3, respectively].

organism: human gut metagenome

source_name: Fecal microbial community

growth_protocol: Unless specified otherwise all incubations took place for 4 hours under anaerobic conditions, in the dark, and at 37°C. Fresh fecal samples from three unrelated healthy adults were diluted 1:10 (w/vol) in freshly prepared BHI (pH7; Becton Dickinson) liquid medium.

extract_protocol: Microbial cells from samples before and after the 4-hour incubations were lysed by a bead beater (BioSpec Products), total RNA was extracted with phenol:chloroform:isoamyl alcohol (pH 4.5, 125:24:1, Ambion 9720), purified using MEGAClear columns (Ambion), and rRNA was depleted via subtractive hybridization (MICROBExpress, Ambion, in addition to custom depletion oligos). The presence of genomic DNA contamination was assessed by PCR with universal 16S rDNA primers. cDNA was synthesized using SuperScript II and random hexamers (Invitrogen), followed by second strand synthesis with RNaseH and E.coli DNA polymerase (New England Biolabs). Samples were prepared for sequencing with an Illumina Hi-Seq instrument after enzymatic fragmentation (NEBE6040L/M0348S). Libraries were quantified by quantitative reverse transcriptase PCR (qRT-PCR) according to the Illumina protocol. qRT-PCR assays are run using ABsoluteTM QPCR SYBR® Green ROX Mix (Thermo Scientific) on a Mx3000P QPCR System instrument (Stratagene, La Jolla, CA). The size distribution of each library was quantified on an Agilent HS-DNA chip.

treatment_protocol: In total, we tested six therapeutic drugs and eight antibiotics (10μg.ml-1 final concentration), in addition to low pH and mutiple controls.

tag: healthy adult

value: Individual C

tag: treatment protocol of gut microbiome

value: untreated (no incubation)

tag: incubation time

tag: collection day


title: HUVECs 1


title: rAC-VEC clone 4


title: Hi-C Progeria (HGPS) Fibroblasts p19

city: Worcester

first: Rachel

middle: Patton

last: McCord

state: MA

address: 364 Plantation St. LRB 570M

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

description:
HGPS-p19
HGPS patient.

data_processing:
Library strategy: Hi-C
Reads were mapped to the hg18 genome using Bowtie2 using the "very-sensitive" settings in an iterative procedure, starting with the first 25 bp of the sequence and iterating to the full 75 bp length as previously described (Imakaev et al., Nature Methods, 2012 [22941365]).
Aligned reads were assigned to restriction fragments and filtered to discard duplicate read pairs (PCR over-amplification products) and molecules for which both ends map to the same restriction fragment. Restriction fragments shorter than 100 bp or longer than 100kb, as well as those with the top 0.5% of read counts, were removed (validPair file).
Reads were assigned to genomic bins of 200 kb, according to the center of their corresponding restriction fragment. The binned interaction maps were then corrected for systematic biases by equalizing the total coverage (1D sum across the matrix) of every bin in the genome using 50 iterations of a normalization procedure previously described (Imakaev et al., Nature Methods, 2012) (IntMatrix file). These matrices were then smoothed with a 1 Mb bin size and 200 kb step size for publication figures.
Genome_build: hg18
Supplementary_files_format_and_content: validPair files: Comment lines describing the inputs to the file are all preceeded by a '#' character. The 3 columns of data (tab delimited) are: 1) The first restriction fragment of the interacting pair (restriction fragment ID number|coordinates); 2) The second restriction fragment of the interacting pair; 3) The total number of unique paired end reads that map to this combination of restriction fragments.
Supplementary_files_format_and_content: IntMatrix files: Contains a matrix of normalized interaction frequencies for every pair of 200 kb bins in the genome. Bin names and genomic coordinates are listed in row and column headers, and then iteratively corrected interaction frequencies are listed in each pair of row and column.

source_name: patient forearm skin biopsy, Hi-C

growth_protocol: Primary human dermal fibroblasts were cultured in MEM (Invitrogen/GIBCO) supplemented with 15% fetal bovine serum (FBS) (Invitrogen) and 2 mM L-glutamine.

extract_protocol:
Hi-C was carried out essentially as described previously (Lieberman-Aiden et al., 2009 [PMID 19815776]). Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP and ligated for 4 hours at 16 C. After reversing the formaldehyde crosslinks by incubation at 65 C with Proteinase K overnight, unligated biotinylated ends were removed by incubation with 15 U T4 DNA polymerase.
The ligation products were fragmented by Covaris sonication to an average size of 200 bp, and then the ideal size for Illumina sequencing (100-300 bp) was selected by Ampure fractionation (0.9x Ampure beads to remove the DNA fragments >300 bp followed by 1.3x Ampure beads to isolate the remaining DNA fragments > 100 bp). The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an 'A' to each end. The biotinylated junctions were then pulled down using MyOne streptavidin beads at a ratio of 1 uL beads per ng of biotinylated DNA. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified. Samples were sequenced on an Illumina GAII instrument using the Paired End 75 bp module.

treatment_protocol: 20 million cells were crosslinked in 1% formaldehyde for each Hi-C experiment.

tag: disease status

value: Hutchinson-Gilford progeria syndrome

tag: tissue

value: forearm skin biopsy

value: fibroblasts

value: male

tag: passage


title: A-seq NO siRNA


title: Hi-C Normal Father Fibroblasts p18

description:
Father-p18
Patient's healthy father.

source_name: normal forearm skin biopsy, Hi-C

value: normal

tag: cell type


title: Hi-C Progeria (HGPS) Fibroblasts p17

description:
HGPS-p17
HGPS patient.


title: C2_tetracyclin

value: tetracyclin

value: 4 hours


title: C2_norfloxacin

value: norfloxacin


title: Hi-C Normal Age-Control Fibroblasts p20

description:
AgeControl-p20
Healthy age-matched control.

source_name: normal skin biopsy, Hi-C

value: skin biopsy

value: female


title: C2_kanamycin

value: kanamycin


title: C2_pH7


title: C2_gDNA

value: gDNA


title: C2_erythromycin

value: erythromycin


title: C2_chloramphenicol

value: chloramphenicol


title: C2_EtOH

value: EtOH


title: C2_doxycycline

value: Individual C

value: doxycycline


title: C1_tetramisole

value: tetramisole


title: C2_ampicillin

value: ampicillin


title: C2_ciprofloxacin

value: ciprofloxacin


title: C1_T0

value: untreated (no incubation)


title: C1_pH7


title: C1_sulfasalazine

value: sulfasalazine


title: C1_pH5


title: C1_nizatidine

value: nizatidine


title: C1_gDNA

value: 4 hours


title: C1_EtOH


title: C1_digitoxin

value: digitoxin


title: B2_pH7

value: Individual B


title: B2_T0


title: C1_phenacetin

value: phenacetin


title: B2_tetracyclin

value: tetracyclin


title: B2_gDNA

value: gDNA


title: C1_digoxin

value: digoxin


title: B2_norfloxacin

value: norfloxacin


title: B2_kanamycin

value: kanamycin


title: B2_erythromycin

value: erythromycin


title: B2_ciprofloxacin


title: B1_T0


title: B2_chloramphenicol

value: chloramphenicol


title: B2_ampicillin


title: B2_doxycycline

value: doxycycline


title: B1_phenacetin


title: rem-1(pk2295) TAP

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description:
Small RNA sequence data
5' barcode TACA, 3' adapter TCGTATGCCGTCTTCTGCTTG

