title: anti-ATF4 (D4B8)

data_processing:
Base-calling was done by Illumina RTA 1.9.35, at Phred+64 qualities.
ChIP-Seq reads were aligned to the human genome (hg19) using Bowtie2 version 2.1.0 using all default settings. Reads that could not be uniquely mapped were discarded.
Read densities were normalized to the total number of aligned reads (reads per million mapped reads - RPM) in a sample using Bedtools version 2.17.0.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig files were generated using Bedtools version 2.17.0. Peak height represents read density in reads per million.

source_name: HAP1, 2 mM histidinol for 24 hours, ATF4 ChIP

growth_protocol: HAP1 cells were re-plated the day before treatment at 1.6x10^7 cells/well in 15 cm tissue culture-treated dishes. Cells were cultured in IMDM supplemented with 10% fetal calf serum, GlutaMAX (Life Technologies), and Penicillin-Streptomycin (Life Technologies).

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed. Chromatin was sheared to an average fragment size of 200 bp using a Covaris S2 ultrasonicator. ATF4-DNA complexes were isolated with antibody and Dynabeads.
ChIP-Seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs), including optional size selection of adapter-ligated DNA and 13 cycles of PCR amplification. Libraries were sequenced on a GAIIx Genome Analyzer (Illumina).

treatment_protocol: Growth media was replaced with fresh media containing 2 mM histidinol (SIGMA, H6647) 24 hours prior to harvest.

tag: chip antibody

value: ATF4 (Cell Signaling Technology, D4B8, Cat. No. 11815, Lot No. 2)


title: anti-ATF4 (ABE387)

status: Public on Aug 28 2015

type: SRA

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

country: USA

institute: NIH/NIAID

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: 2 mM histidinol, 24 hours

value: ATF4 (Millipore, ABE387)


title: AO87_5

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Read counts were derived from HTSeq.scripts.count module in HTSeq-0.6.0 with default parameters.
Peak calling were performed by ChIPseeqer-2.1 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: reads count and peaks files are in .txt format

molecule: total RNA

organism: Mus musculus

growth_protocol: Isolated primary cells were harvested directly from mouse.  No growth culture.

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K4me1/2 antibody (abcam 32356) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.  RNA was purified using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step. DNA was purified using PCR purification columns (QIAGEN).
RNA-seq libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v2. ChIP-seq libraries were prepared using 10ng of DNA and Illumina’s TruSeq ChIP sample prep. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT dsDNA HS Assay (Life Technologies).

treatment_protocol: B220+ cells were purified from mouse lymphoma tumors by immunomagnetic enrichment with CD45R(B220) microbeads (Miltenyi Biotech)

tag: cell type

value: B cell

tag: transduction

value: empty vector

tag: stain

value: tumor


title: B. juncea control (BC) (UNPAIRED)

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq raw reads were processed by NGS-QC toolkit and low-quality as well as adapter-contaminated sequences were discarded. High quality (paired and unpaired) reads were assembled de-novo using SOAPde-novo assembler  independently at eight different K-mers (21, 27, 33, 39, 45, 51, 57, 63). The eight assemblies were subsequently clustered by using CD-HIT-EST [68]. The clustering parameters used were ≥80% query coverage and ≥80% identity. To further clean the data transcripts present in only one of the K-mer assemblies were removed. This was followed by removal of transcripts with less than 1 FPKM in all the three conditions (BC, BDS and BHS). Finally all the transcripts less than 200 bp were removed and the remaining transcripts were functionally annotated using FASTAnnotater tool (http://fastannotator.cgu.edu.tw/) with an e-value cut-off of 0.00001 by taking non-redundant protein database of EMBL (European Molecular Biology Laboratory) as a reference. Gene ontology analysis of transcripts was derived through Uniprot hit accessions and prediction of biochemical pathways was performed by KEGG identifiers (http://www.genome.jp/kegg/).
Supplementary_files_format_and_content: cufdiff_isoform_exp.diff: List of of deferentially expressed transcripts
Supplementary_files_format_and_content: matrix_isoforms.fpkm_tracking: Normalized FPKM values of each sample (Q1=BC, Q2=BDS, Q3=BHTS)

molecule: polyA RNA

organism: Brassica juncea

source_name: 7-day old whole seedling

growth_protocol: Seeds were surface sterilized with 2% sodium hypochlorite solution for 10 minutes (min) on a shaker and then washed five times with double distilled water for three min each. Sterile seeds were hydroponically grown on a muslin cloth wrapped around a small container in a growth chamber at 24°C±1 with 16 hours (h) day/8 h night photoperiod.

extract_protocol:
Total RNA was isolated using GITC-based method from abiotic stress treated and untreated whole seedlings, independently for each time point. Extracted RNA was quantified using spectrophotometer and an aliquot of heat denatured RNA was electrophoresed on denaturing agarose gel to check its integrity. RNA extracted from two different time points were pooled in equimolar amounts and three RNA-Seq libraries- BC (control seedlings), BDS (drought stressed seedlings) and BHS (high temperature stressed) were prepared utilizing NEBNext RNA-Seq library preparation Master Mix Set for Illumina procured from NEB, USA.
Poly A+ RNA was isolated from 10 µg of total RNA using Sera-Mag beads (GE Healthcare, UK) and fragmented chemically at high temperature. Fragmented RNA was qualitatively and quantitatively checked on Bioanalyzer (Agilent, USA). 250 ng of fragmented RNA was used for first strand reverse transcription using random primers followed by second strand synthesis. The ends of double stranded cDNA were repaired and mono-adenylated. Paired end adapters were ligated using Rapid T4 DNA ligase and then size fractionated. Approximately, 350 bp size region was eluted and PCR amplified for 12 cycles. The quality and quantity of prepared libraries was evaluated utilizing Bioanalyzer (Agilent, USA) Ultra-deep parallel sequencing was performed using Illumina Genome Analyzer IIx at University of Delhi South Campus, Delhi, India according to manufacturer’s instructions.

