title: Ago3 IP - artificial piRNA - replicate# 2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

data_processing:
A custom pipeline that generates genome annotations based on that found in http://kaikogaas.dna.affrc.go.jp/
Samples were sequenced in a Illumina HiSeq 2000 platform or Illumina MiSeq.
JX files: Adapter sequences were clipped from the reads and sorted into individual libraries based on the barcodes (which are at the 3′ end). Reads were then mapped to the Bombyx mori genome (http://kaikogaas.dna.affrc.go.jp/; this has the combined data generated by the Silkworm Genome Research Program in Japan and Silkworm Genome Project in China). Only perfectly mapping reads were used for subsequent analyses using custom-built pipelines. Typically, 55% of the small RNA reads (max= 64%, min= 43%, calculated from 17 libraries) mapped to the genome. However, given that the genome assembly is not complete, many of the non-mapped sequences are likely to be perfectly-mapping reads, and are missing in our current analyses. Annotation of reads were carried out using the following databases: a set of Bombyx transposon consensus sequences, coding and miRNA sequences from Silkworm genome database, and a set of our own assemblies for both mRNAs and transposons expressed in the BmN4 cells.
DH files: Reads were sorted into individual libraries based on the barcodes and the 3’ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200). Reads were then aligned to the Siwi-T piRNA precursor sequence (see supplementary information in the associated manuscript) using bowtie (Langmead et al., 2009) allowing no mismatches.  For Vasa binding sites detection, the reads originating from Vasa footprint were aligned to the reporter allowing no mismatch. Counts from two independent libraries were merged together and only the reads longer than 10 nucleotides were used for plotting the coverage.
Genome_build: Bombyx mori genome at http://kaikogaas.dna.affrc.go.jp/

organism: Bombyx mori

source_name: Bombyx mori, BmN4 cells

growth_protocol: Transfected BmN4 cells were used.

extract_protocol: Nucleic acids were isolated from protein complexes immunoprecipitated with the indicated antibodies and resolved by 15% or 20% urea-PAGE. Bands corresponding to piRNAs or the indicated size were excised from the gel and extracted with 400 µl of 0.3M NaCl solution at 25°C overnight. All deep sequencing libraries (except for JX52, JX59 and JX86) were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. JX52, JX59 and JX86 were prepared by ligating homemade RNA adaptors, followed by gel-purification and RT-PCR. Libraries were sequenced on Illumina HiSeq platform (EMBL Heidelberg Gene core facility) or Illumina MiSeq platform (EMBL Heidelberg Gene core facility) .

tag: cell type

value: BmN4 cells

tag: transfection

value: expression of artificial piRNA reporter Siwi T

tag: antibody

value: anti-Ago3  (Xiol et al., 2012, Mol Cell 47, 970-979)

tag: 3' barcode (nebnext primers)

value: TGACCA

tag: 5' barcode


title: 1-cell embryos (small RNA replicate 2)

status: Public on Jun 04 2014

type: SRA

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
1cell_2
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

library_source: transcriptomic

data_processing:
Sequencing reads for each sample and stage were seperately mapped to the transcriptome using bwa with default parameters. For small RNAs reads were mapped to the genome
For mRNAs reads were aggregated across all isoforms of a given gene.
For mRNAs aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
For small RNAs reads were annotated based on the strand and the annotation (i. e. sense or antisense with regards to a given annotation).
For small RNAs all reads of a given annotation were aggregated and converted into reads per million (RPM)
Genome_build: WS190
Supplementary_files_format_and_content: Tab separated txt-file with gene identifiers and expression values in RPKM for mRNAs and RPM for small RNAs.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: 1-cell small RNA library

growth_protocol: Strains were maintained using previously described methods(Brenner, 1974; Stiernagle, 2006) on OP50 seeded NGM plates at permissive temperatures.

extract_protocol:
For small RNA-seq: 1 µg of total RNA per sample were used for small RNA library preparation. First total RNA was treated with RNA 5â?? polyphosphatase (Epicentre Biotechnologies, USA) prior to small RNA library preparation to allow for subsequent cloning of multiphosphorylated endo-siRNAs. Small RNA cloning and library preparation was then performed with the TruSeq Small RNA Sample Preparation Kit (Illumina, USA) according to the manufacturer protocol.
Oocytes: Adult wild-type hermaphrodites (N2) were cut using a razorblade in PBS containing 0.5% BSA and 0.02%Tween. Oocytes were picked by mouth pipetting under a stereo microscope (Leica), washed thoroughly in PBS and lyzed in TriZol LS (Invitrogen, USA). Sperm: Sperm was isolated in principle as described previously(L¹Hernault & Roberts, 1995) from males worms obtained from a fog-2(q71) mutant background strain. Males were cut in cold PBS containing protease inhibitors (Sigma-Aldrich, Germany). Sperm was subsequently purified by filtration (3x40µm, 2x10µm, 1x6µm nylon mesh) and washed twice in cold PBS. Sperm was then activated by incubation in PBS containing 200µg/mL Pronase (Sigma-Aldrich, Germany) for 30 minutes at 24°C and suspended in Trizol LS (Invitrogen, USA) for RNA extraction. 1-cell embryos: 1-cell embryos were obtained by fluorescence activated cell sorting (eFACS) as described previously(Stoeckius et al, 2009) in an FACSAriaIII flow cytometer (BD Biosciences, USA).  Whole worm: Adult worms were washed from NGM plates with M9-Buffer and subsequently washed at least 3 times with M9-Buffer. RNA was isolated from whole worms by bead homogenization (6000 rpm, 5 seconds) in a Precellys24 (Precellys, USA) in Trizol LS reagent (Invitrogen, USA) according to the manufacturers protocols.

tag: strain

tag: temperature

tag: rna source

value: 1-cell embyro

tag: library

value: small RNA library


title: Siwi IP - artificial piRNA - replicate #1

country: Switzerland

value: anti-Siwi (Xiol et al., 2012, Mol Cell 47, 970-979)

value: ATCACG


title: R1_ESC_rep1

status: Public on Jun 05 2014

city: Stanford

first: Christa

last: Buecker

state: California

address: 269 Campus Drive

department: Chemical and Systems Biology

country: USA

institute: Stanford University

description: Mouse embryonic stem cells grown under ESC (serum free, N2B27 based 2i+LIF) or differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR) for 48h

data_processing:
RNA seq libraries were sequenced with Illumina Genome Analyzer
reads were mapped with tophat, FPKM were determined using Cufflinks
Genome_build: mm9 and refseq
Supplementary_files_format_and_content: csv files containing all FPKM

organism: Mus musculus

source_name: embryonic stem cells (ESC)

growth_protocol: All mouse ESC lines were adapted for a minimum of 5 passages to growth in serum free N2B27 based medium supplemented with MEK inhibitor PD0325901 (0.8μM) and GSK3β inhibitor CHIR99021 (3.3μM) in tissue culture dishes pretreated with 7.5μg/ml polyL-ornithine (Sigma) and 5μg/ml laminine (BD) (Hayashi et al., 2011).  To induce EpiLC differentiation, cells were washed with PBS, trypsinized and strained. 200,000 to 300,000 cells per 10cm2 were plated on tissue culture dishes pretreated with 5μg/ml Fibronectin (Millipore) in N2B27 based medium supplemented with 1% KSR (Invitrogen) and 12μg/ml bFGF (Peprotech). Where indicated 20ng/ml Activin A (R&D Scientific) was added.

extract_protocol:
RNAs from two independent biological replicates of ESC culture and two independent biological replicates from EpiLCs were extracted with Trizol (Invitrogen), following the manufacturer's recommendations. 10 μg of total RNA were subjected to two rounds of oligo-dT purification using Dynaloligo-dT beads (Invitrogen). 100 ng of the purified RNA were fragmented with 10x fragmentation buffer (Ambion). Fragmented RNA was used for first-strand cDNA synthesis, using random hexamer primers (Invitrogen) and SuperScript II enzyme (Invitrogen). Second strand cDNA was obtained by adding RNaseH (Invitrogen) and DNA Pol I (New England Biolabs) to the first strand cDNA mix.
The resulting double-stranded cDNA was used for Illumina library preparation and sequenced with Illumina Genome Analyzer.

treatment_protocol: All samples were washed once with PBS and lysed directly on the plate with Trizol.

tag: es cell line

value: R1 ESC

tag: mouse strain

tag: growth


title: N2 whole worm (small RNA replicate 1)

description:
NR_1
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

source_name: whole worm small RNA library

value: whole worm


title: Siwi IP - artificial piRNA - replicate# 2

value: CGATGT


title: Ago3 IP - artificial piRNA - replicate# 1

value: TTAGGC


title: HA Vasa DQAD IP - 12-mer replicate# 2

value: HA-tag

value: anti-HA (sc-805; Santa Cruz)

value: CGGA


title: HA-Vasa DQAD IP - piRNAs replicate# 2

value: GCCAAT


title: 1-cell embryos (polyA replicate 3)

description:
1cell_poly_3
processed data file: data_mRNA_rpkm.txt

source_name: 1-cell embyro poly(A)-extracted mRNA library

extract_protocol:
mRNA-Seq: PolyA RNA was fragmented into approximately 250 nt fragments by chemical fragmentation (200 mM tris acetate pH 8.2, 500 mM potassium acetate, 150 mM magnesium acetate) at 94°C for exactly 3.5 min in a thermocycler. Fragmented RNAs were isolated with RNA Clean beads (Beckman Coulter, USA) according to manufacturerâ??s instructions. Fractionation was checked by capillary electophoresis in a RNA Pico 6000 chip using the Bioanalyzer (Agilent Technologies, USA). First strand cDNA synthesis was accomplished using Superscript III Reverse Transcriptase and random hexamers (Invitrogen, USA), followed by second strand synthesis using DNA Polymerase I and RNaseH (Invitrogen USA). Double-stranded DNA was purified with Agencourt AMPure beads XP (Beckman Coulter, USA) and quality was checked by capillary gelelectrophoresis on the Bioanalyzer with the Agilent DNA 1000 kit (Agilent Technologies, USA). dsDNA libraries subsequently processed for sequencing using the Genomic DNA Sample Prep Kit (Illumina, USA) according to the manufacturerâ??s protocol.
Oocytes: Adult wild-type hermaphrodites (N2) were cut using a razorblade in PBS containing 0.5% BSA and 0.02%Tween. Oocytes were picked by mouth pipetting under a stereo microscope (Leica), washed thoroughly in PBS and lyzed in TriZol LS (Invitrogen, USA). Sperm: Sperm was isolated in principle as described previously(L¹Hernault & Roberts, 1995) from males worms obtained from a fog-2(q71) mutant background strain. Males were cut in cold PBS containing protease inhibitors (Sigma-Aldrich, Germany). Sperm was subsequently purified by filtration (3x40µm, 2x10µm, 1x6µm nylon mesh) and washed twice in cold PBS. Sperm was then activated by incubation in PBS containing 200µg/mL Pronase (Sigma-Aldrich, Germany) for 30 minutes at 24°C and suspended in Trizol LS (Invitrogen, USA) for RNA extraction. 1-cell embryos: 1-cell embryos were obtained by fluorescence activated cell sorting (eFACS) as described previously(Stoeckius et al, 2009) in an FACSAriaIII flow cytometer (BD Biosciences, USA).  Whole worm: Adult worms were washed from NGM plates with M9-Buffer and subsequently washed at least 3 times with M9-Buffer. RNA was isolated from whole worms by bead homogenization (6000 rpm, 5 seconds) in a Precellys24 (Precellys, USA) in Trizol LS reagent (Invitrogen, USA) according to the manufacturers protocols.