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the C. elegans genome (WS220)

organism: Caenorhabditis elegans

source_name: Young adult C. elegans

extract_protocol: Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. RNA was then treated with Tobacco Acid Pyrophosphatase according manufactorers conditions. 5' and 3' adapttors were ligated.

value: Bristol N2 background

value: Young adult C. elegans

tag: rna treatment

value: TAP treated


title: B2_EtOH

value: EtOH


title: B1_pH7


title: B1_tetramisole

value: tetramisole


title: rem-1(pk2452) ox

description:
Small RNA sequence data
5' barcode ACTA, 3' adapter TCGTATGCCGTCTTCTGCTTG

extract_protocol: Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. RNA was then oxidised using NaIO4 and quenched using glycerol. After gel isolation 5' and 3' adaptors were ligated.

value: oxidised


title: B1_pH4

value: 4 hours


title: B1_nizatidine

value: Individual B

value: nizatidine


title: B1_sulfasalazine

value: sulfasalazine


title: B1_pH5


title: B1_digoxin


title: mir164a_col-0

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

description: small RNA profiling

data_processing: Unique sequences listed together with their abundance. SHORE (http://shore.sourceforge.net) was used for removing the sequencing adapters and producing the unique sequence counts.

organism: Arabidopsis thaliana

source_name: Col-0 35S::MIR164ACol-0

growth_protocol: Plants were grown at 23°C in long days (16 h light, 8 h dark) on soil, at 65% humidity

extract_protocol: Total RNA was extracted from leaf tissue using the TRIzol reagent (Invitrogen). Small RNAs were isolated using the mirVana miRNA Isolation Kit (Ambion), starting from 50 μg ot total RNA. The library was prepared as described in Felippes et al, Nucleic Acid Research 2011

treatment_protocol: Plants were transformed with either an empty binary vector (control), or with alleles of MIR164A from either the Col-0 or C24 strain expressed under a constitutive 35S CaMV promoter

tag: genotype/variation

value: transgenic 35S::MIR164ACol-0

value: leaves


title: A2_T0

value: Individual A

value: untreated (no incubation)


title: rem-1(pk2452)

extract_protocol: Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. 5' and 3' adapttors were ligated.

value: untreated


title: B1_gDNA

value: gDNA


title: rem-1(pk2295) ox


title: A2_tetracyclin

value: tetracyclin


title: control

description: small RNA profiling

source_name: Col-0 control

value: control


title: WT TAP

value: Bristol N2 background

value: Young adult C. elegans


title: WT ox


title: rem-1(pk2295)


title: B1_EtOH

value: EtOH


title: A2_norfloxacin

value: norfloxacin


title: WT


title: A2_kanamycin

value: kanamycin


title: A2_gDNA

value: 4 hours


title: small RNA profiling of cotyledons

city: beijing

first: Jinsong

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: IGDB

description: small RNA sequencing

data_processing:
cotyledon_smRNA_unique.txt; genome build: Glyma1.0
The raw data was preprocessed by Fastx-Toolkit pipeline to remove low quality reads and clip adapter sequence (CTGTAGGCACCATCAAT). Reads ranged from 18 to 25nt were collected and mapped to the soybean genome sequence using Burrows-Wheeler Aligner (BWA). Sequences that uniquely matched the genome without any mismatch were subjected to the subsequent analysis.

organism: Glycine max

source_name: cotyledons

growth_protocol: Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.

extract_protocol: By polyacrylamide gel electrophoresis, the small RNA (~17-27nt) was purified from 100μg of total RNA and ligated to a 5’ RNA adapter and a 3’ RNA adapter. Reverse transcription followed by low cycle PCR was performed to obtain sufficient product for SBS sequencing. PCR products were collected by gel purification and resuspended in 10 ul elution buffer (Qiagen).

value: cotyledons

value: 20 days after flowering


title: A2_EtOH


title: A2_pH7


title: B1_digitoxin

value: Individual B

value: digitoxin


title: mir164a_c24

description: small RNA profiling

value: transgenic 35S::MIR164AC24

value: leaves


title: A2_doxycycline

value: Individual A

value: doxycycline


title: A2_erythromycin

value: erythromycin


title: small RNA profiling of leaves

description: small RNA sequencing

data_processing:
leaf_smRNA_unique.txt; genome build: Glyma1.0
The raw data was preprocessed by Fastx-Toolkit pipeline to remove low quality reads and clip adapter sequence (CTGTAGGCACCATCAAT). Reads ranged from 18 to 25nt were collected and mapped to the soybean genome sequence using Burrows-Wheeler Aligner (BWA). Sequences that uniquely matched the genome without any mismatch were subjected to the subsequent analysis.

source_name: leaves

value: 14 days after germination


title: A2_ciprofloxacin

value: ciprofloxacin


title: A2_chloramphenicol

value: chloramphenicol


title: small RNA profiling of stems

description: small RNA sequencing

data_processing:
stem_smRNA_unique.txt; genome build: Glyma1.0
The raw data was preprocessed by Fastx-Toolkit pipeline to remove low quality reads and clip adapter sequence (CTGTAGGCACCATCAAT). Reads ranged from 18 to 25nt were collected and mapped to the soybean genome sequence using Burrows-Wheeler Aligner (BWA). Sequences that uniquely matched the genome without any mismatch were subjected to the subsequent analysis.

source_name: stems

value: stems


title: small RNA profiling of roots

description: small RNA sequencing

data_processing:
root_smRNA_unique.txt; genome build: Glyma1.0
The raw data was preprocessed by Fastx-Toolkit pipeline to remove low quality reads and clip adapter sequence (CTGTAGGCACCATCAAT). Reads ranged from 18 to 25nt were collected and mapped to the soybean genome sequence using Burrows-Wheeler Aligner (BWA). Sequences that uniquely matched the genome without any mismatch were subjected to the subsequent analysis.

source_name: roots

value: roots


title: A2_ampicillin

value: ampicillin


title: mRNA-seq of leaves

data_processing:
leaf_mRNA_unique.txt; genome build: Glyma1.0
Reads were mapped to soybean genome sequence using BWA software with no more than two nucleotides mismatch. Only reads mapped to mo more than two locations of soybean genome were reserved. The reads mapped to two locations were even distributed to the two sites. The gene expression was counted and normalized to RPKM (Reads per Kilobase per Million).

extract_protocol: mRNA-seq library was constructed following Illumina kit’s recommendation. Briefly, Poly-A containing RNA was extracted from 15μg of total RNA using Oligotex kit (Qiagen). Poly-A containing RNA was fragmented and used as template for first strand cDNA synthesis using transcriptase and random primers, followed by second strand cDNA synthesis. End repair and adding an ‘A’ base to the 3’ end were performed to the double stranded cDNA, and then DNA adapter was ligated to the DNA fragment. Finally, adapter-ligated DNA was enriched by 15 cycles of PCR and gel-purified for Illumina sequencing.