treatment_protocol: Seedlings were grown for seven days and then subjected to various abiotic stresses. Drought stress was imposed for 3 h and 12 h by replacing water with high osmolality solution (300 mM mannitol). For imposing high temperature stress, seedlings were placed in a BOD incubator (Scientific systems, India) at 42°C for 30 min and 4 h. Entire seedlings (including the roots) were harvested after specified time intervals, snap frozen in liquid nitrogen and stored at -80°C.  Untreated seedlings were taken as control.

tag: strain

value: var varuna

tag: tissue

value: whole seedling

tag: age


title: OCI-Ly7 rep2 input

data_processing:
FASTQ files were generated and aligned by using the Illumina CASAVA pipeline.
Peak calling was performed using ChIPseeqer pipeline default settings (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277)
Genome_build: hg18
Supplementary_files_format_and_content: txt files

source_name: lymphoma cell line

growth_protocol: cultured cells, IMDM+10%FBS

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K4me2 antibody (abcam 32356) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
Illimunia Truseq ChIPseq protocol

treatment_protocol: 1% formaldehyde for 10 min

value: lymphoma B cells

tag: antibody


title: OCI-Ly7 rep2

value: H3K4me2 antibody (abcam 32356)


title: OCI-Ly7 rep1 input


title: Input

source_name: HAP1, 2 mM histidinol for 24 hours, input


title: OCI-Ly7 rep1


title: B. juncea control (BC) (PAIRED-END)


title: Col-0 16h

city: Exeter

first: ZhengRong

last: Yang

address: Stocker Road

country: United Kingdom

institute: Exeter University

data_processing:
Base Calling carried out using CASAVA v1.8.2
Fastq-Mcf was then used to remove adapter sequences and trim reads of a phred quality score < 20 with the following parameters: -q 20 -l 35 -k 0  -p 15  --max-ns 0 -m 3. ERCC reads were removed using Bowtie v1.0.0 with the following parameters: -S -X 600
Reads were aligned to the reference genomes for Arabidopsis thaliana using TopHat v2.0.8b with the following parameters: -r 200 --mate-std-dev 375 --library-type fr-unstranded.
Reads were quantified at each predicted gene location using htseq-count v0.6.0 with the following parameters: -m union -s yes
These single replicate data were analysed by gFOLD (Feng et al., 2012) using a cutoff of log2 1.6
Supplementary_files_format_and_content: Tab delimited matrix containing raw counts, gene length and the normalised count for each gene in each sample.

organism: Arabidopsis thaliana

source_name: Infected Arabidopsis thaliana leaf tissue

growth_protocol: Arabidopsis Sowing And Plant Growth Conditions: Arabidopsis thaliana seed, Col-0 or jaz5/10, were sown onto ~7cm square pots of sieved compost mix (Levingtons F2 compost+sand (LEV206): vermiculite (medium grade) mixed in a 6:1 ratio) and stratified for 3 days at 4°C in darkness. Seeds were germinated in a controlled environment growth chamber with a 10 h photoperiod (lights on 8am, off 6pm) of 120 µmol m-2 s-  at 23oC (day), 20oC (night) and relative humidity of 65%. Plants were pricked into individual 7cm pots in a 24 cell and plants were grown for 4.5 weeks. Cells were continuously moved in the controlled environment chamber to reduce positional effects.  Pseudomonas growth: Pseudomonas syringae pv. tomato strain DC3000 carrying the empty broad host range vector pVSP61 (Innes et al., 1993) was grown on solidified Kings B media (King et al. 1954) containing rifampicin 50 μg ml-1 and kanamycin 25 μg ml-1. For inoculation, overnight cultures were grown with shaking (200 rpm) at 28oC. Cells were harvested (2000g X 8 min), washed and resuspended in 10 mM MgCl2. Cell density was adjusted to OD600 0.15 ( ~0.75 x 108 colony forming units (cfu) ml-1).

extract_protocol:
Plant RNA extraction: RNA was extracted according to de Torres et al. (2006). The frozen single leaf was ground to a fine powder in a liquid nitrogen pre-cooled mortar. 600µl of Z6 buffer (8M guanidinium hydrochloride, 20mM MES, 20mM EDTA pH7.0) was added and the powder quickly mixed. When thawed, the sample was passed to a 1.5ml microfuge tube and the mortar washed with 100µl of Z6 buffer. The combined sample was extracted with 1 vol. of phenol/chloroform then centrifuged at 4oC for 5 min at maximum speed. The aqueous phase was removed to a new microfuge tube and 1/20 vol. of acetic acid (1M) and 0.7 vol. 100% ethanol added nucleic acids collected after 30min on ice. The resultant RNA pellet was washed in 70% ethanol and resuspended in 100µl of sterile ddH2O. Samples were cleaned up using a Qiagen RNeasy Plant mini kit according to the manufacturers instructions and samples eluted in 30μl in RNAse free water.
2 µl of diluted ERCC RNA control spike-in mix 1 or control spike-in mix 2 (Life Technologies) was added to 1 µg of sample RNA and the volume adjusted to 50 µl.   Sequencing Libraries were prepared usingthe standard  Illumina TruSeq RNA library preparation protocol. on a Sciclone NGS platform. Samples were processed in 96 well hard shell PCR plates (Biorad HSP-9631). Washes were done in 150 µl bead washing solution instead of the 200 µl used in the manual process. Incubations at 65°C and 16°C for mRNA denaturation, and second-strand synthesis were performed on the Sciclone deck. However, the 80°C and 94°C incubations for mRNA elution and fragmentation, and first-strand cDNA synthesis reactions were performed on a thermocycler with heated lid to avoid excess evaporation. Purification and size selection was by Ampure XP bead clean up rather than gel based size selection. Library quality and quantitiy was determined by LabChipGX high sensitivity assay, after diluting the libraries 2µl in 20 µl.

