title: N2_total-2

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
supplementary file: EditingList.txt
Illumina Casava 1.8 sanger base calls

data_processing:
RNAseq: polyA, J2, Input datasets
Basecalls performed using CASAVA version 1.8 or 1.3 (see samples description column)
Aligned fastq files with TopHat v2.0.10 with options: --b2-very-sensitive -g 20 -i 30 -I 5000 --read-edit-dist 3 -N 3 --read-realign-edit-dist 0 --segment-length 25 --segment-mismatches 2 --no-coverage-search  --min-segment-intron 30 --max-segment-intron 5000
Re-aligned unmapped.bam file from tophat using bowtie2 v2.1.0 with options: --local --very-sensitive-local
Merge tophat2 and bowtie2 bam files using samtools merge
PolyA_counts: generate counts (exon and utr only) using ensembl ws220 gtf with HTSeq-count v0.5.4p3 with options: -m intersection-nonempty -i gene_name
PolyA_normalization: counts normalized using Deseq v1.16 estimateSizeFactors
Input and J2_counts: generate counts (utr's,exons,introns included) using ws220 gff file and bedtools intersect v2.16.2 with options: -abam -split -wb -bed
Input and J2_normalization: normalized counts by total reads mapped.
TotalRNAedit_Mapping: To capture A-to-I RNA editing in total RNA-seq reads, we used the Blat-like Fast Accurate Search Tool (BFAST) to align wild type, tdp-1(ok803), and adr-2(gv42) total RNA sequences to WS220 C. elegans genome
TotalRNAedit_editCalls: For wild-type, adr-2(gv42), and tdp-1(ok803) total RNA samples the alignments were piled up using an in house program. We required a minimum base quality of 20, minimum coverage of 10x and a non-reference base proportion between 0.3 and 0.99. Potential edited sites where more than 90% of the reads mapped had the same start and end position were discarded. Sites where more than 90% of the alignments fell within 3bp from the end of the read were also discarded. For each remaining site the strand was inferred to determine the edited base using WS220 gene annotations. Positions where the strand could not be determined or the strand was ambiguous were discarded. Each of the potential edited positions from the wild-type or tdp-1(ok803) samples were compared to the adr-2(gv42) sample at the same position and the site was identified as a an edit if the alternate base proportion in the adr-2(gv42) sample was < 0.05. All regions identified as edited were visually inspected on the IGV browser to confirm the validity of each target. Regions containing reads with multiple base changes (>1 in 100bp read) besides A-to-I conversions (seen as A-to-G compared to the genomic sequence for positive genes and T-to-C for negative genes) were not counted as edited. Editing events mapping to spice junctions were also disregarded. To identify editing in introns enriched by J2 immunoprecipitation that were not identified in the original analysis (due to insufficient read depth), reads mapping to all J2-IP enriched introns were inspected visually on the IGV genome browser and hand-annotated as edited. Intronic sequences were counted as edited if the reads mapping to that intron contained at least 10 reads that encompassed 3 or more independent editing events (indicative of promiscuous editing of highly dsRNA) and these editing events were represented in all three biological replicates of wild type and/or tdp-1(ok803) J2-IP. Again, intronic regions where reads contained multiple changes besides A-to-I conversions compared to the genomic sequence were disregarded as artifact. Identification of inverted repeats/repetitive elements within edited regions was determined by matching an interval file of all edited regions with an interval file containing the coordinates of all repetitive regions in the C. elegans genome (taken from wormbase, genome browser, Repeat Masker track). We required an overlap of at least 50bp between the edited region and the inverted repeat to consider the two regions overlapping.
Genome_build: ws220
Supplementary_files_format_and_content: tab delimited text file containing gene name and normalized counts for each gene

RNAseq: total datasets
Align fastq files with BFAST (see Table E15 in paper)
Identify adr-2 dependent edits: For wild-type, adr-2(gv42), and tdp-1(ok803) total RNA samples the alignments were piled up using an in-house program. Positions in wild type and tdp-1(ok803) samples with a discrepancy between the genomic sequence and mRNA sequence consistent with A-to-I editing (A-G and C-T transitions) were identified. Potential edited positions were compared to the adr-2(gv42) sample and sites also showing A-to-G or C-to-T changes were discarded.
The Integrative Genome Viewer (IGV) tool, count, was used to transform BFAST alignment files into pileups for downstream analysis. Edit locations were used to compare percent editing between wild type and tdp-1(ok803). Only regions containing a minimum of 20 reads/region in both strains were used. The total number of edited nucleotides in each location was divided by the total number of potentially edited nucleotides for each location. A site was considered potentially edited if the site showed evidence of an A-to-I change (read as A-to-G (positive strand genes) or T-to-C (negative strand genes) compared to genomic sequence) in either wild type or tdp-1 mutant RNA- seq. Significant changes in editing were determined by performing a 2-proportional Z- Tests between wild type and tdp-1(ok803) percent edited ratios; p<0.05 for significant changes.
Genome_build: ws220
Supplementary_files_format_and_content: tab delimited text file containing all genes that were identified in our analysis of total RNA that contain A-to-I RNA editing

source_name: whole worm extract

growth_protocol: Maintenance and growth of worms were as described in (Brenner, 1974), and all strains were raised at 15°C or 20°C.

extract_protocol:
Extract for J2-IP experiments was made from young adult animals grown on solid plates at 15°C. Worms used for TDP-1 immunoprecipitation followed by RT-PCR were crosslinked according to (Zisoulis et al, 2010). Worms used for J2-IP were not crosslinked. Extract was prepared by bead beating as described in (Saldi et al, 2007). Extracts were used immediately for immunoprecipitations or dissolved in TRizol (for input RNA).
RNA for poly(A) and total RNA sequencing libraries was extracted from whole animals by TRIzol extraction. Genomic DNA was removed using turboDNAse (Invitrogen). For total RNA libraries, 5μg of RNA was run through a Ribozero column (Epicenter, #R2C1046) to remove ribosomal RNA. For poly(A)-selected libraries, RNA was selected using sera-mag magnetic oligo dT beads (Therma Scientific). Libraries were created using Illumina TruSeq kits (RS-122-2001). RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) were converted into strand-specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080-044) using incrementally increasing temperatures from 42°C-59°C to allow for transcription though structured RNAs. rRNA was not removed from J2-IP RNA samples. Immunoprecipitated DNA from ChIP samples was converted in sequencing libraries using ChIP-Seq DNA Sample Prep Kit (IP-102-1001). Libraries were sequenced on Illumina HiSeq 2000 platforms.

value: N2-CGC B

tag: temperature


title: tdp1_total-1

status: Public on Nov 19 2014

type: SRA

country: USA

description:
supplementary file: EditingList.txt
Illumina Casava 1.3 base calls

library_source: transcriptomic

molecule: total RNA

organism: Caenorhabditis elegans

tag: strain

tag: developmental stage


title: N2_total-3


title: tdp1_total-2


title: tdp1_CHIP-1

description:
supplementary file: TDP1_CHIP-1_peaks.bed
Illumina Casava 1.8 sanger base calls

library_source: genomic

data_processing:
CHIPseq
Basecalls performed using CASAVA version 1.8
fatsq file trimmed from 5' or 3' end if sanger quality score 20 or below.
Aligned with bowtie vs. 0.12.7 default parameters
Peaks called with MACS vs. 1.42 with options: -m 2, 30 -bw 300 --keep-dup=5 -p 1E-2
Genome_build: ws220
Supplementary_files_format_and_content: Bed files with peak coordinates and densities

molecule: genomic DNA

source_name: CHIP from whole worm extract

value: young adult


title: Del_SCR_129/Cast_1_p9 [Illumina HiSeq 2000]

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description:
Del_SCR_129Cast_1_p9.bedgraph
Del_SCR_129Cast_1_p9(129).bedgraph
Del_SCR_129Cast_1_p9(Cast).bedgraph

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 14/02/2014
Reads were aligned to in silico constructed versions of the 129S1 and CastEiJ genomes using Tophat2 running Bowtie2.
Mapped reads were split into 129, Cast or unknown using custom scripts and variant data, only variant bases sequenced with Phred score > 20 (on standard 33 offset) were considered for allele calling
BedGraphs were generated using bedtools v2.17.0 genomecov script with standard settings.
genome build:mm9

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: All cells were maintained on gelatin-coated plates in ES media supplemented with LIF and two inhibitors (2i, CHIR99021 and PD0325901).

extract_protocol:
RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction.
NEBNext mRNA Library Prep Reagent Set for Illumina

treatment_protocol: SCR deleted clones contain a deletion of the Sox2 downstream enhancer which lies between Chr3:34653922-34661217 in the M. musculus genome build mm9.  Deletions were generated in F1 ES cells using gRNA104 (TAGCATACGTCACGCCGGAA) and gRNA112 (ACTGTTCTCGAACACTCTGT) to target the Cas9 nuclease.

tag: genotype

value: ΔSCR(129/Cast), clone 1

tag: passage

value: 9 after colony seletion


title: tdp1_CHIP-RNAseControl

description:
supplementary file: TDP1_CHIP_rnaseControl_peaks.bed
Illumina Casava 1.8 sanger base calls


title: tdp1_total-3


title: N2_total-1


title: tdp1_CHIP-2

description:
supplementary file: TDP1_CHIP-2_peaks.bed
Illumina Casava 1.8 sanger base calls


title: ADR2_total-1


title: tdp1_J2-2

description:
supplementary file: J2NormalizedCounts.txt
Illumina Casava 1.8 sanger base calls

source_name: J2 immunoprecipitated from whole worm extract


title: tdp1_J2-3


title: tdp1_J2-1


title: tdp1_input

description:
supplementary file: Input_normalizedCounts.txt
Illumina Casava 1.8 sanger base calls


title: N2_J2-2


title: N2_J2-3


title: N2_J2-1


title: tdp1_polyA-2

description:
supplementary file: polyA_normalizedCounts.txt
Illumina Casava 1.8 sanger base calls

molecule: polyA RNA


title: N2_input


title: F1 ES [Illumina HiSeq 2000]

description:
F1_ES.bedgraph
F1 ES (129).bedgraph
F1 ES (Cast).bedgraph

value: wild type


title: tdp1_polyA-3


title: tdp1_polyA-1


title: N2_polyA-3


title: Del_SCR_Cast_11 [Illumina MiSeq]

description:
Del_SCR_Cast_11.bedgraph
Del_SCR_Cast_11(129).bedgraph
Del_SCR_Cast_11(Cast).bedgraph

value: ΔSCR(Cast), clone 11

value: 5 after colony seletion


title: N2_polyA-2


title: DcreA

city: Jinan

first: Yuqi

last: Qin

address: 27 Shanda Nan Lu

country: China

institute: Shandong University

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in modifeid Czapek culture medium with 2% glucose as carbon resource for 12 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 48 h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.