value: fem-1(hc17ts)/TX189(OMA-1::GFP) (mother) X CB4856 (father)

value: poly(A)-extracted mRNA library


title: 1-cell embryos (polyA replicate 2)

description:
1cell_poly_2
processed data file: data_mRNA_rpkm.txt


title: 1-cell embryos (polyA replicate 1)

description:
1cell_poly_1
processed data file: data_mRNA_rpkm.txt


title: Siwi IP

value: BmN4 cells


title: HA Vasa DQAD IP - 12-mer replicate #1

value: ACTTGA


title: mEpiSC_RNAseq_rep4

city: Clev

first: Paul

middle: J.

last: Tesar

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

data_processing:
Reads were aligned to mm9 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et al., 2009) with default settings.
FPKM values for RefSeq genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks v2.0.2 (Trapnell et al., 2010). A detailed description of the file format can be found at http://cufflinks.cbcb.umd.edu/manual.html under the subheading "Cufflinks Output"

molecule: polyA RNA

source_name: Epiblast stem cells

growth_protocol: mESCs were grown in Knockout DMEM (Invitrogen) supplemented with 20% Knockout Serum Replacement (KSR) (Invitrogen), 10^3 units/ml recombinant murine Leukemia Inhibitory Factor (LIF) (ESGRO, Millipore), 2mM L- alanyl-L-glutamine dipeptide (Glutamax; Invitrogen), 1x non-essential amino acids (Invitrogen), and 0.1mM 2-mercaptoethanol (Sigma). mESCs were passaged every third day as a single cell suspension using 0.25% trypsin/EDTA and seeded at 3.0x10^4 cells/cm^2 for routine culture. mEpiSCs were cultured in Knockout DMEM supplemented with 20% KSR, 10ng/ml FGF2 (R&D Systems), 2mM Glutamax, 1x non-essential amino acids, and 0.1mM 2-mercaptoethanol and passaged every third day using 1.5 mg/ml collagenase type IV (Invitrogen) and trituration into small clumps of ~10-100 cells. Irradiated mouse embryonic fibroblasts (MEFs) served as a feeder layer for all pluripotent cell types and were maintained with DMEM supplemented with 10% fetal bovine serum, 2 mM glutamax, 1x non-essential amino acids, and 0.1 mM 2- mercaptoethanol. All cells were grown on Nunclon Δ-treated dishes or multiwell plates (Fisher Scientific) coated for 2 hours at 37°C with 0.1% (w/v) porcine gelatin (Sigma).

extract_protocol:
Cells were separated from MEF feeder layer and RNA was extracted from ~2x10^6 cells with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the RNAeasy Plus kit (Qiagen) according to the manufacturer’s protocol.
PolyA+ RNA was prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol.

tag: cell line


title: CB4856 whole worm (polyA replicate 2)

description:
HW_poly_2
processed data file: data_mRNA_rpkm.txt

source_name: whole worm poly(A)-extracted mRNA library


title: mEpiSC_RNAseq_rep2


title: HA-Vasa DQAD IP - piRNAs replicate#1

value: GAAC


title: Ago3 IP

value: anti-Ago3  (Xiol et al., 2012, Mol Cell 47, 970-979)

value: ACAGTG


title: CB4856 sperm (polyA high purity, pronase treated)

description:
HW_sperm_vp
processed data file: data_mRNA_rpkm.txt

source_name: sperm poly(A)-extracted mRNA library

value: sperm


title: mEpiSC_Dnase

library_source: genomic

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used to remove adapter sequences and trim read ends using a quality score cutoff of 20.
DNase-seq data were aligned to mm9 genome assemblies (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Bowtie v0.12.9 (Langmead et al., 2009), allowing reads with ≤ 2 mismatches and randomly assigning reads with > 1 reportable alignment to one alignment site ("-M 1" parameter).
Peaks were detected with MACS v1.4 (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files - Wiggle tracks stepped at 25 bp were generated by MACS, normalized to the median signal by chromosome and converted to bigwig format using the UCSC Genome Browser’s wigToBigWig utility (retrieved from http://hgdownload.cse.ucsc.edu/admin/exe/). bed files - MACS called peaks.

molecule: genomic DNA

growth_protocol: mEpiSCs were cultured in Knockout DMEM supplemented with 20% KSR, 10ng/ml FGF2 (R&D Systems), 2mM Glutamax, 1x non-essential amino acids, and 0.1mM 2-mercaptoethanol and passaged every third day using 1.5 mg/ml collagenase type IV (Invitrogen) and trituration into small clumps of ~10-100 cells. Irradiated mouse embryonic fibroblasts (MEFs) served as a feeder layer for all pluripotent cell types and were maintained with DMEM supplemented with 10% fetal bovine serum, 2 mM glutamax, 1x non-essential amino acids, and 0.1 mM 2- mercaptoethanol. All cells were grown on Nunclon Δ-treated dishes or multiwell plates (Fisher Scientific) coated for 2 hours at 37°C with 0.1% (w/v) porcine gelatin (Sigma).

extract_protocol:
1x10^7 cells were subjected to DNase sequencing as previously described (Song et al., 2011).
Sequencing libraries were prepared as previously described (Song et al., 2011)


title: mEpiSC_RNAseq_rep1


title: mESC_RNAseq_rep4

source_name: Embryonic stem cells


title: fog2 sperm (small RNA replicate 1)

description:
sperm_1
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

source_name: sperm small RNA library

value: small RNA library


title: mESC_RNAseq_rep3


title: PC3_H3K27me3_ChIP-Seq

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

description:
Sample 24
processed data file: PC3_ChromHMM.bed

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v0.12.8 allowing up to 3 mismatches, discarding ambiguous and clonal reads. ChromHMM v1.03 was used to simultaneously partition the genomes of all four cell lines into 15 chromatin states which were collapsed into 9 distinct states manually annotated by comparison to the published ChromHMM model for HMEC cells.
NOMe-seq reads were aligned to hg19 using BSMAP_2.01 and counts of methylated residues vs total sequencing counts at GCH and WCG sites summarized using custom R scripts. NDRs were detected by a 100bp sliding window in 20bp increments chi-squared test of GCH methylation versus the genome background with a p-value cutoff of -log10(p)>15, significant windows overlapped and retained if a minimum 140bp in size.
Genome_build: hg19
Supplementary_files_format_and_content: NDR bed files contain the -log10 pvalue in the name field (4th column). ChromHMM bed files report Consolidated ChromHMM States. GCH/WCG tsv files contain coordinates of cytosines in GCH/WCG genomic contexts and methylation values per cell line in two columns - C is the count of methylated calls and cov is the sequencing coverage at each position

organism: Homo sapiens

extract_protocol:
Nuclei were purified (described for NOMe-Seq) after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared by the USC Epigenome Center following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

tag: chip antibody

value: H3K27me3 (#39155, Active Motif)


title: mESC_RNAseq_rep2


title: Nsl1_ChIP-seq

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling was done with the Illumina pipeline (1.8.2) and FASTQ files have been generated using CASAVA v1.8.2.
The sequence alignment was done by the software Bowtie (0.12.7).
FASTQ files have been generated using CASAVA v1.8.2.
Bed files were generated by the Illumina pipeline (1.8.2).
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: mESCs

extract_protocol:
mESCs were cross-linked with 1% formaldehyde for 10 minutes at room temperature, lysded and shared mechanically using the Covaris E210 to obtain a chromatin fragment size of 200-500bp. For the IP histone-DNA complexes the anti-Msl1 (3208) or anti-Nsl1 (3130) antibodies were used. DNA was purified with Qiaquick (Qiagen) columns.
Ten ng of precipitated DNA was used for Solexa sequencing. To create a genomic library we followed the instructions of NEXTFlex v12.03 (BIO Scientific) for Msl1 and the NEBNext protocol (Biolabs, E6240) for Nsl1. Librarys were validated with the Agilent Bioanalyzer.

tag: age

tag: passages

tag: genotype

value: wt

tag: genetic background


title: PC3_H3K4me3_ChIP-Seq

description:
Sample 26
processed data file: PC3_ChromHMM.bed

value: H3K4me3 (#39160, Active Motif)


title: PrEC_Input_ChIP-Seq

description:
Sample 22
processed data file: PrEC_ChromHMM.bed

source_name: PrEC

value: PrEC

value: None (input)


title: mESC_RNAseq_rep1


title: PC3_H3K27ac_ChIP-Seq

description:
Sample 23
processed data file: PC3_ChromHMM.bed

value: H3K27Ac (#39297, Active Motif)


title: PrEC_RNApolIIp_ChIP-Seq

description:
Sample 21
processed data file: PrEC_ChromHMM.bed

value: RNA Polymerase II (#ab817, Abcam)


title: PrEC_H3K4me3_ChIP-Seq

description:
Sample 20
processed data file: PrEC_ChromHMM.bed


title: PC3_CTCF_ChIP-Seq

description:
Sample 29
processed data file: PC3_ChromHMM.bed

value: CTCF (#07-729, Millipore)


title: PC3_Input_ChIP-Seq

description:
Sample 28
processed data file: PC3_ChromHMM.bed


title: N2 oocytes (small RNA replicate 1)

description:
ooc_1
processed data file: data_small_RNA_rRNA.txt
processed data file: data_small_RNA_miRNA_prec.txt
processed data file: data_small_RNA_miRNA.txt
processed data file: data_small_RNA_u21RNA.txt
processed data file: data_small_RNA_tRNA.txt
processed data file: data_small_RNA_snoRNA.txt
processed data file: data_small_RNA_snRNA.txt
processed data file: data_small_RNA_exon.txt
processed data file: data_small_RNA_intron.txt

source_name: oocytes small RNA library

value: oocytes


title: mEpiSC_RNAseq_rep3


title: N2_background whole worm (polyA replicate 2)

description:
NR_poly_2
processed data file: data_mRNA_rpkm.txt

value: whole worm

value: poly(A)-extracted mRNA library


title: PrEC_H3K27ac_ChIP-Seq

description:
Sample 17
processed data file: PrEC_ChromHMM.bed


title: PrEC_H3K27me3_ChIP-Seq

description:
Sample 18
processed data file: PrEC_ChromHMM.bed


title: MCF7_H3K4me1_ChIP-Seq

description:
Sample 13
processed data file: MCF7_ChromHMM.bed

value: H3K4me1 (#39298, Active Motif)


