title: bud bloomer

city: Erfurt

first: Anne

last: Behrend

address: Kuehnhaeuser Strasse 101

department: Plant Propagantion

institute: Leibniz Institute of Vegetable and Ornamental Crops

data_processing:
data were obtained quality filtered, tag sorted, poly A+ tails and adapter trimmed from vertis Biotechnolgie AG, Freising, Germany
fastq was split in fasta+quals with MIRA 3.0.5 by the convert_project
sequences from plastids, endophytes, mitochondria, and for rRNA, were removed using SeqClean
sequence reads were assembled using the cDNA option of GS DeNovoAssembler (Newbler) 2.5.3 (Roche)
and mapped on backbone assembly (contigs from common assembly of both flower types) using the cDNA option of GS DeNovoAssembler (Newbler) 2.5.3 (Roche)
read numbers were normalized and differentially expressed contigs were identified using the Audic Claverie algorithm (p=0.01, Bonferroni correction) via the web tool IDEG6

organism: Calluna vulgaris

source_name: young flowers

growth_protocol: Plants were kept in the greenhouse in winter and under field conditions in frost free periods.

extract_protocol:
The sampels were ground under liquid nitrogen. From the tissue powder total RNA was isolated using s CTAB based protocol. The total RNA preparations were ananlysed for theit integrity by capillary electrophoresis. Form total RNA polyA+ RNA was prepared which was used for cDNA synthesis.
First-strand cDNA was synthesised using an oligo(dT)-linker primer and M-MLV H- reverse transcriptase. The reaction conditions were chosen such that the lenght og first-stand cDNA was limited to ~ 500-1000nt. Finally, the cDNA was amplified (17 cycles) using a high fidility DNA polymerase. For Titanium sequencing the cDNAs in size range of 500-650 bp were eluted from a preparative agarose gel. Aliquots of the size fractionated cDNAs were analzyed by capillary electrophoresis. 5'-454 Adapter A1 and 3'-454 Adapter B1 were ligated and samples tagged bud (TCTACT bud/ TGTATC wt) .

tag: flower type

value: bud

value: flower

value: Maria


title: Male WT stage B

status: Public on Jan 26 2015

type: SRA

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Vitis vinifera 12X V1 whole genome using CLC Genomics Workbench.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods 2008. In short, exons from all isoforms of a gene were merged to create contigs. The number of reads falling in the exons were counted and normalized by the size of the contig and by the size of the library.
Genome_build: Vitis vinifera (12X V1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

molecule: total RNA

organism: Vitis vinifera subsp. sylvestris

source_name: Flower bud

extract_protocol:
The frozen buds were ground into a fine powder in liquid nitrogen and total RNA was extracted and purified with the SpectrumTMTotal RNA kit (Sigma-Aldrich, Inc, Spain) and Qiagen RNAeasy Mini Spin Columns (Qiagen, Valencia, CA, USA), respectively,according to the manufacturers’instructions. The concentration and purity of total RNA were determined using a Synergy HT Nanodrop system (Biotek, Germany), with the software Gen5TM (Biotek, Germany). The quality of the RNA was confirmed on a denaturing gel electrophoresis. For each sample, 25µg of total RNA were utilized for transcriptome sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Developmental stage B

tag: tissue

value: Flower bud

tag: genotype

value: wild type

tag: gender

value: male


title: Male WT stage D

value: Developmental stage D


title: Female WT stage H

value: Developmental stage H

value: female


title: Female WT stage D


title: Female WT stage G

value: Developmental stage G


title: Female WT stage B


title: input_GATA1s_rep2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

library_source: genomic

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 -m 1 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file with read coverage, peak file in broad peak format

molecule: genomic DNA

organism: Mus musculus

growth_protocol: G1ME cells were grown in alpha-MEM supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin (10 U/mL stock), 1% L-glutamine (mM stock), and 20 ng/mL thrombopoietin. After transduction, cells were cultured in the same media plus 2U/mL of erythropoietin

extract_protocol:
Lysates were clarified from sonicated nuclei and HA-GATA1 or HA-GATA1s DNA complexes were isolated with anti-HA antibody.
Libraries were prepared using the protocol as outlined for Illumina's TruSeq ChIP Sample Prep Kit ( IP-202-1012), except that the libraries were size selected using Agencourt SPRIselect beads for an average size of ~300-325bp prior to PCR amplification. Library quality was assessed using the Aglient Bioanalzyer 2100 and libraries were sequenced on the Illumina HiSeq2000.

treatment_protocol: G1ME cells were transduced with MIGR1-GATA1-HA or MIGR1-GATA1s-HA virus, and harvested 42 hours after transduction for ChIP-seq.

tag: strain background

tag: cell line

tag: cell type

value: immortalized, developmentally arrested megakaryocyte-erythroid progenitors (MEPs) derived from in vitro differentiation of murine Gata1-ES cells

tag: transduced with

tag: timepoint

value: bipotential progenitors at 42 hrs post transduction

tag: chip antibody


title: input_GATA1s_rep1


title: GATA1s_rep1

value: anti-HA


title: input_GATA1fl_rep2


title: GATA1fl_rep2


title: GATA1fl_rep1


title: Hermaphrodite stage B

organism: Vitis vinifera

value: Domesticated

value: hermaphrodite


title: pol2-M644G (run256)

city: Edinburgh

first: Martin

last: Taylor

state: Midlothian

address: Crewe Road

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: Sample name: run256

data_processing:
Sequence reads were aligned to the sacCer3 reference genome with Bowtie2 (version 2.0.0)
Samtools (version 0.1.18) View was used to filter alignments requiring a minimum mapping quality of 30 (Phred scale).
Samtools (version 0.1.18) was used to sort and index the resulting BAM format alignments.
Bedtools (version 2.16.2) bamToBed function was used to generate a Bed file of read mapping coordinates.
Custom code (riboReadEndBedToGidChrM.pl) was applied to the Bed coordinates file to calculate the genomic coordinate of the embedded ribonucleotide (one nucleotide 5' of the 5' read end and on the opposite strand).
Genome_build: sacCer3 (SGD version 64)
Supplementary_files_format_and_content: Bed files where coordinates correspond to single ribonucleotide incorporation sites. Score field shows count of reads in sample that indicate ribonucleotide at indicated strand and position.

organism: Saccharomyces cerevisiae

source_name: Yeast log phase culture

growth_protocol: Yeast strains were grown at 30°C in YPDA to mid log phase (see Supplementary Table 3 for a list of strains) or to saturation for stationary phase.

extract_protocol:
Per 5 OD600 units, cell pellets were resuspended in 200 µl lysis buffer (2% Triton X-100, 1% SDS, 0.5 M NaCl, 10 mM Tris-HCl pH8.0, 1 mM EDTA). An equal volume of TE-equilibrated phenol and glass beads (0.40-0.60 mm Φ, Sartorius) were added, and cells lysed by vortexing for 2 min; 200 µl of TE was then added, followed by an additional 1 min of vortexing. After centrifugation, the aqueous phase was further extracted with equal volumes of phenol:chloroform:isoamylalcohol (25:24:1) and chloroform. Total nucleic acids were precipitated with 1 ml of 100% ethanol, and dissolved in 0.5 M NaCl. RNA was degraded by treatment with 10 μg RNAse A (Roche) for 1 h at room temperature. DNA was finally purified with an equal volume of Ampure XP beads (Beckman Coulter) and eluted in nuclease-free water.
DNA was sonicated using a Bioruptor Plus (Diagenode) to achieve an average fragment length of approximately 400 bp. Fragmented DNA was concentrated by ethanol precipitation and size selected using 1.2 volumes of Ampure XP. DNA was quantified by nanodrop (Thermo Scientific) and up to 5 μg was used for NEBNext End Repair and dA-Tailing (New England Biolabs) following the manufacturer’s guidelines. After the End Repair reaction DNA was purified using 1.2 volumes of Ampure XP. Subsequent steps were performed in the presence of Ampure XP beads, capturing the DNA by adding NaCl and PEG8,000 to final concentrations of 1.25 M and 10% respectively. The trP1 adapter (see below) was attached using NEBNext Quick Ligation with 120 pmol of adapter per μg of DNA for 14-18 h at 16°C.
Terminal transferase (NEB) was then used to block any free 3’ ends with ddATP for 2 h at 37°C, with 20 U of TdT per μg of DNA. After Ampure XP purification, beads were removed and DNA nicked using recombinant RNase H2 (10 pmol per µg of library) or Nb.BtsI (NEB; 10 U per µg) for 2 h at 37°C. RNase H2 purification and reaction conditions were as previously described62. Enzymes were inactivated by heating at 80°C for 20 min, and DNA was purified using 1.8 volumes of Ampure XP. Shrimp Alkaline Phosphatase (Affymetrix; 5 U) was then used to remove 5’ phosphates at 37°C (1 h per μg of library). After heat inactivation for 15 min at 65°C and Ampure XP purification, DNA was denatured by heating at 95°C for 5 min and snap cooling. Subsequently, A adapter (see below; 120 pmol per μg of library) was attached using NEBNext Quick Ligation for 14-18 h at 16°C. Fragments with biotinylated A adapter were captured on streptavidin-coupled M-280 Dynabeads (Life Technologies) following the manufacturer’s guidelines, and non-biotinylated strands were released in 0.15 M NaOH. Single stranded fragments were concentrated by ethanol precipitation.

tag: strain

tag: growth phase

value: log phase culture

tag: enzyme treatment

value: RNase H2

tag: sequencing chip

value: Ion Torrent 318


title: pol2-M644L (run258)

description: Sample name: run258


title: wild type

country: Germany

value: wt

value: flower


title: PB_E-DS11464

city: Seattle

first: Kai-Hsin

last: Chang

state: WA

address: 1705 NE Pacific St.

