title: 180

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH-Science for Life Laboratory

description: Sample 32

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
The paired-end reads were trimmed with respect to quality and remaining adapter sequences using Trim Galore and aligned to the human genome reference hg19 (ENSEMBL v71) with TopHat version 2.0.4
The aligned reads were assembled into transcripts using Cufflinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include output from Cufflinks for each Sample 1-33

source_name: skeletal muscle

extract_protocol:
Trizol® method
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing and clustered on cBot

tag: tissue

value: skeletal muscle

value: male

tag: biopsy location

value: left leg

tag: exercise status

value: trained

value: post-training period 1

tag: original sample id


title: hNSC_CHD8_KD_G_3

status: Public on Jan 21 2015

type: SRA

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

country: USA

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Bowtie (v0.12.9)
zcat /sequencers/sequencerO/runs/131021_SN7001144_0397_AH7LYYADXX/Data/Intensities/BaseCalls/Unaligned/Project_Jc798/Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.fastq.gz | bowtie -B 1 -p 8 --chunkmbs 256 -m 1 -x 1000 /home/jc798/GENOME/contam/contam - --al=131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.contam   --un=131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.unaligned 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.multi ; bowtie -B 1 -p 8 --chunkmbs 256 -m 1 -x 1000 /home/jl56/GENOME/hg19/dna/hg19_nh 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.unaligned 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.bowtie
Custom perl script
Cotney et al, Cell 2013.
RSEQTools (0.6.0)
cat Sample_JCOT_166_141_DFC_Chd8.bowtie | bowtie2mrf genomic > ../mrf/Sample_JCOT_166_141_DFC_Chd8.mrf
RSEQTools (0.6.0) and wigToBigWig
cat Sample_JCOT_148_hNSC_H3K27ac_1.mrf | mrf2wig Sample_JCOT_148_hNSC_H3K27ac_1; cat Sample_JCOT_148_hNSC_H3K27ac_1_chr*.wig | grep -v track > Sample_JCOT_148_hNSC_H3K27ac_1.wig; rm Sample_JCOT_148_hNSC_H3K27ac_1_chr*.wig; wigToBigWig -clip Sample_JCOT_148_hNSC_H3K27ac_1.wig /home/jl56/GENOME/hg19/dna/hg19_nh.chrom.sizes Sample_JCOT_148_hNSC_H3K27ac_1.bw
Tophat (v2.0.9)
tophat -p 8 -G /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf  -o 4_Sample_JCOT_214_004_ --no-novel-juncs --no-novel-indels --read-mismatches 1 --read-gap-length 0 --read-edit-dist 1 --read-realign-edit-dist 0 --b2-N 1 -g 1 -m 0 -M --library-type=fr-firststrand /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome ../Sample_JCOT_214_004_R1.fastq.gz ../Sample_JCOT_214_004_R2.fastq.gz
Htseq (v0.5.4)
samtools view ../4_Sample_JCOT_214_004_/accepted_hits.sorted.bam | htseq-count -q -s reverse - /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf > 4_Sample_JCOT_214_004_counts.txt
Genome_build: hg19 for human samples
Genome_build: mm9 for mouse samples
Genome_build: UCSC KnownGene annotation (05/13/2013)
Supplementary_files_format_and_content: bam (anonymized aligned read cooridinates)
Supplementary_files_format_and_content: bed (peak calls in UCSC bed format)
Supplementary_files_format_and_content: bigWig (signal tracks)
Supplementary_files_format_and_content: counts.txt (abundance measurements per gene reported by HTSeq)

molecule: polyA RNA

organism: Homo sapiens

source_name: human Neural Stem Cells

growth_protocol:
RNA-Seq: H9 derived human neural stem cells (hNSCs) were purchased from Life Science Technology (cat no. N7800100).  Cells were maintained in KnockOu™DMEM/F12 medium (12660-012, Life Science Technology) supplemented with StemPro® supplement (A1050801, Life Science), 20ng/ml basic FGF recombinant protein (GF003, EMD Millipore Corporation), and 20ng/ml EGF recombinant protein (GF144, EMD Millipore Corporation). These cells were cultured as a attached monolayer in tissue culture flasks precoated with the BD Metrigel  ™ hESC-qualified Matrix (354277, BD) in a 37C incubator with 5% CO2.
ChIP-seq: H9 derived human neural stem cells (hNSCs) were purchased from Life Science Technology (cat no. N7800100).  Cells were maintained in KnockOu™DMEM/F12 medium (12660-012, Life Science Technology) supplemented with StemPro® supplement (A1050801, Life Science), 20ng/ml basic FGF recombinant protein (GF003, EMD Millipore Corporation), and 20ng/ml EGF recombinant protein (GF144, EMD Millipore Corporation). These cells were cultured as a attached monolayer in tissue culture flasks precoated with the BD Metrigel  ™ hESC-qualified Matrix (354277, BD) in a 37oC incubator with 5% CO2.  Human brain tissue was excised from frozen brain slabs with a rotary cutting instrument. Mouse embryonic tissue was dissected from E17.5 mouse embryos harvested from timed pregnant mothers.

extract_protocol:
RNA-seq: Total RNA was extracted using the miRNeasy Micro Kit (217084, Qiagen), as described in the manufacturer’s instructions. The step of DNase I digestion was included to avoid potential DNA contamination.
Standard Illumina Multiplexed Paired-End Library Prep performed by the Yale Center for Genome Analysis (YCGA).
ChIP-seq: Nuclei were extracted in six pellet volumes of lysis buffer I (50 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubating on ice for 15 minutes.  Tissue was homogenized with a dounce homogenizer and nuclei were harvested by centrifugation at 2000g for 10 minutes at 4°C.  Nuclei were resuspended in five pellet volumes of nuclear lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubated on ice for 20 minutes.  300 mL nuclear lysates in 1.5 mL tubes were sonicated using a Misonix S4000 with 431A cup horn (10 second pulses, 10 second rest, 20 minutes total, 2°C maintained by circulating chiller).  Following sonication insoluble material was pelleted by centrifugation at 16000g for 10 minutes at 4°C.  A small sample of soluble crosslinked chromatin was purified, checked for correct sonication size range and DNA concentration was measured.  100 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 10 mg of CHD8 antibody.  Samples were incubated overnight at 4°C with rotation.  Beads were precipitated on magnet stand and washed five times with 1 mL of wash buffer (100 mM Tris pH8.0, 500 mM LiCl, 1% NP-40, 1% deoxycholic acid, 1x Roche Complete protease inhibitor, 5mM sodium butyrate) and once with TE.  Immunoprecipiated chromatin was eluted from beads with 50 mL of elution buffer (TE + 1% SDS) at 65°C for 10 minutes.  Crosslinks were reversed overnight at 65°C.  Chromatin was treated with RNAseA and proteinase K then purified with Qiagen PCR cleanup kit.  Concentration of eluted chromatin was measured with PicoGreen (Invitrogen).

treatment_protocol:
RNA-seq: All shRNAs were transfected using Amaxa Nucleofector (Laza) according to the manufacturer’s instructions. The following shRNAs were used: shCHD8 #C (CloneID: V2LHS_201084, Thermo), mature antisense sequence TAAAGACTCCAATGAGCAG); shCHD8#G (Clone ID: V3LHS_311510, Thermo), mature antisense sequence ACTGTTGAATCATCTGCCT). After transfection, cells were grown for 48 hours in KnockOut™ DMEM/F-12 medium.  Cells were then trypsinized by Accutase (Life Science Technology) and sorted on FCS Aria II machine.  Both western blotting and RT-qPCR were used to determine the downregulation of CHD8 expression.
ChIP-seq: Human brain tissue or mouse cortex tissue were briefly homogenized and crosslinked with 1% formaldehyde at room temperature with rotation for 15 minutes.  Crosslinking was quenched with 150 mM glycine. hNSC cells were crosslinked on culture plates, quenched with glycine,  scraped off plates, and transferred to 15 mL conical tubes. Cultured cells or tissue were harvested by centrifugation at 1500g for 5 min at 4C.   Pelleted tissue was washed twice with cold PBS, flash frozen and stored at -80°C.

tag: cell type

value: human Neural Stem Cells (hNSCs)

tag: transfected with

value: shCHD8 #G (CloneID:V3LHS_311510)

tag: time point

value: 48 hours after transfection


title: D2 hybrid 89 clone rep2

city: Pisa

first: Elena

last: Barghini

state: PI

address: Via del Borghetto 80

department: Department of Agriculture, Food and Environment

country: Italy

institute: University of Pisa

data_processing:
Sequenced reads were trimmed for adaptor sequence using trimmomatic version 0.32 with the following parameters:ILLUMINACLIP:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:51
Reads were mapped using CLC-BIO Genomic Workbench 5.1 onto a modified P. trichocarpa unigene model database version 9.1 (only one sequence per gene ID was retained)
Gene expression level was calculated and expressed as mreads per kilobase per million reads mapped (RPKM) as described in Mortazavi et al. (2008)
Genome_build: Ptrichocarpa_210_cds.fa
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Populus x canadensis

source_name: leaf

growth_protocol: Rooted cuttings of hybrids between P. deltoides (L155-079,female) and P. nigra (71077-2-308, male) were cultivated in 20×20 cm 2 pots in the greenhouse, under natural daylight conditions (750 μm m −2 s −1 ,maximal photon flux density), with air temperature maintained at 17–29 °C, and relative humidity from 55 to 90 %.

extract_protocol:
The total RNA was isolated from leaves of single plants with different RWC, according to the method described by Logemann et al. (1987), followed by DNAse  treatments to remove genomic DNA contamination. RNA was purified by phenol/chloroform extraction and was precipitated following standard procedures
RNA-Seq library was generated using the TruSeq RNA-Seq Sample Prep kit, according to the manufacturer’s protocol (Illumina Inc., San Diego, CA, USA)

treatment_protocol: Some hybrid plants 50–70 cm in height were normally watered and watering of others were suspended for 8 and 13 days

tag: genotype

value: Hybrid 89 clone 35

value: leaf

tag: Stage

value: severe drought


title: 126

country: Sweden

description: Sample 31

tag: gender

value: right leg


title: 118

description: Sample 30

value: untrained

value: pre-training period 1


title: dcp2-1 replicate 2

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

country: Germany

institute: University of Heidelberg

data_processing:
Adapter was removed with cutadapt 1.3.
18-26 nt long reads were selected, and among these, only those which are not originated from rRNAs and tRNAs were kept for downstream analysis.
Mapping of reads to TAIR10 genome was performed using bowtie2-2.2.0, with parameters -N 0 --phred33 --very-sensitive ; reads mapped with mismatches were removed from the Bam outputs.
BigWig files for read mapping were generated by converting the strand-specific coverage of TAIR10 genome computed by bedtools with the UCSC bedGraphToBigWig program.
Counting strand-independant of reads 18-26 nt on TAIR10 genes and intergenic regions were performed by bedtools-2.2.1.
Differential expression analysis was performed by DESeq 1.16.0 with default options.
Genome_build: TAIR10
Supplementary_files_format_and_content: BiGWig files for mapping of 18-26 nt long reads (excluding reads from rRNAs and tRNAs) on the TAIR10 genome, for each condition, on each strand.