treatment_protocol: Leaf infiltration: Plants were randomised and for each genotype and time-point 3 fully expanded leaves from four individual plants were either harvested (non-induced) or inoculated with DC3000. For infiltration, a small nick was made on either side of central vascular vein on the abaxial surface and bacterial challenge (OD600 of 0.15) was performed with a 1ml needleless syringe. All inoculations were completed by 11 am and inoculated plants were left under a light bench in the laboratory (22oC). Samples were taken at 6, 8, 12 and 16 hpi. Leaves were harvested by cutting at the petiole/leaf blade junction and were immediately snap-frozen in foil untill used for RNA preparation.

tag: ecotype

tag: genotype/variation

value: wild type

tag: agent

value: Pseudomonas syringae pv. tomato DC3000


title: OCI-Ly1 rep2 input


title: OCI-Ly1 rep1 input


title: OCI-Ly1 rep1


title: OCI-Ly1 rep2


title: anti-ATF4 (sc-200)

value: ATF4 (Santa Cruz Biotechnology sc-200, Lot No. C0513)


title: Viv-2

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

data_processing:
Paired-end sequencing reads aligned to human reference genome (GRCh37/hg19) with Tophat v1.2, using default parameters but allowing 10 alignments.
Cufflinks package used to assemble transcripts and measure relative abundance in FPKM.
Assembled transcripts were compared with RefSeq from UCSC genome browser.
Differential expression was examined using the Cuffcompare and Cuffdiff in the Cufflinks package.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. These are the differential expression files generated by cuffdiff.

source_name: Viv

growth_protocol: Mice, weaned at 3 weeks of age were put on Viv, HFD or SO-HFD for 35 weeks, after which they were sacrificed and their livers were excied and store in RNALater

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen). Sequencing libraries were constructed using the iIllumina TruSeq RNA Sample Prep Kit v2.
RNA libraries were prepared following the manufactor's standard protocol from Illumina.

tag: tissue type

value: mouse liver

value: 38 weeks old mouse

value: Vivarium chow fed mice

tag: length of treatment

value: 35 weeks


title: D4-3

source_name: HFD

value: HFD fed mice (40kcal% total fat(2% Linoleic Acid from soybean oil))


title: D4-1


title: D3-1

source_name: SO-HFD

value: SO-HFD fed mice (40kcal% total fat(10% Linoleic Acid from soybean oil))


title: D3-2


title: B. juncea high temperature stressed (BHS) (PAIRED-END)


title: male adult

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

data_processing:
Sequenced reads were aligned onto the corresponding reference (unpublished, assembly will published under PRJNA270384) using TopHat v1.0.12 with default parameters except -r 20 --mate-std-dev 10 -I 10000 --segment-mismatches 3 --segment-length 24 --solexa1.3-quals；
bam files are dealed to wig files by /tophat-1.4.1.Linux_x86_64/wiggles
Supplementary file display the rpkm files. rpkm are calculated based on bam files from tophit aliger using custom programes. identifiers in the RPKM files are the gene identifier in the corresponding reference.

organism: Papilio xuthus

source_name: whole body

extract_protocol:
total RNA is extracted by TRIzol Reagent
For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: developmental stage

value: adult

tag: Sex

value: male


title: Viv-3


title: female adult

value: female


title: male pupa

value: pupa


title: Viv-1


title: Aspen-Ston1-15-3

city: Quebec City

first: Adam

last: Foster

state: Quebec

address: 8678 rue de la Comtoise

department: CFS

country: Canada

institute: Natural Resources Canada

data_processing:
Illumina Casava1.8 software used for basecalling.
Quality checking: base call quality , consequtive homopolymer, Kmer frequency, base call frequency, overrepresented sequence and basic statisitics was performed in RobiNA - transcriptomics data preprocessor version 1.2.1
Adapter trimining, sliding window trimmer, read length filter to remove reads shorter than 20 bp for all samples. RobiNA - transcriptomics data preprocessor version 1.2.1
Read mapping was performed using Bowtie v1 to reference genome allowing 2 mismatches in a 28 bp seed legnth in RobiNA - transcriptomics data preprocessor version 1.2.1.
Gene expression analysis step - edgeR with BH corrected p-value cutoff 0.05, auto dispersion and min Log-fold change of 1 within RobiNA - transcriptomics data preprocessor version 1.2.1
Unassembled reads were pooled for samples of the same species and de novo assembled using CLC Genomics Workbench version 7 with default settings. Contigs less than 500 bp in legnth were discarded.
Read mapping was performed using Bowtie v1 to reference genome allowing 2 mismatches in a 28 bp seed legnth in RobiNA - transcriptomics data preprocessor version 1.2.1.
Gene expression analysis step - edgeR with BH corrected p-value cutoff 0.05, auto dispersion and min Log-fold change of 1 for samples mapped to lists of contigs
Genome_build: P. trichocarpa V3.0 210
Supplementary_files_format_and_content: Read count files were generated using Bowtie v1 in RobiNA 1.2.1 mapping to either the P. trichocarpa V3 genome of a list of de novo assembled contigs; Digital gene expression analysis files were prouced by edgeR in RobiNA 1.2.1; de novo asssembled contigs (fasta) for each poplar species were produced using CLC Genomics Workbench  version 7 de novo assembler with reads that did not map to the P. trichocarpa v3 genome.