title: MCF7_H3K4me3_ChIP-Seq

description:
Sample 14
processed data file: MCF7_ChromHMM.bed


title: MCF7_H3K27me3_ChIP-Seq

description:
Sample 12
processed data file: MCF7_ChromHMM.bed


title: PrEC_H3K4me1_ChIP-Seq

description:
Sample 19
processed data file: PrEC_ChromHMM.bed


title: MCF7_H3K27ac_ChIP-Seq

description:
Sample 11
processed data file: MCF7_ChromHMM.bed


title: HMEC_Input_ChIP-Seq

description:
Sample 10
processed data file: HMEC_ChromHMM.bed

source_name: HMEC

value: HMEC


title: Msl1_ChIPseq


title: HMEC_H3K4me3_ChIP-Seq

description:
Sample 8
processed data file: HMEC_ChromHMM.bed


title: HMEC_H3K27ac_ChIP-Seq

description:
Sample 5
processed data file: HMEC_ChromHMM.bed


title: HMEC_H3K27me3_ChIP-Seq

description:
Sample 6
processed data file: HMEC_ChromHMM.bed


title: PC3_NOMe-Seq

description:
Sample 4
processed data file: GCH.tsv.gz, WCG.tsv.gz

extract_protocol:
Cells were trypsinized and centrifuged for 3 mins at 500g, then washed in ice-cold PBS and resuspended in 1mL ice-cold Nuclei Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA and 0.5% NP-40,plus protease inhibitors) per 5x106 cells and incubatedon ice for 5 min. Nuclei were recovered by centrifugation at900g for 3 min and washed in Nuclei Wash Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1mM EDTA containing protease inhibitors). Freshly prepared nuclei (2x105 cells) were resuspended in 1X M.CviPI reaction buffer (NEB), then treated with 150U of M.CviPI (NEB; 50,000U/mL) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
Genomic DNA (2 μg) was sonicated using a Covaris instrument to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer analysis (Agilent Technologies). Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt. Magnetic beads were employed for all nucleic acid purifications in subsequent steps.  Following end repair, A-tailing was performed using the dA-tailing module according to manufacturer’s instructions (New England Biolabs). Adapters with a 3’‘T’ overhangs were then ligated to the end-modified DNA. Modified Illumina paired-end (PE) adapters were used. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20μL. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix under the following conditions: 98°C for 2 min, followed by 4 cycles of 98°C for 30 s then 65°C for 15 s and 72°C for 1 min with a final extension for 10 min in 50μL total reaction volume. The final library product was examined on the Agilent Bioanalyzer then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.  Optimal concentrations to get the right cluster density were determined empirically.


title: MCF7_NOMe-Seq

description:
Sample 2
processed data file: GCH.tsv.gz, WCG.tsv.gz


title: HMEC_RNApolIIp_ChIP-Seq

description:
Sample 9
processed data file: HMEC_ChromHMM.bed


title: SL26788

city: Seattle

first: Sangsoon

last: Woo

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description:
Sample 12
20-40 nucleotide fraction donor 6

data_processing:
Base calling were performed on the instrument using the HiSeq Sequencing Control Software (HCS). CASAVA software version 1.8 (Illumina) was used for de-multiplexing and production of FASTQ sequence files.
FASTX application (www.molecularevolution.org) was used to trim adapter sequences from the 3’and 5'-end of the sequence read, discard any sequence of less than 17 nucleotides after trimming, and to collapse identical reads into single entries retaining the read count for each unique sequence.
Non-redundant sequences were then aligned to genomic RNA and mRNA sequences using Bowtie 2 (www.bowtie-bio.sf.net) and the mapped sequences (perfectly matched and mismatched) were retained and aligned to common and abundant non-coding RNAs (tRNAs, rRNAs, snoRNAs). After the perfectly matched reads to non-coding RNAs were removed from the genome/mRNA aligned reads, remaining sequences were further aligned to known mature and precursor miRNAs using the miRBase 19 database (www.mirbase.org). Since a large proportion of sequences did not map to miRNA, an additional alignment to a transcript and non-coding RNA(miscRNA) database (Ensembl version 75) using bowtie2 was performed. Alignment to the specific piRNA database from piRNABank (http://pirnabank.ibab.ac.in/) was also performed.
R script was used to tablulate the read counts for each unique sequence from the alignment results. R/Bioconductor packages were used to tablulate the raw sequence read count for each target database entry. Raw read counts for each RNA class from all samples in the study were then joined in raw data tables. The raw reads were converted to reads per kilobase of target length per million mapped reads (RPKM) using R script.
Genome_build: hg19
Supplementary_files_format_and_content: The .csv files include raw counts and RPKM values for each Sample

source_name: exosomes isolated from cell-free seminal fluid

extract_protocol:
Exosomes were isolated from cell-free seminal fluid by ultracentrifugation over a 30% sucrose/D2O cushion. RNA was extracted using the Exiqon miRCURY RNA isolation kit
ScriptMiner Small RNA-Seq Library Preparation Kit, according to the manufacturer’s instructions, except that following the RNA linker ligation, but before cDNA synthesis, the RNA was fractionated using a 10% acrylamide-urea gel. RNA fragments consisting of inserts of approximately 15-40 nt were excised as a lower band, and RNA fragments containing inserts of approximately 40-100 nt were excised as an upper band.

tag: donor

tag: fraction

value: 20-40 nucleotide fraction


title: SL26787

description:
Sample 11
20-40 nucleotide fraction donor 5


title: HMEC_NOMe-Seq

description:
Sample 1
processed data file: GCH.tsv.gz, WCG.tsv.gz


title: PC3_RNApolIIp_ChIP-Seq

description:
Sample 27
processed data file: PC3_ChromHMM.bed


title: SL26784

description:
Sample 8
20-40 nucleotide fraction donor 2


title: SL26785

description:
Sample 9
20-40 nucleotide fraction donor 3


title: PC3_H3K4me1_ChIP-Seq

description:
Sample 25
processed data file: PC3_ChromHMM.bed


title: SL26779

description:
Sample 3
40-100 nucleotide fraction donor 3

value: 40-100 nucleotide fraction


title: SL26777

description:
Sample 1
40-100 nucleotide fraction donor 1


title: SL26781

description:
Sample 5
40-100 nucleotide fraction donor 5


title: SL26782

description:
Sample 6
40-100 nucleotide fraction donor 6


title: SL26783

description:
Sample 7
20-40 nucleotide fraction donor 1


title: SL26780

description:
Sample 4
40-100 nucleotide fraction donor 4


title: MCF7_Input_ChIP-Seq

description:
Sample 16
processed data file: MCF7_ChromHMM.bed


title: fra2Δ BPQ + CuSO4 treated Rep 3

city: Durham

first: Nigel

last: Robinson

address: South Road

department: Department of Chemistry, School of Biological and Biomedical Sciences

country: United Kingdom

institute: Durham University

data_processing:
Illumina Casava pipeline version 1.8.3 was used for basecalling
Initial quality assessment was based on data passing the Illumina Chastity filtering
The sequence reads were additionally filtered and trimmed using an in-house (BaseClear) filtering protocol
The filtered/trimmed reads were aligned against the reference sequences using the CLCbio 'RNA-Seq' software
Reads per Kilobase of exon model per Million mapped reads (RPKM) (Mortazavi et al. 2008. Nat. Methods. 5: 621-628.) were calculated
Genome_build: NC_001133, NC_001134, NC_001135, NC_001136, NC_001137, NC_001138, NC_001139, NC_001140, NC_001141, NC_001142, NC_001143, NC_001144, NC_001145, NC_001146, NC_001147, NC_001148, NC_001224
Supplementary_files_format_and_content: All processed data files are .txt and contain the transcript abundance (expressed as RPKM) for each of the genes in the above genome build

organism: Saccharomyces cerevisiae

source_name: Logarithmically growing cells in liquid culture

growth_protocol: Logarithmically growing cells were innoculated into liquid YPAD (standard YPD with the addition of 30 mg l-1 adenine) to OD600 nm = 0.1. Where stated the culture was additionally supplemented with 0.1 mM CuSO4 or 0.1 mM CuSO4 and 1.68 μM BPQ. Cells were cultured at 30 °C with rotary shaking for 5 h before harvest.

extract_protocol:
Total RNA was extracted using the Ambion PureLink RNA Mini Kit according to manufacturers instructions
Library construction and sequencing was performed by BaseClear, Netherlands. The Illumina TruSeq RNA-seq library preparation kit was used. The mRNA was purified by polyA capture, fragmented and converted to double-stranded cDNA. DNA adapters were ligated to both ends of the DNA fragments and subjected to PCR amplification. The library was sequenced on the Illumina HiSeq 2500 platform (single read 50 data). Where necessary re-sequencing was performed to yield sufficient data.

treatment_protocol: See growth protocol

value: BY4741 fra2Δ

tag: treatment

value: 1.68 μM BPQ, 0.1 mM CuSO4


title: fra2Δ BPQ + CuSO4 treated Rep 1


title: fra2Δ BPQ + CuSO4 treated Rep 2


title: cumulus cell (CC) GV rep 2

city: Ramat Gan

first: Gil

middle: M

last: Yerushalmi

address: 2 Sheba rd.

department: Obstetrics and Gynecology

country: Israel

institute: Sheba Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to human genome (hg19)using Tophat v1.3.3 using default parameters. Non-unique reads were excluded from downstream analysis
A counting table was generated for all Ensembl genes (release 64). The number of reads overlap each of the annotated genes was counted using the HT-seq python package, using the "union" overlap resolution mode. DESeq v. 1.8.3 within the Bioconductor framework was used for normalization and differential expression analysis. Independent filtering was done first by dropping the 40% genes with lowest overall counts. After applying the statistical test, the resulting p-values were corrected for multiple testing using the Benjamini & Hochberg approach, and genes having p<0.05 and fold change > 2 were called as being significant.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized expression and statistical results of the differentially expressed genes

source_name: Cumulus granulosa

extract_protocol:
Total RNA was extracted from CCs by the Mini RNA Isolation I Kit (Zymo Research Corp., CA), according to manufacturer’s instructions. Following isolation total RNA was tested with a Bioanalyzer (Agilent Technologies 2100). mRNA was purified from Total RNA using pre-prepared Sera-mag Magnetic Oligo(dT) Beads (Thermo Fisher Scientific, MA).
RNA prepared for sequencing according to the standard Illumina protocols (Illumina inc.San Diego, CA) for sequencing of cDNA samples.

tag: tissue

value: ovary


title: cumulus cell (CC) M2 rep 1


title: cumulus cell (CC) GV rep 1


title: cumulus cell (CC) M2 rep 2


title: fra2Δ CuSO4 treated Rep 3

tag: strain

value: 0.1 mM CuSO4


title: fra2Δ CuSO4 treated Rep 1


title: TET1-FL

city: Houston

first: CHUNLEI

last: JIN

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The reads were mapped to human genome (hg19) by TopHat (V2.0.5)
The number of fragments in each known gene from RefSeq database was enumerated using htseq-count from HTSeq package.
The differential expression between samples was statistically accessed by R/Bioconductor package edgeR (V3.0.8) and DESeq (V1.10.1), using the two most similar samples (mTET1-FL and TET1-FL) to estimate the biological variation. Genes with FDR≤0.05 by both edgeR and DESeq and fold change≥2 were called significant.
Genome_build: hg19
Supplementary_files_format_and_content: _fpkm.txt: the FPKM value (fragments per kilobase of exon per million fragments mapped) for each gene. Only genes with >=10 fragments in at least one sample and with no isoform shorter than 200bp are reported.
Supplementary_files_format_and_content: _DE.txt: the significant differentially expressed genes.