organism: Arabidopsis thaliana

source_name: aerial portions

growth_protocol: A. thaliana plants were grown on Bouturage media (Duchefa) in long-day conditions (16 hours light, 8 hours dark) at 15°C and aerial portions were collected 12 days after germination.

extract_protocol:
Total RNA was extracted using the RNAeasy Plant mini kit according to the supplier’s instructions (Qiagen) ; RNA samples enriched for small fractions were obtained with mirVana miRNA Isolation Kit.
Small RNA-seq libraries were performed according to NEBNext Small RNA-seq Multiplex Small RNA Library Prep Set for Illumina, with a different bar code for each sample.

tag: age

tag: genotype/variation

value: dcp2 mutant


title: hNSC_CHD8_KD_C_3

value: shCHD8 #C (CloneID:V2LHS_201084)


title: D2 hybrid 85 clone rep2

value: Hybrid 85 clone 45


title: dcp2-1 replicate 1


title: hNSC_Ctrl_KD_1


title: D2 hybrid 85 clone rep1

value: Hybrid 85 clone 42


title: D1 hybrid 89 clone rep2

value: Hybrid 89 clone 15

value: moderate drought


title: 140

description: Sample 28

value: skeletal muscle

value: male

value: trained


title: Wild type replicate 1

value: wild type


title: 132

description: Sample 27


title: 160

description: Sample 33

value: female

value: post-training period 1


title: D1 hybrid 89 clone rep1

value: Hybrid 89 clone 10

value: leaf


title: C hybrid 89 clone rep2

value: Hybrid 89 clone 8

value: C (control)


title: 155

description: Sample 22

value: left leg


title: 116

description: Sample 26


title: 104

description: Sample 20

value: right leg


title: vcs-6/rdr6 replicate 1

value: vcs-6 and rdr6 double mutant


title: 165

description: Sample 29


title: D1 hybrid 85 clone rep2

value: Hybrid 85 clone 24


title: 108

description: Sample 25

value: untrained

value: pre-training period 1


title: 186

description: Sample 15


title: 220

description: Sample 24


title: Wild type replicate 2


title: 218

description: Sample 23


title: 147

description: Sample 21


title: C hybrid 85 clone rep1

value: Hybrid 85 clone 3


title: 206

description: Sample 13

value: skeletal muscle


title: 208

description: Sample 14


title: D2 hybrid 89 clone rep1

value: Hybrid 89 clone 20

value: severe drought


title: UbxIa-Exd

city: New York

first: Harmen

middle: J

last: Bussemaker

state: NY

address: 1212 Amsterdam Ave MC 2441

department: Biological Sciences

institute: Columbia University

description: wild-type UbxIa-Exd

library_source: genomic

data_processing:
Illumina 2500 fastq files were demultiplexed according to barcode (according to Riley et al, Methods in Molecular Biology, 2014)
For Hox-Exd complexes, 12/14/16-mer affinity tables were constructed from sample-specific Round 3 data together with Round 0 reference data using the method described in Riley et al, Methods in Molecular Biology, 2014 (PMID 25151169).
For Hox monomers, 9-mers affinity tables were constructed from sample-specific Round 3 data (Round 2 for Dfd) together with Round 0 control data using the method described in Riley et al, Methods in Molecular Biology, 2014 (PMID 25151169).
In the 16-mer affinity tables, the variable region (upper case) was extended with the fixed 5' and 3' flanking sequences of the library.
Genome_build: Not applicable - SELEX reads are not aligned to reference genome
Supplementary_files_format_and_content: List of 9/12/14/16-mer relative binding affinity tables derived from R2/R3 and R0 in tab-delimited format

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: recombinant protein

growth_protocol: All plasmids were transformed into BL21(DE3) (Agilent).  5ml overnight bacterial culture was diluted into 200mL (LB) and grown to OD 0.6.  Protein expression was induced with 1mM IPTG for 4 hours at 37C.

extract_protocol:
All His-tagged proteins were purified by cobalt chromatography (Clontech).  Bradford assays and Coomassie staining was used to assess protein quality and concentration.
Libraries were prepared according to methods described in Slattery et al, Cell, 2011 (PMID 22153072) and Riley et al, Methods in Molecular Biology, 2014 (PMID 25151169)

tag: tag

value: histidine

tag: sample type

value: wild-type UbxIa-Exd


title: AntpWT-Exd

description: wild-type Antp-Exd heterodimer

value: wild-type Antp-Exd heterodimer


title: ScrWT-Exd

description: wild-type Scr-Exd heterodimer

value: wild-type Scr-Exd heterodimer


title: 109

description: Sample 10

value: male

value: trained

value: post-training period 1


title: 214

description: Sample 18

value: female


title: 194

description: Sample 16

value: left leg


title: 191

description: Sample 19

value: right leg


title: D1 hybrid 85 clone rep1

value: Hybrid 85 clone 12

value: leaf

value: D1 (moderate drought)


title: 212

description: Sample 17

value: untrained

value: pre-training period 1


title: 207

description: Sample 8

value: skeletal muscle


title: library1_A

description: common reference for AntpWT-Exd, Lab-Exd, Dfd-Exd, UbxIVa-Exd, AbdA-Exd, and AbdB-Exd


title: library1

description: common reference for ScrWT-Exd and UbxIa-Exd


title: 213

description: Sample 12


title: C57BL6/J female OE

city: Bochum

first: Ninthujah

last: Kanageswaran

address: Universitätsstr. 150

department: Biology and Biotechnology

institute: Ruhr-University Bochum

description:
tissue pool of eight adult animals
C57BL6OEfemale

data_processing:
Illumina sequencing was performed on a Genome Analyzer IIx using single end 36-bp (OE) respectively 75-bp (ORNs) reads. In case of C57BL/6J mice and FACS-sorted mice (heterozygous) were sequenced on a HiSeq-2000 by standard Illumina protocols (101-bp, paired end).
RNA-Seq reads were aligned to version mm9 of mouse reference genome and transcriptome using TopHat (v2.0.7) which utilizes the ultra-fast short–read mapping program Bowtie to arrange the alignment
Aligned RNA-Seq reads for each sample were assembled into transcripts and their abundance was estimated by the program Cufflinks (v1.3.3) using the RefSeq mm9 reference transcriptome in Gene Transfer Format (GTF) obtained from the UCSC Genome Bioinformatics database (University of California Santa Cruz)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for sample

organism: Mus musculus

source_name: Olfactory Epithelium

extract_protocol:
Olfactory Epithelia were prepared and pooled from eight individuals for each condition. ORNs were obtained from OMP-GFP mice and enriched by FACS sorting. Subsequently RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol including the optional on-column DNaseI digestion.
Libraries for NGS sequencing were prepared from RNA and subjected to DSN normalization by standard Illumina protocols

tag: strain

value: wildtype

tag: tissue/cell type

value: Olfactory Epithelium (OE)


title: 196

description: Sample 3


title: 177

description: Sample 6


title: library5

description: common reference for ScrLinkGQ-Exd and AntpHT-Exd


title: FACS-sorted ORNs (homozygous)

description:
tissue pool of six adult animals
ORNshomo

source_name: Olfactory Receptor Neurons

value: transgenic OMP-GFP mice, homozygous

value: FACS-sorted olfactory receptor neurons (ORNs)


title: CD1 female OE

description:
tissue pool of eight adult animals
CD1OEfemale


title: library3

description: common reference for ScrArg5A-Exd and AntpQT-Exd


title: library4

description: common reference for AntpHQ-Exd and UbxIa2-Exd


title: FACS-sorted ORNs (heterozygous)

description:
tissue pool of eight adult animals
ORNshetero

value: transgenic OMP-GFP mice, heterozygous


title: 202

description: Sample 7


title: C hybrid 85 clone rep2

value: Hybrid 85 clone 4

value: C (control)


title: 101

description: Sample 9

value: male


title: library2_B

description: common reference for ScrHis-12A,Arg3A-Exd and AntpHQT-Exd


title: 182

description: Sample 2

value: trained

value: post-training period 1


title: 121

description: Sample 5

value: female

value: left leg


title: 138

description: Sample 11

value: right leg


title: library2_A

description: reference for PbFl

value: reference for PbFl


title: 201

description: Sample 4


title: library1_C

description: common reference for PbFl-Exd and Dfd

value: common reference for PbFl-Exd and Dfd


title: 219

description: Sample 1


title: AbdB-Exd

description: wild-type AbdB-Exd

value: histidine

value: wild-type AbdB-Exd


title: UbxIVa-Exd

description: wild-type UbxIVa-Exd

value: wild-type UbxIVa-Exd


title: Dfd

description: wild-type Dfd monomer

value: wild-type Dfd monomer


title: CD1 male OE

description:
tissue pool of eight adult animals
CD1OEmale

value: wildtype

value: Olfactory Epithelium (OE)


title: PbFl-Exd

description: wild-type PbFl-Exd heterodimer

value: wild-type PbFl-Exd heterodimer


title: PbFl

description: wild-type PbFl monomer

value: wild-type PbFl monomer


title: AntpHT-Exd

description: mutant Antp(F-6H, Q6T)-Exd

value: mutant Antp(F-6H, Q6T)-Exd


title: AbdA-Exd

description: wild-type AbdA-Exd

value: wild-type AbdA-Exd


title: AntpLinkQT-Exd

description: mutant Antp(RSQFGKCQE->KRVHLGTSTVNANGE, G4Q, Q6T)


title: library1_B

description: common reference for ScrArg3A-Exd, ScrHis-12A-Exd, ScrHis-12AGQ-Exd, and AntpLinkQT-Exd


title: Dfd-Exd

description: wild-type Dfd-Exd

value: wild-type Dfd-Exd


title: Lab-Exd

description: wild-type Lab-Exd

value: wild-type Lab-Exd


title: ScrLinkGQ-Exd

description: mutant Scr(KRVHLGTSTVNANGE->RSQFGKCQE, Q4G, T6Q)


title: Sucrose_16h

city: Tianjin

first: Bang

last: Wang

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina HiSeq™ 2000 used for sequencing
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 12) with Tophat.
The alignment results were stored in SAM format files for subsequent analysis.
The count of reads uniquely mapped to only one gene for each transcript were calculated by HTseq-count using SAM files and genome annotation as input.
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM).
Genome_build: GCA_000182925.2
Supplementary_files_format_and_content: tab-delimited text files including locus, length, reads, and RPKM

organism: Neurospora crassa OR74A

growth_protocol: Conidia were innoculated at 10^6 conidia/mL and grown 30 h for crop straws or 16 h for sucrose media.