institute: University of Washington

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
PB_E-DS11464.peaks.fdr0.01.hg19.bed: hg19

organism: Homo sapiens

source_name: human mobilized peripheral blood derived erythroblasts

growth_protocol: hESC line H1 were grown on irradiated MEFs and passaged onto matrigel coated plates for MEF free growth in MEF conditioned medium. Erythroblasts from hESCs were derived by embryoid body method. Embryoid bodies were dissociated and cultured in erythroid inducing media. FL and PB derived erythroid cells were obtained by culturing mononuclear cells from FL and CD34+ cells from mobilized PB in the same erythroid inducing media.

extract_protocol: Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibody at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligated to Illumina adapters and made into a Solexa library for sequencing.

tag: ChIP

value: human erythroblasts


title: ES_E-DS11462

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
ES_E-DS11462.peaks.fdr0.01.hg19.bed: hg19

source_name: hESC-H1 line-derived erythroblasts


title: H1_hESC-DS11461

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
H1_hESC-DS11461.peaks.fdr0.01.hg19.bed: hg19

source_name: hESCs-H1 line

value: human embryonic stem cells


title: pol3-L612M (run254)

description: Sample name: run254


title: input_GATA1fl_rep1


title: pol1-L868M (run238)

description: Sample name: run238


title: POL (run237)

description: Sample name: run237

value: POL


title: pol1-L868M (run220)

description: Sample name: run220


title: pol1-L868M (run192)

description: Sample name: run192


title: pol3-L612M (run219)

description: Sample name: run219


title: POL (run195)

description: Sample name: run195


title: POL (run190)

description: Sample name: run190


title: GATA1s_rep2


title: pol1-L868M (run186)

description: Sample name: run186


title: Input control

city: Leuven

first: Jonas

last: Demeulemeester

state: Belgium

address: ON5 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB – KU Leuven

data_processing:
Illumina CASAVA 1.8.2 was used for basecalling
Residual adapter sequences were trimmed and filtered out using fast-x clipper v0.013, option –M15.
Quality reports were generated using FastQC v0.10.1 and reads were checked for PHRED quality, length and contamination.
Reads were mapped to the hg19 human reference assembly (UCSC) using bowtie (v2.1.0)
Peaks were called using ZINBA v2.02.03 with broad=TRUE and threshold=0.01
Genome_build: hg19
Supplementary_files_format_and_content: output bed file from ZINBA

source_name: CD4+ T cells

extract_protocol:
30E7 CD4+ T cells were fixed with 1% formaldehyde (25°C, 10 min) and stopped with 0.125M Glycine. Nuclei were sonicated using a Diagenode Bioruptor (Liege) to produce fragments of ~200 bp. LEDGF/p75-bound chromatin fragments were immunoprecipitated with antibody A300-848.
Libraries were generated according to the Illumina TruSeq DNA Sample preparation guide. Briefly, the immunoprecipitated DNA was end-repaired, A-tailed and ligated to TruSeq adapters. After PCR amplification with 15 cycles and gel size selection of ~300bp fragments, libraries were captured and sequenced using the Illumina HiSeq 2000.

value: Primary CD4+ T cells

value: none (input)


title: POL_BstI (run184)

description: Sample name: run184


title: LEDGF/p75 (PSIP1) ChIP-Seq

value: anti-LEDGF/p75 (Bethyl, A300-848)


title: Rnh201.2 b

city: Research Triangle Park

first: Scott

middle: Alexander

last: Lujan

state: NC

address: 101 T.W. Alexander Drive

department: LMG/LSB

institute: NIEHS

description: Sample 15

data_processing:
Library strategy: Ribo-seq
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.2.1, discarding pairs with one or both reads shorter than 15 nt, additional base trimmed to allow paired-end mapping with bowtie
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 0.12.8 -k1 -v2)
Align remaining pairs to L03 reference genome (bowtie 0.12.8 -m1 -v2 -X10000)
Align end 1 of unmapped pairs to L03 reference genome (bowtie 0.12.8 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, shift 1 base upstream and combine
Combine all technical replicates
Genome_build: L03 reference v2 (see supplementary files)
Supplementary_files_format_and_content: bedGraph, count of Ribo-seq 5' ends per position

growth_protocol: Yeast strains were grown to mid log phase (OD600=0.6) at 30°C in YPDA medium supplemented with 0.25 mg/ml adenine

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
Ribo-seq was performed by hydrolyzing one μg of genomic DNA with 0.3 M KOH for 2 hours at 55°C. Following ethanol-precipitation, the DNA fragments were treated for three minutes at 85°C, phosphorylated with 10 units of 3´-phosphatase-minus T4 polynucleotide kinase (New England Biolabs) for 30 minutes at 37°C, heat inactivated for 20 minutes at 65°C and purified using HighPrep™ PCR beads (MagBio). Phosphorylated products were treated for three minutes at 85°C, ligated to oligo ARC140 (Supplementary Table 1) overnight at room temperature using 10 units of T4 RNA ligase, 25% PEG8000 and 1 mM CoCl3(NH3)6, and purified using HighPrep™ PCR beads (MagBio) . Ligated products were treated for 3 minutes at 85°C. The second strand was synthesized using four units of T7 DNA polymerase (New England Biolabs). The ARC76/ARC77 adapter was annealed to the second strand for five minutes at room temperature and purified using HighPrep™ PCR beads (MagBio). Libraries were PCR amplified using primer ARC49 and primer ARC79 or ARC84 to ARC107, using KAPA HiFi Hotstart ReadyMix (KAPA Biosystems). Libraries were then purified using HighPrep™ PCR beads (MagBio) and pooled for sequence analysis. Paired-end sequencing was performed on a HiSeq2500 sequencer (Illumina) or MiSeq to identify the location of the 5´-DNA ends generated by alkaline hydrolysis.


title: FL_E-DS11463

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
FL_E-DS11463.peaks.fdr0.01.hg19.bed: hg19

source_name: human fetal liver derived erythroblasts


title: pol1-L868M_stat_phase (run38)

description: Sample name: run38

source_name: Yeast stationary phase culture

value: stationary phase culture

value: Ion Torrent P1


title: POL_stat_phase (run37)

description: Sample name: run37


title: pol1-L868M_BstI (run185)

description: Sample name: run185


title: H1_hESC-DS20456

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
H1_hESC-DS20456.peaks.fdr0.01.hg19.bed: hg19


title: pol1-L868M (run36)

description: Sample name: run36


title: FL_E-DS20402

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
FL_E-DS20402.peaks.fdr0.01.hg19.bed: hg19


title: ES_E-DS21037

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
ES_E-DS21037.peaks.fdr0.01.hg19.bed: hg19


title: covS-G457V-4

status: Public on Jan 24 2015

city: Houston

first: Samuel

last: Shelburne

state: TX

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

description: RNA after rRNA depletion

data_processing:
The raw reads in FASTQ format were aligned to the reference genome, MGAS10870, using MOSAIK alignment software with parameters of -hs 15, -mmp 0.06, -mmal,   -minp 0.5, -act 35, -mhp 100, and -m all
The overlaps between aligned reads and annotated genes were counted using HTSeq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). The gene counts were normalized using the scaling factor method implemented in the R package of DESeq2 (version 1.2.10). If the number of overlapped read of any given gene is less than one per million total mapped read for  all samples, this gene was excluded from further analysis.
A negative binomial generalized linear model was fit to each gene expression with strain type as covariates. Then a likelihood-ratio test was applied to examine if there is any difference in the expression of a gene among six strains. The Benjamini-Hochberg method was used to control false discovery rate (FDR). The pairwise comparisons were performed to compare the gene expressions between WT vs any other strain using Wald's tests. The Holm's method was used to calculate adjusted p-value to correct for multiple testing. The calculation was conducted using R (version 3.0.1) with the package of DESeq2 (version 1.2.10)
Genome_build: MGAS10870
Supplementary_files_format_and_content: excel file with normalize counts

organism: Streptococcus sp. 'group A'

source_name: bacteria grown in high magnesium nutrient rich broth

growth_protocol: GAS strains grown in THY +15 mM MgCl2 to mid-exponential phase

extract_protocol:
Cells were lysed using a fast FastPrep approach and RNA was isolated from ruptured cell using an RNeasy Kit (Qiagen)
cDNA was fragmented to 200 bp (mean fragment size) with the S220 Focused-ultrasonicator (Covaris) and used to make barcoded sequencing libraries on the SPRI-TE Nucleic Acid Extractor (Beckman-Coulter).

treatment_protocol: RNA protect was added at 2x volumes to cells and then cells were harvested by centrifugation, snap frozen, and stored at -80 C.

tag: strain/variation


title: covS-G457V-3

description: RNA after rRNA depletion


title: POL (run35)

description: Sample name: run35


title: PB_E-DS20403

data_processing:
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml   standard params for Hi-Seq lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred33-quals, standard params for GAII lanes: bowtie -p 4  --mm   -n 3 -v 3 -k 2  --phred64-quals
Genome Build:
PB_E-DS20403.peaks.fdr0.01.hg19.bed: hg19


title: covS-T284A-3

description: RNA after rRNA depletion


title: covS-T284A-4

description: RNA after rRNA depletion


title: wt_GSNO_4

status: Public on Jan 27 2015

city: Jena

first: Jörg

last: Linde

address: Naumburger Str. 96 a

department: Institute for Bacterial Infections and Zoonoses

institute: Federal Research Institute for Animal Health - Friedrich-Loeffler-Institute

description: 50ml volume in a 250 ml shaking flask, 180rpm.nitrosative stress. single-end,not strand-specific, no PolyA-filter.