value: creA deletion

tag: medium

value: Modifeid Czapek culture medium with 2% glucose as carbon resource

tag: culture time

value: 48 h after transferring washed mycelia to the new medium


title: DlaeA

value: laeA deletion


title: Del_SCR_129_37 [Illumina MiSeq]

description:
Del_SCR_129_37.bedgraph
Del_SCR_129_37(129).bedgraph
Del_SCR_129_37(Cast).bedgraph

value: ΔSCR(129), clone 37


title: Del_SCR_129_15 [Illumina MiSeq]

description:
Del_SCR_129_15.bedgraph
Del_SCR_129_15(129).bedgraph
Del_SCR_129_15(Cast).bedgraph

value: ΔSCR(129), clone 15


title: JKM139_2_T240

status: Public on Nov 20 2014

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Biological replicate 2

data_processing:
Reads were mapped to the S. cerevisiae S288C reference genome (retrieved from SGD) using the version 1.4.1 of TopHat, with a tolerance of 4 mismatches and a maximum size for introns of 2 Kb.
Subsequent analysis used reads uniquely mapped on the reference genome.
Tags densities were normalized on the total number of reads mapped on ORFs.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each gene in each sample

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted using standard hot phenol procedure. rRNAs were depleted from total RNA using the RiboMinus Eukaryote Kit for RNA-Seq (Life Technologies).
Strand-specific total RNA-Seq libraries were prepared from 125 ng of rRNA-depleted RNA using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: strain background

tag: genotype/variation

tag: induction status

value: 240 min after HO induction


title: HeLa shRNA TIAR

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: short hairpin RNA (shRNA)

data_processing:
Short reads were aligned against human genome hg19 with Tophat.
Transcript abundances were calculated with cufflinks.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Homo sapiens

source_name: HeLa cell line, TIAR shRNA

growth_protocol: Adherent HeLa cell lines expressing stably empty (control) or TIA1 and/or TIAR shRNA-pSUPER constructs were cultured under standard conditions as previously reported (Izquierdo JM, Alcalde J, Carrascoso I, Reyes R, Ludeña MD: Knockdown of T-cell intracellular antigens triggers cell proliferation, invasión and tumor growth. Biochem J 2011, 435:337-344).

extract_protocol:
Total RNA from above HeLa cell lines was purified by TRIZOL method (Invitrogen). The quality of the total RNA was tested using the Agilent 2100 Bioanalyzer RNA Nano Chip.
For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol.

tag: cell line

value: HeLa

tag: construct

value: TIAR-shRNA-pSUPER


title: 114

value: 114-2 (wild type)


title: DlaeADcreA

value: double deletion of laeA and creA


title: HeLa shRNA Control

description: short hairpin RNA (shRNA)

source_name: HeLa cell line, control shRNA

value: empty


title: F1 ES [Illumina MiSeq]


title: N2_polyA-1

value: N2-CGC B


title: HeLa shRNA TIA1

description: short hairpin RNA (shRNA)

source_name: HeLa cell line, TIA1 shRNA


title: Dpse_Dam_rep3

status: Public on Nov 18 2014

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description:
DamID-derived DNA
Replicate 3 of Dam-only (control) in D. pseudoobscura

data_processing:
DamID adapters were removed from 5' and 3' ends of reads using cutadapt with the following command: cutadapt -a GATCCTCGGCCGCGACC -g ^GGTCGCGGCCGAGGATC -o sample_cutadapt.fq.gz sample.fq.gz
Reads were mapped to their respective original genomes using bowtie2 with the default parameters.
Mapped reads were converted to bam format, sorted and indexed using SAMtools version 0.1.19.
BEDTools version 2.21.1 was used to convert reads to bed format (bamToBed), and the BEDTools slop utility was used to extend reads to the average library fragment size.
For samples from all non-melanogaster species, UCSC LiftOver was used to translate reads into the dm3 genome assembly. The -minMatch parameter was set to 0.7 for D. simulans and D. yakuba, and it was set to 0.5 for D. pseudoobscura. In all cases, multiple outputs were not permitted.
The position of all GATC fragments in each genome was found using the scanMotifGenomeWide.pl utility from HOMER v4.7. The BEDTools coverage utility was used to count the number of reads overlapping each GATC fragment in each sample, and resulting counts were combined into a count table including all sample and control replicates for each comparison of a Dam-fusion protein vs. Dam-only.
DESeq2 v.1.6.1 was used to test for differential enrichment of Dam-fusion reads versus Dam-only reads in each GATC fragment. Fragments flagged as differentially enriched (log2 fold change >0 and adjusted p-value <0.05 or <0.01) were extracted, and neighboring GATC fragments with less than 100 bp separating them were merged to form binding intervals using an in-house perl script.
Binding profiles were created by using an in-house perl script to extract the normalized log2 fold changes between the fusion protein and Dam-only control calculated by DESeq2 for each GATC fragment.
Genome_build: Varies per sample (dm3, droSim1, droYak2, dp3)
Supplementary_files_format_and_content: Bed files contain the locations of binding intervals (described above). Column 4 shows the number of neighboring GATC fragments that were merged to create each interval. For D. melanogaster, binding intervals called at FDR1 and FDR5 are provided. For all non-melanogaster species, binding profiles are provided for data in the original genome (untranslated) and data that has been translated to the D. melanogaster dm3 genome assembly.
Supplementary_files_format_and_content: Bedgraph files contain binding affinity profiles, which are the normalized log2 fold changes between the fusion protein and Dam-only control for each GATC fragment across the genome. For all non-melanogaster species, binding profiles are provided for data in the original genome (untranslated) and data that has been translated to the D. melanogaster dm3 genome assembly.

organism: Drosophila pseudoobscura

source_name: whole embryos, 0-16 hours

growth_protocol: Flies were grown on standard cornmeal medium at 25 degrees C, with the exception of D. pseudoobscura, which were grown on banana-opuntia-malt medium at 22.5 degrees C. Embryos were collected after overnight lays on a grape juice-agar plate streaked with fresh yeast paste.

extract_protocol:
To extract high-molecular weight genomic DNA, each aliquot of embryos was dechorionated and  homogenized  in a Dounce 15-ml homogenizer in 10 ml of homogenization buffer (10 mM Tris-HCl pH 7.6, 60 mM NaCl, 10 mM EDTA, 0.15 mM spermine, 0.15 mM spermidine, 0.5% Triton X-100). The lysate was then  spun for 10 minutes at 6000g. The supernatant was discarded, and the pellet was  resuspended in 10 ml homogenization buffer, then spun again for 10 minutes at  6000g. The supernatant was again discarded, and the pellet was resuspended in 3  ml homogenization buffer. 300 μl of 20% n-lauroyl sarcosine were added, and the  samples were inverted several times to lyse the nuclei. The samples were treated  with RNaseA followed by proteinase K, then purified by two  phenol-chloroform extractions and one chloroform extraction. DamID samples were prepared from genomic DNA following the DamID protocol from Vogel et al. (Nat Protoc 2, 1467-1478, 2007).
Libraries were prepared as for ChIP-seq by BGI Tech, starting with at least 20 ng of DNA per sample and following standard Illumina protocol (end repair, 3' dA-tailing, ligation of adapters, PCR amplification and size selection for fragments 100-300bp). Libraries were multiplexed with 2 samples per run for the MiSeq and 9-12 samples per lane for the HiSeq. MiSeq libraries were run as 150-bp paired-end reads, while HiSeq libraries were run as 50-bp single-end reads.

treatment_protocol: Each line of flies was transformed with a piggyBac plasmid containing either a Dam-only transgene or a Dichaete-Dam or SoxNeuro-Dam fusion transgene. Transgenic flies were identified by the presence of GFP expression in the eyes.

tag: strain of origin

value: D. pseudoobscura pseudoobscura  (reference strain)

tag: transgene inserted

tag: original genome build

value: dp3 (UCSC)

tag: translated genome build

value: dm3 (UCSC)


title: Dpse_Dam_rep2

description:
DamID-derived DNA
Replicate 2 of Dam-only (control) in D. pseudoobscura


title: Dpse_DichaeteDam_rep1

description:
DamID-derived DNA
Replicate 1 of Dichaete-Dam in D. pseudoobscura
Dpse_DDam_DESeq2_p05_merged.bed
Dpse_DDam_dm3_DESeq2_p05_merged.bed
Dpse_DDam_DESeq2_allGATC.bedgraph
Dpse_DDam_dm3_DESeq2_allGATC.bedgraph


title: Dpse_Dam_rep1

description:
DamID-derived DNA
Replicate 1 of Dam-only (control) in D. pseudoobscura


title: Dpse_DichaeteDam_rep3

description:
DamID-derived DNA
Replicate 3 of Dichaete-Dam in D. pseudoobscura
Dpse_DDam_DESeq2_p05_merged.bed
Dpse_DDam_dm3_DESeq2_p05_merged.bed
Dpse_DDam_DESeq2_allGATC.bedgraph
Dpse_DDam_dm3_DESeq2_allGATC.bedgraph


title: Del_SCR_129/Cast_1_p9 [Illumina MiSeq]

value: ΔSCR(129/Cast), clone 1

value: 9 after colony seletion


title: NPC115D

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to reference geneome (hg19) using tophat spliced aligner.
Cufflinks was used to estimate the transcript abundance against RefSeq gtf downloaded from ucsc table browser.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files with fpkm values for RefSeq genes. (Cufflinks output)

source_name: Nasopharyngeal carcinoma – Primary tumor

extract_protocol:
not provided
Libraries were generated using the TruSeq RNA Sample Preparation kit (Illumina)

tag: tissue

value: Nasopharynx

tag: disease stage

value: Primary tumor

tag: gender

value: MALE


title: NPC8D


title: NPC9D


title: NPC3D


title: CAGE

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

description:
CAGE
For the 5' end, one or two extra Gs between the barcode and real sequence, need to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 13 nt also needs to be trimmed due to 3' end adaptors and unstable qualities.

data_processing:
CAGE: basecalling by CASAVA version 1.8.2. The first 11 nt from 5'end and the last 13nt from 3'end are trimmed off (check sample description).  All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to hg19 by bowtie version 0.12.7 using --strata --best -k 10. Only 5'end of single mapped reads are used in the analysis.
RNASeq: basecalling by CASAVA version 1.8.2. All the reads are mapped by Tophat version 2.0.6, using Tophat -G gencode_version17.gtf --solexa-quals --bowtie-n --segment-length 25 -r 145 --mate-std-dev 250 --library-type fr-secondstrand. The mapped reads are subsequently assembled by cufflinks (v2.0.2) using cufflinks -g gencode_version17.gtf --library-type fr-second.  De novo transcriptomes from the four RNA-seq libraries are then merged by Cuffmerge and compared to the genecode version17 annotation by Cuffcompare (rnaseq_cuffcmp_ids.txt).  Fianlly,  cufflinks FPKM for gene expression is extracted as a single table (rnaseq_gene_cufflinks_FPKM.txt) , raw expression counts are extracted for all the isoforms followed by the normalization by spike-ins (rnaseq_isoform_spikein_norm.txt).
5'p-end sequencing: All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 20 -p 50 and mapped to hg19 by Tophat version 2.0.6, using Tophat -G gencode_version17.gtf --solexa1.3-quals --bowtie-n --segment-length 25 --library-type fr-secondstrand. Only 5'end of single mapped reads are used in the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for cage and 5p include processed 5'end signals, splited by the strands.  Gtf file includes all the assembled transcripts from the process described as above. Tab-delimitated files include a file for gene FPKM expression, a file for transcript spikein-normalized expression, and a id file associating the denovo internal ids with gencode v17 annotated ids.