organism: Populus tremuloides

source_name: Fully expanded leaf

growth_protocol: Trees were propgated in the greenhouse in 3 L pots with supplemented light at 16 h daylengths for 5 months. The five month old trees were transferred to Conviron growth chambers set at 22°C and 16h light with a photosynthetic flux of 90-100 µmol m-2 s-1 and incubated for 4 weeks for a final age of 6 months.

extract_protocol:
RNA was also isolated from 100 mg of liquid nitrogen chilled homogenized leaf tissue using the RNeasy Plant Mini Kit (Qiagen) with in column RNase-Free DNase Set (Qiagen) .
RNA was extracted from each tree sampled and assayed for quality with a 2100 Bioanalyzer and Nanodrop 1000 spectophotometer. All RNA samples had a ratio of the absorbance at 260 and 280nm (A260/280) above 2.0 and were confirmed to be free of genomic DNA. Libraries for each RNA sample were prepared by Brian Boyle at ‘L'Institut de biologie intégrative et des systèmes’ (IBIS) at Université Laval, Quebec City, Quebec, Canada. Each cDNA library was barcoded and six samples were pooled together. TruSeq RNA Sample Preparation Kit v2 was used to prepare DNA for Illumina sequencing

treatment_protocol: One monosporal Sphaerulina isolate from each species was utilized. Isolates were prepared from spore suspensions stored in 25% glycerol at -80ºC.  To obtain conidia for foliar application, storage cultures were seeded to potato dextrose agar (PDA; Difco 213400) plates and grown at 22ºC in the dark for 8 days. Conidia were harvested by flooding plates (20 per isolate) with sterile distilled water, then filtered through 100-µl nylon mesh sterile Falcon® cell strainers (Fisher Scientific, Waltham, MA, USA), centrifuged at 4000 x g for 10 minutes, washed with 40 ml of sterile distilled water and resuspended in sterile distilled water to 1x105 per mL prior to application. Using an airbrush, each tree was sprayed with 10 mL of atomized spore suspension. Three trees from each species were sprayed with water to serve as controls.

tag: inoculation

value: Ston1 conidia

tag: sample time

value: 15 days after inoculation


title: Aspen-Ston1-15-2


title: 5st-instar larva

value: 5st-instar larva


title: female pupa


title: OCI-LY7 input

description: ChIP-seq

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Peak calling were performed by ChIPseeqer-2.1 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak file is in .txt format

source_name: Lymphoma cell line

growth_protocol: GCB-DLBCL cell lines were grown in IMDM with 15%FBS.

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with KMT2D antibody (in-house generated human KMT2D antibody specific for the N-terminus previously described in Hu D. et. al Mol Cell Biol 2013 PMID:24081332) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
KAPA HTP ChIP-seq sample prep kit (KAPA Bioystems)

tag: cell line

value: GCB-DLBCL

tag: genotype

value: wt

value: tumor


title: OCI-LY7

description: ChIP-seq

tag: cell type

value: KMT2D antibody


title: 4st-instar larva

value: 4st-instar larva


title: Aspen-Ston1-15-1


title: D4-2

value: mouse liver

value: 38 weeks old mouse

tag: treatment


title: 3st-instar larva

value: 3st-instar larva


title: D3-3

value: 35 weeks


title: 1st-instar larva

value: 1st-instar larva


title: Aspen-Ston1-4-3

value: 4 days after inoculation


title: ChIP-2-130516

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: anti-H3K4me3 ChIP-seq

data_processing:
ChIP-seq Data Analysis: The ChIP-seq reads were aligned to Arabidopsis thaliana genome TAIR10 by Bowtie v2.1.0 (Langmead and Salzberg, 2012) using default parameters with local alignment model. Duplicated reads and low-mapping-quality reads were identified and removed with SAMtools (Li et al., 2009). Enriched peaks were identified by MACS (Zhang et al., 2008) with default parameters. Density maps of reads for visualization were caculated with SAMtools and programs from UCSC genome, based on read counts of the 200 bp extension of sequencing reads towards the 3’ direction (as described previously described (Ernst et al., 2011)) after total reads normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: 12DAG seedlings

growth_protocol: All Arabidopsis plants were grown at 23°C under long day condition (LD, 16 hours light, 8 hours dark) on 1/2 MS plates. 12DAG seedlings were used for ChIP assays.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) assays were performed using 1 g 12-day-old seedlings as previously described with minor modifications (Lu F. et al., 2010, Cell research 20(3):387-390). For anti-HA ChIP, chromatin was fragmented by Micrococcal nuclease (MNase, NEB M0247S) in the MNase digestion buffer (50 mM Tris pH 8.0, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2) instead of sonication before nuclei lysis. Antibodies used in ChIP were anti-H3K4me3 (Millipore 07-473) and anti-HA (Sigma H6908).
The ChIP-Seq libraries were constructed using NEBNext® DNA Library Prep Master Mix Set for Illumina® (NEB, E6040S). ChIPed DNA was ligated with Illumina single-end genome sequencing adaptors, size fractionated to obtain 300-bp fragments

treatment_protocol: No treatment

value: seedling

tag: chip antibody

value: anti-H3K4me3 (Millipore, catalog# 07-473, lot# 2289139)


title: ChIP-3-130516

description: anti-H3K4me3 ChIP-seq

tag: tissue


title: ChIP-6-130516

description: anti-H3K4me3 ChIP-seq


title: ChIP-1-130516

description: anti-H3K4me3 ChIP-seq

value: Col


title: Aspen-Ston1-1-2

value: Ston1 conidia

value: 1 day after inoculation


title: Aspen-Ston1-4-2


title: 2st-instar larva

value: 2st-instar larva


title: Aspen-Ston1-4-1


title: ZC_3_140207

description: anti-HA  ChIP-seq

value: anti-HA (Sigma, catalog# H6908, lot# 013M4771)