data_processing:
FASTQ files were received from GATC, Konstanz, Germany
Sequenced reads were trimmed for low-quality regions (btrim windowsize 15 average  phredscore20)
Mapping of read pairs using TopHat (v2.0.6; -G GFF ); -maxintronlength 10000) versus the genome from www.candidagenome.org. GFF was produced durign study (see publication for details)
Read counting using htseq-count (-mode union, -s no, -type CDS)
Calculation of RPKM values using raw counts, sum of totally mapped reads and sum of exon length using  GFF file
Genome_build: the genome track downloaded (in July 2013) from http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/current/ was used.
However, there has been an update meanwhile and the file has now moved to archive http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/archive/C_glabrata_CBS138_version_s02-m01-r22_chromosomes.fasta.gz
The information about the version number (sXX-mYY-rZZ) are provided at: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=CAL0000143461
Supplementary_files_format_and_content: xls

organism: Nakaseomyces glabratus

source_name: whole organism

growth_protocol: C. glabrata was routinely cultivated on YPD agar or in broth at 37°C. Candida glabrata was grown in standard nutrient-rich medium, ph4, ph8 and in nitrosative stress (GSNO) conditions. After harvesting RNA, paired-end and strand-specific RNA-Seq was performed on three biological replicates after PolyA filtering respectively. Additionally, a fourth replicate without filtering was sequenced single-end and not strand-specific..

extract_protocol:
Cells  were collected by centrifugation and stored in RNA later until RNA extraction.  Total RNA was isolated using the hot acidic phenol chloroform method. RNA quality was determined with a Bioanalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies) according to the manufacturer's protocol. RNA concentration was determined with a Nanodrop ND1000 (Peqlab)
tagged random primed cDNA libraries were prepared from fragmented polyA-RNA using standard illumina protocols

treatment_protocol: For the pH treatment, C. glabrata was cultivated in M199 pH4 for 14-16 hours. Cells were harvested and cultured under the same condition again. 1x106 cells/ ml were harvested and transfered to fresh M199 pH4 or pH8 for 60 minutes. Cells were harvested and stored in RNAlater prior to RNA isolation. For the GNSO treatment (nitrosative stress) C. glabrata was grown in YPD medium at 37°C and 180 rpm for 14-16 h. 1X106 cells/ml were resuspended in 50 ml of normal YPD or YPD containong 0.6M GNSO (Sigma) for 60 minutes. Cells were harvested and stored in RNAlater prior to RNA isolation.

tag: growth medium

value: YPD + 0.6M GSNO

tag: incubation temperature

tag: incubation time

value: 60 minutes


title: covS-G457V-1

description: RNA after rRNA depletion


title: covS-G457V-2

description: RNA after rRNA depletion


title: pol2-M644G (run28)

description: Sample name: run28


title: pol2-M644L (run29)

description: Sample name: run29


title: covS-E281A-3

description: RNA after rRNA depletion


title: covS-T284A-2

description: RNA after rRNA depletion


title: covS-T284A-1

description: RNA after rRNA depletion


title: pol3-L612M (run25)

description: Sample name: run25


title: covS-E281A-2

description: RNA after rRNA depletion


title: covS-H280V-3

description: RNA after rRNA depletion


title: covS-H280V-2

description: RNA after rRNA depletion


title: covS-H280V-4

description: RNA after rRNA depletion


title: covS-4

description: RNA after rRNA depletion


title: covS-H280V-1

description: RNA after rRNA depletion


title: covS-3

description: RNA after rRNA depletion


title: covS-1

description: RNA after rRNA depletion


title: 10870-4

description: RNA after rRNA depletion

value: MGAS10870 (wild-type)


title: 10870-2

description: RNA after rRNA depletion


title: covS-2

description: RNA after rRNA depletion


title: 10870-1

description: RNA after rRNA depletion


title: G9a mutant (G9a-/-), DCV, Fat Body

city: Nijmegen

first: Ronald

last: van Rij

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences - Radboud University Medical Center

data_processing:
The FASTQ sequence reads were generated using the Illumina Casava pipeline version 1.8.0.
Initial quality assessment was based on data passing the Illumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house filtering protocol from Baseclear BV (Leiden, the Netherlands).
The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.10.0.
Reads were mapped to the reference genome (Drosophila melanogaster dm3, released in April 2006, UCSC Bioinformatics) using TopHat version 1.4.0.
Differential expression analysis between two data sets was performed with the Genomatix analysis suite (using DESeq 1.0.6).
Genome_build: Drosophila melanogaster dm3, released in April 2006, UCSC Bioinformatics
Supplementary_files_format_and_content: Text files contain results of the differential gene expression analysis. All differently regulated transcript are listed, with informations about the gene/transcript itself (TranscriptiD, Refseq number, LocusID, Symbol, GeneID, ContigAccn, Chromosome, strand, start, end and lenght of the transcript, number of exons, and p-value). It then contains the Log2 (fold change), Up/Down regulation, Number of reads in both samples analysed (i.e in mock and DCV), the NE value (the NE-value is based on the number of reads located in the exons of the transcript and is normalized to the length of the transcript and the density of the data set.The NE-value is calculated based on the following formula: NE = c * #readsregion / (#readsmapped * lengthregion), where NE is the normalized expression or enrichment value, #readsregion: the reads (sum of base pairs) of falling into either the transcript or the cluster region, #readsmapped: all mapped reads (in base pairs), lengthregion: the transcript or cluster length in base pairs and c a normalization constant set to 107), and mean and SD of the NE value.
Supplementary_files_format_and_content: Differential expression analysis of gene expression in DCV infected wild-type flies (G9a+/+ or E02) relative to mock.
Supplementary_files_format_and_content: Differential expression analysis of gene expression in DCV infected G9a mutant flies (G9a-/- or G9a DD2 or E37) relative to mock.
Supplementary_files_format_and_content: Differential expression analysis of gene expression in fat body of DCV infected wild-type flies (G9a+/+ or E02) relative to mock.
Supplementary_files_format_and_content: Differential expression analysis of gene expression in fat body of DCV infected G9a mutant flies (G9a-/- or G9a DD2 or E37) relative to mock.
Supplementary_files_format_and_content: Differential expression analysis of gene expression in DCV infected G9a mutants (G9a-/- or G9a DD2 or E37) relative DCV infected wild-type flies (G9a+/+ or E02)
Supplementary_files_format_and_content: Differential expression analysis of gene expression in fat bodies of DCV infected G9a mutants (G9a-/- or G9a DD2 or E37) relative to DCV infected wild-type flies (G9a+/+ or E02)

organism: Drosophila melanogaster

source_name: Dissected Fat body

extract_protocol:
Total RNA was extracted from flies using the phenol/chloroform method using Isol-RNA lysis Agent. Samples were then processed with the Illumina mRNA Truseq Kit.
Library was constructed with the TruSeq mRNA kit from Illumina.

tag: genotype

value: G9a -/- (or G9a DD2, or E37)

tag: sex/age

value: female, 3-5 days old

tag: time point

value: 24h post-infection

tag: tissue

value: fat body

tag: infection

value: DCV


title: G9a mutant (G9a-/-), DCV, Whole Fly

source_name: Whole fly

value: whole fly


title: Wild-type (G9a+/+), DCV, Fat Body


title: Wild-type (G9a+/+), DCV, Whole Fly


title: covS-E281A-4

description: RNA after rRNA depletion


title: Wild-type (G9a+/+), Mock, Fat Body

value: mock


title: Wild-type (G9a+/+), Mock, Whole Fly


title: G9a mutant (G9a-/-), Mock, Whole Fly


title: BT-549 Input [lab: Zhao-DFCI]

status: Public on Jan 23 2015

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned to revision hg19 of the human genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Breast Cancer

growth_protocol: BT-549 cells were grown in RPMI medium supplemented with 10% fetal bovine serum.  They were grown to 80-90% confluence by visual inspection and then cross linked with formaldehyde for ten minutes.

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

tag: cell line

tag: cell line type

value: basal-like breast cancer

value: Breast

tag: cell number

value: 50 million


title: BT-549 H3K27Ac [lab: Zhao-DFCI]

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#

tag: chip antibody lot#


title: ZR-75-1 Input [lab: Zhao-DFCI]

growth_protocol: ZR-75-1 cells were grown in RPMI medium supplemented with 10% fetal bovine serum.  They were grown to 80-90% confluence by visual inspection and then cross linked with formaldehyde for ten minutes.

value: luminal-like breast cancer


title: ZR-75-1 H3K27Ac [lab: Zhao-DFCI]


title: T47D H3K27Ac [lab: Zhao-DFCI]

growth_protocol: Cells were maintained under typical conditions in RPMI +10% FBS.  Cells were grown to 80-90% confluence by visual inspection and then cross linked with formaldehyde for 10 minutes.


title: T47D Input [lab: Zhao-DFCI]

growth_protocol: Cells were maintained under typical conditions in RPMI +10% FBS.  Cells were grown to 80-90% confluence by visual inspection and cross linked with formaldehyde for 10 minutes.


title: MDA-MB-468 H3K27Ac [lab: Zhao-DFCI]

growth_protocol: MDA-MB-468 cells were grown in RPMI medium supplemented with 10% fetal bovine serum.  They were grown to 80-90% confluence by visual inspection and then cross linked with formaldehyde for ten minutes.