source_name: HEK293T cell

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium modified with 10% fetal bovine serum and 100 μg/ml streptomycin-penicillin.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Libraries were prepared from 100 ng of DNase-treated total RNA samples using Encore® Complete RNA-Seq Library System (NuGEN, San Carlos, CA) following the manufacturer’s protocol.

treatment_protocol: mTET1-CD, TET1-CD, mTET1-FL, TET1-FL expression plasmid or empty vector was transfected into HEK293T cells by using OPTI-MEM (Invitrogen) and FuGene HD transfection reagent (Roche). Three days after transfection, overexpressed cells were purified with fluorescent activated cell sortng.

tag: transfection

value: TET1-FL expression plasmid


title: mTET1-CD

value: mTET1-CD expression plasmid


title: fra2Δ CuSO4 treated Rep 2


title: mTET1-FL

value: mTET1-FL expression plasmid


title: SL26786

description:
Sample 10
20-40 nucleotide fraction donor 4


title: VectorControl

value: empty vector


title: fra2Δ untreated Rep 3

value: Untreated


title: cumulus cell (CC) M2 rep 3


title: fra2Δ untreated Rep 2


title: WT BPQ + CuSO4 treated Rep 3

value: BY4741 wild type


title: WT BPQ + CuSO4 treated Rep 2


title: fra2Δ untreated Rep1


title: WT BPQ + CuSO4 treated Rep 1


title: WT CuSO4 treated Rep 3


title: WT untreated Rep 2


title: WT CuSO4 treated Rep 1


title: WT untreated Rep 3


title: mEpiSC_input

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used to remove adapter sequences and trim read ends using a quality score cutoff of 20.
ChIP-seq data were aligned to mm9 genome assemblies (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Bowtie v0.12.9 (Langmead et al., 2009), allowing reads with ≤ 2 mismatches and discarding reads with > 1 reportable alignment ("-m 1" parameter).
Peaks were detected with MACS v1.4 (Zhang et al., 2008), using an aligned input DNA sample as control.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files - Wiggle tracks stepped at 25 bp were generated by MACS, normalized to the median signal by chromosome and converted to bigwig format using the UCSC Genome Browser’s wigToBigWig utility (retrieved from http://hgdownload.cse.ucsc.edu/admin/exe/). bed files - MACS called peaks.

extract_protocol:
ChIPs were performed from 5x10^6 crosslinked mEpiSCs as previously described (Schmidt et al., 2009). The following antibodies were used for ChIP: rabbit anti-H3K4me1 (Abcam #8895), rabbit anti- H3K4me3 (Active Motif #39159), rabbit anti-H3K27ac (Abcam #4729), mouse anti-H3K27me3 (Abcam #6002).
Sequencing libraries were prepared as previously described (Schmidt et al., 2009).


title: WT untreated Rep1


title: mEpiSC_H3K4me3

value: H3K4me3 (Active Motif #39159)


title: mEpiSC_H3K4me1


title: mEpiSC_H3K27ac


title: Rmr1_B73_Hybrid_sRNA_bio1

city: Columbus

first: Joy-El

middle: Renee Barbour

last: Talbot

address: 574 Aronoff Lab, 318 W 12th Ave

department: Molecular and Cell Biology & Molecular Genetics

institute: University of California - Berkeley & The Ohio State University

data_processing:
Basecalls performed using CASAVA version 1.6 (Phred +64 quality scores).
Retained only reads that could have 3' adapter sequences trimmed using CutAdapt (Martin 2011 EMBnet.journal 17.1; code at http://code.google.com/p/cutadapt/) with parameters: -O 7 and –trimmed-only.
Discarded all reads with Ns or basecall qualities below Phred=30 (custom perl scripts).
Collapsed remaining reads into unique read tags and abundances in each library (custom perl script).
Reported all alignments with zero mismatches between the unique read tags and the maize B73 genome (B73 RefGen_v2_5b; http://ftp.maizesequence.org/current/assembly/ZmB73_RefGen_v2.tar.gz; including mitochondrial, plastid and UNKNOWN chromosomes) with Bowtie (version 0.12.8, 64-bit) using options (-f -v 0 -a -B 1 –suppress 6,7,8).
Genome_build: B73 RefGen_v2 (5b)
Supplementary_files_format_and_content: smallRNA_tag_abundance.csv – comma-delimited text file, 12 columns: column 1 = unique read tag sequence, column 2 = number of mappable loci to B73 RefGen_v2 (5b) with zero mismatches,  columns 3-12 = raw abundance of tag in each HQ library.

organism: Zea mays

source_name: immature cob (~4cm)

growth_protocol: Plants were grown under standard greenhouse conditions and immature ~4cm cobs were harvested, flash frozen in liquid nitrogen, and stored at -80C until processed.

extract_protocol:
Previously frozen developing ~4cm immature cobs were ground in liquid nitrogen with a mortar and pestle and total RNAs were isolated using TRIzol reagent (Invitrogen).
The sRNA libraries were constructed using Illumina's sRNA Sequencing Sample Preparation Guide.

tag: rmr1 genotype

value: Rmr1 / Rmr1

value: Pl1-Rh / B73

tag: translocation chromosome between chromosomes 6 & 9 [t6-9 (043-1)]

tag: sequencing chemistry

value: Version 2


title: rmr1-1_het_sRNA_bio2

value: rmr1-1 / Rmr1

value: Pl1-Rh rmr1-1 ^ B73 X Pl1-Rh ^ B73


title: rmr1-1_B73_Hybrid_sRNA_bio1

value: Pl1-Rh rmr1-1 / B73


title: Rmr1_B73_Hybrid_sRNA_bio2


title: Rmr1_MaternalP_sRNA_bio1

data_processing:
Basecalls performed using CASAVA version 1.8 (Phred +33 quality scores).
Retained only reads that could have 3' adapter sequences trimmed using CutAdapt (Martin 2011 EMBnet.journal 17.1; code at http://code.google.com/p/cutadapt/) with parameters: -O 7 and –trimmed-only.
Discarded all reads with Ns or basecall qualities below Phred=30 (custom perl scripts).
Collapsed remaining reads into unique read tags and abundances in each library (custom perl script).
Reported all alignments with zero mismatches between the unique read tags and the maize B73 genome (B73 RefGen_v2_5b; http://ftp.maizesequence.org/current/assembly/ZmB73_RefGen_v2.tar.gz; including mitochondrial, plastid and UNKNOWN chromosomes) with Bowtie (version 0.12.8, 64-bit) using options (-f -v 0 -a -B 1 –suppress 6,7,8).
Genome_build: B73 RefGen_v2 (5b)
Supplementary_files_format_and_content: smallRNA_tag_abundance.csv – comma-delimited text file, 12 columns: column 1 = unique read tag sequence, column 2 = number of mappable loci to B73 RefGen_v2 (5b) with zero mismatches,  columns 3-12 = raw abundance of tag in each HQ library.

value: Pl1-Rh ^ B73

value: Version 3


title: Rmr1_MaternalP_sRNA_bio2


title: rmr1-1_B73_Hybrid_sRNA_bio2


title: B73_PaternalP_sRNA_bio1

value: B73 Elite Inbred


title: B73_PaternalP_sRNA_bio2


title: Trf2 275 Antibody

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Sample trf2_275 was constructed with the following Illumina barcode: AGTTCC
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 1.0.0, allowing only unique alignments with up to 2 mismatches
Genome_build: Release 5
Supplementary_files_format_and_content: BEDGRAPH files contain per-base coverage after extending aligned reads to 110bp

organism: Drosophila melanogaster

source_name: Staged embryos

growth_protocol: D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.

extract_protocol:
ChIPs were performed with whole cell extracts (WCE) from embryos as previously described (Chen et al. 2013) with small modification. 800 mg 2-4h embryos were crosslinked with 1.8% Formaldehyde in 2.4 ml crosslinking buffer with 7.5 ml Heptane for 15 min. After wash with PBT-0.125M glycine twice, embryos were transferred to a 7 ml Douncer homogenizer with 5 ml Buffer A1 (15 mM HEPES, pH 8; 15 mM NaCl; 60 mM KCl; 4 mM MgCl2; 0.5% Triton X-100; 0.5 mM DTT; fresh 1 × Protease Inhibitor Cocktail), and homogenized five times each with the loose fitting and the tight fitting pestles. Homogenized samples were centrifuged 3 min at 4°C at 1500 g, and the pellet was then subsequently washed three times with Buffer A1 and once with Buffer A2 (15 mM HEPES, pH 8; 140 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 1% SDS; 0.5% N-lauroylsarcosine; fresh 1 × Protease Inhibitor Cocktail). Resuspended the pellet with 2.8 ml Buffer A2 and aliquot to 4 EP tubes. Sheared the chromatin with Branson Sonicator 8 × 10s at Power 3. Sheared chromatin was cleaned by centrifuge 10 min at 4°C at 13000 g. Supernatant was collected for ChIP. Aliquot 130ul Rabbit IgG Dynabeads to 4 tubes and wash with PBS-0.5%BSA twice.  Incubated beads with antibodies (10ul for TBP and 30 ul for TRF2) in 700ul PBS-0.5%BSA for 2 h at 4°C. removed PBS-0.5%BSA, added 700 ul sheared chromatin for each tube, and incubated overnight at 4°C. the ChIPed chromatin was washed with RIPA buffer 3 times, and eluted with 200 ul elution buffer + 200ul TE. Incubated the chromatin 30 min at 37°C with RNase (60ug) and 6h at 65°C for reversing the crosslink with Proteinase K (60ug). DNA was clean by phenol/phenol-chloroform-isoamylalcohol extractions and ethanol precipitation. The precipitated DNA was resuspended in 35 μl water.
Libraries for the ChIPed DNA were prepared and barcoded with NEBNext DNA Library Prep Master Mix and Multiplex Oligos for Illumina. For each step, DNA was cleaned with Ampure beads as suggested in the NEB manual.