title: A1_sulfasalazine

value: sulfasalazine


title: A1_phenacetin

value: phenacetin

value: 4 hours


title: A1_pH7


title: mRNA-seq of stems

data_processing:
stem_mRNA_unique.txt; genome build: Glyma1.0
Reads were mapped to soybean genome sequence using BWA software with no more than two nucleotides mismatch. Only reads mapped to mo more than two locations of soybean genome were reserved. The reads mapped to two locations were even distributed to the two sites. The gene expression was counted and normalized to RPKM (Reads per Kilobase per Million).


title: A1_nizatidine

value: nizatidine


title: A1_pH5


title: mRNA-seq of cotyledons

data_processing:
cotyledon_mRNA_unique.txt; genome build: Glyma1.0
Reads were mapped to soybean genome sequence using BWA software with no more than two nucleotides mismatch. Only reads mapped to mo more than two locations of soybean genome were reserved. The reads mapped to two locations were even distributed to the two sites. The gene expression was counted and normalized to RPKM (Reads per Kilobase per Million).

value: 20 days after flowering

value: cotyledons


title: A1_gDNA

value: gDNA


title: A1_T0

value: untreated (no incubation)


title: A1_EtOH

value: Individual A

value: EtOH


title: mRNA-seq of roots

data_processing:
root_mRNA_unique.txt; genome build: Glyma1.0
Reads were mapped to soybean genome sequence using BWA software with no more than two nucleotides mismatch. Only reads mapped to mo more than two locations of soybean genome were reserved. The reads mapped to two locations were even distributed to the two sites. The gene expression was counted and normalized to RPKM (Reads per Kilobase per Million).


title: BS-seq of cotyledons

data_processing:
cotyledon_site.txt; genome build: Glyma1.0
We first obtained the two converted genome sequences, which were respectively derived by conversion of C (cytosine) to T (thymidine) and G (guanine) to A (adenosine). Reads with the conversion of C to T were mapped to the two converted genome sequences by Burrows-Wheeler Aligner (BWA) with no more than two nucleotides mismatch. We extracted the first 75 bases of unmapped reads and performed the alignment again. Only reads mapped to unique site were reserved for further analysis. The Perl scripts were used to recover the converted reads to original sequence and calculated the numbers of C and T for each C in the genome sequence. Methylated cytosine was defined as below: cytosine was covered by no less than two reads, and the sequencing number of C was more than 80% of sequencing number of C plus T.
Column 1: chromosome;Column 2: cytosine location; Column 3: forward strand or reverse strand. +: forward strand, -: reverse strand; Column 4: cytosine type: CG, CHG or CHH; Column 5: sequencing read number of methylated cytosines ;Column 6: sequencing read number of unmethylated cytomsines.

extract_protocol: Briefly, 5 ug genome DNA was extracted from the tissue of roots, stems, leaves, and cotyledons using DNeasy Plant Mini Kit (Qiagen), followed by fragmentation to 50-500 bp with a Bioruptor (Diagenode Sparta). End repair and adding an ‘A’ base to the 3’ end were performed to the DNA fragment and then methylated DNA adapter was ligated to the product. The adapter-ligated DNA of 150-200 bp was purified from agarose gel, followed by two treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen).The bisulfite-converted DNA was amplified by 18 cycles of PCR using uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene) and purified with PCR purification kit (Qiagen).


title: BS-seq of leaves

data_processing:
leaf_site.txt; genome build: Glyma1.0
We first obtained the two converted genome sequences, which were respectively derived by conversion of C (cytosine) to T (thymidine) and G (guanine) to A (adenosine). Reads with the conversion of C to T were mapped to the two converted genome sequences by Burrows-Wheeler Aligner (BWA) with no more than two nucleotides mismatch. We extracted the first 75 bases of unmapped reads and performed the alignment again. Only reads mapped to unique site were reserved for further analysis. The Perl scripts were used to recover the converted reads to original sequence and calculated the numbers of C and T for each C in the genome sequence. Methylated cytosine was defined as below: cytosine was covered by no less than two reads, and the sequencing number of C was more than 80% of sequencing number of C plus T.
Column 1: chromosome;Column 2: cytosine location; Column 3: forward strand or reverse strand. +: forward strand, -: reverse strand; Column 4: cytosine type: CG, CHG or CHH; Column 5: sequencing read number of methylated cytosines ;Column 6: sequencing read number of unmethylated cytomsines.

value: leaves


title: BS-seq of roots

data_processing:
root_site.txt; genome build: Glyma1.0
We first obtained the two converted genome sequences, which were respectively derived by conversion of C (cytosine) to T (thymidine) and G (guanine) to A (adenosine). Reads with the conversion of C to T were mapped to the two converted genome sequences by Burrows-Wheeler Aligner (BWA) with no more than two nucleotides mismatch. We extracted the first 75 bases of unmapped reads and performed the alignment again. Only reads mapped to unique site were reserved for further analysis. The Perl scripts were used to recover the converted reads to original sequence and calculated the numbers of C and T for each C in the genome sequence. Methylated cytosine was defined as below: cytosine was covered by no less than two reads, and the sequencing number of C was more than 80% of sequencing number of C plus T.
Column 1: chromosome;Column 2: cytosine location; Column 3: forward strand or reverse strand. +: forward strand, -: reverse strand; Column 4: cytosine type: CG, CHG or CHH; Column 5: sequencing read number of methylated cytosines ;Column 6: sequencing read number of unmethylated cytomsines.

value: 14 days after germination


title: A1_pH4


title: A1_digitoxin

value: digitoxin


title: BS-seq of stems

data_processing:
stem_site.txt; genome build: Glyma1.0
We first obtained the two converted genome sequences, which were respectively derived by conversion of C (cytosine) to T (thymidine) and G (guanine) to A (adenosine). Reads with the conversion of C to T were mapped to the two converted genome sequences by Burrows-Wheeler Aligner (BWA) with no more than two nucleotides mismatch. We extracted the first 75 bases of unmapped reads and performed the alignment again. Only reads mapped to unique site were reserved for further analysis. The Perl scripts were used to recover the converted reads to original sequence and calculated the numbers of C and T for each C in the genome sequence. Methylated cytosine was defined as below: cytosine was covered by no less than two reads, and the sequencing number of C was more than 80% of sequencing number of C plus T.
Column 1: chromosome;Column 2: cytosine location; Column 3: forward strand or reverse strand. +: forward strand, -: reverse strand; Column 4: cytosine type: CG, CHG or CHH; Column 5: sequencing read number of methylated cytosines ;Column 6: sequencing read number of unmethylated cytomsines.


title: Mnase Hog1 Rep2

city: Barcelona

first: Francesc

last: Posas

address: Dr. Aiguader

country: Spain

institute: UPF

data_processing:
Reads were mapped using GEM mapper version build 539 with default parameters
Calculated heights using Pyicos convert version 1.0.6c default parameters
Calculated enrichment using Pyicos enrichment version 1.0.6c
Genome_build: sarCer2

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast cultures were grown to early log phase.