extract_protocol:
Mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: 1×Vogel’s salts with 2% (w/w) sucrose

value: mycelia


title: ScrHis-12AGQ-Exd

description: mutant Scr(H-12A, Q4G, T6Q)-Exd

value: mutant Scr(H-12A, Q4G, T6Q)-Exd


title: AntpHQ-Exd

description: mutant Antp(F-6H, G4Q)- Exd

value: mutant Antp(F-6H, G4Q)- Exd


title: WheatStraw_30h

source_name: crop straw_mycelia

value: 1×Vogel’s salts with 2% (w/w) ground wheat straw

tag: tissue


title: RiceStraw_30h

value: 1×Vogel’s salts with 2% (w/w) ground rice straw


title: CornStraw_30h

value: 1×Vogel’s salts with 2% (w/w) ground corn straw for 30 h


title: SoybeanStraw_30h

value: 1×Vogel’s salts with 2% (w/w) ground soybean straw


title: ScrHis-12A,Arg3A-Exd

description: mutant Scr(H-12A, R3A)-Exd

value: histidine

value: mutant Scr(H-12A, R3A)-Exd


title: AntpQT-Exd

description: mutant Antp(G4Q, Q6T)-Exd

value: mutant Antp(G4Q, Q6T)-Exd


title: ScrArg3A-Exd

description: mutant Scr(R5A)-Exd heterodimer

value: mutant Scr(R5A)-Exd heterodimer


title: ScrHis-12A-Exd

description: mutant Scr(H-12A)-Exd heterodimer

value: mutant Scr(H-12A)-Exd heterodimer


title: mouse_E17.5_Frontal_Cortex_Chd8_1

source_name: mouse E17.5 Cortex

tag: strain background

tag: developmental stage

value: Embryonic Day 17.5

value: Cortex

tag: chip antibody

value: CHD8 N terminus

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: BarleyStraw_30h

value: 1×Vogel’s salts with 2% (w/w) ground barley straw for 30 h


title: ScrArg5A-Exd

description: mutant Scr(R3A) -Exd heterodimer

value: mutant Scr(R3A) -Exd heterodimer


title: 4922_CD4_Naive_0 [Bisulfite-Seq]

status: Public on Jan 20 2015

city: La Jolla

first: Daniel

last: Salomon

state: CA

address: 10550 N Torrey Pines Rd, MEM-241

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

description: Bisulfite Treated

data_processing:
Basecalls performed using CASAVA versions 1.5-1.8.1
Bisulfite reads were mapped to hg18 with novoalign in bisulfite mode with the following parameters:   novoalign -d [index file] -f [fastq file] -F STDFQ -b 4 -c 8 -a -h 120 -t 240 -s 50 -o SAM
Genome_build: hg18
Supplementary_files_format_and_content: Tab delimited text files containing % methylation by CpG with counts for each base at the indicated position.  Headers are "Gene, Chr, Position, Total_FWD_Reads, FWD_A, FWD_C, FWD_G, FWD_T, %Methylation_FWD, Total_REV_Reads, REV_A, REV_C, REV_G, REV_T, %Methylation_Rev"

source_name: Primary Naïve CD4 T Cell

growth_protocol: Naïve and memooy CD4 cells were negatively selected using magnetic beads (Stem Cell Technologies). CD8 T cells and CD19 B cells were positively selected on magnetic beads (Miltenyi Biotec).

extract_protocol:
Genomic DNA was prepared from cell pellets using an All Prep kit (QIAGEN).  DNA was bisulfite converted using the EpiTect Bisulfite conversion kit (QIAGEN).
Bisulfite treated genomic DNA was amplified by microdroplet PCR amplification on an RDT 1000 (RainDance Technologies) with a custom primer library according to the manufacturer’s instructions.  Briefly, microdroplets containing genomic DNA were merged with microdroplets from the custom primer droplet library.  The custom primer droplet library consists of a collection of individual primer droplets, where each primer droplet contains matched pairs of forward and reverse primer (for each amplicon defined within the primer library.  For primers covering a CpG, a degenerate base (C/T or G/A, depending on the strand) was used at that location. The RDT1000 generated each PCR droplet by pairing a single genomic DNA template droplet with a single primer droplet.  Paired droplets flow past an electrode embedded in the chip and are instantly merged together. All resulting PCR droplets were automatically dispensed as an emulsion into a single PCR tube and transferred to a standard thermal cycler for PCR amplification.  Each sample generated more than 1 million singleplex PCR droplets. Samples were amplified for 55 cycles, the droplet emulsion was broken, and the PCR product was purified over a MinElute column (QIAGEN) following the manufacturer’s recommended protocol. RainDance PCR products were end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. End-repaired products were concatenated using T4 DNA ligase and then fragmented to 200 bp using a Covaris S2. Fragmented PCR product was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified for 15 cycles and library fragments of ~350 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 an Illumina HiSeq 20002000  following the manufacturer's protocols.  100 bp single-end reads were generated with 10 samples per lane.

treatment_protocol: Purified naïve and memory CD4 T cells were cultured in RPMI supplemented with 10% FBS, 100 U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2 with anti-CD3/CD28 activator beads (Invitrogen) for 0 or 48 hours.

tag: activation


title: UbxIa2-Exd

description: wild-type UbxIa-Exd, replicate

value: wild-type UbxIa-Exd, replicate


title: mouse_E17.5_Occipital_Cortex_Chd8_1


title: 5220_CD4_Naive_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: AntpHQT-Exd

description: mutant Antp(F-6H, G4Q, Q6T)-Exd

value: mutant Antp(F-6H, G4Q, Q6T)-Exd


title: 5134_CD4_Memory_48 [RNA-Seq]

description: RNAseq

data_processing:
Basecalls performed using CASAVA version 1.5
RNAseq reads were mapped to hg18 with Tophat v1.4 using default parameters.  No junctions file (-j) or GTF file (-G) was specified.  Gene-level FPKM values were calculated with Cufflinks v2.0.2 in quantitation-only mode (-G) with the GENCODE gene models downloaded from the Human Genome Browser at UCSC in GTF format.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include RPKM for individual files.

source_name: Primary Memory CD4 T Cell

extract_protocol:
RNA was purified from cell pellets with TriZol following standard protocols
Total RNA was converted to cDNA with the Ovation RNA-seq system (NuGEN) following standard protocols.  cDNA was S1 endonuclease digested.  cDNA libraries were end-repaired, A-tailed, and ligated to indexed adapters.  Purified library was amplified with 15 cylces of PCR followed by size selection.  Cluster generation and sequencing was conducted on an Illumina GAIIx following manufacturer's intructions.

value: anti-CD3/CD28 beads, 48 hours


title: 4922_CD4_Memory_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5220_CD4_Memory_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5009_CD4_Memory_48 [RNA-Seq]

description: RNAseq


title: 5134_CD4_Naive_48 [RNA-Seq]

description: RNAseq


title: 5134_CD4_Memory_0 [RNA-Seq]

description: RNAseq


title: 5009_CD4_Naive_48 [RNA-Seq]

description: RNAseq


title: 5009_CD4_Memory_0 [RNA-Seq]

description: RNAseq


title: 5134_CD4_Naive_0 [RNA-Seq]

description: RNAseq


title: 5009_CD4_Naive_0 [RNA-Seq]

description: RNAseq


title: 5053_CD4_Memory_0 [RNA-Seq]

description: RNAseq


title: 5053_CD4_Memory_48 [RNA-Seq]

description: RNAseq


title: 5053_CD4_Naive_48 [RNA-Seq]

description: RNAseq


title: HsW-3

city: Atlanta

first: Hsiao-Lin

middle: V.

state: GA

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA by DNA Core Facility, University of Missouri- Columbia
The raw sequences in Illumina GAIIx sequencing reads were trimmed removing adapter using “fastx_clipper” in the FASTX-Toolkit (version 0.0.13) and smRNAs with lengths between 15 and 40 nt were selected and mapped to the Brachypodium genomic sequences (Bd v1.0 version) using BOWTIE (version 0.12.7).
Classification of small RNAs was performed by BEDTools (v2.10.0) and in-house UNIX shell programming using the following databases: Bd v1.0 annotations for protein coding features downloading from www.Brachypodium.org.
Total number of smRNAs mapped to 3'UTR region of the coding genes were calculated (as raw count) and normalized to the total number of mapped reads multiplied by 106 (rpm, reads per million).
Genome_build: Bd v1.0
Supplementary_files_format_and_content: tab-delimited text files include raw sequence count mapped to 3'UTR region of the coding genes for each Sample.

organism: Brachypodium distachyon

source_name: Brachypodium leaves

growth_protocol: A community standard diploid inbred line of Brachypodium distachyon, Bd21, was used for all experimental treatments. The palea and lemma were carefully peeled off from the mature seeds with fine forceps. The stripped seeds were sterilized by soaking in a solution of 0.615% sodium hypochlorite supplemented with 0.1% Tween 20 for 10 min with occasional rocking. The sterilized seeds were thoroughly rinsed three times with sterile double-distilled water and placed on Murashige and Skoog (1/2 MS)-agar plates (1/2 MS-agar plates hereafter) (4.3 g/l MS salts with vitamins, 3% sucrose, pH 5.8, and 0.4% phytagel). The seeds/plates were cold-treated at 4°C for 2 days to synchronize germination, followed by germination in a light incubator at 22°C with a daily photoperiodic cycle of 16 h light and 8 h dark. Germinated seedlings were transplanted into soil and grown in a light incubator at 22°C with a daily photoperiodic cycle of 16 h light and 8 h dark.

extract_protocol:
Total RNA was isolated from the leaves of unstressed and stress treated plants using TRIzol (Life Technologies) according to the manufacturer’s protocol.
The RNA samples were used for sequencing library construction using the Small RNA sample Prep v1.5 kit and TruSeq Small RNA Sample Prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.  The smRNA libraries were sequenced using the Illumina Genome Analyzer II (by DNA Core Facility, University of Missouri- Columbia) according to the manufacturer’s instructions.

treatment_protocol: For heat stress treatments, plants were either incubated at 42°C for 1 or 3 hours in the temperature and light controlled growth chamber, or immersed in 42°C water for 1 or 3 hours. For cold stress treatment, plants were incubated at 4°C for 6 or 24 hours. For the salt stress treatment, the soil of plants was soaked with 300 mM NaCl until saturation and plants were grown for 48 hours in a light incubator. The leaves of unstressed and stress treated plants were collected and frozen in liquid nitrogen before RNA extraction.

tag: cultivar

tag: stress conditions

value: Heat stress by water immersion for 3 hours

value: leaves


title: HsA-1

value: Heat stress by air incubation for 1 hour


title: HsA-3

value: Heat stress by air incubation for 3 hours


title: HsW-1

value: Heat stress by water immersion for 1 hour


title: Ss-48

value: Salt stress for 48 hours


title: Cs-24

value: Cold stress for 24 hours


title: Bd21

value: unstressed


title: Cs-6

value: Cold stress for 6 hours


title: Sp 1

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

description: Sample 17

data_processing:
We use Rockhopper for alignment and the complete analysis of data
Genome_build: ASM28121v1
Supplementary_files_format_and_content: tab-delimited text files include expression values obtained in Rockhopper for each sample

organism: Pseudomonas putida DOT-T1E

extract_protocol:
Single colonies of P. putida strain DOT-T1E were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: spectinomycin


title: Gm 2

description: Sample 16

value: gentamicin


title: Sp 2

description: Sample 18


title: 5053_CD4_Naive_0 [RNA-Seq]

description: RNAseq


title: Tc 2

description: Sample 12

value: tetracycline


title: Rif 1

description: Sample 13

value: rifampicin


title: Rif 2

description: Sample 14


title: Gm 1

description: Sample 15


title: Cip 2

description: Sample 10

value: ciprofloxacin


title: Tc 1

description: Sample 11


title: Km 1

description: Sample 7

value: kanamycin


title: Km 2

description: Sample 8


title: TDG_WT_fC_protect

city: Chicago

first: Dali

last: Han

state: IL

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) by bismark v0.8.333,using options -n 1 -l 40 -chunkmbs 512.
The numbers of converted and unconverted cytosines were further extracted from each 5fC/5caC-enriched bisulfite-Seq and DIP-CAB-Seq datasets. CpGs with less than 10 reads were discarded.
The difference between bisulfite-Seq and DIP-CAB-Seq datasets were tested by using a Fisher’s exact test. CpGs with a significantly higher unconverted rate (P<0.05 and difference > 1%) in DIP-CAB-Seq were taken as 5fC/5caC-modified cytosines
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files for each dataset was generated by HOMER software
5caC_TDG_KO_site.txt and 5fC_TDG_KO_site.txt data content information:
Column 1: chromosome
Column 2: position
Column 3: orientation
Column 4: Number of C reads in protect sample
Column 5: Number of T reads in protect sample
Column 6: Number of C reads in DIP sample
Column 7: Number of T reads in DIP sample
Column 8: Difference of C% between protect and DIP samples
Column 9: Fisher's exact test P.value.