value: Oregon-R

tag: Stage

value: 2-4h AEL

value: anti-Trf2 275 Antibody (custom polyclonal antibody generated in rabbits)


title: mEpiSC_H3K27me3


title: TET1-CD

value: TET1-CD expression plasmid


title: Trf2 274 Antibody

data_processing:
Sample trf2_274 was constructed with the following Illumina barcode: AGTCAA
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 1.0.0, allowing only unique alignments with up to 2 mismatches
Genome_build: Release 5
Supplementary_files_format_and_content: BEDGRAPH files contain per-base coverage after extending aligned reads to 110bp

value: anti-Trf2 274 Antibody (custom polyclonal antibody generated in rabbits)


title: TBP 517 Antibody

data_processing:
Sample tbp_517 was constructed with the following Illumina barcode: ATCACG
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 1.0.0, allowing only unique alignments with up to 2 mismatches
Genome_build: Release 5
Supplementary_files_format_and_content: BEDGRAPH files contain per-base coverage after extending aligned reads to 110bp

value: anti-TBP 517 Antibody (custom polyclonal antibody generated in rabbits)


title: reporter - HA Vasa DQAD IP - 12mer #1

data_processing:
A custom pipeline that generates genome annotations based on that found in http://kaikogaas.dna.affrc.go.jp/
Samples were sequenced in a Illumina HiSeq 2000 platform or Illumina MiSeq.
JX files: Adapter sequences were clipped from the reads and sorted into individual libraries based on the barcodes (which are at the 3′ end). Reads were then mapped to the Bombyx mori genome (http://kaikogaas.dna.affrc.go.jp/; this has the combined data generated by the Silkworm Genome Research Program in Japan and Silkworm Genome Project in China). Only perfectly mapping reads were used for subsequent analyses using custom-built pipelines. Typically, 55% of the small RNA reads (max= 64%, min= 43%, calculated from 17 libraries) mapped to the genome. However, given that the genome assembly is not complete, many of the non-mapped sequences are likely to be perfectly-mapping reads, and are missing in our current analyses. Annotation of reads were carried out using the following databases: a set of Bombyx transposon consensus sequences, coding and miRNA sequences from Silkworm genome database, and a set of our own assemblies for both mRNAs and transposons expressed in the BmN4 cells.
DH files: Reads were sorted into individual libraries based on the barcodes and the 3’ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200). Reads were then aligned to the Siwi-T piRNA precursor sequence (see supplementary information in the associated manuscript) using bowtie (Langmead et al., 2009) allowing no mismatches.  For Vasa binding sites detection, the reads originating from Vasa footprint were aligned to the reporter allowing no mismatch. Counts from two independent libraries were merged together and only the reads longer than 10 nucleotides were used for plotting the coverage.
Genome_build: Bombyx mori genome at http://kaikogaas.dna.affrc.go.jp/

source_name: Bombyx mori, BmN4 cells

tag: cell type

value: BmN4 cells

value: expression of artificial piRNA reporter Siwi T + HA Vasa DQAD

tag: antibody

value: anti-HA (sc-805; Santa Cruz)

tag: 3' barcode (nebnext primers)

value: ATCACG

tag: 5' barcode


title: WT CuSO4 treated Rep 2

value: BY4741 wild type

value: 0.1 mM CuSO4


title: TBP 518 Antibody

data_processing:
Sample tbp_518 was constructed with the following Illumina barcode: TGACCA
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 1.0.0, allowing only unique alignments with up to 2 mismatches
Genome_build: Release 5
Supplementary_files_format_and_content: BEDGRAPH files contain per-base coverage after extending aligned reads to 110bp

tag: chip antibody

value: anti-TBP 518 Antibody (custom polyclonal antibody generated in rabbits)


title: reporter - HA Vasa DQAD IP - 12mer #2

value: CGATGT


title: rmr1-1_het_sRNA_bio1

value: rmr1-1 / Rmr1

tag: genotype

value: Pl1-Rh rmr1-1 ^ B73 X Pl1-Rh ^ B73


title: SW_WB20_BK11_WM

city: Lincoln

first: Swapna

middle: R.

last: Purandare

state: Nebraska

address: 348 Manter Hall

department: Biological Sciences

institute: University of Nebraska-Lincoln

data_processing:
We mapped sequencing reads to the 36,961 gene predictions of v2.1 annotation of the pea aphid genome (available at aphidbase.com) using the Arraystar Software v.5 (DNAStar Inc.).
Genes with a total raw read count of less than 100 for all 15 libraries were filtered out
The DESeq2 R package  was used to normalize the libraries
Genome_build: v2.1 annotation of the pea aphid genome (available at aphidbase.com)
Supplementary_files_format_and_content: .csv file containing gene expression data normalized using DESeq2 R package

organism: Acyrthosiphon pisum

source_name: Pea aphid whole body

growth_protocol: For asexual winged and wingless females (photoperiod L: D cycle = 16:8,  temperature 18°C), sexual females and males (photoperiod L: D cycle = 13:11 temperature 15°C)

extract_protocol:
RNA was extracted using a phenol/chloroform extraction. RNA was quantified by Qubit and the quality was checked by Bioanalyzer (Agilent)
RNA sequencing libraries were constructed per manufacturer instructions with sample-specific tags (Illumina) and sequenced on an Illumina HiSeq 2000 sequence analyzer

treatment_protocol: We collected whole bodies of 30 adult aphids of each of the five morphs and three clones (total of 15 samples) by flash freezing them in liquid nitrogen. Samples were stored at -80°C. We used three different clones as biological replicates

tag: morph

value: Winged male

tag: age

value: 2 day old adult

tag: growing conditions

value: photoperiod L:D cycle = 13:11,  temperature 15°C


title: HMEC_H3K4me1_ChIP-Seq

description:
Sample 7
processed data file: HMEC_ChromHMM.bed

tag: cell line

value: HMEC

value: H3K4me1 (#39298, Active Motif)


title: SW_WB21_BK11_UWM

value: Wingless male


title: SW_WB22_BK11_SF

value: Sexual female

value: 2-6 day old adult


title: SW_WB19_I18_SF


title: SW_WB17_I18_WM


title: SW_WB16_F1_UWM


title: SW_WB15_F1_WM


title: SW_WB11_BK11_WF

value: Winged female

value: photoperiod L:D cycle = 16:8,  temperature 18°C


title: SW_WB06_I18_WF


title: TET1-CD_DREAM

data_processing:
Sequencing tags were mapped to SmaI sites in the human genome (hg18) and signatures corresponding to methylated (starting with CCGGG…) and unmethylated CpG (starting with GGG…) were enumerated for each SmaI/XmaI site.
The methylation value was calculated as the ratio of the number of tags starting with CCGGG over total number of tags mapped to a given SmaI/XmaI site.
Genome_build: hg18
Supplementary_files_format_and_content: The columns of the processed file are: SmaI_ID(SmaI site ID), Chrom(chromosome of the SmaI site), Pos(position of the SmaI site), MetReads(observed number of tags corresponding to methylated CpG), UnmetReads(observed number of tags corresponding to unmethylated CpG), Methylation(methylation value).

source_name: HEK293T cells

extract_protocol:
mTET1-CD, TET1-CD, mTET1-FL or TET1-FL expression plasmid (containing GFP reporter) was transfected into HEK293T cells by using OPTI-MEM (Invitrogen) and FuGene HD transfection reagent (Roche), followed by fluorescent activated cell sortng to collect GFP positive cells 3 (for mTET1-CD or TET1-CD ) or 7 (for mTET1-FL or TET1-FL ) days after transfection. The genomic DNA was then extracted from those cells.
Five micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for additional 16 hours at 37°C. Digested DNA was purified using QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3´→5´ exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3’ DNA ends created by XmaI digestion and added 3’ dA tails to all fragments. Solexa paired ends adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-375 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Solexa paired end PCR primers using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA) and then ready for paired-end sequencing on Illumina Genome Analyzer II.

tag: cell sorting time

value: 3 days after transfection


title: mTET1-CD_DREAM


title: SW_WB05_F1_SF


title: SW_WB02_F1_UWF

value: Wingless female


title: mTET1-FL_DREAM

value: 7 days after transfection


title: SW_WB01_F1_WF


title: TET1-FL-IP

data_processing:
Sequenced DNA tags were mapped to human genome hg18 using ELAND (Illumina Analysis Pipeline) and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept. CCAT (version 3.0) was used to detect peaks in hMeDIP-Seq samples. The window size was set as 500 bp. Peaks with FDR ≤ 0.05 and fold enrichment to input ≥ 5 were called significant.
Genome_build: hg18
Supplementary_files_format_and_content: The columns of the processed file are: chr(chromosome of the peak), start(start postion of the peak), end(end position of the peak), tags_chip(number of tags in hMeDIP sample), tags_control(number of tags in Input sample), fold_change(fold change of hMeDIP to Input), FDR(false discovery rate).

extract_protocol:
mTET1-CD, TET1-CD, mTET1-FL or TET1-FL expression plasmid (containing GFP reporter) was transfected into HEK293T cells by using OPTI-MEM (Invitrogen) and FuGene HD transfection reagent (Roche), followed by fluorescent activated cell sortng to collect GFP positive cells 3 (for mTET1-CD or TET1-CD ) or 7 (for mTET1-FL or TET1-FL ) days after transfection. The genomic DNA was then extracted from those cells.
Before hydroxymethylated DNA immunoprecipitation (hMeDIP) reaction, genomic DNA samples were sonicated into a desirable fragment size of 100~500 bp. The purified sonicated DNA was then prepared for adapter ligation as per Illumina’s standard protocol (Illumina, San Diego, CA) with minor modifications. In brief, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow enzyme (DNA Polymerase I Large Fragment) and T4 polynucleotide kinase (NEB, Ipswich, MA). The blunt phosphorylated DNA fragments were treated with Klenow fragment (3’ to 5’ exo minus) (NEB) and dATP to add an ‘A’ base to the 3’ end. Solexa paired ends adapters were ligated to the ends of the DNA fragments using Quick T4 DNA Ligase (Enzymatics, Beverly, MA). The resulting DNA products were subsequently subjected to hMeDIP for purifying 5hmC-containing DNA fragments. The immunoprecipitated and input control DNA were size selected by electrophoresis in a 2% agarose gel. A slice corresponding to 300 (± 25) bp size window based on DNA ladder was cut out. The DNA extracted from agarose was amplified with PCR (10-15 cycles) by using Solexa paired end PCR primers and Phusion™ High-Fidelity DNA Polymerase (NEB). The resulting sequencing library was finally cleaned with AMPure magnetic beads (Agencourt, Beverly, MA) and ready for single-read sequencing on Illumina Genome Analyzer II.