title: CY1838 input

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

data_processing:
Fastq files were used to map reads to yeast genome(saccer3) with or Bowtie 0.12.9
Mapped reads were counted and  used to calculate the p value and log2 ratio of Ip vs Input or histone modifications in mutant vs wt
log2 ratio of Ip vs  input were used to plot with metagene profiles and distance to telomere.
log2 ratio of histone modifications in mutant vs wt were used to plot with metagene profiles.
Genome_build: sacCer3_2011
Supplementary_files_format_and_content: see README file

growth_protocol: Cells were synchronized in G2/M with nocodazole, released into alpha-factor and harvested at O.D of 0.6

extract_protocol:
Samples were crosslinked with formaldehyde, digested with micrococcal nuclease and subjected to chromatin immunoprecipitation using an Arp5 antibody
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol

tag: strain

value: WT


title: CY1838 Arp5

tag: antibody

value: Arp5 antibody from Abcam (ab12099).


title: arp5_K4Me3_A12

growth_protocol: Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol

treatment_protocol: Cells were crosslinked with formaldehyde

value: Anti H3K4me3 antibody are from Active Motif, 39159


title: covS-E281A-1

description: RNA after rRNA depletion

tag: strain/variation


title: arp5_Input_A8


title: arp5_K79Me3

value: Anti H3K79me3 antibody are from Grunstein Lab


title: BY4741_K4Me3_A11


title: 10870-3

description: RNA after rRNA depletion

value: MGAS10870 (wild-type)


title: BY4741_K79Me3


title: BY4741_Input_A7


title: mRNA_CY1315_ino80_BIOO-BC12

data_processing:
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8 or Bowtie
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
mapped reads(sam file) were used to cacullate the mRNA level and log2 ratio of mutants vs WT using customed script
log2 ratio of mutants vs wt were used to plot with metagene profiles.
Genome_build: sacCer3_2011
Supplementary_files_format_and_content: see README file

source_name: CY337 Background

extract_protocol:
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol. For ChIP-Seq, Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 following the manufacturer’s protocol

value: CY337 Background


title: G9a mutant (G9a-/-), Mock, Fat Body

value: G9a -/- (or G9a DD2, or E37)

value: female, 3-5 days old


title: mRNA_sir3_BIOO-BC7

source_name: BY4741 Background

value: BY4741 Background


title: mRNA_ies6_BIOO-BC9


title: mRNA_arp5_BIOO-BC8


title: mRNA_BY4741_BIOO-BC6


title: ies2_2_AR005


title: WT_CY337_AR007


title: ino80_CY1315_AR008


title: MDA-MB-468 Input [lab: Zhao-DFCI]


title: ies6_2_AR004


title: ies2_AR005


title: arp5_2_AR003


title: arp5_AR003


title: sir3_AR004


title: BY4741_AR001


title: 10 hr Input

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using Bowtie (Langmead et al., 2009). Duplicated reads were filtered (allowing no more than 2 reads at the same location).
Two programs were used to infer enriched binding regions (peaks): QuEST (Valouev et al., 2008) and MACS (Zhang et al., 2008). As negative control for defining background binding to the Rorγt analysis, we used an antibody for the isotype control immunoglobulin (IgG), and anti-RORγt antibody in a RORγt-deficient population. As a negative control for the Foxp3 analysis we used the Foxp3 antibody in EL4 cells (with no exogenous Rorc). As negative control for the EL4 peaks we used cells with no exogenous Rorc.  The output of the two programs is a list of enriched binding regions (peaks) together with an estimate of statistical significance. For QuEST we retain all the peaks with p-value<10-8; for MACS we used a p-value cutoff of 10-8 or estimated FDR below 5%. We then applied a post-processing step, consolidating all the peaks that for a given algorithm (QuEST or MACS) was detected (up to a distance of 50bp) with all of the controls. We report this unified set of peaks. Associated p-values are minimum over QuEST or MACS.
Genome_build: mm9
Supplementary_files_format_and_content: TDF format; generated with igvtools count program

source_name: embryonic stem cells

growth_protocol: tet-ON Oct4 ESCs were maintained in ESC media containing 15% tetracycline-free FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and trancription factor-DNA complexes were isolated with antibody.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Retinoic-acid differentiated tetON-Oct4 ESCs were treated with either PBS or doxycyline to induce expression of Oct4. These cells were fixed with formaldehyde, lysed using cell lysis buffer, sonicated to shear chromosomal DNA to 250-750 bp size, immunoprecipitated using antibodies against Oct4, Jmjd1c and Spt16.

tag: cell type

value: embryonic stem cells

value: input


title: 0 hr Input


title: Sperm1A

city: Uppsala

first: Hans

last: Ellegren

address: Norbyvägen 18D

department: Ecology and Genetics

country: Sweden

institute: Uppsala University

data_processing:
Data filtering including removing adaptor sequences, contamination and low-quality reads from raw reads, using in-house programs.
Filtered reads were then aligned to the WASHUC2 assembly version of the chicken genome using SOAPaligner-v2.21
The number of reads covering each cytosine site were separated into those corresponding to mC (i.e., non-converted upon bisulfite treatment) and those corresponding to C (i.e., converted upon bisulfite treatment).
Genome_build: WASHUC2
Supplementary_files_format_and_content: cout files are a vertical arrangement format of each cytosine, one line contains information for one cytosine. The columns are 1. Chromosome ID; 2. Position; 3. Strand (+/-); 4. Cytosine pattern (CG/CHH/CHG); 5. Cytosine sequence context; 6. Copy number; 7. Methyl-reads number; 8. Non-methyl-reads number; 9. Binomial distribution expected values

organism: Gallus gallus

source_name: sperm cells

extract_protocol:
DNA was extracted from 100 µl of chicken sperm, directly frozen upon sampling. Thawed sperm cells were washed twice in water and 200 µl of Laird’s lysis buffer (Tris-Col 100mM, EDTA 5 mM, NaCal 20 mM, SDS 2%, DTT 40 mM and proteinase K 500 µg/ml) was then added and was incubated overnight at 50°C. The sample was then purified by two rounds of phenol-chloroform/chloroform extraction followed by ethanol precipitation.
Standard Illumina paired-end protocol

value: sperm cells

tag: developmental stage

value: adult


title: Oct4-0hr_ChIPSeq


title: TKO_DNMT3B1_SETD2_bisulfite_seq single

status: Public on Jan 22 2015

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
fastq files from MiSeq and HiSeq experiments were pooled and split to 50bp length
fastq files were directly processed and mapped using standard settings for single-end bisulfite sequencing in QuasR in R (http://www.bioconductor.org/packages/release/bioc/html/QuasR.html)
methylation values were extracted with QuasR, and only CpGs were analyzed that were overed at least ten times
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values: chr, CG_start, CG_end, tot_reads_TK_D3A2, meth_read_TK_D3A2, tot_reads_TK_D3B1, meth_read_TK_D3B1

growth_protocol: DNMT1,3a,3b-triple-null embryonic stem cells (Tsumura et al., 2006), 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:
Genomic DNA was extracted using Proteinase K digest followed by phenol extraction and ethanol precipitation, followed by RNase treatment. Genomic DNA was sonicated using a Bioruptor (7 cycles) to 200-500 bp. Fragmented, pre-methylated phage T7 DNA and unmethylated lambda DNA were spiked in as converson control.
6 ug DNA were end-repaired, poly-adenylated and ligated to methylated, paired-end adapters from Illumina. Ligated DNA fragments were purified on 2% agarose gels. Fragmetns between 350-400bp were extracted and bisulfite conversion was performed using the Qiagen Epitect bisulfite kit. Converted DNA was amplified for 10 cycles and cleaned up with Ampure beads.

tag: genotype

value: TKO, SETD2-KO


title: Jmjd1c-10hr_ChIPSeq


title: mRNA_sir3arp5_BIOO-BC10

value: sir3Δ, arp5Δ


title: Spt16-10hr_ChIPSeq


title: BY4741_2_AR001


title: 5066_day2_monosomes

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

growth_protocol: ESC were cultured in regular LIF containing media or placed in non-adherent, liquid differentiation condititions where embryoid bodies were collected 48 hrs post-seeding.

extract_protocol:
Cells were lysed in polysome lysis buffer, an aliquote was kept (input) and remaining volume was loaded and separated on sucrose gradients. RNA was extracted from sucrose fractions using Rneasy columns (qiagen)
TruSeq RNA

treatment_protocol: Cells were treated for 15min with cyclohexamide to fix ribosomes

value: Differentiated embryoid body

tag: state

value: Differentiated embryoid body (day 2)

tag: sucrose fraction

value: monosomes

value: wild-type

value: R1 (established in August 1991, from a 3.5 day blastocyst produced by crossing two 129 substrains, 129S1/SvImJ and 129X1/SvJ


title: 5066_day2_F1

tag: tissue

value: polysomes


title: Oct4-10hr_ChIPSeq


title: 5066_day2_input


title: ies6_AR002


title: sir3_2_AR002


title: 5066_day0_F1

value: undifferentiated


title: TKO_DNMT3B1_bisulfite_miseq

data_processing:
fastq files from MiSeq and HiSeq experiments were pooled and split to 50bp length
fastq files were directly processed and mapped using standard settings for single-end bisulfite sequencing in QuasR in R (http://www.bioconductor.org/packages/release/bioc/html/QuasR.html)
methylation values were extracted with QuasR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values: chr, CG_start, CG_end, tot_reads_TK_D3A2, meth_read_TK_D3A2, tot_reads_TK_D3B1, meth_read_TK_D3B1


title: 5066_18_day2_monosomes


title: 5066_18_day0_monosomes


title: 5066_day0_input


title: 5066_18_day0_F1


title: 5066_18_day0_input


title: 5066_day0_monosomes


title: 5066_18_day2_input


title: TKO_DNMT3A2_bisulfite_hiseq2000


title: Retired Mature

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

description: Sample 18

data_processing:
library strategy: mRRBS (multiplexed reduced representation bisulfite sequencing)
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse  genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS

source_name: retired_mammary cells

growth_protocol: Virgin and pregnant state C57BL/6 female mice were maintained in the Harvard Institute of Medicine animal facility.