title: egg

value: egg


title: ZC_4_140207

description: anti-HA  ChIP-seq


title: ZC_3_131216

description: anti-HA  ChIP-seq


title: ZC_6_140207

description: anti-HA  ChIP-seq


title: ZC_2_131216

description: anti-HA  ChIP-seq


title: Aspen-mock-3

value: mock-water

value: 0 days after inoculation


title: Aspen-mock-2


title: Aspen-mock-1


title: HESC Protected Control VAT1L MiSeq

status: Public on Aug 27 2015

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

data_processing:
Data processing of reads: Reads mapping to the bait, or to the Illumina adapters was masked using a customized script and BLAT. The masked libraries were subsequently mapped to a Bgl II-“digested” version of the GRCh37-based reference genome using BWA v.0.7.9a. The number of reads with MapQ greater than 10 was recorded for each BglII fragment in each library using custom Python scripts. Additional checks were performed to ensure that the fragments do not overlap blacklisted regions (Duke Excluded and DAC Blacklisted Regions).
Reference genome used in mapping: GRCh37.71 was downloaded from Ensembl. Each chromosome (1...22, X, Y, MT) was digested with BglII. Each BglII fragment is stored in the resulting fasta reference as a separate entry as chromo_bglII-start_bglII-end (i.e.: chr11_51323245_51328383). Additionally, both K12 Ecoli (NC_000913.2) and PhiX (NC_001422.1) were added to the reference to capture the PhiX sequencing spike-in control and contamination traces from Ecoli DNA, which is used in different experiments.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files for each Sample include interactors and bridges, and their corresponding read count.

source_name: HESC Protected Control VAT1L MiSeq

growth_protocol: The HESC line HS181 (Hovatta et al., 2003) was cultured as described previously (Imreh et al., 2004). In brief: cells were kept at 37°C, 6.8% CO2, high humidity, in HESC medium (=80% KO DMEM + 20% SR + 2 mM L-glutamine  + 1% non-essential amino acids + 0.1 mM β-mercapoethanol + 4 ng/ml bFGF). For feeder cells, human foreskin fibroblasts (hFS) (CRL-2429) were cultured in Iscove's Medium + 10% FCS, irradiated with 35 Gy and seeded at a concentration of 2.1 × 104 cells/cm2. The HS181 cells were dissociated using Dispase enzyme (10 mg/ml) and mild mechanical splitting. Embryoid bodies (EBs) were produced using Dispase and kept in HESC medium without bFGF for 12 days in Petri dishes.

extract_protocol:
Standard Sollexa preparation.
Library preparation for MiSeq sequencing: Nextera XT DNA sample preparation kit (FC-131-10244C) and Nextera XT index kit (FC-131-1001) were used to generate the libraries of 4C samples prepared from HESCs crosslinked in the presence or absence of Olaparib. Paired end sequencing with long read length (150 bp × 2) was performed on Illumina Miseq according to the instructions using MiSeq reagent kit v2 (MS-102-2001, Illumina).

treatment_protocol: BglII-digested chromatin from formaldehyde-fixed HESCs and EBs was used for preparation of 4C samples in the presence of protease inhibitors, as has been described earlier. The removal of PAR was performed by incubating the crosslinked chromatin with 25ng/ml (final concentration) recombinant PARG (Trevigen) in the presence of 2 mM DTT and 4mM vanadyl-ribonucleoside (final concentration; New England Biolabs) in Bgl II restriction buffer at 25°C for one day and two weeks at 37°C. To assess influence by any contaminating RNAse during this time period, boiled RNAse A (0.8 mg/ml) was added to parallel samples for the same period of time. The amplification of the interacting samples from the H19 ICR bait, which is enriched in repeats, necessitated the use of multiple, nested primers to reduce the presence of bait sequences as follows: F1 core: cgatgt tag tcgcat gag tgtcta t; R1 core: cat ggg tat ttctggaggctt ct; (94°C -3min, 4 x (98°C -20 sec, 70°C -20min, 68°C -20min); 25 x (98°C -20sec, 70°C -1.5 min, 68°C -20 min)); F2: gat tag gctcccagccatgcatg;R2: gggtcatctgggaat agg acactc (94°C -3 min, 27 x (98°C -20 sec, 58°C -1.5 min, 68°C -20 min)); F3: gataagagcgaaactctgtc; R3:cactcatgggagccgcac (94°C -3 min, 26 x (98°C -20 sec, 56°C -1 min, 68°C -20 min)); F4: cagaaa att atgacaatgaaag; R3: cactcatgggagccgcac (94°C -3 min, 23 x (98°C -20 sec, 59.5°C -30 sec, 68°C -20 min)).