source_name: HEK293 Flp-In T-Rex cells

extract_protocol:
Purelink (Ambion)
CAGE (PMID: 21938627)

tag: reporter gene

value: no gene inserted in Flp-In locus

tag: barcode

value: a mix of 3 barcodes (AGACAGCAG, CTTCAGCAG, GATCAGCAG ) and 30 % phiX as spike in.


title: Del_SCR_129/Cast_1_p5 [Illumina MiSeq]

description:
Del_SCR_129Cast_1_p5.bedgraph
Del_SCR_129Cast_1_p5(129).bedgraph
Del_SCR_129Cast_1_p5(Cast).bedgraph

tag: strain

tag: genotype

tag: passage

value: 5 after colony seletion


title: 5p_XRN1_SMG6

description:
5'p-end sequencing
cytoplasmic 5'-monophosphate poly(A)+ RNA

source_name: HEK293 b-39 (Flp-In T-Rex) cells

extract_protocol:
Digitonin (cytoplasmic) extract, phenol/chloroform, MicroPoly(A) Purist (Ambion)
Ligation of RNA adapter to 5'-end of RNAs with 5'-monophosphate. cDNA synthesis with adapter-tagged random hexamer primers. Size-selection (~300-400 bp; inserts of ~200-300 bp). PCR-amplification with adapter-compatible primers. Solexa sequencing from 5'-end original RNA molecule.

value: b-globin PTC39 reporter expressed from Flp-In locus

value: SMG6/XRN1 depletion


title: 5p_XRN1_UPF1

value: UPF1/XRN1 depletion


title: rnaseq_XRN1

description:
RNASeq
cytoplasmic poly(A)+ RNA
processed data files: rnaseq_gene_cufflinks_FPKM.txt, rnaseq_isoform_spikein_norm.txt and rnaseq_cuffcmp_ids.txt

extract_protocol:
Digitonin (cytoplasmic) extract, phenol/chloroform, MicroPoly(A) Purist (Ambion)
ScriptSeq v2 (Epicentre)

value: XRN1 depletion

value: ACATCG


title: Del_SCR_129_15 [Illumina HiSeq 2000]

value: ΔSCR(129), clone 15


title: 5p_control

value: control (EGFP siRNA-treated)


title: 5p_XRN1


title: Dpse_DichaeteDam_rep2

description:
DamID-derived DNA
Replicate 2 of Dichaete-Dam in D. pseudoobscura
Dpse_DDam_DESeq2_p05_merged.bed
Dpse_DDam_dm3_DESeq2_p05_merged.bed
Dpse_DDam_DESeq2_allGATC.bedgraph
Dpse_DDam_dm3_DESeq2_allGATC.bedgraph

value: D. pseudoobscura pseudoobscura  (reference strain)

value: dp3 (UCSC)


title: Dyak_Dam_rep2

description:
DamID-derived DNA
Replicate 2 of Dam-only (control) in D. yakuba

organism: Drosophila yakuba

value: droYak2 (UCSC)

value: dm3 (UCSC)


title: Dyak_Dam_rep1

description:
DamID-derived DNA
Replicate 1 of Dam-only (control) in D. yakuba


title: Dsim_Dam_rep2

description:
DamID-derived DNA
Replicate 2 of Dam-only (control) in D. simulans

organism: Drosophila simulans

value: droSim1 (UCSC)


title: Dsim_Dam_rep3

description:
DamID-derived DNA
Replicate 3 of Dam-only (control) in D. simulans


title: WT_zeb_5d_R2

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

data_processing:
read quality control (FastQC)
low quality read trimming (FASTX tools)
mapping to Arabidopsis TAIR10 (TopHat)
retrieving number of reads per gene coordinates (qualimap)
Genome_build: TAIR10
Supplementary_files_format_and_content: readcounts per gene for each of the libraries and RPKM values

organism: Arabidopsis thaliana

source_name: shoot apex

growth_protocol: plants were grown for seven days on solid ½ MS media at 16 h light: 8 h dark at 21°C.

extract_protocol:
dissected shoot apices (hypocotyl and roots, cotyledons and trie leaves were cut away with a razor blade) were flash frozen and RNA was extracted using the RNeasy Mini Kit (Qiagen) with additional on column DNAse I (Roche) digest
RNA libraries were prepared for sequencing using RNA TruSeq kit (Illumina) using standard protocol

treatment_protocol: 7 days old plants were transferred to control ½ MS plates and freshly prepared drug media for specified times.

tag: ecotype

value: shoot apical meristem

tag: exposure time

value: 5 days


title: Dyak_DichaeteDam_rep2

description:
DamID-derived DNA
Replicate 2 of Dichaete-Dam in D. yakuba
Dyak_DDam_DESeq2_p05_merged.bed
Dyak_DDam_dm3_DESeq2_p05_merged.bed
Dyak_DDam_DESeq2_allGATC.bedgraph
Dyak_DDam_dm3_DESeq2_allGATC.bedgraph


title: WT_zeb_5d_R1


title: Dsim_SoxNDam_rep2

description:
DamID-derived DNA
Replicate 2 of SoxNeuro-Dam in D. simulans
Dsim_SoxNDam_DESeq2_p05_merged.bed
Dsim_SoxNDam_dm3_DESeq2_p05_merged.bed
Dsim_SoxNDam_DESeq2_allGATC.bedgraph
Dsim_SoxNDam_dm3_DESeq2_allGATC.bedgraph


title: Dsim_SoxNDam_rep3

description:
DamID-derived DNA
Replicate 3 of SoxNeuro-Dam in D. simulans
Dsim_SoxNDam_DESeq2_p05_merged.bed
Dsim_SoxNDam_dm3_DESeq2_p05_merged.bed
Dsim_SoxNDam_DESeq2_allGATC.bedgraph
Dsim_SoxNDam_dm3_DESeq2_allGATC.bedgraph


title: WT_mock_5d_R2


title: Dyak_DichaeteDam_rep1

description:
DamID-derived DNA
Replicate 1 of Dichaete-Dam in D. yakuba
Dyak_DDam_DESeq2_p05_merged.bed
Dyak_DDam_dm3_DESeq2_p05_merged.bed
Dyak_DDam_DESeq2_allGATC.bedgraph
Dyak_DDam_dm3_DESeq2_allGATC.bedgraph


title: rnaseq_XRN1_UPF1

tag: genotype/variation

value: TCAAGT


title: Dsim_DichaeteDam_rep3

description:
DamID-derived DNA
Replicate 3 of Dichaete-Dam in D. simulans
Dsim_DDam_DESeq2_p05_merged.bed
Dsim_DDam_dm3_DESeq2_p05_merged.bed
Dsim_DDam_DESeq2_allGATC.bedgraph
Dsim_DDam_dm3_DESeq2_allGATC.bedgraph


title: rnaseq_XRN1_SMG6

tag: cell line

value: GATCTG


title: atr_MMC_R2


title: WT_mock_5d_R1


title: atr_MMC_R1


title: atr_zeb_R2


title: Dsim_DichaeteDam_rep1

description:
DamID-derived DNA
Replicate 1 of Dichaete-Dam in D. simulans
Dsim_DDam_DESeq2_p05_merged.bed
Dsim_DDam_dm3_DESeq2_p05_merged.bed
Dsim_DDam_DESeq2_allGATC.bedgraph
Dsim_DDam_dm3_DESeq2_allGATC.bedgraph


title: Dyak_Dam_rep3

description:
DamID-derived DNA
Replicate 3 of Dam-only (control) in D. yakuba


title: Dsim_DichaeteDam_rep2

description:
DamID-derived DNA
Replicate 2 of Dichaete-Dam in D. simulans
Dsim_DDam_DESeq2_p05_merged.bed
Dsim_DDam_dm3_DESeq2_p05_merged.bed
Dsim_DDam_DESeq2_allGATC.bedgraph
Dsim_DDam_dm3_DESeq2_allGATC.bedgraph


title: PCBP2 iCLIP in JFH-1 Huh7

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

institute: Stanford University

description:
replicates 1 and 2
library strategy: iCLIPseq

data_processing:
Reads were filtered for quality, PCR duplicates removed using the random barcode, 5' and 3' adaptor sequences were trimmed and reads were mapped to hg19 and a custom noncoding RNA index [We constructed a custom index of human short repetitive noncoding RNAs (including snRNAs and Y RNAs) as well as the full 42kb human rDNA locus. These sequences were obtained from Rfam (for short repetitive RNAs) and GenBank (for the rDNA locus, GenBank ID: U13369.1). The index was build with each RNA as a tandem element in a single FASTA file which was then used to make a bowtie2 index. This bowtie2 index was then used to map sequencing reads after which unmapped reads were aligned to the hg19 build of the human genome.].
Crosslinked nucleotides were identified as the first nucleotide of each trimmed read. Crosslinked nucleotides were only analyzed if present at least 6 between the biological replicates.
Genome_build: hg19; AB047639.1
Supplementary_files_format_and_content: The bigWig file provided contains processed Crosslinked nucleotides from the DDX21_SAT iCLIP experiment (i.e., trimmed, mapped, and processed data mapping to hg19, excluding reads that mapped to the custom index we built). Data presented is an intersection of the two biological replicates.