extract_protocol:
Genomic DNA was collected using phenol/chloroform extraction
mRRBS (multiplexed reduced representation bisulfite sequencing) libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil

treatment_protocol: Mammary glands from different reproductive stages were digested to purify different cell types from the mouse epithelium.

tag: gender

value: female

tag: age

value: Retired Breeders

value: mammary gland

value: mammary epithelial mature luminal cells


title: Day 16 Pregnant Stem

description: Sample 10

source_name: Day16_pregnant_mammary cells

value: D16 pregnant

value: mammary epithelial stem cells


title: Day 19 Pregnant Mature

description: Sample 15

source_name: Day19_pregnant_mammary cells

value: D19 pregnant


title: Day 16 Pregnant Progenitor

description: Sample 11

value: mammary epithelial luminal progenitor cells


title: Day 16 Pregnant Mature

description: Sample 12


title: Day 10 Pregnant Progenitor

description: Sample 8

source_name: Day10_pregnant_mammary cells

value: D10 pregnant


title: Day 10 Pregnant Mature

description: Sample 9


title: Day 19 Pregnant Progenitor

description: Sample 14


title: Day 10 Pregnant Stem

description: Sample 7


title: Week 9 Virgin Stem

description: Sample 4

source_name: non-pregnant_mammary cells

value: 9 week virgin


title: Week 3 Virgin Mature

description: Sample 3

value: 3 week virgin


title: Week 9 Virgin Progenitor

description: Sample 5


title: Week 3 Virgin Progenitor

description: Sample 2


title: Week 9 Virgin Mature

description: Sample 6


title: Retired Progenitor

description: Sample 17


title: mRNA_CY337_BIOO-BC11

value: CY337 Background

value: WT


title: Embryoid Bodies derived from mES cells Jarid2 -/- rescue with Jarid2 BAC H3K27me3 IP, replicate 1

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Single-end 100bp reads were mapped on the Mouse reference genome (mm9) using the Bowtie2 software (v2.1.0, Langmead B. et al. 2012) allowing one mismatch in the seed (22bp) and reporting one location in case of multiple mapping hits.
PCR duplicates were then removed using PicardTools (v1,65)
For Jarid2 and Jarid2K116me2 ChIP-seq :  Peak calling was performed with MACS (v1.4.2, (Zhang et al., 2008)) With default parameters, Using the Input sample as control. Significant peaks were identified with a minimum FDR of 15%.
For H3K27me3 ChIP-seq: Peak calling was performed with MACS2 (v2.0.10, (Zhang et al., 2008)) With a DNA fragment size estimated during library preparation, Using the Input sample as control. The broad parameter is enabled in order to call for histone enriched regions. Significant peaks were identified with a minimum FDR of 5%.
Genome_build: mm9
Supplementary_files_format_and_content: bed files are the output of peak calling. Scores represent -10*log10(p-value)
Supplementary_files_format_and_content: BigWig files are generated with HOMER (v3.17)

source_name: embryoid bodies

growth_protocol:
Sample 1 to 10 Undifferentiated cells maintained ESC serum + LIF on gelatin coated plate
Sample 11 to 16:Embryoid bodies (EBs) are formed by hanging drop method. Cells are diluted at 1000 cells/20μl drop in ES media in absence of LIF. After 2 days EBs are flushed in low adherence plates. ES medium is changed every day.

extract_protocol:
Formaldehyde cross-linking 1,1% for 10 minutes.
Libraries were prepared accordingly to manufactures (TruSeq ChIP sample Prep Kit, Illumina). Sequencing was performed on Hi-Seq 2500 Illumina single reads 100bp.

treatment_protocol: mES cells are supplemented with LIF (ESGRO)

value: H3K27me3 IP (abcam 6002)

value: ESC induced to differentiate by the Hanging Drop Method, LIF removal for 8 days


title: Embryoid Bodies derived from mES cells Jarid2 -/- rescue with Jarid2 K116A BAC H3K27me3 IP, replicate 1


title: Week 3 Virgin Stem

description: Sample 1


title: Embryonic Stem cells Jarid2 -/- rescue with Jarid2 BAC H3K27me3 IP, replicate 2

value: ESC Serum + LIF grown


title: Embryoid Bodies derived from mES cells Jarid2 -/- H3K27me3 IP, replicate 1


title: Embryonic Stem cells Jarid2 -/- H3K27me3 IP, replicate 2


title: Embryonic Stem cells Jarid2 -/- rescue with Jarid2K116A BAC H3K27me3 IP, replicate 2


title: Embryonic Stem cells Jarid2 -/- rescue with Jarid2K116A BAC H3K27me3 IP, replicate 1


title: Retired Stem

description: Sample 16


title: Embryoid Bodies derived from mES cells Jarid2 -/- rescue with Jarid2 K116A BAC H3K27me3 IP, replicate 2


title: Embryoid Bodies derived from mES cells Jarid2 -/- rescue with Jarid2 BAC H3K27me3 IP, replicate 2


title: TKO_DNMT3B1_SETD2_bisulfite_seq paired-end

value: TKO, SETD2-KO

value: embryonic stem cells


title: Embryonic Stem cells Jarid2 -/- input


title: Embryonic Stem cells (E14) Jarid2 K116me2 IP

value: Jarid2 K116me2 IP (this study, Sanulli et al.)


title: Day 19 Pregnant Stem

description: Sample 13

value: female

value: mammary gland


title: Embryonic Stem cells Jarid2 -/- H3K27me3 IP, replicate 1


title: Embryonic Stem cells (E14) Jarid2 IP

value: Jarid2 IP (Li et al. Gene & development 2010)


title: TKO_DNMT3B1_bisulfite_hiseq2000


title: TKO_DNMT3A2_bisulfite_miseq


title: Embryonic Stem cells Jarid2 -/- rescue with Jarid2 BAC H3K27me3 IP, replicate 1


title: esiGFP-r1

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
TopHat 2.0.9 is used to align reads to reference genome. The tophat parameters are: -g 1 -r 100 --mate-std-dev 200, others are default. For strand-specific data, use --library-type fr-secondstrand
Then use wiggles to convert into wig file
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: Hela cells (cervical cancer cells)

growth_protocol: HeLa cells were cultured in complete DMEM media containing 10% NCS, 1% Pen/Strep, 1%NEAA.

extract_protocol:
Total RNA from control esiRNA and PRMT9 esiRNA transfected HeLa cells were extracted using the Trizol reagent.
We used Epicenter’s ScriptSeq V2 to prepare the libraries for all 4 samples.
We performed 75-nt pair-end strand-specific RNA sequencing.

treatment_protocol: Hela cells were transfected with control esiRNA or esiRNA targeting PRMT9 (1ug esiRNA/10cm dish). Cells were left for 72 hours before they were harvested for RNA extraction.

tag: cell line

value: Hela

tag: transfection

value: control esiRNA


title: Embryonic Stem cells (E14) input


title: Embryoid Bodies derived from mES cells Jarid2 -/- H3K27me3 IP, replicate 2


title: esiGFP-r2


title: esiPRMT9-r2

value: esiRNA targeting PRMT9 (1ug esiRNA/10cm dish)


title: esiPRMT9-r1


title: LNCaP_GRO-seq_siTOP1_1h_dht_replicate-D

city: La Jolla

first: Michael

middle: G

last: Rosenfeld

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

description: GRO-seq, siTOP1, 1h treatment with 100 nM DHT

data_processing:
Library strategy: GRO-Seq
GRO-Seq was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp  (Luo et al., 2013: PLoS one 8, no. 5, e65632). The bedGraph files were prepared using HOMER (http://homer.salk.edu/homer/) software.
Genome build: hg18
Supplementary files format and content: bedGraph (GRO-seq tag density)

growth_protocol: LNCaP cells were seeded on dishes in RPMI-1640 supplemented with 10% FBS and allowed to attached overnight. The following day, the cells were washed twice with PBS and fed with phenol-free DMEM supplemented with 5% charcoal:dextran FBS. One day later, the cells were transfected using Lipofectamine 2000 and 20 pmol mL-1 siRNA diluted in Opti MEM reduced serum media without phenol red (Life Technologies). The transfection media was removed after 16 h incubation and the cells were washed twice with PBS. Fresh, phenol-free DMEM supplemented with 5% charcoal:dextran FBS and Penicillin/Streptomycin was added to the dishes. 48h post transfection, the cells were treated with 100 nM for 1h, and then harvested.

extract_protocol: For GRO-Seq, ~20 million cell nuclei from DHT- or vehicle-treated, siCTL or gene-specific siRNA-transfected LNCaP cells were extracted and harvested, and RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.

value: LNCaP

tag: molecule

value: nascent RNA


title: 5066_18_day2_F1

value: Differentiated embryoid body

value: Differentiated embryoid body (day 2)

value: polysomes

value: R1 (established in August 1991, from a 3.5 day blastocyst produced by crossing two 129 substrains, 129S1/SvImJ and 129X1/SvJ


title: LNCaP_GRO-seq_siControl_1h_vehicle_replicate-D

description: GRO-seq, siControl, 1h treatment with vehicle

growth_protocol: LNCaP cells were seeded on dishes in RPMI-1640 supplemented with 10% FBS and allowed to attached overnight. The following day, the cells were washed twice with PBS and fed with phenol-free DMEM supplemented with 5% charcoal:dextran FBS. One day later, the cells were transfected using Lipofectamine 2000 and 20 pmol mL-1 siRNA diluted in Opti MEM reduced serum media without phenol red (Life Technologies). The transfection media was removed after 16 h incubation and the cells were washed twice with PBS. Fresh, phenol-free DMEM supplemented with 5% charcoal:dextran FBS and Penicillin/Streptomycin was added to the dishes. 48h post transfection, the cells were treated with ethanol for 1h, and then harvested.