title: HEB Protected Control MiSeq

source_name: HEB Protected Control MiSeq

value: HS181-derived embryoid bodies


title: HEB Protected PARG MiSeq

source_name: HEB Protected PARG MiSeq


title: HESC Protected Olaparib 10m MiSeq

source_name: HESC Protected Olaparib 10m MiSeq


title: HESC Protected Olaparib 24h MiSeq

source_name: HESC Protected Olaparib 24h MiSeq


title: Aspen-Ston1-1-3


title: Aspen-Ston1-1-1


title: cdk8∆ pRS315 vector_03

city: Vienna

first: Alwin

last: Koehler

address: Dr.-Bohr-Gasse 3/9

country: Austria

institute: Max F. Perutz Laboratories

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Saccharomyces cerevisiae reference genome (Ensembl R64-1-1 release) using TopHat version 2.0.9
After alignment reads were associated with known genes based on annotations derived from Ensembl and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.0.1, Biocunductor version 2.12)
For statistical testing data were log transformed using voom approach in the limma package.
For visualization and result files the TMM normalised counts are represented as RPKM values.
Ensembl R64-1-1 release
Supplementary_files_format_and_content: tab delimited text file including RPKM values for each sample

organism: Saccharomyces cerevisiae

source_name: Sample 12

growth_protocol: An overnight culture of yeast grown in SDC-Leu was diluted to OD 0.1-0.2 the next day. 8 ml of  SDC-Leu culture grown to OD of 0.6-0.8 was harvested by centrifugation at 4000 rpm. Cells were washed once with 2 mL water and snap frozen in liquid nitrogen.

extract_protocol:
RNA was extracted by hot Phenol method. DNA was digested, RNA purified by a second Phenol Chlorofom extraction.
rRNA was removed with Ribozero Kit (Epicentre) following manufacturers instructions. Libraray was generated following the instructions of the NEB RNA ultra Kit for library preparation

treatment_protocol: Cells were untreated and grown under standard conditions.

tag: transformation

value: pRS315 vector


title: cdk8∆ pRS315 vector_02

source_name: Sample 11


title: cdk8∆ pRS315 vector_01

source_name: Sample 10


title: sac3∆ pRS315 Sac3 R288D_03

source_name: Sample 9

value: pRS315 Sac3 R288D


title: HESC Protected PARG MiSeq

source_name: HESC Protected PARG MiSeq


title: sac3∆ pRS315 vector_02

source_name: Sample 5


title: ZC_1_131216

description: anti-HA  ChIP-seq


title: sac3∆ pRS315 Sac3 R288D_01

source_name: Sample 7


title: sac3∆ pRS315 13MYC-SAC3 WT_03

source_name: Sample 3

value: pRS315 13MYC-SAC3


title: untreated KhES-1, replicate1

city: Chuou-ku

first: Masatoshi

last: Ohgushi

state: Kobe

address: 2-2-3 Minatojima-minamimachi,

country: Japan

institute: RIKEN Center for Developmental Biology

data_processing:
Basecalls were performed using illumina RTA  software (version 1.17.21.3) and reads were de-multiplexed using bcl2fastq ( version 1.8.3).
Quality check of the reads was performes using FastQC(version 0.10.1). Ascertaining the high quality of sequencing, reads were mappedto hg19 human genome assembly using Tophat (version 2.0.8b) with default parameter settings.
Number of reads originating from genes were quantified by cuffdiff program in Cufflinks package (version 2.1.1). These count values were subsequently used to test for differential expression using edgeR(version 3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized expression values for each sample

source_name: dox-untreated tet-shLbc hESCs

growth_protocol: hESC colonies were cultured on matrigel-coated 6-well plate using MEF-conditioned standard 10%KSR medium and maintained at 37C and 2% CO2.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) using the company-provided protocol. On the culture plate, cells were lysed in 700uL buffer RLT and spun through QIAshredder (Qiagen) prior to RNA extraction.
Libraries were prepared using 1μg of total RNA, according to the protocol of TruSeq RNA Sample Prep Kit v2

treatment_protocol: Dox solution was added to the culture at a final concentration of 1 μg/ml, and cultured for 72 hr with daily medium changes.

value: untreated

tag: strain

value: tet-shLbc:Bcl-XL KhES-1


title: AKAP-Lbc-depleted KhES-1, replicate2

source_name: dox-treated tet-shLbc hESCs

value: dox-treated


title: untreated KhES-1, replicate3


title: AKAP-Lbc-depleted KhES-1, replicate1


title: sac3∆ pRS315 13MYC-SAC3 WT_01

source_name: Sample 1


title: sac3∆ pRS315 vector_01

source_name: Sample 4


title: untreated KhES-1, replicate2


title: sac3∆ pRS315 13MYC-SAC3 WT_02

source_name: Sample 2


title: HESC Protected Control MiSeq

source_name: HESC Protected Control

tag: cell line (background)

value: human embryonic stem cells (HESCs)


title: AKAP-Lbc-depleted KhES-1, replicate3


title: Prespawning ground, female 2, OE P3

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
processed data files:
DiffExpr_Location_7-12_vs_1-6_Salmo_salar_3_mismatches.xlsx;
DiffExpr_Location_7-12_vs_1-6_Oncorhynchus_keta_de_novo.xlsx

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
In strategy 1, reads were aligned to 48,223 Salmo salar cDNA sequences (downloaded from NCBI) allowing 3 mismatches per 50 nt read (3 mismatches ~ 94% identity) using TopHat (version 2.0.5) (Trapnell et al., 2009)
In strategy 2, reads were aligned to a de novo assembled Chum salmon olfactory rosette contig reference file using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel

DiffExpr_Location_7-12_vs_1-6_Oncorhynchus_keta_de_novo.xlsx;
The reference FASTA file (Oncorhynchus_keta_cDNA.fa) was made as follows: A total of ~250 million paired-end 2 x 50 nt reads (~25 Gb data) from all 12 RNAseq libraries were combined and used in a single de novo assembly to generate cDNA sequences corresponding to mRNAs that are expressed in the O.keta olfactory placodes. This resulted in 98,542 cDNA contigs ranging in size from 200 - 17,327 nt.