extract_protocol:
Samples were initially quantified with the double-strand specific Quanti-iT dsDNA HS Assay Kit (Invitrogen) to make sure enough starting material had been provided (usually 10ng). Following end-repair of DNA by incubation with T4 DNA polymerase and Klenow fragment (NEB), DNA was purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and 3’à5’ exo- Klenow fragment (NEB). DNA was purified using MinElute spin columns (Qiagen) and double-stranded adapters (Adapter1/Adapter2) were ligated to the DNA using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel and fragments in the size range of interest (aproximately 250 bp plus 65 bp of adapters for usual ChIP samples and 150 bp for MNAse digested ChIP samples) were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, Adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 and 2.0 (in this step adapters are extended to a total of 112 bp). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer, and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match.
Libraries were quantified by TaqMan Universal PCR Master Mix, No AmpErase kit (Applied Biosystems-Roche) and specific oligos and probe.    DNA was loaded into a lane of a single-read flow cell for cluster generation using a single-read cluster generation kit v4 (Illumina). During this process, DNA molecules are immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of the sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer IIx instrument for sequencing, and 36 sequencing cycles were performed, using v4 SBS kits sequencing kits. Each flow cell we run on the Genome Analyzer IIx contains a PhiX control lane (loaded at a concentration of 4pM), used to monitor run quality.

treatment_protocol: Exposed to osmostress (0.4M NaCl) for 5 minutes for Hog1 immunoprecipitation (anti-HA 12CA5) and for 10 minutes for RNA Pol II immunoprecipitation (8WG16, Covance)

tag: background strain

tag: genotype

tag: chip antibody

tag: condition

value: not exposed to osmostress


title: Mnase Hog1 10'

value: exposed to osmostress


title: Mnase WT 10'

value: wildtype


title: A1_tetramisole

data_processing:
Pre-processing of raw reads: trimmed ends to min score = 20 and minimum length = 20, required both pairs, concatenated each trimmed pair
Mapped reads to 539 human-associated genomes (http://www.hmpdacc.org/) using SSAHA (version 2; parameters: -best 1 -score 20 -solexa)
The number of transcripts assigned to each gene was then tallied.
Supplementary_files_format_and_content: Counts files were generated. Values are total reads assigned and fraction reads assigned (#reads/total reads) [columns 2 and 3, respectively].

value: tetramisole


title: Hog-HA 5'

value: anti-HA 12CA5


title: Mnase WT Rep1


title: Hog-HA 0' Rep1


title: Hog-HA 0' Rep2


title: Pol 2 Hog1 0' Rep 2

value: 8WG16 Covance


title: Pol 2 WT 10'


title: Pol 2 WT 0' Rep 2


title: LaminA ChIP, HGPS, p16, rep2

description:
LaminA-HGPS-p16-R2
HGPS patient.

data_processing:
DNA fragments were sequenced by the Illumina Genome Analyzer 1G and aligned to the hg18 genome assembly using ELAND.
We removed reads that mapped to satellite repeat regions as defined in hg18. To avoid PCR amplification artifacts, we applied a stringent filter to remove duplicated reads by allowing only one mapped read at any position in the genome in one direction.
Genome_build: hg18
Supplementary_files_format_and_content: .bed files contain mapped sequence reads that are filtered as described above.

source_name: patient forearm skin biopsy, lamin ChIP

extract_protocol:
Cells and nuclei were lysed, and then chromatin was sonicated on ice for 12 times 20 seconds at 30% amplitude with a microtip attached to a Branson 450 sonifier. Immunoprecipitations were performed overnight with 15-25 μg of antibody (mouse anti-H3K27me3 [Abcam ab6002], mouse anti-lamin A/C [Millipore MAB3211], goat anti-lamin A/C N18) coupled to Dynal Protein G Magnetic Beads. Beads were washed 5 times in RIPA buffer and 1 time in ice-cold PBS. DNA was eluted in Elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS).
DNA was prepared for sequencing as recommended by Illumina/Solexa 1G.

treatment_protocol: Cells were grown to confluency and then crosslinked in 1% formaldehyde.

value: Hutchinson-Gilford progeria syndrome

value: forearm skin biopsy

value: fibroblasts

tag: gender

value: male

tag: cell line

value: goat anti-lamin A/C N18

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number


title: Pol 2 Hog1 0' Rep 1


title: C1_pH4

tag: healthy adult

value: Individual C

tag: treatment protocol of gut microbiome

value: 4 hours


title: Mnase WT Rep2


title: LaminA ChIP, HGPS, p16, rep1

description:
LaminA-HGPS-p16-R1
HGPS patient.

value: mouse anti-lamin A/C

value: Millipore


title: Pol 2 WT 0' Rep 1


title: LaminA ChIP, Father, p16, rep2

description:
LaminA-Father-p16-R2
Patient's healthy father.

source_name: normal forearm skin biopsy, lamin ChIP

value: normal


title: LaminA ChIP, Father, p16, INPUT, rep2

description:
LaminA-Father-p16-R2-INPUT
Patient's healthy father.

source_name: normal forearm skin biopsy, input


title: LaminA ChIP, Father, p16, rep1

description:
LaminA-Father-p16-R1
Patient's healthy father.


title: A1_digoxin

value: Individual A

value: digoxin

tag: incubation time

tag: collection day


title: LaminA ChIP, Father, p16, INPUT, rep1

description:
LaminA-Father-p16-R1-INPUT
Patient's healthy father.

tag: disease status

tag: tissue


title: H3K27me3 ChIP, HGPS, p17, INPUT

description:
H3K27me3-HGPS-p17-R2-INPUT
HGPS patient.

source_name: patient forearm skin biopsy, input

tag: cell type

tag: passage


title: H3K27me3 ChIP, HGPS, p14, INPUT

description:
H3K27me3-HGPS-p14-R1-INPUT
HGPS patient.


title: H3K27me3 ChIP, HGPS, p17

description:
H3K27me3-HGPS-p17-R2
HGPS patient.

source_name: patient forearm skin biopsy, H3K27me3 ChIP

value: mouse anti-H3K27me3

value: Abcam


title: H3K27me3 ChIP, HGPS, p14

description:
H3K27me3-HGPS-p14-R1
HGPS patient.


title: Mnase Hog1 Rep1

value: not exposed to osmostress


title: H3K27me3 ChIP, Father, p19

description:
H3K27me3-Father-p19-R2
Patient's healthy father.

source_name: normal forearm skin biopsy, H3K27me3 ChIP


title: H3K27me3 ChIP, Father, p19, INPUT

description:
H3K27me3-Father-p19-R2-INPUT
Patient's healthy father.


title: H3K27me3 ChIP, Age Control, p17, INPUT

description:
H3K27me3-AgeControl-p17-INPUT
Healthy age-matched control.

source_name: normal skin biopsy, input

value: skin biopsy

value: female


title: H3K27me3 ChIP, Father, p14

description:
H3K27me3-Father-p14-R1
Patient's healthy father.

value: forearm skin biopsy


title: H3K27me3 ChIP, Age Control, p17

description:
H3K27me3-AgeControl-p17
Healthy age-matched control.

source_name: normal skin biopsy, H3K27me3 ChIP

value: fibroblasts


title: H3K27me3 ChIP, Father, p14, INPUT

description:
H3K27me3-Father-p14-R1-INPUT
Patient's healthy father.

value: male


title: LaminA ChIP, HGPS, p16, INPUT, rep2

description:
LaminA-HGPS-p16-R2-INPUT
HGPS patient.