title: LNCaP_GRO-seq_siControl_1h_dht_replicate-D

description: GRO-seq, siControl, 1h treatment with 100 nM DHT

growth_protocol: LNCaP cells were seeded on dishes in RPMI-1640 supplemented with 10% FBS and allowed to attached overnight. The following day, the cells were washed twice with PBS and fed with phenol-free DMEM supplemented with 5% charcoal:dextran FBS. One day later, the cells were transfected using Lipofectamine 2000 and 20 pmol mL-1 siRNA diluted in Opti MEM reduced serum media without phenol red (Life Technologies). The transfection media was removed after 16 h incubation and the cells were washed twice with PBS. Fresh, phenol-free DMEM supplemented with 5% charcoal:dextran FBS and Penicillin/Streptomycin was added to the dishes. 48h post transfection, the cells were treated with 100 nM DHT for 1h, and then harvested.


title: LNCaP_GRO-seq_siTOP1_1h_vehicle_replicate-D

description: GRO-seq, siTOP1, 1h treatment with vehicle


title: LNCaP_TOP1_ChIP-seq_30min_dht

description: ChIP-seq with BLRP-tagged TOP1, 30min treatment with 100 nM DHT

data_processing:
ChIP-seq was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp (Luo et al., 2013: PLoS one 8, no. 5, e65632). The regions with DHT-increased/DHT-decreased TOP1-binding were calculated using SICER (with  background control from 3 combined repeats from GEO database: GSM1543795). The TOP1 peaks were calculated with MACS. The 43653 peak summits in 64569 DHT-increased regions and 15073 peak summits in 26321 DHT-decreased regions were saved in "GSE63202_43653summitsIn64569increasedTOP1regions.bed.gz" and "GSE63202_15073summitsIn26321decreasedTOP1regions.bed.gz" files respectively in GEO database: GSE63202.  Please note, not all regions have clearly defined peaks.
Genome build: hg18
Supplementary file format and content: BED (peaks)

growth_protocol: LNCaP cells were engineered to express BirA enzyme and the Tet-Repressor. This parental line was used to generate inducible cells that express biotin-tagged human topoisomerase I under the control of a Tet-on promoter that can be induced with doxycycline to obtain protein expression level similar to the endogenous one. Biotin ligase recognition peptide (BLRP)-tagged TOP1 cells were used for the ChIP experiment. Following doxycycline (2 μg/mL) induction for 24 h, the cells were stimulated with 100 nM DHT for 30 min and fixed with 1% formaldehyde for 10 min at room temperature.

extract_protocol: Isolated nuclei were sonicated and precipitation was carried out with Streptavidin Magnetic Microspheres (Solulink). Beads were washed with standard ChIP buffers. Additional extensive washes (4 times/20 min each with 1% SDS in TE buffer and two times with 1% Triton X-100 in TE buffer) were performed, before TEV (Life Technologies) cleavage. DNA was purified using QIAquick spin columns (Qiagen).

tag: chip antibody

value: BLRP-tagged TOP1


title: LNCaP_PRO-cap_1h_vehicle

description: PRO-cap, 1h treatment with vehicle

data_processing:
Library strategy: PRO-cap
PRO-cap was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp  (Luo et al., 2013: PLoS one 8, no. 5, e65632). The bedGraph files were prepared using HOMER (http://homer.salk.edu/homer/) software. The clusters of PRO-cap transcriptional initiation sites were predicted using HOMER software and bidirectionally transcribed loci were defined similarly to previously published analysis of CAGE tag clusters for FANTOM5 samples (Andersson et al., 2014: Nature 507, 455-461). We identified divergent (reverse-forward) clusters of PRO-cap pairs separated by at most 574 bp, which resulted in 7873 in vehicle treated samples.
Genome build: hg18
Supplementary files format and content: BED (peaks), bedGraph (PRO-cap tag density)

source_name: PRO-cap, 1h treatment with vehicle

growth_protocol: LNCaP cells were purchased from ATCC and maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Omega Scientific), 2mM L-Glutamine and Penicillin/Streptomycin. The cells were starved in phenol-free DMEM (Lonza) supplemented with 5% charcoal: dextran stripped fetal bovine serum (Omega Scientific) for 72 hours.

extract_protocol: PRO-cap was performed as previously described [Kwak, H., et al., Science 339, 950-953 (2013)] by using ~ 20 million nuclei isolated from LNCaP cells starved for 72 hours and treated with ethanol for 1h.


title: LNCaP_GRO-seq_siMRE11_1h_vehicle_replicate-C

description: GRO-seq, siMRE11, 1h treatment with vehicle


title: LNCaP_GRO-seq_siMRE11_1h_dht_replicate-C

description: GRO-seq, siMRE11, 1h treatment with 100 nM DHT


title: LNCaP_GRO-seq_siControl_1h_dht_replicate-B

source_name: GRO-seq, siControl, 1h treatment with 100 nM DHT


title: LNCaP_GRO-seq_siMRE11_1h_dht_replicate-B

source_name: GRO-seq, siMRE11, 1h treatment with 100 nM DHT


title: LNCaP_GRO-seq_siNKX3.1_1h_vehicle_replicate-A

description: GRO-seq, siNKX3.1, 1h treatment with vehicle


title: LNCaP_GRO-seq_siControl_1h_dht_replicate-C


title: LNCaP_PRO-cap_1h_dht

description: PRO-cap, 1h treatment with 100 nM DHT

data_processing:
Library strategy: PRO-cap
PRO-cap was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp  (Luo et al., 2013: PLoS one 8, no. 5, e65632). The bedGraph files were prepared using HOMER (http://homer.salk.edu/homer/) software. The clusters of PRO-cap transcriptional initiation sites were predicted using HOMER software and bidirectionally transcribed loci were defined similarly to previously published analysis of CAGE tag clusters for FANTOM5 samples (Andersson et al., 2014: Nature 507, 455-461). We identified divergent (reverse-forward) clusters of PRO-cap pairs separated by at most 574 bp, which resulted in 10275 in +DHT treated samples.
Genome build: hg18
Supplementary files format and content: BED (peaks), bedGraph (PRO-cap tag density)

source_name: PRO-cap, 1h treatment with 100 nM DHT

extract_protocol: PRO-cap was performed as previously described [Kwak, H., et al., Science 339, 950-953 (2013)] by using ~20 million nuclei isolated from LNCaP cells starved for 72h  and treated with 100 nM DHT for 1h.


title: LNCaP_GRO-seq_siNKX3.1_1h_dht_replicate-A

description: GRO-seq, siNKX3.1, 1h treatment with 100 nM DHT


title: LNCaP_GRO-seq_siMRE11_1h_vehicle_replicate-B

source_name: GRO-seq, siMRE11, 1h treatment with vehicle


title: LNCaP_GRO-seq_siControl_1h_vehicle_replicate-B

source_name: GRO-seq, siControl, 1h treatment with vehicle


title: LNCaP_GRO-seq_siControl_1h_dht_replicate-A


title: LNCaP_GRO-seq_siControl_1h_vehicle_replicate-C


title: LNCaP_GRO-seq_siTOP1_1h_dht_replicate-A

source_name: GRO-seq, siTOP1, 1h treatment with 100 nM DHT


title: LNCaP_GRO-seq_siControl_1h_vehicle_replicate-A


title: LNCaP_MRE11_ChIP-seq_15min_dht

description: ChIP-seq with MRE11 antibody, 15min treatment with 100 nM DHT

data_processing:
ChIP-seq was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using BFAST (Homer et al., 2009: PloS one 4, e7767). The peaks were calculated with MACS software.
Genome build: hg18
Supplementary files format: BED (peaks)

source_name: ChIP-seq with MRE11, 15min treatment with 100 nM DHT

growth_protocol: LNCaP cells were purchased from ATCC and maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Omega Scientific), 2mM L-Glutamine and Penicillin/Streptomycin and starved in phenol-free DMEM (Lonza) supplemented with 5% charcoal: dextran stripped fetal bovine serum (Omega Scientific) for 72 hours. Cells were synchronized with 2.5 μM alpha-amanitin (Sigma) for 2 hours, washed twice with PBS and released. Cells were treated with 100 nM DHT for 15 min prior to fixation with 1% formaldehyde for 15 min at RT.

extract_protocol: Chromatin immunoprecipitation experiments were done as previously described (Garcia-Bassets et al., 2007: Cell 128, 505-518).

value: MRE11 (Abcam; Ab397)


title: LNCaP_AR_ChIP-seq_1h_dht

description: ChIP-seq with AR antibody, 1h treatment with 100 nM DHT

data_processing:
ChIP-seq were sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SMALT, www.sanger.ac.uk/resources/software/smalt). The peaks were calculated with MACS software, the histone marks and background control are from GEO database (GSE27824). AR-enhancers were identified based on the epigenetic signatures. We identified 6545 AR-enhancers (AR-binding with H3K4me1 and H3K27Ac marks, histone modifications that co-localize with active enhancers, that exclude 574 AR-binding sites within 1000bp from H3K4me3 region with strong signal (promoter mark) and 2536 AR-binding sites away (≥1000bp) from any of those marks).
Genome_build: hg18
Supplementary files format and content: BED (peaks)

source_name: ChIP-seq with AR, 1h treatment with 100 nM DHT

growth_protocol: LNCaP cells were purchased from ATCC and maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Omega Scientific), 2mM L-Glutamine and Penicillin/Streptomycin.