tag: fraction

value: IP


title: mTET1-FL-Input

tag: transfection

value: Input


title: mTET1-FL-IP


title: TET1-CD-Input


title: mTET1-CD-IP


title: MCF7_RNApolIIp_ChIP-Seq

description:
Sample 15
processed data file: MCF7_ChromHMM.bed

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v0.12.8 allowing up to 3 mismatches, discarding ambiguous and clonal reads. ChromHMM v1.03 was used to simultaneously partition the genomes of all four cell lines into 15 chromatin states which were collapsed into 9 distinct states manually annotated by comparison to the published ChromHMM model for HMEC cells.
NOMe-seq reads were aligned to hg19 using BSMAP_2.01 and counts of methylated residues vs total sequencing counts at GCH and WCG sites summarized using custom R scripts. NDRs were detected by a 100bp sliding window in 20bp increments chi-squared test of GCH methylation versus the genome background with a p-value cutoff of -log10(p)>15, significant windows overlapped and retained if a minimum 140bp in size.
Genome_build: hg19
Supplementary_files_format_and_content: NDR bed files contain the -log10 pvalue in the name field (4th column). ChromHMM bed files report Consolidated ChromHMM States. GCH/WCG tsv files contain coordinates of cytosines in GCH/WCG genomic contexts and methylation values per cell line in two columns - C is the count of methylated calls and cov is the sequencing coverage at each position

value: RNA Polymerase II (#ab817, Abcam)


title: TET1-CD-IP


title: mTET1-CD-Input


title: SW_WB12_BK11_UWF


title: SW_WB18_I18_UWM


title: Meunna_High_KPY_2

status: Public on Jun 03 2014

city: Acton

first: Saravanan

last: Thavamanikumar

state: ACT

address: Clunies Ross Street

institute: CSIRO

description: Sample 8

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed low-quality sequence, then mapped to Eucalyputs grandis reference genome using Tophat
Read counts of each gene were used for differential gene expression analyis with edgeR package. Raw red counts were used in edgeR packge. BAM files from TopHat package were analyzed with BEDTools packaged to obtain read counts mapping to different transcripts represented in the GTF annotation file. These read counts were used in statistical tests of differential expression between control and stress treatments.
Genome_build: Egrandis_v1.0 [http://www.phytozome.net/eucalyptus.php]
Supplementary_files_format_and_content: tab-delimited text files include readcounts for each gene and each sample

organism: Eucalyptus nitens

growth_protocol: Trees are growing in natural environment

extract_protocol: Cambial scraps from trees were flash frozen on dry ice, and RNA was harvested using modified CTAB method. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Trees from KPY extremes were sampled

tag: strain

tag: tissue

value: xylem

value: 20 years


title: Meunna_Low_KPY_2

description: Sample 11


title: Meunna_High_KPY_3

description: Sample 9


title: Florentine_Low_KPY_2

description: Sample 5


title: Florentine_Low_KPY_3

description: Sample 6


title: Florentine_Low_KPY_1

description: Sample 4


title: Meunna_Low_KPY_1

description: Sample 10


title: TET1-FL_DREAM


title: Florentine_High_KPY_3

description: Sample 3


title: Florentine_High_KPY_1

description: Sample 1


title: TET1-FL-Input


title: Meunna_High_KPY_1

description: Sample 7


title: H929_PU1

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

description: ASCII shift tag: 64

data_processing:
Basecalls performed using CASAVA version 1.6 and 1.8 (see ASCII shift tag of RAW files; 64 for version 1.6 of CASAVA and 33 for version 1.8)
If required reads were converted to fastq format (Solexa --> Sanger quality score)
Before aligning, reads were trimmed to remove adapters and low confidence regions using a python script. A 4 base sliding window was run along each read, if the average Q Phred score for a window was < 20 the read was trimmed at the window start, finally any match to adapter sequences were trimmed
Trimmed reads were aligned using Bowtie2 with the --very-senstive parameter.  The resultant SAM files were converted to BAM using Samtools with the quality filter set to 20 (i.e. -q 20)
The BAM files were analysed for peaks using GEM, with quality filter set to 1 (i.e. -q 1)
ChIP-seq quality was assessed by cross-correlation using the MaSC and Phantompeakqual programs.   Reads were extended to the length reported by MaSC, scaled to reads per million and converted to BigWig files.  These were used for visualisation of the data and also for fold-change analysis for the SPIB knock-down ChIP-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: BED files (converted from GEM events); BigWig coverage files (Used for ChIP-seq fold change analysis)

source_name: Multiple myeloma

growth_protocol:
OCI-Ly3 and OCI-Ly10 were grown in IMDM with Glutamax™ (Life Technologies™), 10% HIFBS, 50µM betamercaptoethanol. Each batch of chromatin from each cell line were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.
H929 were grown in RPMI 1640, 10% HIFBS, 1% L-Glutamine. Each batch of chromatin were harvested from 2*10^7 cells. Batches were pooled together and distributed in aliquots. Individual CHIP were obtained from 4*10^6 cells.

extract_protocol:
Cell fixation and chromatin sonication were optimised for each cell line in order to obtain enrichment of DNA fragments between 200-500bp. Chromatin was pre-cleared with BSA saturated Protein A sepharose (Thermo Scientific). A fraction of the chromatin was then incubated overnight at 4°C with the appropriate antibody (in duplicate) and then immunoprecipitated with BSA saturated Protein A sepharose (Thermo Scientific) for 4 hours at 4°C. Following washing to remove aspecificity, each IP was eluted from the Protein A sepharose overnight. DNA was then purified with standard phenol/chloroform extraction and quantified using Quant-iT™ Picogreen® dsDNA Broad-Range Assay Kit (Life Technologies™).
IRF4, PU.1 and SPIB CHIP-seq libraries from OCI-LY3, OCI-LY10 and H929 were generated using the Illumina ChIP-seq Sample Prep Kit (Illumina®) according to manufacturer’s instructions. The BATF and the SPIB knockdown libraries were generated using the Microplex Library Preparation™ Kit (Diagenode) following manufacturer's instructions, and size selected using Agencourt® AMPure® XP beads (Beckman Coulter®).

treatment_protocol: SPIB knockdown on OCI-Ly3 were obtained by transfecting SPIB siRNA s13354 and scramble siRNA (Ambion, Life Technologies™) using Amaxa® Nucleofector® system and Amaxa® Cell line Nucleofector® Kit V (Lonza), setting D.023. Cells were harvested after 48hrs and the efficiency and the degree of the knockdown was assessed by RT-PCR and Western blot.

value: Multiple myeloma

value: sc-352X, Santa Cruz


title: H929_SPIB

description: ASCII shift tag: 64

value: In-house (Leeds University)


title: Meunna_Low_KPY_3

description: Sample 12


title: H929_IRF4

description: ASCII shift tag: 64

value: sc-28696X, Santa Cruz


title: OCILY10_SPIB

description: ASCII shift tag: 64

source_name: ABC DLBCL

value: Diffuse large B-cell lymphoma (DLBCL)


title: SW_WB07_I18_UWF

value: 2 day old adult


title: OCILY10_PU1

description: ASCII shift tag: 64


title: OCILY10_IRF4

description: ASCII shift tag: 64


title: Florentine_High_KPY_2

description: Sample 2


title: OCILY3_SPIB

description: ASCII shift tag: 64


title: OCILY3_PU1

description: ASCII shift tag: 64


title: OCILY3_Input

description: ASCII shift tag: 64


title: OCILY3_IRF4

description: ASCII shift tag: 64


title: OCILY3_SPIB-SPIBkd

description:
ASCII shift tag: 33
SPIB siRNA transfection


title: Control_rep1

city: Chicago

first: Chonghui

last: Cheng

state: IL

address: 303 E Superior Street, Robert H. Lurie Comprehensive Cancer Center 5-119

department: Hematology/Oncology Division, Feinberg School of Medicine

institute: Northwestern University

data_processing:
Paired-end RNA-Seq reads were mapped to human genome (hg19) and transcriptome (Ensembl release 68) using method described previously (Bahn et al. 2012; Li et al. 2012). First, reads were mapped with Bowtie-0.12.7 to hg19 using the following command line: 'bowtie --sam-nosq -S -k 80 -e 140 -n 3 -l 20 -q --phred33-quals -p 2 -y'. Second, reads were mapped with Bowtie-0.12.7 to transcriptome (Ensembl release 68) using the following command line: 'bowtie --sam-nosq -S -k 80 -e 140 -n 3 -l 20 -q --phred33-quals -p 2 -y'. Third, reads were mapped with Blat to hg19 using the following command line: 'blat -minIdentity=75 -tileSize=11 -fine'. Two reads in a pair were mapped separately. Alignments of a read with more than 10 mismatches were discarded. Read pairs were then examined for uniqueness and correct pairing. A uniquely mapped pair was required to have less than five mismatches on each read and not to map to anywhere else in the genome or transcriptome as a pair with less than or equal to 10 mismatches each.
Genome_build: hg19
Supplementary_files_format_and_content: txt files

source_name: LM2 cells

growth_protocol: Control and hnRNPM shRNA-expressing LM2 cells were seeded at a density of 1.6 x 10^6 in 10 cm plates in DMEM, supplemented with 10%FBS, L-glutamine, penicilin, and streptomycin.

extract_protocol:
Cells were collected in 1ml Trizol at 48 h after plating. RNA was extracted according to the RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: control


title: hnRNPM KD_rep2

value: hnRNPM siRNA treated


title: Control_rep2


title: OCILY3_Input-SPIBkd


title: OCILY3_IRF4-SPIBkd


title: H929_Input

description: ASCII shift tag: 64


title: OCILY3_IRF4-Scrm

description:
ASCII shift tag: 33
Scramble transfection


title: OCILY3_PU1-Scrm


title: OCILY10_Input

description: ASCII shift tag: 64


title: OCILY3_SPIB-Scrm


title: iaa3 + BR RNA-Seq replicate 2

first: Eunkyoo

last: Oh

state: CA

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

description: RNA-Seq of iaa3 + BR replicate 2

data_processing:
Basecalls performed using CASAVA version 1.?
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome_build: TAIR9

organism: Arabidopsis thaliana

source_name: Etiolated iaa3 seedlings treated with 100 nM brassinolide

growth_protocol: Seedlings were grown on medium containing 2 µM propiconazole (PPZ) in the dark for 5 days and treated with mock or 100 nM BL for 4 hr before harvesting.

extract_protocol: Total RNA was extracted by using the Spectrum Plant Total RNA kit (Sigma, USA). Libraries were constructed using TruSeqTM RNA Sample Preparation Kit (Illumina) according to the manufacturer’s procedure.

value: Etiolated seedlings


title: iaa3 RNA-Seq replicate 1

description: RNA-Seq of iaa3 replicate 1

source_name: Etiolated iaa3 seedlings


title: Col-0 + BR RNA-Seq replicate 2

description: RNA-Seq of Col-0 + BR replicate 2

source_name: Etiolated wild type (Col-0) seedlings treated with 100 nM brassinolide


title: Col-0 + BR RNA-Seq replicate 1

description: RNA-Seq of Col-0 + BR replicate 1


title: Col-0 RNA-Seq rep 1

description: RNA-Seq of Col-0 replicate 1

source_name: Etiolated wild type (Col-0) seedlings


title: OCILY3_PU1-SPIBkd


title: Seed 9WAF

city: Higashi-Hiroshima

first: Kazuya

last: Koyama

state: Hiroshima

address: 3-7-1, Kagamiyama

department: Fundamental Reesearch Division

country: Japan

institute: National Research Institute of Brewing

description: Sample 9

data_processing:
Tags were extracted from sequence data of multiplexed samples, which were analyzed by Illumina Genome Analyzer II. Sequence reads were sorted by index seqence into separate files. From each read in each file, 26-bp sequence upstream anchoring enzyme site (CATG) was extracted. Extracted 26-bp sequences (tags) were counted. Non singleton tags were extracted in each sample and used for transcript profiling. These process was done by script written in Perl.
Supplementary_files_format_and_content: Tab-delimited text files include tag sequences and tag counts per million total tags for each Sample.

organism: Vitis vinifera

source_name: Seed 9WAF

extract_protocol:
Total RNA was extracted, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with a previously described procedure (Reid et al. BMC Plant Biology 6:27). Quality control was performed with the Agilent 2100 Bioanalyzer.
Ds-cDNA was synthesized using biotinylated dT primer. After digestion of cDNA with anchoring enzymes NlaIII, digested fragments were associated streptavidin magnetic beads. Adapters were ligated to cDNA ends on the beads and adapter-cDNA was digested with EcoP15I. Released fragments after enzyme digestion were ligated to adapter encoding barcode. Obtained fragments were once amplified PCR and applied to sequence analysis.