growth_protocol: Huh7 cells were grown in DMEM with 10% FBS, 1% nonessential amino acids, and 200uM L-glutamine

extract_protocol:
Lysates were clarified from sonicated Huh7 cells and PCBP2-RNA complexes were isolated with an anti-PCBP2 antibody.
Libraries were prepared according to the standard iCLIP protocol (PMID: 24184352), substituting the 3' RNA adaptor for one with a 3'-Biotin blocking moity. Subsequent steps utalized a Streptavidin-Biotin capture strategy to eliminate the need for precipiations between biochemical reactions. Each sequencing read conatins a 13 nt random (D's and N's) and experimental (XXXX) "DDDNNXXXXNNNN". The experimental barcodes are described in (PMID: 24184352)

treatment_protocol: Huh7 cells were either uninfected or infected with the JFH-1 isolate of HCV at a multiplicity of infection of 0.01

tag: host cell line

tag: infection

value: JFH-1 isolate of HCV

tag: rip antibody

value: anti-PCBP2 (Sigma Aldrich, catalog number R4155)


title: atr_zeb_R1


title: Dyak_DichaeteDam_rep3

description:
DamID-derived DNA
Replicate 3 of Dichaete-Dam in D. yakuba
Dyak_DDam_DESeq2_p05_merged.bed
Dyak_DDam_dm3_DESeq2_p05_merged.bed
Dyak_DDam_DESeq2_allGATC.bedgraph
Dyak_DDam_dm3_DESeq2_allGATC.bedgraph

tag: strain of origin

tag: transgene inserted

tag: original genome build


title: PCBP2 iCLIP in uninfected Huh7

value: uninfected


title: Dmel_Dam_rep3

description:
DamID-derived DNA
Replicate 3 of Dam-only (control) in D. melanogaster

organism: Drosophila melanogaster

tag: translated genome build


title: atr_mock_R2

tag: tissue

value: 0 h


title: atr_mock_R1


title: Dsim_Dam_rep1

description:
DamID-derived DNA
Replicate 1 of Dam-only (control) in D. simulans


title: WT_MMC_R1


title: WT_MMC_R2


title: Dmel_SoxNDam_rep3

description:
DamID-derived DNA
Replicate 3 of SoxNeuro-Dam in D. melanogaster
Dmel_SoxNDam_DESeq2_p01_merged.bed
Dmel_SoxNDam_DESeq2_p05_merged.bed
Dmel_SoxNDam_DESeq2_allGATC.bedgraph


title: Dsim_SoxNDam_rep1

description:
DamID-derived DNA
Replicate 1 of SoxNeuro-Dam in D. simulans
Dsim_SoxNDam_DESeq2_p05_merged.bed
Dsim_SoxNDam_dm3_DESeq2_p05_merged.bed
Dsim_SoxNDam_DESeq2_allGATC.bedgraph
Dsim_SoxNDam_dm3_DESeq2_allGATC.bedgraph


title: Dmel_SoxNDam_rep2

description:
DamID-derived DNA
Replicate 2 of SoxNeuro-Dam in D. melanogaster
Dmel_SoxNDam_DESeq2_p01_merged.bed
Dmel_SoxNDam_DESeq2_p05_merged.bed
Dmel_SoxNDam_DESeq2_allGATC.bedgraph


title: Dmel_Dam_rep2

description:
DamID-derived DNA
Replicate 2 of Dam-only (control) in D. melanogaster


title: WT_zeb_R2


title: Dmel_DichaeteDam_rep2

description:
DamID-derived DNA
Replicate 2 of Dichaete-Dam in D. melanogaster
Dmel_DDam_DESeq2_p01_merged.bed
Dmel_DDam_DESeq2_p05_merged.bed
Dmel_Ddam_DESeq2_allGATC.bedgraph


title: WT_mock_R1

value: 0 days


title: WT_zeb_R1


title: Dmel_DichaeteDam_rep1

description:
DamID-derived DNA
Replicate 1 of Dichaete-Dam in D. melanogaster
Dmel_DDam_DESeq2_p01_merged.bed
Dmel_DDam_DESeq2_p05_merged.bed
Dmel_Ddam_DESeq2_allGATC.bedgraph


title: K5-Cre+ single cells

status: Public on Nov 17 2014

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: distal lung epithelium

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells. In addition, one "no cell control" was prepared using reagents without any cell input in a PCR tube.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Mice were administered 3 doses of  0.25 mg / g body weight tamoxifen in 50 ul corn oil, with each dose seperated by 48 hours, and animals were housed 1 week prior to sacrifice.  Lungs were exposed via standard procedures and perfused with PBS.  After installation with agarose and subsequent hardening by a brief incubation on ice, each lobe was cut away from the mainstem bronchi. The proximal-most ¼ of each lobe surrounding the bronchi was then cut away to minimize the inclusion of basal cells in the cell preparation.  Cells were incubated for 30 min at room temperature with anti-integrin B4, anti-EpCam-PE, and sytox blue, washed, and sorted.

value: lung

tag: age

value: 6-8 weeks


title: H3K4me3 ChIP-seq in Suz12GT (aka Suz12(Bgal/Bgal)) ESC-derived Spinal Motor Neuron lineage cells

city: Cambridge

first: Laurie

middle: A

last: Boyer

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Sequences were extended +200 bp for histone marks and allocated in 25-bp bins.
A Poissonian model was used to determine statistically enriched bins with a P-value threshold set at 1x10-9 as described previously (Marson et al., 2008).  Additionally, we required that genomic bins were at least 5 fold over input to be considered enriched peaks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstad et al. Cell 2012).

source_name: differentiated cells (ESCs were subjected to Spinal motor Neuron in vitro directed differentiation)

growth_protocol: ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Cells were then preplated - plated on cell culture plates without gelatin for 20 minutes to allow the MEFs to attach and thus deplete the cell population of MEFs - before collection for ChIP.

extract_protocol: The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification: Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on (high), 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Millipore 07-473 antibody was used in the ChIP.  The ChIP DNA was then used to prepare sequencing libraries as described in Schmidt et al., 2009. For this study, a 1:40 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was amplified for 18 cycles. The samples were then examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

tag: time

value: d5 (of in vitro differentiation)

tag: cell type

value: ESC-derived Spinal Motor Neuron lineage Cells

value: mutant in Suz12

tag: mutant cell line reference

value: Pasini et al., 2007

tag: chip antibody

value: anti-H3K4me3 (Millipore, catalog# 07-473)


title: Dmel_Dam_rep1

description:
DamID-derived DNA
Replicate 1 of Dam-only (control) in D. melanogaster

value: dm3 (UCSC)


title: H3K4me3 ChIP-seq in Suz12GT (aka Suz12(Bgal/Bgal)) ESCs

source_name: ES cells

value: ESCs

tag: strain


title: DDX21 iCLIP Biological replicate 2

description: iCLIP-seq protocol

data_processing:
Sequencing reads were trimmed of the 3’ adaptor, filtered for quality and length (>20nt insert), PCR duplicates removed, and 5’ adaptor trimmed.
Processed reads were mapped with bowtie2 (parameters –m 1 and –v 2). Mapped reads were collapsed to RT stops as the first nucleotide of each read. RT stops from biological replicates were intersected. Reads passing this filtering were then used for assignment to known protein and noncoding RNAs in hg19.
DDX21_iCLIPseq_RTstops.bw = bigWig file of high confidence RT stops from merged biological replicates of DDX21 iCLIPseq. Located on series entry.
Genome_build: hg19

source_name: HEK293 Cells

growth_protocol: HEK293 were grown under standard tissue culture conditions

extract_protocol:
Lysates were clarified from sonicated HEK293 and DDX21-RNA complexes were isolated with anti-Flag and anti-HA antibodies.
Libraries were prepared according to the standard iCLIP protocol (PMID: 24184352)

tag: antibody 1

value: FLAG-M2, Sigma-Aldrich, Cat# A2220-5ML

tag: antibody 2

value: HA, Pierce, Cat# 26181

value: embryonic kidney


title: CC10- B4+ single cells and K5-Cre+ single cells

description: all are processed FPKM files

tag: genotype


title: DDX21 iCLIP Biological replicate 1

description: iCLIP-seq protocol

tag: cell line


title: rnaseq_control

description:
RNASeq
cytoplasmic poly(A)+ RNA
processed data files: rnaseq_gene_cufflinks_FPKM.txt, rnaseq_isoform_spikein_norm.txt and rnaseq_cuffcmp_ids.txt

tag: reporter gene

value: b-globin PTC39 reporter expressed from Flp-In locus

tag: genotype/variation

value: control (EGFP siRNA-treated)

tag: barcode

value: CGTGAT


title: H3K4me3 ChIP-seq in WT E14 ESCs

value: wild type


title: IMR90 iPS  (RNA-Seq)

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Supplementary_files_format_and_content: ICF_normReadcounts.txt matrix listing normalized read counts
Raw reads from the Illumina HiSeq2000 were mapped to the hg18 genome and Refseq genes using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.1) were filtered out
Poisson statistics were performed on the read counts of genes that passed filtering

source_name: induced pluripotent stem cell

growth_protocol: hESCs and hiPSCs were maintained in DME supplemented with 20% KSR, nonessential amino acids (Invitrogen), L-Glutamine (Mediatech), Penn/Strep, 2-mercaptoethanol with a feeder layer of MEFs as previously described (Shen et al., 2006).

extract_protocol:
RNA was isolated using Trizol (Invitrogen) while DNA was isolated using PureLinkTM genomic DNA purification kit (Invitrogen).
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: hESCs and hiPSCs were passaged onto feeder free gelatin coated plates twice before harvesting RNA

value: embryonic stem cell


title: ICF1-1 iPS rep 2  (RNA-Seq)

value: induced pluripotent stem cell


title: Dmel_DichaeteDam_rep3

description:
DamID-derived DNA
Replicate 3 of Dichaete-Dam in D. melanogaster
Dmel_DDam_DESeq2_p01_merged.bed
Dmel_DDam_DESeq2_p05_merged.bed
Dmel_Ddam_DESeq2_allGATC.bedgraph

tag: strain of origin

tag: transgene inserted


title: hiPS2  (RNA-Seq)


title: Ctrl

city: La Jolla

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
control rat neonatal cardiomyocytes
strand specific polyA+ RNA-Seq

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the rat genome (rn4) with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Reads counts per gene were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: rn4
Supplementary_files_format_and_content: The processed data file contains normalized read counts for all RefSeq annotated gene in the rat genome.  The read counts were normalized to the total number of reads found in RefSeq exons in each experiment (normalized to the average between the experiments).  The columns in the file are: 1) RefSeq ID, 2) chr, 3) gene start, 4) gene end, 5) strand, 6) avg. mRNA length, 7) Number of copies in the genome, 8) annotation, 9) normalized counts for Ctrl, 10) normalized counts for anti-miR-99/100 and Let-7

organism: Rattus norvegicus

source_name: neonatal cardiomyocytes

growth_protocol: The method has been described before (Eulalio et al., 2012). Briefly, ventricles from neonatal rats (post-natal day 0) were separated from the atria, cut into pieces and then dissociated in calcium and bicarbonate-free Hanks with HEPES (CBFHH) buffer containing 1.75_mg_ml_1 trypsin (BD Difco) and 10_µg_ml_1 DNase II (Sigma), under constant stirring, at room temperature in eight to ten 10-min steps, collecting the supernatant to fetal bovine serum (FBS, Life Technologies) after each step. The collected supernatant was centrifuged to separate the cells, which were then resuspended in Dulbecco's modified Eagle medium 4.5_g_l_1 glucose (DMEM, Life Technologies) supplemented with 5% FBS, 20_µg_ml_1 vitamin B12 (Sigma) and with 100_U_ml_1 of penicillin and 100_µg_ml_1 of streptomycin (Sigma). The collected cells were passed through a cell strainer (40_µm, BD Falcon) and then seeded onto uncoated 100-mm plastic dishes for 2_h at 37_¡C in 5% CO2and humidified atmosphere. The supernatant, composed mostly of CMs, was then collected and pelleted. Cells were resuspended in antibiotic-free media, counted and plated at the appropriate density; cultures of neonatal rat ventricular CMs prepared using this procedure yielded consistently a purity of >90%.