extract_protocol: Chromatin immunoprecipitation experiments were done as previously described [Garcia-Bassets et al., 2007 Cell 128, 505-518].

treatment_protocol: The cells were starved in phenol-free DMEM (Lonza) supplemented with 5% charcoal:dextran stripped fetal bovine serum (Omega Scientific) for 72 hours followed by stimulation with 100 nM 5alpha-dihydrotestosterone (DHT) for 1h.

value: AR (Santa Cruz; sc-816)


title: LNCaP_MRE11_ChIP-seq_0min

description: ChIP-seq with MRE11 antibody, 0min

source_name: ChIP-seq with MRE11, 0min

growth_protocol: LNCaP cells were purchased from ATCC and maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Omega Scientific), 2mM L-Glutamine and Penicillin/Streptomycin and starved in phenol-free DMEM (Lonza) supplemented with 5% charcoal:dextran stripped fetal bovine serum (Omega Scientific) for 72 hours. Cells were synchronized with 2.5 μM alpha-amanitin (Sigma) for 2 hours, washed twice with PBS and released. Cells were treated with ethanol for 15 min prior to fixation with 1% formaldehyde for 15 min at RT.

value: MRE11 (Abcam; Ab397).


title: LNCaP_background_control_for_TOP1_ChIP-seq_repeat1-3

description: ChIP-seq, background control for TOP1, 3 repeats were combined

data_processing:
ChIP-seq was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp  (Luo et al., 2013: PLoS one 8, no. 5, e65632). This background control is for TOP1 ChIP-seq (GEO: GSM1543791 and GSM1543792). The bedGraph files were prepared using HOMER (http://homer.salk.edu/homer/) software and reads from all 3 repeats.
Genome build: hg18
Supplementary file format and content: bedGraph (GRO-seq tag density)

source_name: ChIP-seq, background control for TOP1

growth_protocol: LNCaP cells were purchased from ATCC and maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Omega Scientific), 2mM L-Glutamine and Penicillin/Streptomycin and starved in phenol-free DMEM (Lonza) supplemented with 5% charcoal: dextran stripped fetal bovine serum (Omega Scientific) for 72 hours.  Cells were treated with ethanol for 1 h prior to fixation with 1% formaldehyde for 10 min at RT.

extract_protocol: Chromatin immunoprecipitation experiments were done as previously described [Garcia-Bassets, I. et al., Cell 128, 505-518 (2007)].

value: background


title: 15kGy_irradiated

city: Austin

first: Chen-Hsun

last: Tsai

state: Texas

address: Room 3.416, 200 E. Dean Keeton St. Stop C0400

department: McKetta Department of Chemical Engineering

institute: Univ. of Texas at Austin

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to D. radiodurans whole genome using bowtie2.2.0
All intergenic loci mapped with over 100 reads per base and longer than 30 nt were annotated as potential sRNA candidates. Specific counts were calculated for 25 identified sRNAs.
Genome_build: ASM856v1; NC_001263.1 and NC_001264.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

growth_protocol: The strain Deinococcus radiodurans R1 (ATCC-13939) was grown overnight at 30° (D. radiodurans) in TGY broth (1% tryptone/0.1% glucose/0.5%yeast extract) to exponential phase (OD600 = 1).

extract_protocol:
Cells were pelleted and resuspended in TRIzol reagent (Invitrogen, 15596-026), and lysed using a bead-beater (Bio Spec Products Inc, 3110BX) with four 100s pulses. The top aqueous phase containing RNA was extracted with chloroform:isoamyl (24:1) alcohol  and precipitated with isopropanol. The resulting pellet was dissolved in RNAse-free water. RNA concentration was measured by spectrophotometer and stored in -20° C for short term use. The integrity and purity of total RNAs were verified with spectrometer (OD260/OD280) and RNA gel staining.
cDNA libraries were prepared from total RNAs that extracted from irradiated or non-irradiated cells. We used NEBNext® Small RNA Libray Prep Set for Illumina® (New England Biolabs Inc. E7330S) to prepare cDNA for all samples with the  protocol provided by the manufacturer.

treatment_protocol: D. radiodurans cells were cultured to exponential (OD600 = 1) phase, packed, frozen with dry ice and transported in sterilized plastic bags for irradiation. Samples were thawed at room temperature at the radiation facility before irradiation. These samples were kept cold on wet ice (0°C) while irradiated with a 10 MeV, 18 kW LINAC b-ray source at the National Center for Electron Beam Research, Texas A&M University. Cell samples were subjected to sham and 15 kGy (250Gy/s) exposures. This initial high radiation exposure was designed to elicit a strong enough response that would allow detectable differential expression of sRNAs by Northern blotting. Cells were diluted 4-5 fold to OD600 =1 and recovered in fresh culture (TGY) medium for 2 hours at 30° C immediately following irradiation and processed for RNA extraction or stored at -80° C for future analysis. Cell survival rates were measured by plating recovered sham and irradiated cells on TGY plates for colony forming units (CFU) comparison.

tag: treatment


title: LNCaP_TOP1_ChIP-seq_30min_vehicle

description: ChIP-seq with BLRP-tagged TOP1, 30min treatment with vehicle

growth_protocol: LNCaP cells were engineered to express BirA enzyme and the Tet-Repressor. This parental line was used to generate inducible cells that express biotin-tagged human topoisomerase I under the control of a Tet-on promoter that can be induced with doxycycline to obtain protein expression level similar to the endogenous one. Biotin ligase recognition peptide (BLRP)-tagged TOP1 cells were used for the ChIP experiment. Following doxycycline (2 μg/mL) induction for 24 h, the cells were stimulated with ethanol for 30 min and fixed with 1% formaldehyde for 10 min at room temperature.


title: Sham_irradiated


title: ICC24 (RNA-seq)

city: New York

first: Daniela

last: Sia

address: 1425 Madison Avenue

department: Liver Diseases

institute: Icahn school of Medicine at Mount Sinai

description: tumoral tissue of ICC23

data_processing:
For RNA-seq, between 20 and 25 million 100 base pair (bp) reads were generated for each of 7 matched-normal samples. Actual alignment of the raw cDNA reads was carried out by tophat-fusion and de novo assembly of transcript level reads was carried out by Cufflinks. Briefly, tophat-fusion breaks up individual reads into 25 bp segments, which are mapped independently to the reference build hg19 via bowtie. Following Edgren et al, we used the following filtration scheme to identify fusion events: 1) BLAST sequence around putative breakpoint to hg19 build to identify and remove paralogous sequences; 2) Filter fusions based on the number of reads that support the putative fusion breakpoints, setting the minimum number of such spanning reads conservatively; 3) compute scores of distributions of coverage of reads around the putative breakpoints, rejecting non uniformly covered reads; 4) fusions between adjacent genes were rejected as read-through transcript events, with a minimum distance of 100 kb; 5) finally, we considered a read to support a fusion if it mapped to both sides of breakpoint by at least a minimum fusion anchor length of 25bp, or generally about a quarter of a read length.
For exome-seq, the experiments achieved high quality in the metrics of high read quality, high mapping rate, low duplication rate and adequate coverage of the target regions.  PCR and optical duplicates, low-quality (Q<20) and non-uniquely mapped reads were successfully removed. Remaining reads were aligned to the human genome reference 19th version using BWA.  Afterwards, somatic single nucleotide variants (SNV) and small indels were identified through VarScan2.  We calculated p-value using Fisher’s Exact Test for all putative mutation sites based on the distribution of read support for different alleles in tumor and matched normal samples.  The VarScan2 software was employed in above analyses because of their desirable feature in detecting mutations in low purity or heterogeneous cancer samples.  Purity information was factored in Mutant allele frequency estimations.
Genome_build: human genome 19
Supplementary_files_format_and_content:

source_name: iCCA patient,  liver

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted from homogenized cholangiocarcinoma samples and their normal conterparts usingTRizol Regent (Invitrogen). Quantity of RNA was measured using Quant-iT Ribogreen RNA assay kit and quality was assessed using a Bioanalyzer. One µg of RNA was used for subsequent RNA-seq library generation. DNA was isolated using the ChargeSwitch® gDNA Mini Tissue Ki/t (Invitrogen) after tissue disruption with a homogenizer. DNA quantity was assessed through Quant-It PicoGreen dsDNA Assay kit (Invitrogen) and its integrity confirmed by agarose gel.
For RNA-seq, the sequencing library was prepared with the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, total RNA was poly-A-selected and then fragmented. The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina recommended 6 bp barcode bases are introduced at one end of the adaptors during PCR amplification step. The size and concentration of the RNAseq libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer. The mRNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's protocol (Illumina, CA, USA). For exome-seq, total genomic DNA library is generated following the manufacturer protocol (NEBNext DNA Library Prep Master Mix Set for Illumina, New England Biolabs, Ipswich, MA). For whole exome sequencing (WES), the library then undergoes solution-based hybridization to an oligonucleotide pool designed to enrich for the whole exome regions of interests. The library is captured by following the manufacturer protocol (SeqCap EZ Human Exome Library v3.0 User Guide. Roche NimbleGen. Madison, WI).