DiffExpr_Location_7-12_vs_1-6_Salmo_salar_3_mismatches.xlsx:
The reference FASTA file consisted of 48,223 Salmo salar cDNA sequences downloaded from NCBI, and thus the identifiers in the *mismatches.xlsx (GI numbers) are searchable in http://www.ncbi.nlm.nih.gov/nuccore
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Function description; sample 7; sample 8; sample 9; sample 10; sample 11; sample 12; sample 1; sample 2; sample 3; sample 4; sample 5; sample 6; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Oncorhynchus keta

extract_protocol:
Olfactory rosettes were obtained from each individual, flash frozen in liquid nitrogen and stored at -80 °C till RNA extraction. Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, USA) and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each individual was prepared from 2 microgram total RNA, using the Illumina TruSeq™ RNA Sample Prep Kit v2  following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin of specimen

value: caught on Oct. 5, 2011 at a 75 km upstream site in Chitose River (pre-spawning site at 43°83’ N, 141°66’ E)

tag: gender

value: female

value: olfactory rosette


title: Prespawning ground, male 2, OE P9

value: male


title: sac3∆ pRS315 Sac3 R288D_02

source_name: Sample 8


title: Prespawning ground, male 3, OE P10


title: Prespawning ground, female 1, OE P2


title: Prespawning ground, male 1, OE P7


title: Prespawning ground, female 3, OE P4


title: sac3∆ pRS315 vector_03

source_name: Sample 6


title: Ishikari Bay, male 3, OE I7

source_name: Ishikari Bay_male_olfactory rosette

value: caught on Oct. 2, 2011 at the coastal zone of the Pacific Ocean in the Ishikari Bay (43°23’ N, 141°13’ E)


title: Ishikari Bay, male 2, OE I5


title: Ishikari Bay, male 1, OE I2


title: Ishikari Bay, female 2, OE I9

source_name: Ishikari Bay_female_olfactory rosette


title: Ishikari Bay, female 3, OE I10


title: Mouse5_IL-10SingPos

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

description: SMARTer amplification

data_processing:
sequenced using the Illumina HiSeq platform
alignment to the mm9 genome was performed by STAR and BWA
raw gene alignment counts was performed using featureCounts program
normalization of raw count values performed by trimmed mean of M (TMM) analysis
differences in transcript expression between populations was assessed using the edgeR package in R
Genome_build: mm9
Supplementary_files_format_and_content: counts.txt contains the raw counts; expr.txt contains the normalized expression values; diffs.txt contains the differential expression stats.

source_name: IL-10+IL-18R– FACS-sorted Treg Cells

extract_protocol:
Cells were FACS-sorted directly into TRIzol LS (Life Technologies) reagent and 2ng of total extracted RNA was amplified using SMARTer Amplification (CloneTech)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genetic background

value: lung

value: Treg

tag: infection

tag: day post-infection


title: Mouse5_IL18RSingPos

description: SMARTer amplification

source_name: IL-10–IL-18R+ FACS-sorted Treg Cells


title: Mouse5_DoubleNeg

description: SMARTer amplification

source_name: IL-10–IL-18R– FACS-sorted Treg Cells


title: Mouse4_IL18RSingPos

description: SMARTer amplification


title: Mouse3_IL-10SingPos

description: SMARTer amplification


title: Mouse4_IL-10SingPos

description: SMARTer amplification


title: Mouse3_IL18RSingPos

description: SMARTer amplification


title: Mouse3_DoubleNeg

description: SMARTer amplification


title: Mouse2_IL-10SingPos

description: SMARTer amplification


title: Mouse2_DoubleNeg

description: SMARTer amplification


title: HEB RNAse

data_processing:
Data processing of reads: Reads mapping to the bait or to the Illumina adapters were masked using a customized script and BLAT. The masked libraries were subsequently mapped to a Bgl II-“digested” version of the GRCh37-based reference genome using BWA v.0.5.9. The number of reads with MAPQ greater than 10 was recorded for each BglII fragment in each library using custom Python scripts. Additional checks were performed to ensure that the fragments do not overlap blacklisted regions (Duke Excluded and DAC Blacklisted Regions). To properly distinguish between true signal and noise the approach described in (Williams et al., 2014) was adopted. Specifically, significance cut-offs per chromosome were calculated from the top fifth percentile of 10,000 calculations of a false discovery rate lower than 0.01, and the non-reproducible interactors were filtered accordingly.
Reference genome used in mapping: GRCh37.71 was downloaded from Ensembl. Each chromosome (1...22, X, Y, MT) was digested with BglII. Each BglII fragment is stored in the resulting fasta reference as a separate entry as chromo_bglII-start_bglII-end (i.e.: chr11_51323245_51328383). Additionally, both K12 Ecoli (NC_000913.2) and PhiX (NC_001422.1) were added to the reference to capture the PhiX sequencing spike-in control and contamination traces from Ecoli DNA, which is used in different experiments.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files for each Sample include interactors and bridges, and their corresponding read count.

source_name: HEB RNAse


title: HESC RNAse

source_name: HESC RNAse


title: Mouse1_IL18RSingPos

description: SMARTer amplification


title: HEB Protected 2

source_name: HEB Protected


title: Ishikari Bay, female 1, OE I4

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
In strategy 1, reads were aligned to 48,223 Salmo salar cDNA sequences (downloaded from NCBI) allowing 3 mismatches per 50 nt read (3 mismatches ~ 94% identity) using TopHat (version 2.0.5) (Trapnell et al., 2009)
In strategy 2, reads were aligned to a de novo assembled Chum salmon olfactory rosette contig reference file using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel

DiffExpr_Location_7-12_vs_1-6_Oncorhynchus_keta_de_novo.xlsx;
The reference FASTA file (Oncorhynchus_keta_cDNA.fa) was made as follows: A total of ~250 million paired-end 2 x 50 nt reads (~25 Gb data) from all 12 RNAseq libraries were combined and used in a single de novo assembly to generate cDNA sequences corresponding to mRNAs that are expressed in the O.keta olfactory placodes. This resulted in 98,542 cDNA contigs ranging in size from 200 - 17,327 nt.