extract_protocol:
Total RNA of all samples was extracted using Rneasy Mini Kit (Qiagen) per manufacturer's instructions
RNA libraries were prepared for sequencing using strand-specific Illumina TruSeq kits per the manufacturer's instructions

treatment_protocol: Neonatal cardiomyocytes were isolated and mock-transduced or transduced with anti-miR-99/100 and anti-Let-7a/c containing AAV2/9 for 7 days

tag: developmental stage

value: neonate

value: cardiomyocyte

tag: treatment

value: transfected with empty adeno-associated virus (AAV)


title: AntiMir

description:
miR-99/100 and Let-7 knockdown rat neonatal cardiomyocytes
strand specific polyA+ RNA-Seq

value: transfected with adeno-associated virus (AAV) containing anti-miR-99/100 and anti-Let-7 shRNAs for knockdown


title: ICF1-2 iPS  (RNA-Seq)


title: ICF1-1 iPS (MethylC-Seq)

description: bisulfite converted genomic DNA

data_processing:
Each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000.
Reads were mapped to the hg18 genome via BS-Seeker
BED files contain the ratio of methylated cytosines to total cytosines covered at single base position
only cytosines with at least 3 or more covered reads were considered
Genome_build: hg18
Supplementary_files_format_and_content: ICF1-1iPS_CG.bed BED file of all CG methylation covered by at least 3 reads
Supplementary_files_format_and_content: ICF1-2iPS_CG.bed BED file of all CG methylation covered by at least 3 reads

growth_protocol: ICF hiPSCs were generated by using transducing ICF patient fibroblasts with Yamanaka factors

extract_protocol:
hiPSCs were passaged onto feeder free gelatin coated plates twice before harvesting DNA
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: hiPSCs were maintained in DME supplemented with 20% KSR, nonessential amino acids (Invitrogen), L-Glutamine (Mediatech), Penn/Strep, 2-mercaptoethanol with a feeder layer of MEFs as previously described (Shen et al., 2006).


title: ICF1-1 iPS rep 1 (RNA-Seq)


title: ICF1-2 iPS  (MethylC-Seq)

description: bisulfite converted genomic DNA


title: H3K4me3 ChIP-seq in E14 ESC-derived Spinal Motor Neuron lineage cells

value: d5 (of in vitro differentiation)

value: ESC-derived Spinal Motor Neuron lineage Cells


title: WT_mock_R2

tag: ecotype

tag: tissue

value: shoot apical meristem

tag: exposure time

value: 0 days


title: small RNA seq of control RNAi of staged young adults

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: small RNAs were isolated using the Illumina V1.5 sRNA kit from wild type animals treated with control RNAi by feeding bacteria programmed to express L4440 vector RNA to L2 larvae and grown to adulthood and  sequenced using Illumina GAII

data_processing:
[ChIP-Seq] FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ≥ 30).
Transcription factor binding sites were determined and scored using SPP peak caller (Kharchenko et al. 2008).
High confidence binding events were identified using IDR (Irreproducible Discovery Rate)
A cross-replicate threshold was obtained using a 5% IDR score threshold.  Additionally, a rescue threshold method was also determined using IDR scoring.  A final rank threshold for each data set was calculated by combining the cross-replicate and rescue threshold scores.  Finally, reads from all replicates were pooled and the SPP and IDR framework was applied again to rank peaks by signal-score. The final rank threshold score determined from the individual replicates was used as a significance threshold for the ranked pooled-data peaks.
[RNA-Seq] Raw FASTQ files were processed and log2 reads-per-million (RPM) values were calculated for each sequence for normalization purposes. Reads were then aligned to known miRNA and 21U-RNA sequences extracted from C. elegans genome WS215, allowing for one mismatch.
Genome_build: [ChIP-Seq] WS220
Genome_build: [RNA-Seq] WS215
Supplementary_files_format_and_content: [ChIP-Seq] Bedgraph files were generated as an output of the SPP program
Supplementary_files_format_and_content: [RNA-Seq] Tab-delimited .txt files report abundance counts.

source_name: staged young adults (N2) treated with control (L4440) RNAi

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation.  Starved L1s were plated on peptone-enriched NGM plates seeded with OP50, and grown until the desired developmental stage at 20˚C except for YL457 and YL524 which were grown at 25˚C to enhance transgene expression. In addition, growth at 25˚C induced temperature-sensitive sterility for YL524 strain, which harbors glp-1(q224).  Worms were harvested and washed free of bacteria in M9.

extract_protocol:
For all ChIP-seq samples, worms  were crosslinked in 2% formaldehyde in M9 buffer for 30 minutes rotating at room temperature.  Crosslinking was quenched with 1M Tris pH 7.5, followed by two washes with M9, and one wash with FA buffer containing protease inhibitors.  Final Triton X-100 concentration in all FA buffers used was either 1% (ChIP-seq data used in the tissue-specific analysis) or 5% (ChIP-seq data sets showing the developmental time course).  Worm pellets were flash-frozen in liquid nitrogen and stored at -80˚C.  Using the Fisher Scientific Sonic Dismembrator 550 (Pittsburgh, PA), samples were sonicated with a microtip on ice for sixteen cycles of 10 sec on, and 60 sec off on the “microtip” setting to fragment the majority of DNA within 200-800bp range.  Sonicated extract containing 2mg of protein was immunoprecipitated as previously described (Zhong et al., 2010) with 7.5µg of anti-GFP antibody (gift from Anthony Hyman) or anti-Pol III antibody (gift from Jason Lieb).
ChIP-seq library preparation for enriched DNA and the genomic DNA input control for at least two biological replicates was performed as described in (Zhong et al. 2010), except Qiagen MinElute PCR purification and gel extraction kits were used after the Klenow step.  Libraries were multiplexed as described in Lefrancois et al. (2009) in order to sequence four samples in a single flow cell using the Illumina Genome Analyzer II platform.
L1 animals were fed bacteria expressing RNAi clones from the Ahringer library (Fraser et al., 2000) until collection at the young adult stage. RNAi-treated young adults were harvested in TRIzol reagent (Invitrogen, Carlsbad, CA). Total RNA was then treated with DNA-free DNAseI (Ambion, Austin, TX).
A total of 5 µg of DNAse-treated RNA harvested from snpc-4(RNAi) and wildtype young adult animals was subjected to the Illumina small RNA v1.5 sample preparation kit and 22-30 bp small RNAs were sequenced

value: YA

value: whole animal


title: small RNA seq of SNPC-4(RNAi) of staged young adults

description: small RNAs were isolated from wild type animals treated with snpc-4(RNAi) by feeding bacteria programmed to express snpc-4 ds RNA to L2 larvae and grown to adulthood and  sequenced using Illumina GAII

source_name: staged young adults (N2) treated with snpc-4(L4440) RNAi


title: Dmel_SoxNDam_rep1

description:
DamID-derived DNA
Replicate 1 of SoxNeuro-Dam in D. melanogaster
Dmel_SoxNDam_DESeq2_p01_merged.bed
Dmel_SoxNDam_DESeq2_p05_merged.bed
Dmel_SoxNDam_DESeq2_allGATC.bedgraph

tag: original genome build

value: dm3 (UCSC)

tag: translated genome build


title: SNPC-4 ChIP from somatic cells of staged young adults (1%)

description: ChIP was performed with anti-GFP of GFP-tagged SNPC-4

source_name: staged young adults from YL524 [glp-1;OP179 (germ cell-deficient SNPC-4-GFP transgenic strain)]

value: soma

tag: chip'ped factor

tag: chip antibody

value: anti-GFP antibody (gift from Anthony Hyman)

tag: strain


title: SNPC-4 ChIP from germ cells of staged young adults (1%)

source_name: staged young adults from YL457 (germline-specific SNPC-4-GFP transgenic strain)

value: germline


title: RPC-1 input in staged, intact young adults (1%)

description: input

source_name: staged young adults (N2)

value: anti-Pol III antibody (gift from Jason Lieb)


title: RPC-1 ChIP in staged, intact young adults (1%)

description: ChIP was performed with anti-RPC-1


title: SNPC-4 input from somatic cells of staged young adults (1%)

description: input


title: SNPC-4 input from germ cells of staged young adults (1%)

description: input


title: Dicer WT Fibroblasts

first: Sara

middle: J

last: Gosline

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

data_processing:
Reads were aligned using TopHat v1.4.0
DESeq v 1.10.1 was used to normalize the reads between WT and KO
Genome_build: mm9
Supplementary_files_format_and_content: DESeq v1.10.1 output is included for all RefSeq transcripts including normalized read counts for the combined replicates, fold change and p-value representing significance of differential expression between WT and KO.

source_name: adult mesenchymal stem cells

growth_protocol: Monoclonal immortalized Dicer WT and KO MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.

extract_protocol:
PolyA-collected mRNA was obtained via the Qiagen miRNeasy kit from subconfluent WT and KO fibroblasts that were lysed using QIAzol directly in the dish. The Illumina Tru-Seq kit was used for sequence preparation, which began with an input amount of 1 µg t
The final libraries were size-selected to 300 +/- 25 bp on a 2% agarose gel for (50/50) paired end sequencing on an Illumina HiSeq 2000 machine.

value: Dicer f/f

tag: cell type

value: fibroblasts


title: SNPC-4 ChIP in staged young adults (1%)

source_name: staged young adults from OP179 (SNPC-4-GFP transgenic strain)


title: SNPC-4 input in staged young adults (1%)

description: input


title: Dicer KO Fibroblasts

value: Dicer -/-


title: siFoxk1_non-starved_RNA-seq

city: New York

first: Brian

last: Dynlacht

state: NY

address: 522 First Avenue

institute: New York University School of Medicine

data_processing:
RNA-seq reads for each library were aligned to the mouse genome build mm9 using Tophat 2.0.9 and Bowtie 2.1.0 with the “-G genes.gtf” and “–no-novel-junctions” options, where genes.gtf contains the UCSC coding transcripts in GTF format.
The transcriptome for each library was assembled using Cufflinks 2.1.1 with the default options.
The transcriptomes were merged using Cuffmerge, and differential expression analyses was performed using Cuffdiff with the “-u” and “-M mask.gtf” options, where mask.gtf contains mitochondrial RNA, tRNA, or rRNA transcripts that were masked from these analyses.
genome_build: mm9
supplementary_files_format_and_conten: Tab-delimited TXT files contain FPKM data and their corresponding confidence intervals for each gene.