treatment_protocol: Three treatments on the clusters of the same vines were performed: light exposure (control), shading with light-proof boxes from flowering onward (shade), shading during 2 weeks (14 days) from the onset of the treatment and then light exposed (shade/light exposure). Berry samples from the grape clusters of the three treatments were collected 3 days after removal of light-proof boxes (17 days after flowering)

tag: index sequence

value: GCCC

tag: total tag counts

tag: developmental stage

value: 9 weeks after flowering

value: seed

tag: light regime

value: light exposure


title: Seed 7WAF

description: Sample 8

source_name: Seed 7WAF

value: GACG

value: 7 weeks after flowering


title: hnRNPM KD_rep1


title: SL26778

description:
Sample 2
40-100 nucleotide fraction donor 2

data_processing:
Base calling were performed on the instrument using the HiSeq Sequencing Control Software (HCS). CASAVA software version 1.8 (Illumina) was used for de-multiplexing and production of FASTQ sequence files.
FASTX application (www.molecularevolution.org) was used to trim adapter sequences from the 3’and 5'-end of the sequence read, discard any sequence of less than 17 nucleotides after trimming, and to collapse identical reads into single entries retaining the read count for each unique sequence.
Non-redundant sequences were then aligned to genomic RNA and mRNA sequences using Bowtie 2 (www.bowtie-bio.sf.net) and the mapped sequences (perfectly matched and mismatched) were retained and aligned to common and abundant non-coding RNAs (tRNAs, rRNAs, snoRNAs). After the perfectly matched reads to non-coding RNAs were removed from the genome/mRNA aligned reads, remaining sequences were further aligned to known mature and precursor miRNAs using the miRBase 19 database (www.mirbase.org). Since a large proportion of sequences did not map to miRNA, an additional alignment to a transcript and non-coding RNA(miscRNA) database (Ensembl version 75) using bowtie2 was performed. Alignment to the specific piRNA database from piRNABank (http://pirnabank.ibab.ac.in/) was also performed.
R script was used to tablulate the read counts for each unique sequence from the alignment results. R/Bioconductor packages were used to tablulate the raw sequence read count for each target database entry. Raw read counts for each RNA class from all samples in the study were then joined in raw data tables. The raw reads were converted to reads per kilobase of target length per million mapped reads (RPKM) using R script.
Genome_build: hg19
Supplementary_files_format_and_content: The .csv files include raw counts and RPKM values for each Sample

source_name: exosomes isolated from cell-free seminal fluid

tag: donor

value: 40-100 nucleotide fraction


title: Skin 9WAF

description: Sample 6

source_name: Skin 9WAF

value: TCCA

value: skin


title: Seed 2WAF

description: Sample 7

source_name: Seed 2WAF

value: GCGG

value: 2 weeks after flowering


title: Skin 2WAF (shade)

description: Sample 3

source_name: Skin 2WAF (shade)

value: GACC

value: shade


title: OCILY10_BATF

description: ASCII shift tag: 33

tag: cell type

value: Diffuse large B-cell lymphoma (DLBCL)

tag: chip antibody

value: sc-100974X, Santa Cruz


title: Skin 7WAF

description: Sample 5

source_name: Skin 7WAF

value: GACT


title: Skin 2WAF (light exposure)

description: Sample 2

source_name: Skin 2WAF (light exposure)

value: GCGT


title: Flower

description: Sample 1

source_name: Flower

value: GCGA

value: flowering

value: flower


title: DR1-Amp

city: Seoul

first: Aram

last: Heo

address: Anam Campus, Anam-dong 5-ga, Seongbuk-gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

description: control

data_processing:
Base-calling: CASAVA v1.8
Alignment: CLC Genomics Workbench 6.5.1
Generation of normalized abundance measurement: CLC Genomics Workbench 6.5.1
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: normalized abundance measurement

organism: Acinetobacter oleivorans DR1

extract_protocol: Total RNA was isolated from 5 ml of expoenetial cells treated Ampicillin 100 µg/ml for 15min, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina HiSeq to generate paired-end 100-bp reads.

tag: genotype

value: Wild type

tag: growth phase

value: exponential


title: DR1-Km

description: control

data_processing:
Base-calling: CASAVA v1.8
Alignment: CLC Genomics Workbench 6.5.1
Generation of normalized abundance measurement: CLC Genomics Workbench 6.5.1
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: normalized abundance measurements

extract_protocol: Total RNA was isolated from 5 ml of expoenetial cells treated Kanamycin 4µg/ml for 15min, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina HiSeq to generate paired-end 100-bp reads.


title: OCILY3_Input-Scrm


title: Scrambled-3 biological replicate 2

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

data_processing:
The paired end sequencing reads were mapped to the mm9 reference genome using the TopHat2 spliced read mapper. Specified options were mate-inner-dist, mate-std-dev and library-type (fr-firststrand). mate-inner-dist and mate-std-dev were assesed individually for each sequenced library based on the output of the sequencer for average fragment size and CV value. TopHat2 version used was v2.0.7
The mapping was followed up by counting the reads that mapped each genomic feature (gene) employing htseq-count with the stranded option set to reverse. The annotations from the ensembl release 67 were used as reference for counting. The package version of HTSeq we used was 0.5.3
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are two column tab separated. First column contains gene id from Ensembl release 67. Second column is the number of reads that were mapped to that gene. Last five rows contain some extra information on couting.

source_name: Mouse male feeder-free embryonic stem cells

growth_protocol: The feeder-dependent mouse female ES cell line F1-21.6 was cultivated on mitomycin-C-inactivated MEFs. The feeder-independent mouse male ES cell line WT26, was cultivated on gelatin-coated dishes in ES cell culture media KnockOut-DMEM (Gibco, Cat. No. 10829-018) supplemented with 1 % L-glutamine (Gibco, Cat. No. 25030-081), 1 % penicillin/streptavidin (Gibco, Cat. No. 15070-063), 1% Non- essential amino acids (Gibco, Cat. No. 11140-050), 1 % Sodium Pyruvate, 1 % 2-mercaptoethanol. All ESC media contained 15 % FBS and 1000 U/ml (for feeder-free) or 2000 U/ml (for feeder-dependent) of leukemia inhibitory factor (LIF). Male and female NPC lines were derived from previously mentioned ES cell lines and cultured in N2B27 medium (StemCell Sciences) containing 10 ng/mL EGF and FGF (Preprotech) on gelatin-coated flasks.

extract_protocol:
Total RNA was extracted from WT26 ESC and NPC as biological triplicates using TRIzol® Reagent and treated with the TURBO Dnase kit (Ambion).
For RNA-seq analysis, cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit with 3 ug DNase-treated samples for paired-end sequencing (50 bp reads)

tag: passages

value: Approximately 30


title: Scrambled-3 biological replicate 1

value: Mouse male feeder-free embryonic stem cells


title: Scrambled-2 biological replicate 1


title: Scrambled-2 biological replicate 2


title: Scrambled-1 biological replicate 2


title: OCILY3_BATF

description: ASCII shift tag: 33

tag: cell line


title: Skin 2WAF (shade/light exposure)

description: Sample 4

source_name: Skin 2WAF (shade/light exposure)

value: GACA

value: shade/light exposure


title: Col-0 RNA-Seq rep 2

city: Stanford

description: RNA-Seq of Col-0 replicate 2

value: Etiolated seedlings


title: NSL3 biological replicate 2


title: Scrambled-1 biological replicate 1


title: NSL3 biological replicate 3


title: NSL3 biological replicate 1


title: iaa3 RNA-Seq replicate 2

description: RNA-Seq of iaa3 replicate 2


title: HA Vasa DQAD IP - long RNAs (200nt)

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

institute: University of Geneva

source_name: Bombyx mori, BmN4 cells

extract_protocol: Nucleic acids were isolated from protein complexes immunoprecipitated with the indicated antibodies and resolved by 15% or 20% urea-PAGE. Bands corresponding to piRNAs or the indicated size were excised from the gel and extracted with 400 µl of 0.3M NaCl solution at 25°C overnight. All deep sequencing libraries (except for JX52, JX59 and JX86) were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. JX52, JX59 and JX86 were prepared by ligating homemade RNA adaptors, followed by gel-purification and RT-PCR. Libraries were sequenced on Illumina HiSeq platform (EMBL Heidelberg Gene core facility) or Illumina MiSeq platform (EMBL Heidelberg Gene core facility) .

value: BmN4 cells

value: HA-tag

tag: antibody

value: anti-HA (sc-805; Santa Cruz)

tag: 3' barcode (nebnext primers)

tag: 5' barcode


title: Msl2 biological replicate 1

tag: strain


title: PrEC_NOMe-Seq

city: Darlinghurst

first: Aaron

last: Statham

institute: Garvan Institute of Medical Research

description:
Sample 3
processed data file: GCH.tsv.gz, WCG.tsv.gz

source_name: PrEC

extract_protocol:
Cells were trypsinized and centrifuged for 3 mins at 500g, then washed in ice-cold PBS and resuspended in 1mL ice-cold Nuclei Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA and 0.5% NP-40,plus protease inhibitors) per 5x106 cells and incubatedon ice for 5 min. Nuclei were recovered by centrifugation at900g for 3 min and washed in Nuclei Wash Buffer (10mM Tris,pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1mM EDTA containing protease inhibitors). Freshly prepared nuclei (2x105 cells) were resuspended in 1X M.CviPI reaction buffer (NEB), then treated with 150U of M.CviPI (NEB; 50,000U/mL) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
Genomic DNA (2 μg) was sonicated using a Covaris instrument to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer analysis (Agilent Technologies). Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt. Magnetic beads were employed for all nucleic acid purifications in subsequent steps.  Following end repair, A-tailing was performed using the dA-tailing module according to manufacturer’s instructions (New England Biolabs). Adapters with a 3’‘T’ overhangs were then ligated to the end-modified DNA. Modified Illumina paired-end (PE) adapters were used. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20μL. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix under the following conditions: 98°C for 2 min, followed by 4 cycles of 98°C for 30 s then 65°C for 15 s and 72°C for 1 min with a final extension for 10 min in 50μL total reaction volume. The final library product was examined on the Agilent Bioanalyzer then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.  Optimal concentrations to get the right cluster density were determined empirically.

value: PrEC


title: Scrambled-2 biological replicate 3


title: Msl1 biological replicate 1


title: Msl1 biological replicate 2


title: Msl1 biological replicate 3


title: MOF biological replicate 3


title: MOF biological replicate 1


title: Scrambled-1 biological replicate 3


title: KANSL3 replicate B (NPC)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were aligned to the genome (version mm9) using bowtie2 with standard parameters
The following reads were removed for down-stream analysis: mitochondrial genome, random chromosomes, mapping quality < 2, those with XS: flag in the bam file
Peak calling was performed with MACS (1.4.2), only peaks that were called in both replicates were used for downstream analyses
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage module of deepTools (https://github.com/fidelram/deepTools), normalizing to 1x coverage.