treatment_protocol: not applicable

tag: material type

value: fresh-frozen

value: liver

value: intrahepatic cholangiocarcinoma


title: ICC16 (RNA-seq)

description: tumoral tissue of ICC15


title: ICC18 (RNA-seq)

description: tumoral tissue of ICC17


title: ICC14 (RNA-seq)

description: tumoral tissue of ICC13


title: ICC10 (RNA-seq)

description: tumoral tissue of ICC9


title: ICC12 (RNA-seq)

description: tumoral tissue of ICC11


title: ICC15 (RNA-seq)

description: non-tumoral tissue of ICC16

value: surrounding non-tumoral tissue


title: ICC8 (RNA-seq)

description: tumoral tissue of ICC6


title: ICC23 (RNA-seq)

description: non-tumoral tissue of ICC24


title: ICC13 (RNA-seq)

description: non-tumoral tissue of ICC14


title: ICC9 (RNA-seq)

description: non-tumoral tissue of ICC10


title: ICC11 (RNA-seq)

description: non-tumoral tissue of ICC12


title: LNCaP_GRO-seq_siTOP1_1h_vehicle_replicate-A

source_name: GRO-seq, siTOP1, 1h treatment with vehicle


title: ICC6 (RNA-seq)

description: non-tumoral tissue of ICC8


title: ICC24 (Exome-seq)

description:
tumoral tissue of ICC23
library strategy: Exome-seq


title: ICC23 (Exome-seq)

description:
non-tumoral tissue of ICC24
library strategy: Exome-seq


title: ICC22 (Exome-seq)


title: ICC21 (Exome-seq)

description:
non-tumoral tissue of ICC22
library strategy: Exome-seq


title: ICC18 (Exome-seq)

description:
tumoral tissue of ICC17
library strategy: Exome-seq


title: ICC12 (Exome-seq)

description:
tumoral tissue of ICC11
library strategy: Exome-seq


title: ICC14 (Exome-seq)

description:
tumoral tissue of ICC13
library strategy: Exome-seq


title: ICC10 (Exome-seq)

description:
tumoral tissue of ICC9
library strategy: Exome-seq


title: ICC13 (Exome-seq)

description:
non-tumoral tissue of ICC14
library strategy: Exome-seq


title: ICC17 (Exome-seq)

description:
non-tumoral tissue of ICC18
library strategy: Exome-seq


title: ICC15 (Exome-seq)

description:
non-tumoral tissue of ICC16
library strategy: Exome-seq


title: ICC11 (Exome-seq)

description:
non-tumoral tissue of ICC12
library strategy: Exome-seq


title: ICC9 (Exome-seq)

description:
non-tumoral tissue of ICC10
library strategy: Exome-seq


title: ICC16 (Exome-seq)

description:
tumoral tissue of ICC15
library strategy: Exome-seq


title: ICC8 (Exome-seq)

description:
tumoral tissue of ICC6
library strategy: Exome-seq


title: ICC6 (Exome-seq)

description:
non-tumoral tissue of ICC8
library strategy: Exome-seq


title: ICC17 (RNA-seq)

description: non-tumoral tissue of ICC18


title: rep2_FEA4_ChIP

status: Public on Jan 21 2015

city: St. Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

description:
rep2_FEA4_MACS_peaks.bed
rep2_FEA4_MACS_summits.bed

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina MiSeq platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
ChIP-seq reads were aligned to the maize reference genome (AGPv2) using Bowtie (v.0.12.7;(Langmead et al., 2009)) and peak calling was performed with MACS version 1.4.0rc2 using only uniquely mapped reads (Zhang et al., 2008). Peaks were identified as significantly enriched (p<1e-05) in each of the ChIP-seq libraries compared to input DNA.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files are output of MACS.1.4.0rc2.  The peaks.bed file includes (from left to right columns) chromosome, peak start, peak stop, -10*log10(pval).  The summits.bed file includes (from left to right columns) chromosome, summit start, summit stop, tag pileup at summit.

organism: Zea mays

source_name: 2-5mm tassel primordia

growth_protocol: Developing tassel primordia, approximately 2-5mm in size, were harvested from FEA4-YFP plants grown in the field at CSHL uplands farm facility.

extract_protocol:
Following dissection, inflorescences were immediately cross-linked in buffer containing 1% formaldehyde for 15 minutes under vacuum, followed by addition of glycine to a concentration of 0.1 M, which was infiltrated for 5 minutes.  Following three washes with distilled water, the cross-linked tissues were dried with paper towels and flash frozen in liquid nitrogen.
Chromatin extracts from YFP-FEA4 plants were immunoprecipitated with anti-GFP (ab290, Abcam) antibody.  Protein A dynabeads (Invitrogen) blocked with yeast tRNA and BSA were used to capture antibody-chromatin complexes (Morohashi et al., 2012).  Following purification of immunoprecipitated DNA, libraries were constructed using the Ovation Low Input DR kit (Nugen) and barcoded to allow multiplexed sequencing.  Two input and two IP libraries were sequenced on one run of an Illumina MiSeq machine.

treatment_protocol: These experiments used families containing a transgene integration event that complemented the mutant (A399S1-7), and expression of the transgene was verified by fluorescence microscopy.

value: anti-GFP

value: 2-5mm tassel primordia

tag: experiment

value: ChIPseq

value: normal B73


title: rep1_FEA4_ChIP

description:
rep1_FEA4_MACS_peaks.bed
rep1_FEA4_MACS_summits.bed


title: fea4_mut_rep3_ear

description: all_genes_expression_values_supp_table.txt

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina HiSeq2000 platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software on the HiSeq as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
Tophat (version 2.0.9) was used to align reads to the maize reference genome (AGPv2) based on an a priori set of 110,028 predicted maize gene models (Working Gene Set v5b.60; maizesequence.org).  We then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks (version 2.0.2) and a high-confidence subset of 39,656 maize gene models, the Filtered Gene Set (FGS v5b.60; maizeseqeunce.org).  Differential expression analysis was carried out using the R package DESeq (v.1.14.0;(Anders and Huber, 2010). An adjusted p-value of < 0.05 was used to call differentially expressed genes after multiple testing correction.  Further details are provided in Supplemental Methods in associated Pautler et al. paper.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Single processed data file for RNAseq analysis includes expression information for all Filtered Gene Set (FGS) genes based on analysis with Cufflinks v.2.0.2 and differential expression analysis with DESeq.  Gene is called significant for differential expression if adjusted p-value < 0.05.  Normalized read count averages among all samples (baseMean.Avg), wild-type biological replicates (baseMean.wt) and fea4 mutant biological replicates (baseMean.fea4) based on DESeq analysis.  These values were used in determine fold changes.  Raw read counts for each sample and normalized fragments per kilobase per million reads (FPKM) based on Cufflinks analysis.

source_name: 1mm ear primordia

growth_protocol: fea4-ref was isolated from an M2 screen of EMS-mutagenized A619 inbred maize, and was deposited in the Maize Genetics Co-Op Stock Center as fea179.  The mutation was introgressed 4-5 times into various inbred lines for phenotypic analysis in segregating families.  fea4-rel*09-5171 and fea4-rel*07-167 were found in a screen for enhancers of ramosa2 in the A619 inbred background.  Ear primordia from segregating populations were collected from field grown plants at the CSHL uplands farm facility.

extract_protocol:
Total RNA was extracted from pools of ear tissue using the PicoPure RNA Isolation kit (Life Technologies), according to manufacturer instructions.  Messenger RNA was enriched by two successive purifications with oligo-dT coupled dynabeads (Invitrogen).
Approximately 50ng of mRNA was used as input for the ScriptSeq v2 RNAseq system (Epicentre).  This kit allowed the addition of barcoded adapters (Index #4,5,6,7) to enable multiplexed sequencing in a single lane of an Illumina HiSeq2000.  Prior to sequencing, the average size distribution of the libraries was verified on a high sensitivity bioanalyzer chip.  The libraries were diluted to 10nM and concentration was verified by qPCR using standards (KAPA Biosystems).

treatment_protocol: Triplicate pools of more than ten 1mm ears were harvested from homozygous fea4 mutants and heterozygous wild-type sibling plants. Freshly dissected ear tissue was fixed in ice-cold acetone, followed by vacuum infiltration for 20 minutes, and three acetone changes of one hour each.

value: 1mm ear primordia

value: RNAseq

value: fea4/fea4 homozygous mutant


title: rep1_input

value: input


title: fea4_mut_rep2_ear


title: wt_rep2_ear

value: fea4/+ heterozygous


title: wt_rep1_ear


title: fea4_mut_rep1_ear


title: hNSC_CHD8_KD_G_2

city: Philadelphia

first: Justin

last: Cotney

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

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

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.

value: human Neural Stem Cells (hNSCs)

tag: transfected with

value: shCHD8 #G (CloneID:V3LHS_311510)

tag: time point

value: 48 hours after transfection


title: hNSC_CHD8_KD_G_0

tag: cell type


title: hNSC_CHD8_KD_G_1


title: hNSC_CHD8_KD_C_2

value: shCHD8 #C (CloneID:V2LHS_201084)


title: hNSC_CHD8_KD_C_1


title: hNSC_Ctrl_KD_3


title: hNSC_Ctrl_KD_2


title: hNSC_Ctrl_KD_0


title: hNSC_CHD8_KD_C_0


title: rep2_input


title: hNSC_non_transfected_1


title: hNSC_non_transfected_0


title: wt_rep3_ear


title: hNSC_Chd8_3

value: CHD8 N terminus

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: dcp2-1/rdr6 replicate 2

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

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: genotype/variation

value: dcp2 and rdr6 double mutant


title: vcs-6/rdr6 replicate 2

value: vcs-6 and rdr6 double mutant


title: hNSC_Chd8_2


title: dcp2-1/rdr6 replicate 1


title: vcs-6 replicate 2

value: vcs-6 mutant


title: vcs-6 replicate 1