source_name: myoblasts

growth_protocol: C2C12 myoblasts (Sigma) were grown in DMEM supplemented with 10% fetal bovine serum, 20 mM L-glutamine, 100 IU penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAgen) with QIAshredder columns and in-column DNaseI digestion as per the manufacturer’s instructions. RNA was eluted from the column in nuclease-free water.
RNA was polyA-selected and libraries were constructed using Illumina's TruSeq method.

treatment_protocol: Cells were starved by first rinsing twice with pre-warmed Hank’s Balanced Salt Solution (HBSS) and incubating in pre-warmed HBSS supplemented with 10 mM HEPES pH 7.5, 100 IU penicillin, and 100 mg/mL streptomycin for 4 h.

tag: cell line


title: siNS_non-starved_RNA-seq


title: siNS_starved_RNA-seq


title: SNPC-4 ChIP in staged young adults (5%)


title: SNPC-4 input in staged young adults (5%)

description: input


title: SNPC-4 ChIP in staged L4s (5%)

source_name: staged L4 larvae from OP179 (SNPC-4-GFP transgenic strain)


title: GTF2B_ChIP-seq neonate

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

data_processing:
ChIP-Seq analysis done by Active Motif (Data Explained in the file attached in PDF format)
The 50-nt sequence reads ("tags") identified by the sequencing service (using Illumina'sHi Seq) are mapped to the genome using BAM algorithm. Alignment information for each tag is stored in BAM format. Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Since the 5'-ends of the tags represent the end of a ChIP/IP-fragments, the tags are extended in silico (using Active motif software)at their 3' -ends to a length of 150-250 bp, depending on the average fragemtn length in the size selected library. To identify the density of fragemnts (extendend tags) along the genome, the genome is divided into 32 nt bins and the number of fragments in each bin is determined. This information is stored in a BAR (binary Analysis results) file that can be reviewed in a browser such as Affymetrix' Integrated Genome Browser (IGB).
An interval is a discrete genomic region, defined by the chromosome number and a start and end coordinate. Intervals represent the locations of the fragment density peaks. For each BAR file, Intervals are calculated and complied into BED files (Browser Extensible Data). A typical threshold setiing is in the range of 10-20, but may be adjusted depending on the number of tags sequenced or based on information on positive and negative test sites, independent estimates for the false discovery rate (FDR), and/or the intent to generate a stringent or relaxed analysis. The applied threshold can be found in the Assay Results report. For an interval to be called, it must contain 3 consecutive bins with fragment densities greater than the threshold.
To compare peak metrics between two samples, overlapping intervals are grouped into"Active regions', which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval (=union of overlapping Intervals). In locations where only one sample has an interval, this interval defines the Active Region. Active regions are useful to consider because the location and the lenghts of the intervals are rarely exactly the same when comparing different samples.
Genome_build: mm9
Supplementary_files_format_and_content: BAR, spreadsheets contain peaks

source_name: whole heart

growth_protocol: Hearts from 1-2day old C57Bl/6 mice undergoing physiological postnatal growth were extracted.

extract_protocol: ChIP, Library construction and Illumina sequencing performed by Active Motif

treatment_protocol: C57Bl/6 mice (12wks, ~26gms, male) were subjecetd to transaortic coartation (standard protocol described in detail in related publication Sayed et al, 2013) for 4days before hearts were extracted for analysis.

value: whole heart

tag: pathology

value: Postnatal heart

tag: age

value: 1-2 day

value: anti-GTF2B (sc-225)


title: GTF2B_ChIP-seq adult

value: Normal heart

value: 12 wk


title: ChIP-seq_input

data_processing:
Sequenced reads had the adapter sequences trimmed and were aligned to the mm9 genome build using BWA 0.7.5a with default options.
Reads mapping to a single genomic locus were selected and PCR duplicates were removed using the SAMtools (version 0.1.19) command "samtools rmdup".
BEDTools was used to generate BED6 and BEDGRAPH files, assuming DNA fragment lengths are an average of 250 bp. The BEDGRAPH data was normalized to the number of million reads present in the respective experiment after alignment and PCR-duplicate removal.
Using the BED6 files, peak-calling was performed using the Qeseq algorithm (Micsinai, M. et al. Nucleic Acids Res. 40(2012)) with the following parameters: “-s 100 -c 15 -p 0.00005”
Using the normalized BEDGRAPH files, BIGWIG files were generated using UCSC's bedGraphToBigWig script.
genome_build: mm9
supplementary_files_format_and_conten: BED files contain the coordinates of enriched regions detected by Qeseq. BIGWIG files display the normalized number of million reads present at each genomic base of all reads after PCR duplicate removal but before peak-calling.

extract_protocol:
Crosslinked, sonicated lysates were spun down to remove debris and protein-DNA complexes were immuno-precipitated. Immuno-complexes were washed, and protein-DNA complexes were eluted. After reversing crosslinks overnight at 65 C, the complexes were treated with RNase and proteinase K. DNA was isolated by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Air-dried input and ChIP DNA was resuspended in nuclease-free water.
ChIP and input DNA was end-repaired (End-It DNA End Repair, Epicentre #ER0720), had 'A' nucleotides added to the 3' ends of blunt ends (Klenow Fragement, NEB #M0212L), and ligated to adapters with 'T' overhangs using T4 DNA Ligase (Enzymatics #L6030-HC-L). Libraries were size-selected at ~350 bp (DNA fragment plus adapters) from a 2% agarose gel, gel extracted (QIAgen Gel extraction kit), and LM-PCR amplified (NEB Phusion High Fidelity PCR Master Mix, #M0531S) with 18 cycles. Libraries were then purified off AMPure XP magnetic beads to remove adapter dimers. All libraries were checked for the absence of adapter dimers by agarose gel and for the presence of quantitative ChIP enrichment at positive control loci prior to sequencing. Library concentrations were determined by PicoGreen assay.

value: none (input)


title: Eed-d5-2_RRBS

data_processing:
The sequencing data were analyzed as previously described (Gu et al., 2011).
Reads were mapped against an in-silico modified mouse genome (UCSC mm9, with inferred MspI restriction and genome-wide conversion of C to T and G to A) using maq (v 0.7.1-9) with the parameters  -D -s 0 -M c -e 100 C.
Read pileups were obtained using samtools mpileup, and for each CpG position, the number of reads bearing a modified or unmodified read was tallied and summed across the dinucleotide, and the fraction methylated was used for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: For each CpG position with at least one sample with 10x coverage, # of methylated C / number of bases are reported, summed over the CpG motif on both strands. The file is organized as chromosome, position, dinucleotide, and for each sample #modified Cs:coverage

source_name: in vitro differentiated cells

growth_protocol: ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Before collection or in vitro differentiation, cells were briefly plated on non-gelatinized tissue culture plates to remove MEFs.

extract_protocol: Reduced representation bisulfite sequencing was performed as published (Gu et al., 2011) and sequenced on an Illumina Hi-Seq.

value: Eednull

value: day 5 of Spinal Motor Neuron in vitro directed differentiation

tag: background

tag: replicate number

tag: differentiation

value: ESCs were subjected to Spinal motor Neuron in vitro directed differentiation as previously described (Wichterle and Peljto, 2008). Cells were collected at day 5.


title: GTF2B_ChIP-seq TAC

value: Hypertrophied heart subjected to Transaortic coarctation (TAC) for 4days


title: Foxk1_ChIP-seq

value: Santa Cruz sc-13450, Lot D1911


title: Eed-d5-1_RRBS


title: Sin3A_ChIP-seq


title: Eed-d0-1_RRBS

value: ES cells


title: Eed-d0-2_RRBS


title: Input DNA


title: Suz12Dd5-2_RRBS


title: Suz12Dd5-1_RRBS


title: MACS 2

city: Woodbury

first: Megan

last: Crow

state: New York

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description: Dissociated DRG neurons were washed in Dulbeccos PBS then resuspended in 120µl MACS buffer (Miltenyi autoMACS HBSS-based washing solution with 0.5% bovine serum albumin). 30µl of biotinylated non-neuronal antibody cocktail was added (Miltenyi MACS Neuron Isolation Kit) and cells incubated at 4°C for 5min. After washing in MACS buffer, cells were resuspended in 120µl MACS buffer with 30µl anti-biotin microbeads (Miltenyi MACS Neuron Isolation Kit) and incubated at 4°C for 10min. Cells were then run through a LD exclusion column placed in a QuadroMACS separator (Miltenyi Biotech), which retained all microbead-conjugated, non-neuronal cells so that only neurons were eluted. For MACS-sorted preparations, eluted pure neurons were then centrifuged, resuspended in Trizol and snap frozen

data_processing:
FastQ files were aligned to the UCSC mm10 build of the mouse genome using TopHat2 (Kim et al., 2013), with the multiple alignment parameter (-g) set to two.
Aligned bam files from separate lanes were combined using the Merge Bam tool from SamTools (Li et al., 2009)
fragments per kilobase per million (FPKM) estimates were obtained using Cufflinks version 2.1.1 (Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM estimates for all samples in .txt form

source_name: Dorsal root ganglion

extract_protocol:
RNA was extracted from intact, unsorted and MACS-sorted samples using the RNeasy micro kit (Qiagen). Each sample (each n) comprised material from 1, 2 or 8 mice in the intact, unsorted and MACS-sorted groups, respectively. RNA integrity was assessed on an Agilent2100 Bioanalyzer (Agilent, Santa Clara, CA) and the RNA integrity number of each sample was >8.
PolyA-selected RNA was used for complimentary DNA library preparation using the NEBNext Ultra direction RNA Library Prep Kit according to manufacturer’s instructions (NEB, Ipswich, MA).  100 bp reads were sequenced on the Illumina HiSeq2500 platform in replicate flow cells.

value: adult

tag: ex vivo/cultured

value: magnetically isolated


title: Suz12Dd0-2_RRBS


title: AB2 individual Anti-DMC1

city: Bethesda

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly. BWA was used to align genomic DNA and H3K4me3 ChIP-Seq data, while the pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome.
For SSDS DMC1 data, hotspots were called using MACS version 2.0.10 and matched control data. The following MACS arguments were used (--nomodel; --shiftsize: 400; --bw: 1000; -q: 0.1). For the H3K4me3 ChIP-Seq experiment, SICER v1.1 (Zang et al., 2009) was used for peak calling. The following arguments were used (species: hg19; redundancy threshold: 1; window size: 200; fragment size: 200; effective genome fraction: 0.8; gap size: 200; FDR: 0.1).
Genome_build: hg19
Supplementary_files_format_and_content: For each SSDS experiment, the associated BED file contains all ssDNA fragments identified for that sample. The bed file columns are as follows:  1. Chromosome  2. Fragment start  3. Fragment end  4. Read1Quality_Read2Quality  5. ITRLength_microhomologyLength  6. Fragment strand; Peak positions called by MACS or SICER are available on the series record.