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: ES cell lines were cultured in feeder-free gelatin-coated pleates in Dulbecco's Modified Eagle (DMEM) supplemented with 15% FBS, 2mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1x non-essential amino acids, 1,000 units/mL LIF, 1x pen/strp.

extract_protocol:
Sonicated mESC genomic DNA (average 400 bp) was subjected to four parallel 5fC/5caC DNA IP. For each DIP assay, 1 μL (anti-5fC) or 0.5 μL (anti-5caC) of antiserum was used. The immunoprecipitated DNA was combined and subjected to either traditional bisulfite treatment or chemical-assisted bisulfite treatment. Hydroxylamine protection of 5fC on immunoprecipitated DNA was performed with 10 mM O-ethylhydroxylamine (Aldrich, 274992) in 100 mM MES buffer (pH = 5.0) at 37°C for 4 h. Protection of 5caC was performed with 20 mM NHS (Aldrich 130672), 2mM EDC (Pierce, 77149), in 75mM MES buffer (pH=5.0) at 37°C for 0.5 h.
After buffer exchange to 100 mM sodium phosphate (pH=7.5) and 150 mM NaCl, the pre-activated 5caC was incubated with 10 mM (4-aminomethyl)benzylazide at 37°C for 1 h. 50 ng of bisulfite treated DNA was tagged with Illumina compatible adapter and amplified to an appropriate library concentration using EpiGnome Methyl-Seq kit (Epicentre-Illumina). Libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer DNA 1000 Chip.

treatment_protocol: DNA library coupled with DNA immunoprecipitation of 5fC and 5caC, chemical protection of 5fC and 5caC, bisulfite treatment

tag: antibody

tag: treatment

value: chemical protection

tag: genotype/variation

value: Tdg fl/fl


title: Cm 2

description: Sample 6

value: chloramphenicol


title: TDG_WT_fC_DIP

tag: strain

value: traditional bisulfite


title: TDG_KO_fC_protect

value: Tdg -/-


title: TDG_WT_caC_protect


title: TDG_WT_caC_DIP


title: Cm 1

description: Sample 5


title: TDG_KO_fC_DIP


title: HITseq_SPT5

city: Frederick

first: Xiaolin

last: Wu

state: MD

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

data_processing:
library strategy: HITseq
Basecalls performed with Illumina software.
Sequence reads (fastq) were trimmed on both ends for LTR sequences and linker sequences.
Trimmed sequences represent HIV integration junction were mapped to mouse genome mm9 using BLAT
Sites were filtered: PE read must map to the same chr, on opposite strand, and within 1kb of distance
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: LEDGF-/- MEF cells

growth_protocol: LEDGF-/- MEF cells were electroporated with plasmid encoding fusion protein.  Cells were then infected with HIV virus 24 hrs later and grew for additional 3 days.

extract_protocol:
Genomic DNA was extracted from HIV infected cells
HIV integration junction sites were amplified by LM-PCR with one primer to the LTR and the other to the linker.  Nested PCR was carried out to clean the product. PCR products were then sequenced using standard Illumina paired end sequencing on GAIIx (70bp) or HiSeq (100bp).

tag: cell type

value: MEF

tag: genotype

value: LEDGF-/-

tag: plasmid encoding protein fused to ledgf-ibd

tag: infection

value: HIV


title: HITseq_NABP2


title: HITseq_INTS9


title: Ap 2

description: Sample 4

value: ampicillin


title: HITseq_NABP1


title: DNMT3B1_ChIPseq Set2d-KO

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
basecalls using CASAVA
fastq to fasta conversion
reads were aligned to mm9 mouse genome using BOWTIE, allowing up to 2 missmatches
coordinates of unique reads that map only once to the mouse genome were converted to WIG format
Genome_build: mm9
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells  were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).

extract_protocol:
For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 150 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.
ChIP-seq library using Illumina TruSeq library protocol with index adapters. Four to five libraries with different barcodes were pooled at equimolar ratios per lane

value: embryonic stem cells


title: C hybrid 89 clone rep1

value: Hybrid 89 clone 6

tag: tissue

value: leaf

tag: Stage

value: C (control)


title: LB 1

description: Sample 1

value: control


title: Cip 1

description: Sample 9


title: DNMT3A2_ChIPseq Set2d-KO


title: TDG_KO_caC_DIP


title: HITseq_NELFE

value: NELFE


title: DNMT3A2_ChIPseq low

value: wild type

value: mock


title: H3K9me1-ChIP-Seq-of-WT-RA

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with only unique mapped reads were kept
Data were filtered using samtools to remove potential PCR duplicates
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 300 bp, and then normalized to 10 M of depth. FPKM were obtained by Tophat and Cufflinks based on UCSC mm9 known genes annotation.

source_name: RA-treated WT ESC

growth_protocol: ES cells were maintained in the presence of feeders in standard ES medium (DMEM supplemented with FBS, nucleosides, non-essential amino acids, glutamine, LIF and β-mercaptoethanol. ES cells were cultured in feeder free conditions in 2i medium (citation) for 2 passages to eliminate feeder cells prior to further analysis.

extract_protocol:
Chromatin Immunoprecipitation were performed according to Diagenode IDeal ChIP-seq Kit with minor modifications. Briefly, 2 million cells were harvested in PBS and crosslinked in 1% formaldehyde for 2 minutes. After sonication, chromatin from 1 million cells was subjected to ChIP using IDeal ChIP-seq Kit. For RNA-Seq, RNA samples were extracted using Trizol reagent, and genomic DNA contaminations were eliminated with TurboTM DNase (Life technologies).
ChIP-seq libraries were constructed with KAPA Library Preparation Kits and single-end sequenced with Hiseq 2000. For RNA-Seq, total RNA were extracted and the subsequent library preparation steps were carried out according to standard Illumina procedures at the NIBS sequencing center and subjected to single-end sequencing.

treatment_protocol: For RA induction, 1 uM all-trans retinoic acid was added into medium and LIF was withdrawn simultaneously.

value: 1 uM all-trans retinoic acid (RA)

tag: strain background

value: C57BL/6 (mixed)

tag: chip antibody

value: H3K9me1, Ab8896 (Abcam)


title: LB 2

description: Sample 2


title: H3K9me1-ChIP-Seq-of-Mutant-RA

source_name: RA-treated Mutant ESC

value: GLP mutant (GLP 3A) homozygous


title: HITseq_NELFCD

value: NELFCD


title: H3K9me1-ChIP-Seq-of-Mutant-ESC

source_name: Mutant ESC

value: untreated


title: HITseq_NELFB

value: MEF

value: LEDGF-/-

value: NELFB


title: H3K9me2-ChIP-Seq-of-Mutant-RA.rep3

value: H3K9me2, mAbcam 1220


title: HITseq_NELFA

value: NELFA

value: HIV


title: RNA-Seq-of-Mutant-ESC-untreated.rep2


title: input-of-Mutant-ESC-untreated.rep3


title: H3K9me2-ChIP-Seq-of-Mutant-ESC.rep3


title: Ap 1

description: Sample 3

value: ampicillin


title: RNA-Seq-of-Mutant-ESC-RA-treated.rep2


title: TDG_KO_caC_protect

value: chemical protection

value: Tdg -/-


title: HITseq_INTS11


title: HITseq_INTS3


title: HITseq_INIP

value: INIP


title: input-of-WT-RA.rep3

value: wild type


title: H3K9me2-ChIP-Seq-of-WT-RA.rep3

value: 1 uM all-trans retinoic acid (RA)


title: H3K9me1-ChIP-Seq-of-WT-ESC

source_name: WT ESC

value: C57BL/6 (mixed)


title: H3K9me2-ChIP-Seq-of-WT-ESC-untreated.rep3


title: input-of-WT-ESC-untreated.rep3


title: RNA-Seq-of-Mutant-ESC-RA-treated.rep1


title: 5284_CD19 [Bisulfite-Seq]

description: Bisulfite Treated

source_name: Primary CD19 B Cell


title: RNA-Seq-of-WT-ESC-untreated.rep2


title: input-of-Mutant-ESC-untreated.rep2


title: H3K9me2-ChIP-Seq-of-Mutant-ESC.rep2


title: input-of-ChIPSeq-Mutant-RA.rep2


title: RNA-Seq-of-WT-ESC-RA-treated.rep1


title: RNA-Seq-of-Mutant-ESC-untreated.rep1


title: input-of-ChIPSeq-Mutant-RA.rep3


title: 5220_CD19 [Bisulfite-Seq]

description: Bisulfite Treated


title: RNA-Seq-of-WT-ESC-RA-treated.rep2


title: RNA-Seq-of-WT-ESC-untreated.rep1


title: input-of-WT-RA.rep2


title: H3K9me2-ChIP-Seq-of-WT-RA.rep2


title: 5211_CD19 [Bisulfite-Seq]

description: Bisulfite Treated


title: input-of-WT-ESC-untreated.rep2


title: 4922_CD19 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5284_CD8 [Bisulfite-Seq]

description: Bisulfite Treated

source_name: Primary CD8 T Cell


title: H3K9me2-ChIP-Seq-of-Mutant-RA.rep2


title: 5220_CD8 [Bisulfite-Seq]

description: Bisulfite Treated


title: Dicer KO (replicate 1)

city: Research Triangle Park

first: Paula

last: Stein

state: NC

address: 111 T.W. A;exander Dr.

department: Reproductive and Developmental Biology Laboratory

institute: NIEHS

data_processing:
Basecalls performed with Illumina base calling software [Illumina Real time analysis(RTA) 1.13.48]
Reads were mapped to the mm10 transcriptome and genome using Tophat (version 2.0.7) with parameters '--read-mismatches 1 --read-gap-length 1 --read-edit-dist 1 --max-multihits 100 --no-discordant --b2-very-sensitive --transcriptome-max-hits 100 --library-type fr-unstranded --no-coverage-search –no-novel-juncs'
Transcript abundance was calculated using HTSeq (version 0.6.1).
Differential expression analysis was performed using DESeq version 1.10.0
Genome_build: mm10
Supplementary_files_format_and_content: Text format with columns [transcript_ID, raw_read_counts].