value: Hutchinson-Gilford progeria syndrome


title: wild type PyYMWT

status: Public on Oct 27 2012

first: Wonjong

last: Moon

address: 307 Westlake Avenue North, Suite 500

institute: Seattle BioMed

description: Wild-type (Py17XNL)

data_processing:
Illumina Genome Analyzer II GA2 HiSeq and CASAVA 1.8.2 for base calling
Additional quality control was applied to the datasets by clipping or removing poor quality reads and N's by ea-utils toolkit (http://code.google.com/p/ea-utils/), with -p 10 and -q 7 settings, then mapped to P. yoelii YM strain reference  genome using tophat version 1.4.1 with default parameters
The differential transcript abundances between samples were measured in Fragments per kilobase of transcript per million mapped fragments (FPKM) using  Cuffdiff by a protocol from Trapnell C. et al. (2012) Nature.
RNA-Seq differential analysis was visualized by CummeRbund
Transcripts with P values of less than 0.01 and at least 4-fold difference in expression (i.e., log fold > 2) were selected to identify the most differentially regulated genes.
Coverage plots were generated to examine the RNA distribution of reads across selected genes-of-interest by comparing the number of unique reads present at each nucleotide position
Genome_build: P. yoelii YM strain version 1 (GeneDB.org)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Plasmodium yoelii yoelii 17XNL

source_name: mosquito salivary glands

growth_protocol: Salivary gland sporozoites were isolated by manual microdissection from A. stephensi mosquitoes 14 days after a single infectious blood meal.

extract_protocol:
RNA was isolated by the Qiagen RNeasy Miniprep Kit with an added DNaseI treatment module.
Library was constructed by Expression Analysis, Inc using the Illumina TruSeq RNA sample preparation kit using standard methods.

treatment_protocol: Salivary gland sporozoites were purified twice over DEAE resin to remove mosquito contaminants.

value: Wild type

value: mosquito salivary glands

value: sporozoites


title: LaminA ChIP, HGPS, p16, INPUT, rep1

description:
LaminA-HGPS-p16-R1-INPUT
HGPS patient.


title: PyPuf2KO

description: pypuf2-knock out transgenic type

value: pypuf2-knock out transgenic type


title: Seedling biological replicate 1

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seedlings were collected six days after imbibition.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

source_name: Soybean seedling six days after imbibition

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (MM), and late- (LM) maturation, pre-dormancy (PD1 and PD2) stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected. For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.

extract_protocol: Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.Approximately one microgram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Two libraries were constructed from genomic DNA isolated from seed coat. One library was spiked in ~ three nanogram of unmethylated lambda DNA as all other libraries; the other library was spiked in ~ three nanogram of methylated lambda DNA to serve as a control for over conversion (i.e. conversion of methylated cytosine to uracil) during the bisulfite conversion step. The methylated lambda DNA was generated by treating unmethylated lambda DNA with CpG Methyltransferase (New England BioLabs). Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: developmental stage

value: 6 days after imbibition

value: seedling


title: mos2-2 rep1

city: Beijing

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
Raw reads from Illumina sequencing were mapped to the Arabidopsis genome using TopHat (Trapnell et al., 2009).
Cuffdiff (Trapnell et al., 2010) was used for expression level estimation (given in FPKM, Fragments Per Kilobase of transcript per Million mapped reads) and differential expression analysis (measured by q-value, multiple testing correction of p-value) with default parameters. Transcripts were considered as differentially expressed when they satisfied the criteria: fold-change>=2 and q-value<0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each samples

source_name: seedlings

growth_protocol: The Arabidopsis thaliana lines used in this study are all in the Columbia (Col-0) background. mos2-2 is a T-DNA insertion line (SALK_033856). All plants were grown at 16-h-light/8-h-dark photoperiod.

extract_protocol:
Total RNAs were isolated from two-week-old seedlings of Col-0 and mos2-2 using TRizol (Invitrogen) and mRNAs were purified using Oligotex mRNA Mini Kit (Qiagen)
cDNA libraries were generated for Illumina GAIIx platform according to the manufacturer’s instructions (Illumina)

tag: ecotype

tag: genotype

value: 14 day old seedlings


title: Cotyledon of seedling biological replicate 1

description: Cotyledons were carefully collected from seedlings six days after imbibition.

source_name: Soybean cotyledons of Seedling six days after imbibition

value: cotyledon from seedling


title: mos2-2 rep2


title: Col-0 rep1

value: wild type


title: MethylCap-seq_323N

status: Public on Oct 26 2012

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

data_processing:
Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequence reads were aligned to the human (hg18) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the 36 bp sequence reads uniquely aligning to the genome were considered for further analysis. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Homo Sapiens hg18 genome assembly.
Genome_build: hg18
Supplementary_files_format_and_content: The file "MergedPeaks_normalized_tagdensity.gz" contains processed data for 24 patient sample pairs. It is a tab-delimited text file. MethylCap-seq was performed on 24 micro-dissected tumors and an equal number of matched microscopically normal tissue samples (48 DNA methylation profiles in total). Enriched regions (peaks) were called for each sample on the basis of a Poisson distribution of overlapping sequence reads within a dynamic window. A false discovery rate (FDR) was calculated relative to the total covered sequence, and peaks with an FDR of ≤10-6 were selected. All peaks from the 48 samples were merged. Per sample the number of tags overlapping each region of interest was calculated and normalized by dividing by the total number of aligned reads of the sample, and the length of the peak.
Supplementary_files_format_and_content: The file "MergedPeaks_normalized_tagdensity_add_5_samples.gz" contains processed data for 5 patient sample pairs. It is a tab-delimited text file. MethylCap-seq was performed on 5 tumors and an equal number of matched normal tissue samples. The peaks identified with the larger sample set was used, per sample the number of tags overlapping each region of interest was calculated and normalized by dividing by the total number of aligned reads of the sample, and the length of the peak.

source_name: normalcolontissue

extract_protocol:
MethylCap (Capturing of methylated DNA) was done using in automated procedure using a SX-8G/IP-StarTM robot (Diagenode). 2 µg of His6–GST–MBD (Diagenode) was incubated with 1 µg of fragmented DNA in binding buffer (BB, 20 mM Tris–HCl pH 8.5, 0.1% Triton X-100) with 200 mM NaCl in a final volume of 200 µl. This solution is mixed at 4 °C for 2 h. Magnetic GST-beads were prepared by washing 35 µl of a well-mixed beads suspension (Promega) with 200 µl of binding buffer + 200 mM NaCl at 4 °C. The suspension was mixed and a magnet was used to collect the beads. After removal of the supernatant the procedure is repeated once. After the second wash the supernatant is removed, but the beads are not allowed to get dry. The GST–MBD solution is added to the washed beads and this suspension is mixed for another hour at 4°C. After removal of the supernatant (the ‘flow-through’) the beads–GST–MBD–DNA complexes are washed/eluted. 200 µl of binding buffer with increasing concentrations of NaCl is added and the suspension is rotated for 10 min at 4 °C. Beads are captured on the magnet, and the supernatant is collected. Three different eluates were collected (LOW, MEDIUM, HIGH), corresponding 500 mM, 600 mM and 800 mM NaCl. For MethylCap-seq the MEDIUM and HIGH eluates were used separately.
1 to 30 ng of DNA was used for library preparation using the ChIP-seq DNA sample Prep Kit (Illumina, cat# IP-102–1001) using the recommended protocol. After ligation of adapters, a 300 bp band is excised using the E-Gel system (Invitrogen), which correspond to a 234 bp fragment of genomic DNA. PCR enrichment of adapter-ligated DNA was done using 14 to 16 cycles of PCR.