source_name: Testis

extract_protocol:
For H3K4me3 CHiP-Seq and DMC1 SSDS protocols, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 and H3K4Me3 ChIP were performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-H3K4Me3 samples were prepared according to manufacturer’s protocol (Illumina) and anti-DMC1 libraries were prepared following the method described in (Khil et al., 2012).  For genomic DNA sequencing, DNA was sheared using a Covaris S series (Covaris, MS, USA) focused-ultrasonicator. Standard sequencing library construction was done using enzymes from New England Biolabs according to the protocol provided by Illumina. The PCR amplified library was size selected on a 2% agarose gel to extract the 300 to 500 bp band.

tag: antibody

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

tag: genotype

value: PRDM9A / PRDM9B

tag: sequencing technique

value: SSDS


title: MACS 1


title: Suz12Dd0-1_RRBS

source_name: ES cells


title: MACS 3


title: AB1 individual Input DNA_for_H3K4me3_ChIP

value: DNA-Seq


title: Suz12GTd5-2_RRBS


title: MACS 4


title: AB1 individual genomic DNA_paired-end

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly. BWA was used to align genomic DNA and H3K4me3 ChIP-Seq data, while the pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome.
For SSDS DMC1 data, hotspots were called using MACS version 2.0.10 and matched control data. The following MACS arguments were used (--nomodel; --shiftsize: 400; --bw: 1000; -q: 0.1). For the H3K4me3 ChIP-Seq experiment, SICER v1.1 (Zang et al., 2009) was used for peak calling. The following arguments were used (species: hg19; redundancy threshold: 1; window size: 200; fragment size: 200; effective genome fraction: 0.8; gap size: 200; FDR: 0.1).
Genome_build: hg19
Supplementary_files_format_and_content: For each SSDS experiment, the associated BED file contains all ssDNA fragments identified for that sample. The bed file columns are as follows:  1. Chromosome  2. Fragment start  3. Fragment end  4. Read1Quality_Read2Quality  5. ITRLength_microhomologyLength  6. Fragment strand; Peak positions called by MACS or SICER are available on the series record. The VCF file on the series record contains the variant calls.


title: Dissociated 3

description: Mice were euthanized with a terminal dose of pentobarbital and decapitated. Dorsal root ganglia were taken from all levels as previously described (Malin et al., 2007). For experiments on intact ganglia, DRG were snap frozen using liquid nitrogen, before being homogenized in Trizol (Invitrogen). For unsorted and MACS-sorted preparations, DRG were washed in F12 medium followed by incubation in dissociating enzymes (3mg/mL dispase, 0.1% collagenase and 200U/ml DNAse, all from Roche) for 30min at 37°C. Dissociation enzymes were then removed and replaced with F12. Cells were triturated 5 times using a P1000 tip to disrupt the tissue. Cells in suspension were retained, and fresh F12 was added to the remaining undisrupted material. This process was repeated 5 times. Cells in suspension were filtered through a 40µm filter and centrifuged for 5min at 150G. For unsorted preparations, cells were resuspended in Trizol at this point and snap frozen.

value: acutely dissociated


title: AB1 individual Anti-H3K4me3

value: Anti-H3K4me3 Millipore (#07-473)

value: ChIP-Seq


title: E14d5-2_RRBS

value: E14 wild type


title: Dissociated 2


title: E14d0-1_RRBS


title: Suz12GTd0-2_RRBS


title: Suz12GTd0-1_RRBS


title: E14d0-2_RRBS


title: SNPC-4 input in staged L4s (5%)

description: input

tag: developmental stage

tag: tissue

value: whole animal

value: anti-GFP antibody (gift from Anthony Hyman)


title: Suz12D d0 RNA

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Bowtie v. 0.12.7, Tophat v1.3.2 and Cufflinks v 1.2.1 and Cuffdiff were utilized to determine the expression levels of genes (Trapnell et al., 2012), using a NCBIN37, ENSEMBL-based annotation and flags -p 4, -r 170,  --segment-length 20 --segment-mismatches 1 --solexa1.3-quals --no-novel-juncs
Cufflinks was guided using the same annotation as Tophat with flags -b -u -p 6
Genome_build: mm9 (iGenome)
Supplementary_files_format_and_content: Txt file containing a table of RPKM values for each sample described in the study

extract_protocol: RNA was isolated using Trizol according to manufacturer’s instructions, including optional step in protocol. RNA quality was determined by Agilent Bioanalyzer. RNA-seq libraries were prepared as previously described (Wamstad et al., 2012). A final round of size selection by Agencourt AMPure XP beads was performed to remove small fragments such as primers. Sequencing was run on either an Illumina GA-2 or Hi-Seq (barcoded). .


title: Intact 4

description: Mice were euthanized with a terminal dose of pentobarbital and decapitated. Dorsal root ganglia were taken from all levels as previously described (Malin et al., 2007). For experiments on intact ganglia, DRG were snap frozen using liquid nitrogen, before being homogenized in Trizol (Invitrogen).

value: ex vivo


title: Intact 2


title: Eed- d0 RNA

value: Eednull


title: Suz12D d5 RNA

value: day 5 of Spinal Motor Neuron in vitro directed differentiation

value: ESCs were subjected to Spinal motor Neuron in vitro directed differentiation as previously described (Wichterle and Peljto, 2008). Cells were collected at day 5.


title: Dissociated 4


title: Eed- d5 RNA


title: AA2 individual genomic DNA

value: PRDM9A / PRDM9A


title: Intact 1

value: adult


title: Intact 3


title: E14 d0 RNA

value: ES cells


title: E14 d5 RNA


title: Suz12GT d5 RNA


title: ST7_Suz12GT_K27

description: ChIP was performed by hand, not on the IPstar, and sequenced on a whole lane of an Illumina GA2. Older dataset used to validate our general findings in Suz12GT H3K27me3 profile.

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Sequences were extended +200 bp for histone marks and allocated in 25-bp bins.
A Poissonian model was used to determine statistically enriched bins with a P-value threshold set at 1x10-9 as described previously (Marson et al., 2008).  Additionally, we required that genomic bins were at least 5 fold over input to be considered enriched peaks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstad et al., 2012).

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed based on the protocol as previously described (Lee et al., 2006), with modifications and adaptations. Briefly, a Diagenode bioruptor was used for sonication of formaldehyde-crosslinked cells on high for 30s on/ 30s off for 45 cycles in sonication buffer (20mM Tris-HCl; 150mM NaCl; 2mM EDTA; 0.1mM SDS; 1% Triton X-100; protease inhibitor (Thermo-scientific)). The Diagenode IP-star was also used for automation of the ChIP protocol in all but ST7_Suz12GT_K27, according to the manufacturer’s specifications. After purification of DNA, samples were used for to prepare libraries for Illumina sequencing. Library preparation is performed essentially as previously described (Schmidt et al., 2009); the amplification and size selection steps are reversed in order, and size selection was performed using Agencourt Ampure XP beads. Sequencing was run on an Illumina Hi-Seq (barcoded).

value: H3K27me3 (Millipore 07-449)


title: ST1334_Eed-d5_K27


title: AB1 individual genomic DNA_single-end

value: PRDM9A / PRDM9B


title: Dissociated 1


title: CJ7 wt RNA

description: prepared and sequenced with ST20; use as wt control for batch normalization.


title: ST1333_Eed-d0_K27


title: ST1328_Suz12Dd5_K27


title: Input DNA

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using DNANexus
peaks were called using QuEST with the following setting: ChIP estimate threshold (20),ChIP extension fold enrichment (3), and a ChIP-to-background fold enrichment (3)
Genome_build: hg19

source_name: HEK293 Cells

extract_protocol:
Lysates were clarified from sonicated HEK293 nuclei and histone-DNA complexes were isolated with anti-DDX21 antibody.
Libraries were prepared according to NEBNext kit.

tag: antibody 1

tag: antibody 2

value: embryonic kidney


title: AA1 individual genomic DNA

value: DNA-Seq


title: ST1312_Suz12GTd5_K27

tag: chip antibody


title: DDX21_SAT mutant iCLIP Biological replicate 1

description: iCLIPseq

data_processing:
Barcodes and adaptor sequences were trimmed and iCLIPseq reads were aligned to hg19 using bowtie as previously described (PMID: 24184352). Crosslinked nucleotides were identified as the first base of each trimmed read.
Crosslinked nucleotides were only analyzed if present at least twice in both biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : the bigWig file provided contains processed Crosslinked nucleotides from the DDX21_SAT iCLIP experiment. Data presented is an intersection of the two biological replicates

extract_protocol:
Lysates were clarified from sonicated HEK293 and DDX21_SAT-RNA complexes were isolated with anti-Flag and anti-HA antibodies.
Libraries were prepared according to the standard iCLIP protocol (PMID: 24184352). Each sequencing read conatins a 13 nt random (D's and N's) and experimental (XXXX) "DDDNNXXXXNNNN". The experimental barcodes are described in (PMID: 24184352)

treatment_protocol: HEK293 cells were transduced with a doxycycline inducible FH-DDX21_SAT mutant construct. Before assaying cells were treated with 0.25ug/mL doxycycline for 24 hours to express the FH-DDX21_SAT. Cells were then processed for iCLIP under previously described conditions (PMID: 24184352)

tag: genotype/variation

value: SAT mutant


title: DDX21_SAT mutant iCLIP Biological replicate 2

description: iCLIPseq

source_name: HEK293 Cels

tag: cell type


title: ST1331_Suz12GTd0_K27

tag: cell line


title: WT -GLU noCHX Ribo-seq

first: Pavanapuresan

last: Vaidyanathan

address: 68-341, 31 Ames Street

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. After subtractive hybridization to remove rRNA, fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR. CHX was omitted from all steps.

data_processing:
align first 21nt of reads to rRNA, with up to 3 mismatches allowed, discarding any reads that map
align first 21nt of remaining reads to entire yeast genome, allowing up to 3 mismatches
align remaining unmapped reads to splice junction sequences, and merge with genome mapping
Reads whose 5' ends map from 12nt 3' of CDS start to 14nt 5' of CDS end are assigned to that gene (first 8 codons are omitted to avoid artifacts due to the use of cylcoheximide in library preparation)
RPKMs are computed as reads per kilobase of CDS sequence per million reads mapping to all CDSs
Genome_build: Saccharomyces cerevisiae May 26 2010
Supplementary_files_format_and_content: tab-delimited tables of reads and RPKMs for all genes and samples.

growth_protocol: Yeast were grown to mid-exponential phase (OD~0.7) at 30C in YPD

extract_protocol:
frozen cell pellets were thawed in lysis buffer and lysis was performed with glass beads as described in the text. Extracts were clarified by a 20' spin at 11,500 rpm in an SS-34 rotor
Footprints: 50 OD units of extract were treated with 50U of RNAse1 and subsequently purified from the monosome region of a sucrose gradient. RNA was extracted by hot acid phenol. Total RNA: RNA was extracted from 50 OD of extract by SDS and hot acid phenol, and poly(A) RNA was purified on DynaBeads. RNA was fragmented at 95C with zinc chloride

treatment_protocol: Cells were treated with 100ug/ml cycloheximide, then harvested by centrifugation. Cell pellet was frozen in liquid nitrogen.