source_name: Full-grown germinal vesicle-intact oocyte

extract_protocol:
Twenty oocytes were lysed in NuGen lysis buffer and cDNA synthesis was performed using the Ovation RNA-Seq System V2 (Nugen) kit.  The resulting cDNA was fragmented into 200bp using Covaris shearing.
Ovation Ultralow DR Multiplex System (Nugen)

value: Dicer null


title: Dicer WT (replicate 2)

value: Dicer wild-type

value: Full-grown germinal vesicle-intact oocyte


title: Dicer KO (replicate 2)


title: Dicer KO (replicate 3)


title: CH

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

data_processing:
RNA-seq: the cDNA library with a fragment length range of 200 bp (±25 bp) was constructed and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000).
Filtering: the trimming adapter sequences were removed and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the software
Gene annotation: for annotation of unigenes using various bioinformatics approaches, the unigenes were firstly searched against the Nr, COG, KEGG and Swiss-Prot protein database using local BLASTx with E value cutoff of 10-5.
Gene Expression Analysis: Gene expression levels were measured in the RNA-Seq analysis as reads per kilobase of exon model per million mapped reads (RPKM). The DEseq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR < 0.01).
Supplementary_files_format_and_content: The excel file contain the gene name, gene length, RPKM value, the number of total reads and the number of unique reads

organism: Boehmeria nivea

source_name: roots

growth_protocol: The seedlings were prepared with shoot-cutting reproduction method. The rooted seedlings were each transplanted in a pot (15 cm in diameter and 12 cm in depth) with nutritious soils (clay: sand: organic matter = 1:1:1, v/v) and cultured in a climate-controlled chamber (14 h light photoperiod; 80% RH; 26 ± 2°C).

extract_protocol:
To prepare samples for digital gene expression analysis, roots of three individual CK or CH plants sampled at the same time point were equally pooled and constituted a sample.Total RNA of each sample was extracted using an EASYspin plus Total RNA kit (Aidlab, Beijing, China) following the protocol. Quality and yield of RNA were determined by agarose gel electrophoresis and Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.
RNA of CK (equally mixed RNA of 3 time points) and CH (equally mixed RNA of 3 time points) samples were used to construct the cDNA library, respectively, with a fragment length range of 200 bp (±25 bp). Then, the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000) according to the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: For preparing challenge (CH) and mock-challenge plants (CK), One milliliter water with or without 150 nematodes were added directly near the roots of each ramie seedling. Three independent biological replications were performed for both inoculated and control plants. One, 3 and 5 days after inoculation (dpi), inoculated and un-inoculated plants were uprooted, the roots of each plant were washed with tap water and blotted dry.

value: roots

tag: developmental stage

value: 30 day old

value: Qingdaye

value: Pratylenchus coffeae infected


title: Ago2 null (replicate 2)

value: Ago2 null


title: CK

value: uninfected


title: 5134_CD4_Naive_0 [Bisulfite-Seq]

description: Bisulfite Treated

tag: activation


title: 5134_CD4_Naive_48 [Bisulfite-Seq]

description: Bisulfite Treated

value: anti-CD3/CD28 beads, 48 hours


title: Dicer WT (replicate 1)


title: 4922_CD8 [Bisulfite-Seq]

description: Bisulfite Treated


title: Ago2 null (replicate 1)


title: 5211_CD8 [Bisulfite-Seq]

description: Bisulfite Treated


title: Ago2 ADH (catalytically inactive), replicate 1

value: Catalytically inactive Ago2


title: Ago2 fl/fl (replicate 3)

value: Ago2 wild-type


title: Ago2 ADH (catalytically inactive), replicate 3


title: 5234_CD4_Naive_48 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5211_CD4_Naive_48 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5234_CD4_Naive_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: Ago2 fl/fl (replicate 2)


title: H3K9me2-ChIP-Seq-of-WT-ESC-untreated.rep2

value: untreated

value: H3K9me, mAbcam 1220


title: Ago2 ADH (catalytically inactive), replicate 2


title: Dicer WT (replicate 3)


title: 5234_CD4_Memory_48 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5234_CD4_Memory_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: 5211_CD4_Memory_48 [Bisulfite-Seq]

description: Bisulfite Treated


title: Ago2 fl/fl (replicate 1)


title: ES_DNMT3B1_DRB

source_name: embryonic stem cells, 75 uM DRB, 10 h

treatment_protocol: 75 uM 5,6-dichloro-1-b-D-ribofuranosylbenzimidazole (DRB) in DMSO were directly added to the growth medium and incubated for ten hours

value: embryonic stem cells

value: wild type


title: ES_DNMT3B1_S277P_rep2

source_name: embryonic stem cells, mock treatment


title: ES_DNMT3B1_S277P_rep1


title: 5211_CD4_Memory_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: NP_DNMT3B1_rep1

source_name: neuronal progenitor cells, mock treatment

value: neuronal progenitor cells


title: NP_DNMT3B1_rep2


title: TKO_DNMT3B1


title: ES_DNMT3B1_rep1


title: ES_DNMT3B1_rep2


title: ES_DNMT3A2_rep2


title: 5134_CD4_Memory_0 [Bisulfite-Seq]

description: Bisulfite Treated


title: input-of-ChIPSeq-Mutant-RA.rep1

growth_protocol:
mouse strain: The targeting vectors were constructed and electro-transfected into R1 ES cells. Positive clones were picked and screened by genomic PCR. To confirm the targeting events resulted in a functional and correctly mutated allele, DNA fragments that spanning the targeting vectors were amplified from cDNA and sequenced. The correct ES clones were used to produce chimeras. F1 heterozygous mice were obtained by crossing chimera with C57BL/6 female mice.
ES cells were maintained in the presence of feeders in standard ES medium (DMEM supplemented with FBS, nucleosides, non-essential amino acids, glutamine, LIF and β-mercaptoethanol. ES cells were cultured in feeder free conditions in 2i medium (citation) for 2 passages to eliminate feeder cells prior to further analysis.

value: C57BL/6 (mixed)

value: GLP mutant (GLP 3A) homozygous

value: embryonic stem cells (ESCs)

tag: treated with

value: 1 uM all-trans retinoic acid (RA)


title: H3K9me2-ChIP-Seq-of-Mutant-RA.rep1

tag: vendor

value: Abcam

value: mAbcam 1220


title: input-of-Mutant-ESC-untreated.rep1


title: input-of-WT-RA.rep1


title: ES_DNMT3B1_S280P


title: H3K9me2-ChIP-Seq-of-WT-RA.rep1


title: H3K9me2-ChIP-Seq-of-WT-ESC-untreated.rep1


title: input-of-WT-ESC-untreated.rep1


title: Primitivo_Soft_3

status: Public on Jan 19 2015

city: Verona

first: Mélanie

last: Massonnet

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology Department

institute: University of Verona

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence
Sequenced reads were aligned onto Vitis vinifera reference genome PN40024 (12x), using the program TopHat v2.0.6, with default parameters.
Mapped reads were used to reconstruct the transcripts using the program Cufflinks v2.0.2 and the V1 version of the 12x draft annotation of the grapevine genome.
Reconstructed transcripts were merged into a single non-redundant list of 29287 transcripts, using the program Cuffmerge, from the Cufflinks package. Using this novel list of transcripts, the normalized mean expression of each transcript was calculated in FPKM (Fragments Per Kilobase of Mapped reads) for each triplicate using the geometric normalization method.
Genome_build: Vitis vinifera reference genome PN40024
Supplementary_files_format_and_content: tab-delimited text file including mean FPKM values of the biological triplicate for each variety at each stage

organism: Vitis vinifera

source_name: berry pericarp

growth_protocol: Grape berries were collected from five red-skin-coloured Vitis vinifera cultivars, all cultivated in the same experimental vineyard (Conegliano, Veneto region, Italy), during the 2011 season.

extract_protocol:
Total RNA was extracted from approximately 400 mg of berry pericarp tissue (entire berries without seeds) ground in liquid nitrogen, using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with some modifications. The sixty non-directional cDNA libraries were prepared from 2,5 µg of total RNA using the Illumina TruSeq RNA Sample preparation protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Primitivo

tag: growth stage

value: Soft berries

tag: biological replicate


title: 5076_CD4_Memory_48 [Bisulfite-Seq]

description: Bisulfite Treated

source_name: Primary Memory CD4 T Cell


title: 5134_CD4_Memory_48 [Bisulfite-Seq]

description: Bisulfite Treated


title: Primitivo_Soft_2


title: Primitivo_Harv_1

value: Berries ripe for harvest


title: Primitivo_Harv_3


title: Primitivo_Soft_1


title: Primitivo_Harv_2


title: Primitivo_Touch_2

value: Berries beginning to touch


title: Primitivo_Touch_1


title: TKO_DNMT3A2


title: Primitivo_Pea_1

value: Pea-sized berries


title: Primitivo_Pea_3


title: Primitivo_Pea_2


title: ES_DNMT3A2_rep1


title: Refosco_Harv_2

value: Refosco


title: Refosco_Harv_1


title: H3K9me2-ChIP-Seq-of-Mutant-ESC.rep1

tag: genotype/variation


title: Refosco_Soft_3


title: Refosco_Soft_2


title: Refosco_Touch_3


title: Refosco_Soft_1


title: Refosco_Touch_2


title: Refosco_Pea_3


title: Refosco_Pea_2


title: Refosco_Pea_1


title: Refosco_Touch_1


title: Negroamaro_Harv_2

value: Negro amaro


title: Negroamaro_Harv_3


title: Negroamaro_Harv_1


title: Negroamaro_Soft_2


title: Negroamaro_Touch_2


title: Negroamaro_Touch_1


title: Negroamaro_Pea_3


title: Negroamaro_Soft_3


title: Negroamaro_Touch_3


title: Primitivo_Touch_3


title: Refosco_Harv_3


title: Negroamaro_Pea_2


title: Barbera_Harv_1

value: Barbera


title: Barbera_Harv_2


title: Barbera_Harv_3


title: Negroamaro_Pea_1


title: Barbera_Soft_3


title: Barbera_Soft_2


title: Barbera_Soft_1


title: Barbera_Touch_3


title: Barbera_Touch_2


title: Barbera_Touch_1


title: Barbera_Pea_3


title: Barbera_Pea_2


title: Sangiovese_Harv_3

value: Sangiovese


title: Sangiovese_Soft_3


title: Sangiovese_Harv_2


title: Sangiovese_Touch_3


title: Sangiovese_Harv_1


title: Sangiovese_Soft_1


title: Sangiovese_Soft_2


title: Sangiovese_Touch_1


title: Sangiovese_Pea_3


title: r2d2_r2d2_soma_beta

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

institute: Ludwig-Maximilians University

data_processing:
Reads were first sorted according to their sample index, then the 3'-adapter sequence and everything else 3'-of it was removed.
Reads were sorted into unique sequences with sequence counts
Reads were size-selected for 21-23 nt or 24-29-30 nt length .
Genome_build: n.a.
Supplementary_files_format_and_content: is a text file with the read sequence and the number of occurrences.