value: normal colon tissue

tag: technique

value: MethylCap-sequencing

tag: starting molecule

value: genomic DNA

tag: antibody/capture

value: Protein domain:His6–GST–MBD (Diagenode)


title: MethylCap-seq_738T

source_name: tumorcolontissue

value: tumor colon tissue


title: MethylCap-seq_62N


title: MethylCap-seq_295N


title: MethylCap-seq_738N


title: MethylCap-seq_480N


title: MethylCap-seq_62T


title: MethylCap-seq_323T


title: MethylCap-seq_480T


title: MethylCap-seq_295T


title: Atf5+/+ olfactory epithelium, biological rep 1

type: RNA

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

hyb_protocol: The Affymetrix GeneChip Hybridization, Wash and Stain Kit was used for hybridization on cartridge arrays.

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

data_processing: RMA method in Affy package from Bioconductor was used in R to summarize the probe level data and normalize the dataset to remove across array variation. Moderated t-test in Limma package was used to determine whether a gene’s expression level differed between Atf5+/+ and Atf5-/-. Genes with a fold change ≥1.5 and p-value <0.001 were considered significant.

label: biotin

source_name: Olfactory epithelium from 3 Atf5+/+ P0 mice

label_protocol: The Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix) was used for fragmentation and labeling . The labeling is single color, using Affy’s Labeling Reagent, i.e. Biotin Allonamide Triphophate.

growth_protocol: P0 mice from an Atf5+/- intercrossing were sacrificed and dissected to collect the olfactory epithelium.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions and further purified using a Qiagen RNeasy Kit. The Ambion WT Expression Kit was used to prepare the cDNA from total RNA.

treatment_protocol: Septa and turbinates were collected from P0 C57BL6 mice of Atf5+/+ and Atf5-/-.

tag: strain

value: olfactory epithelium (septa and turbinates)


title: Atf5-/- olfactory epithelium, biological rep 3

source_name: Olfactory epithelium from 3 Atf5-/- P0 mice


title: Atf5+/+ olfactory epithelium, biological rep 3


title: Atf5+/+ olfactory epithelium, biological rep 2


title: Atf5-/- olfactory epithelium, biological rep 1


title: Col-0 rep2


title: ChIP-seq_HCT116_DKO_H3K27me3

data_processing:
Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequence reads were aligned to the human (hg18) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the 36 bp sequence reads uniquely aligning to the genome were considered for further analysis. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Homo Sapiens hg18 genome assembly.
Genome_build: hg18
Supplementary_files_format_and_content: The file "MergedPeaks_normalized_tagdensity.gz" contains processed data for all patient samples. It is a tab-delimited text file. MethylCap-seq was performed on 24 micro-dissected tumors and an equal number of matched microscopically normal tissue samples (48 DNA methylation profiles in total). Enriched regions (peaks) were called for each sample on the basis of a Poisson distribution of overlapping sequence reads within a dynamic window. A false discovery rate (FDR) was calculated relative to the total covered sequence, and peaks with an FDR of ≤10-6 were selected. All peaks from the 48 samples were merged. Per sample the number of tags overlapping each region of interest was calculated and normalized by dividing by the total number of aligned reads of the sample, and the length of the peak.

source_name: HCT116 with homozygous deletion of DNMT3b and DNMT1 (Rhee et al Nature 2002)

growth_protocol: HCT116 WT and DKO cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (all Gibco/Invitrogen) at 37 °C in 5% CO2 atmosphere.

extract_protocol: HCT116 cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4°C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sheared using a Biouptor (Diagenode). Sonicated chromatin was centrifuged for 5 min and then incubated overnight with 3 µg of antibody and protein A/G beads (Santa Cruz). Beads were washed six times with different buffers at 4°C: twice with solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, HEG, once with the solution same as before but with 500 mM NaCl, once with solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, HEG and twice with HEG. Precipitated chromatin was eluted with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3), incubated at 65°C for 4 h in the presence of 200 mM NaCl, phenol extracted and precipitated with 20 µg of glycogen at -20°C overnight.

treatment_protocol: No specific treatments

value: ChIP-sequencing

value: chromatin

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


title: ChIP-seq_HCT116_DKO_H3K4me3

extract_protocol: HCT116 cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4°C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sheared using a Biouptor (Diagenode). Sonicated chromatin was centrifuged for 5 min and then incubated overnight with 2 µg of antibody and protein A/G beads (Santa Cruz). Beads were washed six times with different buffers at 4°C: twice with solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, HEG, once with the solution same as before but with 500 mM NaCl, once with solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, HEG and twice with HEG. Precipitated chromatin was eluted with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3), incubated at 65°C for 4 h in the presence of 200 mM NaCl, phenol extracted and precipitated with 20 µg of glycogen at -20°C overnight.

value: anti-H3K4me3 (Diagenode)


title: ChIP-seq_HCT116_WT_H3K4me3


title: RNA-seq_HCT116_DKO

extract_protocol: 100µg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit, QIAGEN), followed by DNaseI treatment (QIAGEN). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNeasy MinElute Cleanup Kit, QIAGEN). cDNA was synthesized using 5µg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). ds-cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (MinElute Reaction Cleanup Kit, QIAGEN).

value: ds-cDNA-sequencing

value: RNA


title: RNA-seq_HCT116_WT

value: poly(A) selection (Oligotex mRNA Mini Kit, QIAGEN)


title: ChIP-seq_HCT116_WT_H3K27me3


title: MethylCap-seq_HCT116_DKO

extract_protocol: MethylCap (Capturing of methylated DNA) was done using in automated procedure using a SX-8G/IP-StarTM robot (Diagenode). 2 µg of His6–GST–MBD (Diagenode) was incubated with 1 µg of fragmented DNA in binding buffer (BB, 20 mM Tris–HCl pH 8.5, 0.1% Triton X-100) with 200 mM NaCl in a final volume of 200 µl. This solution is mixed at 4 °C for 2 h. Magnetic GST-beads were prepared by washing 35 µl of a well-mixed beads suspension (Promega) with 200 µl of binding buffer + 200 mM NaCl at 4 °C. The suspension was mixed and a magnet was used to collect the beads. After removal of the supernatant the procedure is repeated once. After the second wash the supernatant is removed, but the beads are not allowed to get dry. The GST–MBD solution is added to the washed beads and this suspension is mixed for another hour at 4°C. After removal of the supernatant (the ‘flow-through’) the beads–GST–MBD–DNA complexes are washed/eluted. 200 µl of binding buffer with increasing concentrations of NaCl is added and the suspension is rotated for 10 min at 4 °C. Beads are captured on the magnet, and the supernatant is collected. Three different eluates were collected (LOW, MEDIUM, HIGH), corresponding 500 mM, 600 mM and 800 mM NaCl. For MethylCap-seq the MEDIUM and HIGH eluates were used separately.