source_name: Neuronal progenitor cells

growth_protocol: The feeder-independent mouse male ES cell line WT26 (a kind gift from the lab of  T. Jenuwein), was grown on gelatin-coated dishes in ES cell culture media KnockOut-DMEM supplemented with 1% L-glutamine, 1% penicillin/streptavidin, 1% Non- essential amino acids, 1% Sodium Pyruvate, 1% 2-mercaptoethanol. All ESC media contained 15% FBS and 1000 U/ml (for feeder free) or 2000U/ml (for feeder-dependent) of leukemia inhibitory factor (LIF). NPC lines were derived from previously mentioned ES cell lines and cultured in N2B27 medium (StemCell Sciences) containing 10 ng/mL EGF and FGF (Preprotech) on gelatin-coated flasks. The cells were kept in a humidified incubator at 37°C and 5% CO2 and were passed when reaching 80-90% confluency.

extract_protocol:
Nuclei were isolated, resuspended in RIPA Lysis Buffer, sheared using Diagenode Bioruptor Plus Sonicator and chromatin was immunoprecipitated with the respective antibodies.
Library preparation was carried out following Illumina standard protocols for paired-end sequencing

treatment_protocol: Mouse ES cells were differentiated into neuronal progenitor cells. In brief, ESC (1x106 cells) were deprived of feeders and plated on 0.1 % gelatin-coated dishes in N2B27 medium and grown for 7 days. During that period of time, the medium was changed every day. Next, cells were dissociated from the plate using accutase and approximately 3 x 10e6 cells were plated in a petri dish to induce formation of embryoid bodies (in N2B27 medium supplemented with 10 ng/ml EGF and FGF2). After 72 hours, embryoid bodies were transferred to 0.1 % gelatin-coated dishes and allowed to attach to the bottom leading to expansion of NPC cells. NPC lines were maintained in N2B27 medium supplemented with EGF and FGF2 (10ng/ml each), on 0.1 % gelatin- coated flasks.

value: ES-derived neural progenitor cells

value: KANSL3 (SIGMA, HPA035018)


title: MSL2 replicate B (NPC)

value: MSL2 (SIGMA, HPA003413)


title: KANSL3 replicate A (NPC)


title: TAF7LKO-mRNA-seq-BAT

city: Berkeley

first: Haiying

last: Zhou

address: 188 Li Ka Shing Center

department: MCB

institute: HHMI/UCB

data_processing:
Mapping sequencing reads to the genome: Sequenced reads were mapped to the 2012 assembly of the mouse genome (UCSC version mm10) using Bowtie with the command-line options ‘-c -q -n 2 -l 48 -m 1’, thereby keeping for further analyses only reads that mapped uniquely to the genome with at most two mismatches at the first 48 bases.
Digital gene expression of mRNA-seq: The reads were than mapped to the mouse transcriptome (version mm10), using TopHat (Trapnell et al., 2009), version v1.4.0., using default parameters. We then applied cufflinks (Trapnell et al., 2010), version v1.3.0, using the default parameters except: --max-mle-iterations 1, to estimate the digital expression levels at each transcript.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: abundance

source_name: TAF7L knockout brown adipose tissue(3-month old)

extract_protocol:
Total RNAs were extracted individually from 1-month-old WT and Taf7lKO mice interscapular BAT (6 of each group) by RNeasy Plus Mini Kit (Qiagen Inc., Germantown, MD).
mRNA-seq libraries preparation and deep sequencing: 6 extracted RNAs from WT and Taf7l KO BAT were pooled with equal amount and 4 μg of WT and Taf7l KO pooled RNA samples was used to purify mRNA and subsequently converted into to mRNA-seq library using mRNA-Seq Sample Prep Kit (Illumina Inc., San Diego, CA) and sequenced on an Illumina HiSeq 2000 sequencer.qualities of the libraries were assessed by 2100 Bioanalyzer (Functional Genomics Laboratory, Berkeley,CA) and then subjected to multiplexed ultra-high throughput sequencing on an Illumina HiSeq 2000 sequencer (GSL core facility, UC Berkeley, CA) as previously described (Zhou et al., 2013),  each sample yielded ∼40–50 million reads.
Preparation of mRNA-seq libraries on mRNA extracted from wild type and Taf7l KO brown adipose tissue precisely followed the instructions from Illumina (Illumina Inc.), qualities of the libraries were assessed by 2100 Bioanalyzer and then subjected to multiplexed ultra-high throughput sequencing on an Illumina HiSeq 2000 sequencer (GSL core facility, UC Berkeley, CA).

value: TAF7L KO

tag: tissue

value: brown adipose tissue

tag: age

value: 1 mo

tag: genetic background


title: MOF replicate A (NPC)

value: MYST1 (BETHYL, A3000992A)


title: MOF replicate B (NPC)


title: MSL2 replicate A (NPC)


title: Input replicate B (NPC)


title: KANSL3 replicate B (ESC)

source_name: Embryonic stem cells

value: mouse embryonic stem cells


title: KANSL3 replicate A (ESC)


title: MSL2 replicate B (ESC)


title: Input replicate A (NPC)


title: Msl2 biological replicate 3

value: Approximately 30


title: Msl2 biological replicate 2

value: Mouse male feeder-free embryonic stem cells


title: MSL2 replicate A (ESC)


title: MSL1 replicate B (ESC)

value: MSL1 (in-house, Rabbit Polyclonal, Final Bleed)


title: MSL1 replicate A (ESC)


title: MOF replicate B (ESC)


title: MOF replicate A (ESC)


title: MCRS1 replicate B (ESC)

value: MCRS1 (Proteintech, 11362-1-AP)


title: Input replicate B (ESC)


title: MOF biological replicate 2


title: WT-mRNA-seq-BAT

source_name: wild type brown adipose tissue(1-month old)

value: wild type


title: methyl-C-seq_DKO_rep1

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

institute: Uiversity Hospital Zurich

description: bisulfite-converted genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.4
MethylC-Seq reads were mapped as previously described (Lister et al., Nature, 2009). Briefly, reads were trimmed until encountering a base with PHRED score <= 2 and bases near the 3' end were trimmed if the adapter sequence was included. For the purpose of mapping, all cytosines were computationally converted to thymines, to be reverted back to their original state after mapping. The Bowtie program(Langmead et al. 2009) was then used to align these computationally converted reads to computationally converted copies of hg18. Non-uniquely mapping reads were discarded
Non-monoclonal reads were filtered out using the Picard software
Using the Samtools Pileup command, for each genomic position the number of reads with match and mismatch were counted in a strand sepcific manner, more specifically, the number of methylated and non-methylated reads per CpG were determined. Individual bases with Phred score < 20 were filtered out. The genome was then divided up into bins of 100 bp and the CpG methylation ratio was calculated by capturing the number of methylated CpG reads in comparison to all reads at CpG for each bin by combining the two replicates and by combining plus- and minus-strand. The methylation ratios per 100bp were used to compose bigwig files.
Genome_build: mm9

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.

extract_protocol:
Genomic DNA was extracted from mESCs and was spiked in with unmethylated lambda DNA (Promega). The DNA was fragmented by sonication.
The DNA was fragmented by sonication. Purified DNA fragments were end-repaired. After A-tailing reaction, fragments were ligated to paired-end cytosine-methylated adapters provided by Illumina. Size-selected adaptor-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified, and sequenced following standard protocols from Illumina.

value: Dnmt3a/3b DKO


title: methyl-C-seq_WT_rep1

description: bisulfite-converted genomic DNA

value: wildtype


title: input DNA H3K9me3 KO

description: ChIP-Seq reads were mapped by bowtie to mm9, keeping only uniquely mapping reads and discarding all but one of clonal reads. Wig files combining H3K9m3 ChIP-seq and the respective input were generated by caclulating reads per 100bp bin for ChIP and 500bp bin for Input and per million reads. The ChIP bin values were divided by the input bin values.

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
Wig files combining H3K9m3 ChIP-seq and the respective input were generated by caclulating reads per 100bp bin for ChIP and 500bp bin for Input and per million reads. The ChIP bin values were divided by the input bin values.
Genome_build: mm9

growth_protocol: mESCs were grown on gelatinized plates in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

treatment_protocol: Setdb1 CKO cells were treated with 800nM of 4-OHT for 4 days and further cultured without treatment for 2 days to induce Setdb1 deletion

value: Setdb1 conditional KO


title: input DNA H3K9me3 wt


title: Mut1

city: Portland

first: Huilan

last: Yao

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

description: Sample 3

data_processing:
EDA done with FASTQC
Alignment done with Bowtie allowing 2 mismatches (only utilizing uniquely mapping reads in the analysis)
Differential expression analysis at the gene level was conducted via linear modeling in edgeR
All p-values were False Discovery Rate adjusted
Further filtering for validation was based on fold change (Mut/WT) > |2| and having >50 reads  and FDR adjusted p-value < 0.05
Genome_build: MM9
Supplementary_files_format_and_content: text files with raw read counts (total counts) and differential expression results (differential expression total)

source_name: Mutant_fetal_liver cells

extract_protocol:
Total RNA was extracted following the manufacturer's protocol.
2ug total RNA from pooled samples was used to make one sequencing library using the Illumina mRNA-seq Sample Preparation Kit (San Diego, CA)

treatment_protocol: Fresh isolated fetal livers were mechanically dissociated by pipetting up and down in PBS containing 0.5% BSA and 2mM EDTA. Single cell suspension were stained with Propidium Iodide as well as antibody against to CD71 and TER119. Cells were FACS sorted directly into TRIzol LS reagent.

tag: strain background

tag: genotype/variation

value: Mutant (Rcor1-/- )

tag: development stage

value: fetal liver cells

tag: surface marker


title: Mut2

description: Sample 4

tag: cell type


title: control2

description: Sample 2

source_name: control_fetal liver cells

value: control (Rcor1+/+ and Rcor1+/-)


title: control1

description: Sample 1


title: WT_RNASeq.rep1

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads trimmed to 36bp length and were aligned to the mm9 genome assembly using TopHat giving rise to bam files
BigWig files were created based on TopHat output, as Bam files were used to calculate read density file using the genomeCoverage script from the Bedtools suite. For comparability, read density numbers were normalized by a factor based on total number of reads per sample
Genome_build: mm9

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's instruction. Ribosomal RNA was removed using RiboMinus Eukatyote Kit (Invitrogen).
The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al. 2009).


title: input DNA 1

description: ChIP-Seq reads were mapped by bowtie to mm9, keeping only uniquely mapping reads and discarding all but one of clonal reads. Wig files combining H3K9m3 ChIP-seq and the respective input were generated using the SPP package for R and binning the data into non-overlapping 100bp bins.

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
wig files were generated by combining CHIP and respective Input files using SPP for R
Genome_build: mm9

tag: chip antibody


title: WT_RNASeq.rep2

tag: genotype


title: methyl-C-seq_DKO_rep2

description: bisulfite-converted genomic DNA


title: methyl-C-seq_DKO_rep paired end

description: bisulfite-converted genomic DNA


title: input DNA 2


title: methyl-C-seq_WT_rep2 paired end

description: bisulfite-converted genomic DNA


title: methyl-C-seq_WT_rep2

description: bisulfite-converted genomic DNA


title: MCRS1 replicate A (ESC)

value: MCRS1 ( Proteintech, 11362-1-AP)