source_name: head & thorax

growth_protocol: flies were reared on standard yeast / cornmeal / molasses medium and harvested 5 days after eclosion.

extract_protocol:
The dissected body parts (head&thorax vs. ovaries) were ground in Trizol with a micro-pestle, then phase separation and precipitation was perfomed according to the manufacturer's instructions.
Total RNA was isolated using Trizol and size-selected on polyacrylamide/urea gels [~18-30 nt). In a first ligation step, pre-adenylated 3'-linkers were ligated to the 3'-end of the small RNAs (AMP-5'p=5'pCTGTAGGCACCATCAATdideoxyC-3') in the absence of ATP. After gel-purification of the ligation products, a 5'-Adapter was ligated in the presence of ATP  5('-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3'). Following reverse transcription with 5'-ATTGATGGTGCCTACAG-3', PCR was performed to append Adapter sequences for Illumina sequencing as well as indexes for multiplexing. A constant 5'-primer  (5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3') was combined with one of four 3'-index primers (5'-CAAGCAGAAGACGGCATACGAGGATCCGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGACAGCTGGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGATCTAGAGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACgaATCGATGATTGATGGTGCCTACAG-3'). Sequencing was single-end (75 nt length), 3'-adapters and indexes were sequenced together with the small RNAs.

treatment_protocol: no special treatment was performed on the live animals

tag: chemical treatment of isolated rna

value: oxidation and beta-elimination

value: head & thorax

value: r2d2 homozygous mutant


title: double mutant

city: Taipei

first: June-Tai

state: (Click to Select US State)

address: No.4, Sec. 1, Roosevelt Rd.

country: Taiwan

institute: National Taiwan Univeristy

data_processing:
A total of 90 million single-end reads, with an average length of 70 bps, was obtained for each sample.
Overrepresented sequences reported by FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) were filtered out by Trimmomatic
The first 10 bps of each sequencing read as well as sequences at read end with quality score ≤ 20 were trimmed, yielding approximately 50 million reads in each sample.
Sequenced reads were then aligned to the D. melanogaster genome (UCSC dm3/FlyBase r5.23) using TopHat (v2.0.9)
Differentially expressed genes between dBRWD3PX2/PX2 and dBRWD3PX2/+ or between dBRWD3PX2/+ and dBRWD3PX2/PX2, yemGS21861/GS21861 were compiled by using Cufflinks (v2.0.2), based on a false discovery rate (FDR) ≤ 0.1 as the cut-off.
Genome_build: UCSC dm3/FlyBase r5.23
Supplementary_files_format_and_content: fpmk

source_name: 3rd instar larval brain

growth_protocol: flies are culture in 25℃.

extract_protocol:
RNA is extracted by the TRIzol method (Invitrogen). Total RNA was treated with DNase I (2 μg) to remove DNA contamination and purified by TRIzol again. Samples were then subjected to ribosomal RNA removal using the Ribo-Zero™ Gold Kits (Epicentre Cat. #RZG1224),
100 ng of the rRNA-depleted RNAs were used for sequencing library preparation by Ion Total RNA-Seq Kit v2 (Life Technologies PN4475936 & PN4479789) according to the manufacturer's instructions.

treatment_protocol: third instar larval brains were isolated for brain transcriptome stduies

tag: tissue type

value: brian

value: 3rd instar larval stage

tag: strain

value: dBRWD3PX2/PX2, yemGS21861/GS21861


title: Sangiovese_Touch_2


title: control

value: brain


title: loqs_loqs_soma_beta

tag: genotype

value: Loqs homozygous mutant


title: loqs_het_soma_beta

value: Loqs heterozygous mutant


title: single mutant


title: r2d2_het_soma_beta

value: r2d2 heterozygous mutant


title: r2d2_r2d2_ovary_beta

source_name: ovary

value: ovary


title: Sangiovese_Pea_1


title: loqs_het_ovary_beta


title: r2d2_het_ovary_beta


title: r2d2_r2d2_soma


title: Negroamaro_Soft_1

value: Soft berries


title: Barbera_Pea_1

value: Pea-sized berries


title: r2d2_het_ovary


title: loqs_loqs_soma


title: Sangiovese_Pea_2


title: WT 24hr rep3

first: Jonathan

middle: Ross

last: Hart

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

description: Breast Epithelial cell line

data_processing:
Basecalls performed using CASAVA version v1.8.2
Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20
Aligned with Bowtie 2.1.0 and Tophat 2.0.10 using Gencode v19 junctions
Samtools 0.1.19-44428cd to make a bam, sort, index
Raw counts were generated using htseq_count 0.6.1 using the UCSC HG19 known gene transcripts from Illumina iGenomes
edgeR 3.2.4 in R 3.1.0 were used to normalize counts between samples and to make comparisons between groups.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized reads in CPM for each detected gene along with differential gene expression log2 (fold change) and p-values for each time point

source_name: WT 24hr rep3

growth_protocol: 500k Cells were seeded in 10cm petri dishes in DMEM/F12 growth medium.  After 24 hours, medium was changed to MCDB-170 serum free media.  Cells were allowed to grow an additional 24 hours.  Medium was changed once more and cells harvested at 0, 6, 12, 24 hours post medium exchange.

extract_protocol:
Total RNA was extracted using Trizol following standard protocol.  1mL Trizol was added directly to cells, RNA was separated from protein and DNA using 200uL chloroform.  Aqueous layer was removed and total RNA was precipitated using 500uL isopropanol precipitation.    This precipitate was redissolved and precipitated with 250uL DEPC treated water folled by 750uL anhydrous ethanol.  Pellet was redissolved in 200uL DEPC treated water. Residual DNA was eliminated using Ambion Dneasy kits.
Nugen Ovation protocol

treatment_protocol: No drug treatments

tag: cell line

tag: time


title: WT 24hr rep2

description: Breast Epithelial cell line

source_name: WT 24hr rep2


title: loqs_loqs_ovary

tag: tissue


title: loqs_het_ovary


title: loqs_het_soma


title: WT 12hr rep3

description: Breast Epithelial cell line

source_name: WT 12hr rep3


title: WT 12hr rep1

description: Breast Epithelial cell line

source_name: WT 12hr rep1


title: WT 0hr rep3

description: Breast Epithelial cell line

source_name: WT 0hr rep3


title: WT 0hr rep1

description: Breast Epithelial cell line

source_name: WT 0hr rep1


title: H1047R 0hr rep3

description: Breast Epithelial cell line

source_name: H1047R 0hr rep3


title: WT 0hr rep2

description: Breast Epithelial cell line

source_name: WT 0hr rep2


title: loqs_loqs_ovary_beta


title: r2d2_het_soma


title: H1047R 0hr rep2

description: Breast Epithelial cell line

source_name: H1047R 0hr rep2


title: r2d2_r2d2_ovary


title: H1047R 0hr rep1

description: Breast Epithelial cell line

source_name: H1047R 0hr rep1


title: WT 6hr rep3

description: Breast Epithelial cell line

source_name: WT 6hr rep3


title: WT 6hr rep2

description: Breast Epithelial cell line

source_name: WT 6hr rep2


title: WT 6hr rep1

description: Breast Epithelial cell line

source_name: WT 6hr rep1


title: WT 24hr rep1

description: Breast Epithelial cell line

source_name: WT 24hr rep1


title: WCE-ZR751_ChIP-seq

city: Paris

first: Ronan

last: Chaligné

address: 26, Rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Supplementary_files_format_and_content: Each sample contains three bedgraph files.
Supplementary_files_format_and_content: 1. ChrX full bedgraph display
Supplementary_files_format_and_content: 2. ChrX allele1 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: 3. ChrX allele2 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: Final SNP list: List of final SNPs derived from ChIP-seq, mRNA-seq and Exome-seq used for allele specific analysis
Datasets were subjected to two types of quality control. FASTQC-0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of sequencing and potential adapter or cross contaminants. Average sequencing quality (phred score) per base was above 30 (Q ≥ 30) for all datasets. In addition, aligned datasets were then subjected toNGS-QC ((Mendoza-Parra et al., 2013); www.ngs-qc.org) to assess the robustness of enrichment. The majority of data sets were of «triple A» quality, no data set was below «triple B». For exome-seq and ChIP-seq, alignment was performed using BWA-MEM-0.7.7 (Li and Durbin, 2009) with default parameters, which simultaneously checks for both global and local alignment for reads. Alignment was followed by three sets of filters to prevent bias in the analysis. 1) duplicate reads (PCR clonal reads) were filtered out using Picard tools-1.86 (http://picard.sourceforge.net) 2) reads with mapping quality less than 10 were filtered out using Bamtools-2.2.3 (https://github.com/pezmaster31/bamtools) and 3) reads with more than one alignment reported were filtered out using in-house scripts. Further analysis was carried out on processed alignment file which is around 10-100M reads after these filters.
To prepare the allele information for each cell-line for allele-specific analysis down the line, SNP analysis was carried out along with SNP6 data. To identify novel variation (apart from known SNPs from SNP6 data), SNP analysis was carried out on all three ChIP-seq, Exome-seq and RNA-seq data individually. ChIP-seq data of different marks (H3K4me3, H3K27me3, RNA Pol II and Input) were merged for each cell line to increase the depth and confidence for variation calling. Variation calling was performed for each cell line separately for ChIP-seq and Exome-seq following the best practice GATK-2.6.5 pipeline by filtering reads with Mapping quality ≥ 1 (Van der Auwera GA et al., 2013; http://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq). Variation calling for RNA-seq was carried out following the methods of Piskol, Robert et al., 2013 to avoid artifacts specific to RNA- seq data (Piskol et al., 2013). A final list of allele information was generated by combining the SNP information from the different data sets for each cell line. To increase the allele-specific sensitivity for the alignment, reads were additionally realigned in an allele-specific manner following the method of Satya et al. (Satya et al., 2012). Read counts for each allele and SNP position were extracted for each mark using in-house scripts. SNP positions with at least three reads from both alleles were considered as heterozygous positions.
Peak calling was performed using HOMER ((Heinz et al., 2010); http://homer.salk.edu/homer/index.html) with default parameters. For H3K27me3 and RNA Pol II, the'style' parameter was chosen as 'histone' due to the broad patterns for this mark, whereas for H3K4me3, which generally give sharp peaks, the parameter 'factor' was chosen. Genomic context annotation over identified peaks were carried out using the HOMER annotation module but with basic annotation by excluding references other than coding genes and non-coding RNA.
A gene-based analysis of annotation integration was carried out using in-house scripts to integrate all annotation from peak and variation calling (informative SNP counts, read depths, homo/heterozygous SNP count and weighted allelic imbalance). To include annotations from regulatory regions 1Kb sequences upstream from the TSS and downstream of the TES were considered. A weighted arithmetic average was calculated for each gene by calculating average Allelic Imbalance (AI) where each SNP's AI was weighted by its read depth.
To illustrate the comparisons across cell lines, ChIP-seq data were normalized using an in-house developed tool called 'Epimetheus', which is based on quantile normalization (manuscript under preparation). Read Count Intensity (RCI) was calculated for a window of 100bp bin size across chromosomes and then these intensities were normalized using quantile normalization from the limma package. The impact of normalization was assessed using MA plots before and after normalization. Specified genomic feature based normalized RCI was constructed, which are illustrated in Figure 6. For TSS-centered plots and heatmaps, a separate TSS-based normalization was carried out with 20bp bin size to obtain higher resolution.
Genome_build: hg19

source_name: Human Breast Cancer Cells

growth_protocol: Human Mammary Epithelial Cells (HMEC, Invitrogen) were grown in serum-free medium (HuMEC, Invitrogen). WI-38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS).