title: MethylCap-seq_HCT116_WT


title: MethylCap-seq_40N

source_name: normal colon tissue


title: MethylCap-seq_41T

source_name: tumor colon tissue


title: MethylCap-seq_40T


title: MethylCap-seq_39T


title: MethylCap-seq_38N


title: MethylCap-seq_37T


title: MethylCap-seq_38T


title: Atf5-/- olfactory epithelium, biological rep 2


title: MethylCap-seq_37N


title: MethylCap-seq_35N


title: MethylCap-seq_36T


title: MethylCap-seq_34T


title: MethylCap-seq_35T


title: MethylCap-seq_36N


title: MethylCap-seq_34N


title: MethylCap-seq_33T


title: MethylCap-seq_33N


title: MethylCap-seq_41N


title: MethylCap-seq_32T


title: MethylCap-seq_32N


title: MethylCap-seq_39N


title: MethylCap-seq_24N


title: MethylCap-seq_24T


title: MethylCap-seq_31T


title: MethylCap-seq_31N


title: MethylCap-seq_23T


title: MethylCap-seq_22T


title: MethylCap-seq_22N


title: MethylCap-seq_19T


title: MethylCap-seq_18T


title: MethylCap-seq_18N


title: MethylCap-seq_21N


title: MethylCap-seq_16N


title: MethylCap-seq_15T


title: MethylCap-seq_15N


title: MethylCap-seq_7T


title: MethylCap-seq_8T


title: MethylCap-seq_14T


title: MethylCap-seq_14N


title: MethylCap-seq_8N


title: MethylCap-seq_7N


title: MethylCap-seq_3T


title: MethylCap-seq_23N


title: MethylCap-seq_3N


title: Pol 2 Hog1 10'

source_name: Yeast

tag: background strain

tag: chip antibody

value: 8WG16 Covance

tag: condition

value: exposed to osmostress


title: MethylCap-seq_2T


title: MethylCap-seq_2N


title: MethylCap-seq_19N


title: MethylCap-seq_21T


title: MethylCap-seq_1N


title: MethylCap-seq_1T


title: RNASeq_Dcp1aKD_Rep2

city: Baltimore

first: Yixian

last: Zheng

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing: The densities of RNA-seq reads (in reads per kilo-bases per million reads, RPKM)  were normalized to the library size and the number of sites in 20bp sliding windows along the genome.

source_name: Embryonic Stem Cell

growth_protocol: V6.5 ESCs (derived from the F1 hybrid of 129SvJae/C57BL/6) were maintained in DMEM (Dulbecco's modified Eagle's medium) supplemented with 15% fetal calf serum, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 1000 U/ml recombinant leukemia inhibitory factor (LIF; Millipore), and 30 U/ml Penicillin/Streptomycin (the ESC medium) either with or without a feeder layer.  For feeder-free culture, V6.5 ESCs and their derivatives were grown on plates coated with gelatin (Millipore).

extract_protocol:
Following Illumina True-Seq DNA Sample Preparation V2 protocol and Illumina True-Seq RNA Sample Preparation V2 protocol
Using TruSeq RNA Sample Preparation Kit, Box B, part # 15013136. Step 1: poly-A RNA Purify using oligo dT magnetic beads. Step 2: Synthesize First Strand cDNA using SuperScript II reagents. Step 3: Synthesize Second Strand cDNA using Second Strand Master Mix. Step 4: Perform End Repair of DNA from step 3 using End Repair Mix. Step 5: Adenylate 3' Ends using ATL mix. Step 6: Ligate Adapters using Ligase Mix. Step 7: Enrich DNA Fragments using PCR Primer Cocktail.

treatment_protocol: For analysis Dcp1a knockdown, shRNA plasmids targeting the mouse Dcp1a mRNAs (Open Biosystems,  shRNA-2:TRCN0000096665) were used. Viral media was collected 48 hours after co-transfection and the ESCs were directly infected with the virus 24 hours after initial plating of the ESCs with 8mM polybrene. The infected ESCs were selected for 24 hours post infection with ESCs media containing 2mM puromycin.

tag: background mouse strain

tag: genotype/variation

value: Dcp1a KD


title: RNASeq_WT

value: WT


title: RNASeq_Dcp1aKD

treatment_protocol: For analysis Dcp1a knockdown, shRNA plasmids targeting the mouse Dcp1a mRNAs (Open Biosystems, shRNA-1:TRCN0000096664) were used. Viral media was collected 48 hours after co-transfection and the ESCs were directly infected with the virus 24 hours after initial plating of the ESCs with 8mM polybrene. The infected ESCs were selected for 24 hours post infection with ESCs media containing 2mM puromycin.


title: RNASeq_WT_CtrlForDcp1aKD


title: RNASeq_Utf1KO

value: Utf1 KO


title: MethylCap-seq_16T

value: MethylCap-sequencing


title: H3_WT

extract_protocol:
Following Illumina True-Seq DNA Sample Preparation V2 protocol and Illumina True-Seq RNA Sample Preparation V2 protocol
Using ChIP-Seq DNA Sample Prep Kit Part # 11257047. Step 1: Perform End Repair of ChIP enriched DNA using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. Step 2: Add ?A? Bases to the 3' End of the DNA Fragments from step 1 using Klenow buffer and Klenow exo. Step 3: Ligate Adapters to DNA Fragments from step 3 using DNA ligase. Step 4: Size (300-400bp) Select the Library by 2% agarose gel with TAE buffer.

tag: antibody vendor/catalog

value: Abcam, ab1791


title: H3_Utf1KO


title: H3_WT_Rep2


title: H3K27me3_Utf1KO_Rep2

value: Abcam, ab6002


title: H3K27me3_Utf1KO


title: H3K27me3_WT_Rep2


title: Suz12_Utf1KO

value: Cell Signaling, 3737


title: Suz12_Utf1KO_Rep2


title: Suz12_WT_Rep2


title: Suz12_WT


title: H3K4me3

value: Cell Signaling, 9751


title: BirA-Control

value: streptavidin beads

value: Invitrogen 656-01 Dynabeads® MyOne? Streptavidin T1


title: ML [RNA-seq]

city: Changchun

first: Mingyuan

last: Liu

state: Jilin

address: 5333 Xian Road

department: Institute of Zoonosis

institute: Jilin University

data_processing:
The cDNA library products were sequenced using the Illumina HiSeq 2000
The raw reads were mapped to the reference sequence  using SOAPaligner/soap2.21.
The calculation of Unigene expression used RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: Trichinella spiralis-3.7.1
Processed data is in file GSE39328_all_gene_expression.txt linked to the Series record.