tag: strain


title: ST46_E14d5_K27


title: ST45_E14d0_K27


title: WT -GLU noCHX fast harvest Ribo-seq

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. After subtractive hybridization to remove rRNA, fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR. CHX was ommitted from all steps. Samples were harvested by filtration and freezing in liquid nitrogen, followed by cryomilling.


title: RAD001 (26uM)-treated NRASG12V/Mll-AF9 AML cells replicate 3

status: Public on Nov 16 2014

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

data_processing:
Illumina 1.5 software used for basecalling.
RNA-seq reads were mapped to mm9_canonical genome assembly and NCBI37/mm9 gtf using TopHat version 2.0.4.
FPKMs were calculated by Cuffdiff, minimum alignment count = 10, false discovery rate = 0.05
Genome_build: mm9_canonical
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample (DMSO, PD, RAD, GDC in triplicate)

source_name: NRASG12V/Mll-AF9 AML cells

growth_protocol: Primary NRASG12V/Mll-AF9 AML cells were plated in RPMI media with 10% FBS, 1 ng/ml GM-CSF and treated with inhibitors or vehicle for 24 hours.  At 24 hours, RNA was extracted from the cells.

extract_protocol:
Rneasy from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: Cells were plated with DMSO vehicle or GDC0941 (20 uM), PD325901 (20uM), or RAD001 (26 uM).

value: (FVB/n X C57/BL/6J) F1


title: NRASG12V On

data_processing:
Illumina 1.5 software used for basecalling.
RNA-seq reads were mapped to mm9_canonical genome assembly and NCBI37/mm9 gtf using TopHat version 2.0.4.
FPKMs were calculated by Cuffdiff, minimum alignment count = 10, false discovery rate = 0.05
Genome_build: mm9_canonical
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: NRASG12V/Mll-AF9 AML

growth_protocol: SCID/Beige mice were injected with NRASG12V/Mll-AF9 leukemia cells via tail vein and aged to develop full blown leukemia (20 days, WBC > 100,000/ul)

extract_protocol:
Qiagen Rnesay RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: Doxycycline intraperitoneal injections at time 0 and doxycycline drinking water at time 0 until sacrifice.

tag: phenotype

value: NRASG12V expression on


title: NRASG12V Off 72

value: NRASG12V expression off


title: GDC0941 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 3


title: GDC0941 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 1


title: NRASG12V Off 96


title: GDC0941 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 2


title: RAD001 (26uM)-treated NRASG12V/Mll-AF9 AML cells replicate 1


title: RAD001 (26uM)-treated NRASG12V/Mll-AF9 AML cells replicate 2


title: PD325901 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 2


title: NRASG12V Off 48


title: PD325901 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 3


title: ST1324_Suz12Dd0_K27

tag: background


title: DMSO-treated NRASG12V/Mll-AF9 AML cells replicate 2


title: DMSO-treated NRASG12V/Mll-AF9 AML cells replicate 1


title: WRR−

status: Public on Nov 15 2014

city: Guangzhou

first: Zhenhui

last: Li

address: Tianhe District Wushan road

institute: South China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gallus gallus whole genome using TopHat.
To estimate the expression of each gene, the total number of reads mapped to its unigenes were calculated and normalized with FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Gallus_gallus.Galgal4.73

organism: Gallus gallus

source_name: Spleen

extract_protocol:
Total RNA was extracted from each spleen using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: strains

value: Recessive White Rocks

tag: group

value: Uninfected Recessive White Rocks

tag: age

value: 140-day old


title: PD325901 (20uM)-treated NRASG12V/Mll-AF9 AML cells replicate 1


title: DDX21-ChIPSeq

value: DDX21, Novus Biologicals,  Cat# BP100-1781

value: DDX21, Novus Biologicals,  Cat# NBP1-83310


title: WRR+

value: J subgroup avian leukosis virus (ALV-J) infected Recessive White Rocks


title: DMSO-treated NRASG12V/Mll-AF9 AML cells replicate 3


title: WT +GLU noCHX fast harvest Ribo-seq


title: Induced beta cell d60

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

description:
D60.meth
Please note that the fastq files (for acinar, d10, d30, d60 samples) contain reads from both HiSeq 2000 and HiSeq 2500. The initial sequencing was performed on HiSeq 2000, but resequencing on HiSeq 2500. All the reads were merged into one fastq file for convenience.

data_processing:
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse  genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain methylation information for each CpG covered by mRRBS. For each CpG, the methylation is shown as the number of times the CpG was methylated over the total times the CpG was measured.

source_name: Induced beta cell

growth_protocol: Rag1-/- were obtained from Jackson Labs (http://jaxmice.jax.org/strain/002216.html).  For β- cell induction, 100ul (>1x 10^9 pfu) of purified adenovirus was directly injected into the splenic lobe of the dorsal pancreas.

extract_protocol:
Cherry+  induced beta cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience), RNA samples were extracted by Trizol
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil

treatment_protocol: Pancreata were perfused through the common bile duct.  After removing endogenous islets, the acinar fraction was digested with liberase and Elastase (Roche) into single cells.

tag: strain background

value: Pancreas

tag: tissue/cell type

value: Cherry+  induced beta cells

tag: samples collected at

value: day 60


title: Induced beta cell 7m

value: 7 months


title: Induced beta cell d10

description:
D10.meth
Please note that the fastq files (for acinar, d10, d30, d60 samples) contain reads from both HiSeq 2000 and HiSeq 2500. The initial sequencing was performed on HiSeq 2000, but resequencing on HiSeq 2500. All the reads were merged into one fastq file for convenience.

value: day 10


title: Acinar

description:
Acinar.meth
Please note that the fastq files (for acinar, d10, d30, d60 samples) contain reads from both HiSeq 2000 and HiSeq 2500. The initial sequencing was performed on HiSeq 2000, but resequencing on HiSeq 2500. All the reads were merged into one fastq file for convenience.

source_name: Acinar

value: Acinar cells


title: GT22

city: Houston

first: Han

last: Liang

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Cencer

data_processing:
The raw reads were aligned to the human genome (hg19) using SOLiD BioScope (version 1.3) whole transcriptome analysis protocol with default parameters and the alignments with properly-paired reads were saved in BAM format for further analysis.
The read counts per gene were calculated using R packages, Rsamtools (1.10.2) and GenomicFeatures (1.12.1).
The read counts were normalized to scale the raw library sizes using the weighted trimmed mean of M-values implemented in R package, edgeR (3.0.8).
If the number of overlapped read of any given gene is less than one per million total mapped read for 95% of the samples, this gene was excluded from further analysis.
A negative binomial generalized linear model was fit to each gene expression and the Wald test was performed to identify differentially expressed genes. The Benjamini-Hochberg method was used to control false discovery rate (FDR). These calculations were performed in R (2.15.1) using edgeR (3.0.8).
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is a data matrix saved in ASCII format. The rows are genes and columns are samples. Each entry is count per million, which is normalized read count per gene per sample divided by library size and multiplying by one million.

source_name: Gastric cancer, stomach

extract_protocol: RNA isolation, library preparation (paired-end, 50nt and 35nt), template bead preparation and SOLiD v 4.0 sequencing followed standard protocols provided by Life Technologies (Carlsbad, California, USA)

tag: tissue type

value: gastric cancer tumor

tag: class

value: IIB

tag: location

value: Body


title: GT21

value: IIIC


title: GT20

value: IA


title: GT19

value: GE junction


title: GT15

value: IIIB


title: GT12


title: GT11


title: GT14


title: GT16

value: IIIA


title: GT9

value: IIA

value: Distal


title: GT10

value: Proximal


title: GT8


title: GT7

value: Artrum


title: Endogenous beta cell

description: Beta.meth

source_name: Endogenous beta cell

tag: tissue

value: Pancreas

value: Endogenous beta cell


title: GT5

value: IB


title: GT4


title: GN22

source_name: Normal tissue, stomach

value: normal gastric tissue


title: GT3


title: GT2


title: GT1


title: Induced beta cell d30

description:
D30.meth
Please note that the fastq files (for acinar, d10, d30, d60 samples) contain reads from both HiSeq 2000 and HiSeq 2500. The initial sequencing was performed on HiSeq 2000, but resequencing on HiSeq 2500. All the reads were merged into one fastq file for convenience.

value: Cherry+  induced beta cells

value: day 30


title: GN20


title: WTmyc_input

city: Coventry

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
Sequence fragments with unique outer coordinates were mapped to the danRer7 genome build using Bowtie with the following parameters: -5 3 -3 30 –n 3 –y –k 2 –m 2 –best.
Peaks were called for each ChIP sample relative to their paired input sample using MACS with the following parameters: --gsize 1.3e+9 –tsize 67 -mfold 8 –pval 5e-10 for Tbx6-myc ChIP samples and –mfold 4 for the wild type Myc tag control ChIP.
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Tab delimited text files containing genomic coordinates of identified ChIP-seq peaks with associated confidence score

organism: Danio rerio

source_name: whole zebrafish embryos

growth_protocol: Embryos grown in E3 embryo medium at 28.5 degrees celcius and heat-shocket for one hour at 37 degrees celcius prior to fixation

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification from was used to obtain chromatin of appropriate fragment size. Desired protein-DNA complexes were isolated using antibody.  Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Kit (Part# FC-121-2001). Briefly, DNA was end-repaired the supplied polymerase mix. The blunt, phosphorylated ends were adenylated to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.
Library construction was performed using the Illumina TruSeq DNA Sample Prep Kit according to manufacturers protocol with the exception that Illumina adapters were diluted 1:100 prior to use.

treatment_protocol: Embryos fixed in 1.85% formaldehyde for 15 mins prior to chromatin extraction

value: Weslyan University wild type

tag: Stage

value: 10S plus 1h at 37 degrees celcius

tag: antibody


title: WTmyc_ChIP

value: anti-myc

tag: antibody vendor

value: Abcam

tag: antibody catalog


title: GT13

value: gastric cancer tumor

value: IIIC


title: GT18

value: Body


title: GT17

value: IIIA


title: Tbx6myc_input1

description: merged Input1 and Input2

tag: strain


title: GN17


title: GN16


title: Tbx6myc_ChIP1

description: merged ChIP1 and ChIP2


title: GN15


title: GT6


title: GN14


title: GN8


title: GN21


title: GN9

value: Distal


title: GN7


title: GN13


title: GN12


title: GN10

value: Proximal


title: GN11

value: GE junction


title: GN6


title: GN3


title: GN2


title: GN4


title: GN1


title: GN5


title: GN18


title: GN19