extract_protocol:
Phenol/chlorophrom extraction was used for gDNA isolation.
Standard Illumina protocols are followed.
ChIP-seq: Bioo Scientific NEXTflex kit is used (Catalog: 514120, 48 reactions)
ChIP-seq: Libraries were prepared according to the standard Illumina protocol and sequenced with the HiSeq2500 system. Single end sequencing was carried out to obtain around 25-150 million (M), 100bp long reads per sample.

tag: gender

value: Female

tag: cell type

value: Luminal

tag: antibody


title: WCE-SKBR3_ChIP-seq


title: mutant-1 miR277

description: TTgaaggttttgggctgcgtcacaggcatgcatttgcactgaaacTATCTGAAGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTT

data_processing:
Reads were first sorted according to their sample index, then the 3'-adapter sequence and everything else 3'-of it was removed.
Reads were size-selected for 17-30 nt length.
Reads were sorted into unique sequences and sequence counts => e.g. wt_miR277_unique.txt
Genome_build: n/a
Supplementary_files_format_and_content: Reads were sorted into unique sequences and sequence counts

source_name: transgenic fruit fly abdomen

growth_protocol: flies were maintained on standard cornmeal/molasses medium

extract_protocol:
severed abdomina were ground with a micro-pestle in trizol
Total RNA was isolated using Trizol and size-selected on polyacrylamide/urea gels [~18-30 nt). In a first ligation step, pre-adenylated 3'-linkers were ligated to the 3'-end of the small RNAs (AMP-5'p=5'pCTGTAGGCACCATCAATdideoxyC-3') in the absence of ATP. After gel-purification of the ligation products, a 5'-Adapter was ligated in the presence of ATP  5('-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3'). Following reverse transcription with 5'-ATTGATGGTGCCTACAG-3', PCR was performed to append Adapter sequences for Illumina sequencing as well as indexes for multiplexing. A constant 5'-primer  (5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3') was combined with one of four 3'-index primers (5'-CAAGCAGAAGACGGCATACGAGGATCCGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGACAGCTGGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGATCTAGAGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACgaATCGATGATTGATGGTGCCTACAG-3'). Sequencing was single-end (either 50, 75 or 78 nt length), 3'-adapters and indexes were sequenced together with the small RNAs.

treatment_protocol: The abdomen was severed from the rest of the fly with microscissors

tag: transgene

value: mutant-1 miR277

tag: transgene sequence

value: abdomen

tag: genetic background


title: WT 12hr rep2

description: Breast Epithelial cell line

source_name: WT 12hr rep2


title: mutant-2 miR277

description: TTgaaggttttgggctgtcgtaccagatagtgcatttgcactgaaacTATCTGAAGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTT

value: mutant-2 miR277


title: WCE-WI38_ChIP-seq

source_name: Human Embryonic Lung Fibroblasts

value: Normal Cells


title: wt miR277

description: TTGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGAAGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTT

value: wt miR277


title: H1047R 6hr rep2

description: Breast Epithelial cell line

source_name: H1047R 6hr rep2


title: H1047R 6hr rep1

description: Breast Epithelial cell line

source_name: H1047R 6hr rep1


title: H1047R 6hr rep3

description: Breast Epithelial cell line

source_name: H1047R 6hr rep3


title: RNAPolII-MDAMB436_ChIP-seq

data_processing:
Supplementary_files_format_and_content: Each sample contains three bedgraph files.
Supplementary_files_format_and_content: 1. ChrX full bedgraph display
Supplementary_files_format_and_content: 2. ChrX allele1 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: 3. ChrX allele2 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: Overall annotation matrix: A matrix excel file with gene-based peak annotation information and allele specific read counts with allelic imbalance ratio.
Supplementary_files_format_and_content: Final SNP list: List of final SNPs derived from ChIP-seq, mRNA-seq and Exome-seq used for allele specific analysis
Datasets were subjected to two types of quality control. FASTQC-0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of sequencing and potential adapter or cross contaminants. Average sequencing quality (phred score) per base was above 30 (Q ≥ 30) for all datasets. In addition, aligned datasets were then subjected toNGS-QC ((Mendoza-Parra et al., 2013); www.ngs-qc.org) to assess the robustness of enrichment. The majority of data sets were of «triple A» quality, no data set was below «triple B». For exome-seq and ChIP-seq, alignment was performed using BWA-MEM-0.7.7 (Li and Durbin, 2009) with default parameters, which simultaneously checks for both global and local alignment for reads. Alignment was followed by three sets of filters to prevent bias in the analysis. 1) duplicate reads (PCR clonal reads) were filtered out using Picard tools-1.86 (http://picard.sourceforge.net) 2) reads with mapping quality less than 10 were filtered out using Bamtools-2.2.3 (https://github.com/pezmaster31/bamtools) and 3) reads with more than one alignment reported were filtered out using in-house scripts. Further analysis was carried out on processed alignment file which is around 10-100M reads after these filters.
To prepare the allele information for each cell-line for allele-specific analysis down the line, SNP analysis was carried out along with SNP6 data. To identify novel variation (apart from known SNPs from SNP6 data), SNP analysis was carried out on all three ChIP-seq, Exome-seq and RNA-seq data individually. ChIP-seq data of different marks (H3K4me3, H3K27me3, RNA Pol II and Input) were merged for each cell line to increase the depth and confidence for variation calling. Variation calling was performed for each cell line separately for ChIP-seq and Exome-seq following the best practice GATK-2.6.5 pipeline by filtering reads with Mapping quality ≥ 1 (Van der Auwera GA et al., 2013; http://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq). Variation calling for RNA-seq was carried out following the methods of Piskol, Robert et al., 2013 to avoid artifacts specific to RNA- seq data (Piskol et al., 2013). A final list of allele information was generated by combining the SNP information from the different data sets for each cell line. To increase the allele-specific sensitivity for the alignment, reads were additionally realigned in an allele-specific manner following the method of Satya et al. (Satya et al., 2012). Read counts for each allele and SNP position were extracted for each mark using in-house scripts. SNP positions with at least three reads from both alleles were considered as heterozygous positions.
Peak calling was performed using HOMER ((Heinz et al., 2010); http://homer.salk.edu/homer/index.html) with default parameters. For H3K27me3 and RNA Pol II, the'style' parameter was chosen as 'histone' due to the broad patterns for this mark, whereas for H3K4me3, which generally give sharp peaks, the parameter 'factor' was chosen. Genomic context annotation over identified peaks were carried out using the HOMER annotation module but with basic annotation by excluding references other than coding genes and non-coding RNA.
A gene-based analysis of annotation integration was carried out using in-house scripts to integrate all annotation from peak and variation calling (informative SNP counts, read depths, homo/heterozygous SNP count and weighted allelic imbalance). To include annotations from regulatory regions 1Kb sequences upstream from the TSS and downstream of the TES were considered. A weighted arithmetic average was calculated for each gene by calculating average Allelic Imbalance (AI) where each SNP's AI was weighted by its read depth.
To illustrate the comparisons across cell lines, ChIP-seq data were normalized using an in-house developed tool called 'Epimetheus', which is based on quantile normalization (manuscript under preparation). Read Count Intensity (RCI) was calculated for a window of 100bp bin size across chromosomes and then these intensities were normalized using quantile normalization from the limma package. The impact of normalization was assessed using MA plots before and after normalization. Specified genomic feature based normalized RCI was constructed, which are illustrated in Figure 6. For TSS-centered plots and heatmaps, a separate TSS-based normalization was carried out with 20bp bin size to obtain higher resolution.
Genome_build: hg19

value: Basal-Like Carcinoma

value: Santa Cruz; sc-9001; H-224


title: H1047R 24hr rep3

description: Breast Epithelial cell line

source_name: H1047R 24hr rep3


title: RNAPolII-ZR751_ChIP-seq


title: WCE-HMEC_ChIP-seq

source_name: Human Mammary Epithelial Cells

value: HMEC


title: WT 6hr rep4

description: Breast Epithelial cell line

source_name: WT 6hr rep4


title: H1047R 24hr rep1

description: Breast Epithelial cell line

source_name: H1047R 24hr rep1


title: RNAPolII-WI38_ChIP-seq


title: WCE-MDAMB436_ChIP-seq


title: H3K27me3-ZR751_ChIP-seq

value: Millipore; ab07449


title: RNAPolII-HMEC_ChIP-seq


title: RNAPolII-SKBR3_ChIP-seq


title: H1047R 12hr rep3

description: Breast Epithelial cell line

source_name: H1047R 12hr rep3


title: Basal 2 dL #2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
Sample name: MCL1-DL
MCL1-DL_BC2CTUACXX_ATCACG_L002_R1
Raw data file batch date: Aug. 9, 2013

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling.
Reads were aligned to the mouse genome by subread version 1.4.4.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: GRCm38 (mm10, NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: mammary gland, basal cells, 2 day lactation

growth_protocol: Luminal and basal cells were sorted directly from mouse mammary glands.

extract_protocol:
FACS-sorted cells were lysed for RNA preparation using the QIAGEN RNeasy Plus Mini-kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

tag: strain/background

value: FVB/N

value: wild type

value: female

value: mouse mammary gland

tag: immunophenotype

value: basal cell population

tag: developmental stage

value: 2 day lactation


title: Basal 2 dL #1

description:
Sample name: MCL1-DK
MCL1-DK_BC2CTUACXX_TTAGGC_L002_R1
Raw data file batch date: Aug. 9, 2013

tag: genotype/variation


title: H3K27me3-MDAMB436_ChIP-seq

value: Female


title: H1047R 12hr rep2

description: Breast Epithelial cell line

source_name: H1047R 12hr rep2


title: Basal 18.5 dP #2

description:
Sample name: MCL1-DJ
MCL1-DJ_BC2CTUACXX_CGATGT_L002_R1
Raw data file batch date: Aug. 9, 2013