organism: Trichinella spiralis

source_name: muscle larvae

extract_protocol: cDNA libraries were prepared  according  to  the  manufacturer’s  instructions  (Illumina).  The poly(A)-containing mRNA molecules were purified using Oligo(dT) Beads (Illumina)from 20  g of total RNA from each sample. Tris-HCl (10 mM) was used to elute the mRNA from the magnetic beads. To avoid priming bias when synthesizing cDNA, mRNA was fragmented before the cDNA synthesis. Fragmentation was performedusing divalent cations at an elevated temperature. The cleaved mRNA fragments were converted into double-stranded cDNA using SuperScript II, RNaseH and DNA Pol I, primed by random primers. The resulting cDNA was purified using the QIAquick PCR  Purification  Kit  (Qiagen).  Then,  cDNA  was  subjected  to  end  repair  and phosphorylation  using  T4  DNA  polymerase,  Klenow  DNA  polymerase  and  T4 Polynucleotide  Kinase  (PNK).  Subsequent purifications were performed using the QIAquick  PCR  Purification  Kit  (Qiagen).  These  repaired  cDNA  fragments  were 3’-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single ‘A’ base overhang at the 3’ end for subsequent ligation to the adapters. Illumina PE adapters were ligated to  the  ends  of  these  3’-adenylated  cDNA  fragments  and  then  purified  using  theMinElute PCR Purification Kit (Qiagen).  To select a size range of templates for downstream enrichment, the products of the ligation reaction were purified on a 2% TAE- Certified Low-Range Ultra Agarose (Bio-Rad,  Hercules,  CA,  USA). cDNA fragments (200 ± 20 bp) were excised from the gel and extracted using the QIAquick Gel Extraction Kit (Qiagen). Fifteen rounds of PCR amplification were performed to enrich the adapter-modified cDNA library using primers complementary to the ends of the adapters (PCR Primer PE 1.0 and PCR Primer PE 2.0; Illumina). The 200 ± 20 bp PCR products were purified using QIAquick Gel Extraction Kit (Qiagen), using the  MinElute  spin  columns  (Qiagen).

treatment_protocol: Total RNA was extracted using the Invitrogen TRIzol® Reagent and then treated with RNase-free DNase I (Ambion,  Guangzhou,  China) for 30 minutes. The integrity of total RNA was checked using an Agilent 2100 Bioanalyser.

value: muscle larvae


title: NBL [NA-seq]

source_name: newborn larvae

value: newborn larvae


title: Utf1

treatment_protocol: BirA-expressing ES cells

value: BirA-expressing


title: Ad [RNA-seq]

source_name: adults

value: adults


title: Input


title: H3_Utf1KO_Rep2


title: C. remanei XX 1

status: Public on Oct 25 2012

city: College Park

first: Eric

middle: S.

last: Haag

address: 4094 Campus Drive

department: Department of Biology

institute: University of Maryland

data_processing:
base were called with RTA (specific release indicated for each raw file;  see column E below)
C. briggsae reads were trimmed to 36bp to correspond to data obtained for the other species
reads were used to generate de novo transcriptome assemblies using SOAPdenovo v1.05, k-mer size 23. The contigs shorter than 50bp, at the tips smaller than 2k or whose coverage was low were removed.
reads were aligned to either genome reference sequences using TopHat v1.2.0 (-p 4 -i 40) or to the do novo assemblies using Bowtie v0.12.7 (-v 2 -m 3 -p 4 -q --best)
expression values for contigs were calculated as Reads Per Kilobase of contigs per Million mapped reads, expression values for gene models were assessed using Cufflinks v1.0.3  (default parameters, using gene annotation files from ENSEMBL release 9 and 14 for C. briggsae)
only genes or contigs whose expression were detected consistently across the three biological replicates were considered for further analyses. Statistical differential expression between sexes was assessed by linear regression models taking into account effect of sex and machine variation (HiSeq vs GAII)
Genome_build: C. japonica, C. elegans, C. brenneri, C.remanei, C. briggsae: Wormbase release WS224
C. japonica CJ302, C. elegans WS220, C. brenneri CB601, C.remanei CR2, C. briggsae CB4

organism: Caenorhabditis remanei

source_name: whole animal

growth_protocol: C. remanei, C. japonica, C. brenneri, and C. elegans  were maintained at 20˚C on OP50-seeded NGM agar plates , using 2.2% agar to discourage burrowing. C. briggsae was maintained at 25˚C  to prevent production of intersexual germ cells in the XX sex. To avoid inbreeding depression in obligately outcrossing strains, large populations were maintained by transferring large chunks from two independent plates per passage.

extract_protocol:
Worms were roughly synchronized by hypochlorite / bleach treatment, and at least 400 XX or 600 XO  L4 and young adult worms per replicate were hand-picked.  Worms were washed and resuspended in 50 microliters of RNA-ase free water. 250mL of TRI-Reagent (Molecular Research Center) were added and the samples were frozen at ‑80˚C. Samples were thawed and lysed using a plastic pestle. RNA was purified using phenol/chloroform extractions, isopropanol precipitations, and DNaseI treatment.
Single-ended cDNA libraries were prepared according to manufacturer’s protocol (Illumina)

tag: temperature (deg.c)

value: L4 & adult females

tag: rna

value: poly-A RNA

tag: base calling software version


title: C. japonica XO 1

organism: Caenorhabditis japonica

value: L4 & adult males


title: C. remanei XO 1


title: C. japonica XX 1


title: C. japonica XO 3


title: C. brenneri XX 1

organism: Caenorhabditis brenneri


title: C. brenneri XX 3


title: C. brenneri XO 3


title: C. japonica XX 3


title: C. brenneri XO 2


title: C. brenneri XX 2


title: C. japonica XX 2


title: H3K27me3_WT


title: A3-1 Ribosome profiling - siLuc

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: rpf-siLuc

data_processing: Sequence reads were mapped to a mouse genome assembly (mm9) using GSNAP with maximum 10% mismatches (for CLIP and untreated PolyA RNA-seq) or 5% mismatches (for RPF or the rest of PolyA RNA-seq). The best hits with maximum two mismatches that aligns to single position of genome were counted for RNA-seq transcript level expression. For RPF and CLIP lanes, the reads were aligned again to non redundant subset of RefSeq transcripts with fixed of single nucleotide polymorphisms detected in RNA-seq. 5'-most 26nt of tag reads were used for alignment of RPF and siRNA-treated RNA-seq reads. Transcript-level tag count were calculated using intersectBed with modified annotations of RefSeq, miRBase, RepeatMasker, rfam and tRNAdb. The detailed description of the analysis pipeline is available on supplementary methods section of the paper.

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cell were incubated in DMEM media containing 20% FBS, non-essentail amino acid and LIF at 37℃.

extract_protocol:
We purified the RNA using TRIzol according to manufacturer's protocol for PolyA+ RNA-seq samples, and we followed the conventional phenol extraction protocol (Ambion Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1)) for CLIP-seq and ribosome profiling libraries.
sucrose gradient sedimentation, RNA purification and Illumina sequencing for ribosome profiling

treatment_protocol: Mouse embryonic stem cell were treated with siRNA for luciferase or for Lin28a and incubated for 48 hours.

tag: library strategy

value: Ribosome profiling

tag: cell line

tag: clip antibody

tag: sirna sequence

tag: rna subset

value: ribosome-bound RNA


title: A3-1 Ribosome profiling - siLin28a


title: A3-1 PolyA+ RNA-seq - siLuc

description: polya-siLuc

extract_protocol:
We purified the RNA using TRIzol according to manufacturer's protocol for PolyA+ RNA-seq samples, and we followed the conventional phenol extraction protocol (Ambion Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1)) for CLIP-seq and ribosome profiling libraries.
RNA purification, oligo-dT enrichment, fragmentation and Illumina sequencing for RNA-seq

value: RNA-Seq

value: polyA RNA


title: A3-1 PolyA+ RNA-seq - siLin28a