source_name: mammary gland, basal cells, 18.5 day pregnancy

value: 18.5 day pregnancy


title: ZR751_Exome

data_processing:
Library strategy: Exome-Seq
Supplementary_files_format_and_content: Final SNP list: List of final SNPs derived from ChIP-seq, mRNA-seq and Exome-seq used for allele specific analysis
Datasets were subjected to two types of quality control. FASTQC-0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of sequencing and potential adapter or cross contaminants. Average sequencing quality (phred score) per base was above 30 (Q ≥ 30) for all datasets. In addition, aligned datasets were then subjected toNGS-QC ((Mendoza-Parra et al., 2013); www.ngs-qc.org) to assess the robustness of enrichment. The majority of data sets were of «triple A» quality, no data set was below «triple B». For exome-seq and ChIP-seq, alignment was performed using BWA-MEM-0.7.7 (Li and Durbin, 2009) with default parameters, which simultaneously checks for both global and local alignment for reads. Alignment was followed by three sets of filters to prevent bias in the analysis. 1) duplicate reads (PCR clonal reads) were filtered out using Picard tools-1.86 (http://picard.sourceforge.net) 2) reads with mapping quality less than 10 were filtered out using Bamtools-2.2.3 (https://github.com/pezmaster31/bamtools) and 3) reads with more than one alignment reported were filtered out using in-house scripts. Further analysis was carried out on processed alignment file which is around 10-100M reads after these filters.
To prepare the allele information for each cell-line for allele-specific analysis down the line, SNP analysis was carried out along with SNP6 data. To identify novel variation (apart from known SNPs from SNP6 data), SNP analysis was carried out on all three ChIP-seq, Exome-seq and RNA-seq data individually. ChIP-seq data of different marks (H3K4me3, H3K27me3, RNA Pol II and Input) were merged for each cell line to increase the depth and confidence for variation calling. Variation calling was performed for each cell line separately for ChIP-seq and Exome-seq following the best practice GATK-2.6.5 pipeline by filtering reads with Mapping quality ≥ 1 (Van der Auwera GA et al., 2013; http://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq). Variation calling for RNA-seq was carried out following the methods of Piskol, Robert et al., 2013 to avoid artifacts specific to RNA- seq data (Piskol et al., 2013). A final list of allele information was generated by combining the SNP information from the different data sets for each cell line. To increase the allele-specific sensitivity for the alignment, reads were additionally realigned in an allele-specific manner following the method of Satya et al. (Satya et al., 2012). Read counts for each allele and SNP position were extracted for each mark using in-house scripts. SNP positions with at least three reads from both alleles were considered as heterozygous positions.
Peak calling was performed using HOMER ((Heinz et al., 2010); http://homer.salk.edu/homer/index.html) with default parameters. For H3K27me3 and RNA Pol II, the'style' parameter was chosen as 'histone' due to the broad patterns for this mark, whereas for H3K4me3, which generally give sharp peaks, the parameter 'factor' was chosen. Genomic context annotation over identified peaks were carried out using the HOMER annotation module but with basic annotation by excluding references other than coding genes and non-coding RNA.
A gene-based analysis of annotation integration was carried out using in-house scripts to integrate all annotation from peak and variation calling (informative SNP counts, read depths, homo/heterozygous SNP count and weighted allelic imbalance). To include annotations from regulatory regions 1Kb sequences upstream from the TSS and downstream of the TES were considered. A weighted arithmetic average was calculated for each gene by calculating average Allelic Imbalance (AI) where each SNP's AI was weighted by its read depth.
To illustrate the comparisons across cell lines, ChIP-seq data were normalized using an in-house developed tool called 'Epimetheus', which is based on quantile normalization (manuscript under preparation). Read Count Intensity (RCI) was calculated for a window of 100bp bin size across chromosomes and then these intensities were normalized using quantile normalization from the limma package. The impact of normalization was assessed using MA plots before and after normalization. Specified genomic feature based normalized RCI was constructed, which are illustrated in Figure 6. For TSS-centered plots and heatmaps, a separate TSS-based normalization was carried out with 20bp bin size to obtain higher resolution.
Genome_build: hg19

extract_protocol:
Phenol/chlorophrom extraction was used for gDNA isolation.
Standard Illumina protocols are followed.
Exome: SureSelect® array-capture (Affymetrix) has been used.
Exome: DNA exome-sequencing has been done by paired-reads lane 2x100 bp after a SureSelect® array-capture. Sequencing has been performed on high-throughput Illumina HiSeq sequencer.

value: Luminal


title: Basal virgin #2

description:
Sample name: MCL1-DH
MCL1-DH_BC2CTUACXX_CAGATC_L002_R1
Raw data file batch date: Aug. 9, 2013

source_name: mammary gland, basal cells, virgin

value: virgin


title: H3K27me3-HMEC_ChIP-seq


title: MDAMB436_Exome


title: SKBR3_Exome


title: H3K27me3-WI38_ChIP-seq


title: Basal virgin #1

description:
Sample name: MCL1-DG
MCL1-DG_BC2CTUACXX_ACTTGA_L002_R1
Raw data file batch date: Aug. 9, 2013


title: H3K4me3-ZR751_ChIP-seq

value: Abcam; ab8580


title: ZR751_mRNA

data_processing:
Supplementary_files_format_and_content: Each sample contains three bedgraph files.
Supplementary_files_format_and_content: 1. ChrX full bedgraph display
Supplementary_files_format_and_content: 2. ChrX allele1 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: 3. ChrX allele2 specific display of bedgraph only on SNP positions
Supplementary_files_format_and_content: Expression results: fpkm_tracking for genes standard output from cufflinks
Supplementary_files_format_and_content: Final SNP list: List of final SNPs derived from ChIP-seq, mRNA-seq and Exome-seq used for allele specific analysis
Datasets were subjected to two types of quality control. FASTQC-0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of sequencing and potential adapter or cross contaminants. Average sequencing quality (phred score) per base was above 30 (Q ≥ 30) for all datasets. In addition, aligned datasets were then subjected toNGS-QC ((Mendoza-Parra et al., 2013); www.ngs-qc.org) to assess the robustness of enrichment. The majority of data sets were of «triple A» quality, no data set was below «triple B». For exome-seq and ChIP-seq, alignment was performed using BWA-MEM-0.7.7 (Li and Durbin, 2009) with default parameters, which simultaneously checks for both global and local alignment for reads. Alignment was followed by three sets of filters to prevent bias in the analysis. 1) duplicate reads (PCR clonal reads) were filtered out using Picard tools-1.86 (http://picard.sourceforge.net) 2) reads with mapping quality less than 10 were filtered out using Bamtools-2.2.3 (https://github.com/pezmaster31/bamtools) and 3) reads with more than one alignment reported were filtered out using in-house scripts. Further analysis was carried out on processed alignment file which is around 10-100M reads after these filters.
To prepare the allele information for each cell-line for allele-specific analysis down the line, SNP analysis was carried out along with SNP6 data. To identify novel variation (apart from known SNPs from SNP6 data), SNP analysis was carried out on all three ChIP-seq, Exome-seq and RNA-seq data individually. ChIP-seq data of different marks (H3K4me3, H3K27me3, RNA Pol II and Input) were merged for each cell line to increase the depth and confidence for variation calling. Variation calling was performed for each cell line separately for ChIP-seq and Exome-seq following the best practice GATK-2.6.5 pipeline by filtering reads with Mapping quality ≥ 1 (Van der Auwera GA et al., 2013; http://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq). Variation calling for RNA-seq was carried out following the methods of Piskol, Robert et al., 2013 to avoid artifacts specific to RNA- seq data (Piskol et al., 2013). A final list of allele information was generated by combining the SNP information from the different data sets for each cell line. To increase the allele-specific sensitivity for the alignment, reads were additionally realigned in an allele-specific manner following the method of Satya et al. (Satya et al., 2012). Read counts for each allele and SNP position were extracted for each mark using in-house scripts. SNP positions with at least three reads from both alleles were considered as heterozygous positions.
Peak calling was performed using HOMER ((Heinz et al., 2010); http://homer.salk.edu/homer/index.html) with default parameters. For H3K27me3 and RNA Pol II, the'style' parameter was chosen as 'histone' due to the broad patterns for this mark, whereas for H3K4me3, which generally give sharp peaks, the parameter 'factor' was chosen. Genomic context annotation over identified peaks were carried out using the HOMER annotation module but with basic annotation by excluding references other than coding genes and non-coding RNA.
A gene-based analysis of annotation integration was carried out using in-house scripts to integrate all annotation from peak and variation calling (informative SNP counts, read depths, homo/heterozygous SNP count and weighted allelic imbalance). To include annotations from regulatory regions 1Kb sequences upstream from the TSS and downstream of the TES were considered. A weighted arithmetic average was calculated for each gene by calculating average Allelic Imbalance (AI) where each SNP's AI was weighted by its read depth.
To illustrate the comparisons across cell lines, ChIP-seq data were normalized using an in-house developed tool called 'Epimetheus', which is based on quantile normalization (manuscript under preparation). Read Count Intensity (RCI) was calculated for a window of 100bp bin size across chromosomes and then these intensities were normalized using quantile normalization from the limma package. The impact of normalization was assessed using MA plots before and after normalization. Specified genomic feature based normalized RCI was constructed, which are illustrated in Figure 6. For TSS-centered plots and heatmaps, a separate TSS-based normalization was carried out with 20bp bin size to obtain higher resolution.
Genome_build: hg19

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure.
Standard Illumina protocols are followed.
mRNA: total RNA was enriched for polyadenylated RNA (polyA mRNA).
mRNA : RNA-sequencing correspond of paired-reads lane 2x100 bp sequencing on poly-A RNA purified  and were prepared according to the standard Illumina protocol. Sequencing has been performed on high-throughput Illumina HiSeq sequencer.


title: H3K4me3-MDAMB436_ChIP-seq


title: H1047R 24hr rep2

description: Breast Epithelial cell line

source_name: H1047R 24hr rep2


title: Luminal 2 dL #2

description:
Sample name: MCL1-LF
MCL1-LF_BC2CTUACXX_CTTGTA_L001_R1
Raw data file batch date: Aug. 9, 2013

source_name: mammary gland, luminal cells, 2 day lactation

value: luminal cell population


title: MDAMB436_mRNA

source_name: Human Breast Cancer Cells


title: Luminal 2 dL #1

description:
Sample name: MCL1-LE
MCL1-LE_BC2CTUACXX_TAGCTT_L001_R1
Raw data file batch date: Aug. 9, 2013


title: WI38_Exome

value: Normal Cells


title: H3K4me3-HMEC_ChIP-seq


title: H3K4me3-WI38_ChIP-seq


title: H3K4me3-SKBR3_ChIP-seq


title: WI38_Clone39_mRNA


title: SKBR3_mRNA


title: Luminal 18.5 dP #1

description:
Sample name: MCL1-LC
MCL1-LC_BC2CTUACXX_GCCAAT_L001_R1
Raw data file batch date: Aug. 9, 2013

source_name: mammary gland, luminal cells, 18.5 day pregnancy


title: Luminal 18.5 dP #2

description:
Sample name: MCL1-LD
MCL1-LD_BC2CTUACXX_GGCTAC_L001_R1
Raw data file batch date: Aug. 9, 2013


title: WI38_Clone42_mRNA

source_name: Human Embryonic Lung Fibroblasts


title: Luminal virgin #1

description:
Sample name: MCL1-LA
MCL1-LA_BC2CTUACXX_GATCAG_L001_R1
Raw data file batch date: Aug. 9, 2013

source_name: mammary gland, luminal cells, virgin


title: Luminal virgin #2

description:
Sample name: MCL1-LB
MCL1-LB_BC2CTUACXX_TGACCA_L001_R1
Raw data file batch date: Aug. 9, 2013


title: Basal 18.5 dP #1

description:
Sample name: MCL1-DI
MCL1-DI_BC2CTUACXX_ACAGTG_L002_R1
Raw data file batch date: Aug. 9, 2013


title: H3K27me3-SKBR3_ChIP-seq