DiffExpr_Location_7-12_vs_1-6_Salmo_salar_3_mismatches.xlsx:
The reference FASTA file consisted of 48,223 Salmo salar cDNA sequences downloaded from NCBI, and thus the identifiers in the *mismatches.xlsx (GI numbers) are searchable in http://www.ncbi.nlm.nih.gov/nuccore

Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Function description; sample 7; sample 8; sample 9; sample 10; sample 11; sample 12; sample 1; sample 2; sample 3; sample 4; sample 5; sample 6; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj


title: UT_SCC59A

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: Primary cSCC cells

data_processing:
RNA sequencing reads obtained from the instrument were aligned against the human reference genome (GRCh37 assembly) using the standard whole transcriptome pipeline and the colorspace alignment tool provided by Applied Biosystems and distributed with the instrument.
Data were filtered using the following specifications:  FC=2, LogFC=1, Ptype=FDR, P=0.05.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalization was performed using limma package (Bioconductor)

source_name: Cutaneous squamous cell carcinoma 59A

growth_protocol: NHKEs and cSCC cell lines were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
The whole transcriptome libraries were constructed following the Whole Transcriptome Analysis Kit procedure (SOLiD™, Applied Biosystems, Foster City, CA).

treatment_protocol: NHEK and cSCC cell lines were serum starved for 24 hourse and the cell lysates were harvested.

value: Cutaneous SCC

tag: sample type

value: Derived from cSCC tumors


title: UT_SCC115

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 115


title: HEB Protected PARG

source_name: HEB Protected PARG

value: HS181-derived embryoid bodies


title: HEB RNAse replicate 2


title: HESC Protected PARG

source_name: HESC Protected PARG


title: UT_SCC7

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 7


title: UT_SCC105

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 105


title: Mouse1_DoubleNeg

description: SMARTer amplification


title: UT_SCC118

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 118


title: UT_SCC12A

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 12A


title: Smarca4_KD_H3_ChIP

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Barcode adapter sequences removed
Reads mapped to mm9 genome using Bowtie, and allowing 1 mismatch
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4C overnight with constant rotation. H3 antibody (abcam, ab1791), H2AZ antibody (abcam, ab4174), Klf4 antibody (kind gift from Dr. Ng from the Genome Institute of Singapore) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 2% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing (50 bp) was performed on an Illumina HiSeq2000

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection

value: ESC line E14

tag: genotype/variation

value: Smarca4 KD


title: Mouse4_DoubleNeg

description: SMARTer amplification


title: NHEKPC

description: Primary keratinocytes

source_name: Normal human epidermal keratinocyt PC

value: Keratinocyte

value: Derived from non-UV exposed epidermis


title: HEB RNAse replicate 1


title: Smarca4_KD_H2AZ_ChIP


title: HEB Protected 1


title: HESC Protected replicate 1

source_name: HESC Protected


title: Smarca4_KD_Klf4_ChIP

value: Klf4 (kind gift from Dr. Ng from the Genome Institute of Singapore)


title: Smarca4_KD_Klf4_INPUT

value: none (Klf4_INPUT)


title: UT_SCC111

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 111


title: SE T6 Weeks-b

city: Columbus

first: Katelin

middle: Libby

last: Hansen

state: OH

address: 333 W. 10th Ave

department: Neuroscience

institute: The Ohio State University

data_processing:
Base-calling was conducted with the standard Illumina Analysis Pipeline 1.0 (Firescrest-Bustard)
Eight FASTQ sequence files (sequencing reads plus quality information) were generated and mapped to the mouse genome (UCSC mm9) using the Bowtie algorithm with default settings.
A C++ program was used to count the number of uniquely mapped reads within exons of Ref-Seq genes (UCSC Genome Browser mm9 annotation)
RefSeq gene sequence counts were median normalized and overlapping gene IDs were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with raw and normalized reads for each sample, as well as fold change values

source_name: Hippocampus

extract_protocol:
Twelve hours, ten days, or six weeks after induction of SE, animals were sacrificed by cervical dislocation and hippocampi were removed bilaterally and subjected to total RNA extraction by TRIzol (Invitrogen #15596-018) as per manufacturer instructions. Polyadenylated RNA was purified by Dynabeads® mRNA purification kit (Life Technologies #61006). As per manufacturer protocol, 1µg of total RNA was incubated at 50°C for 2 min and placed on ice. The sample was added to Dynabeads® with 50µL binding buffer, mixed thoroughly at room temperature for 5 min, washed twice, and then eluted into 10 µL 10 mM Tris-HCl (pH 7.5) by heating to 70°C for 2 min. Purified mRNA was treated with DNase I (Life Technologies #18068015) at 37°C for 30 min followed by 70°C for 5 min. For first strand synthesis, 10µL of the digestion product, 1µL oligo(dT)18 (500 ug/ml), and 1μl 10 mM dNTP mix were mixed. Samples were heated to 65°C for 5 minutes and incubated on ice. Four microliters of 5X First-Strand Buffer, 2μl of 0.1 M DTT, and 1μl of RNaseOUT Recombinant RNase Inhibitor (Life Technologies #10777-019) were added and incubated at 37°C for 2 min. One microliter of MMLV reverse transcriptase (Life Technologies #26025) was added to samples, which were then incubated at 37°C for 50 minutes, followed by a five-minute inactivation at  70°. cDNA was then treated with NEBNEXT mRNA second strand synthesis  mix (neb #e6112) and incubated for 2.5 hours at  16°C, followed by sonication for 10 seconds.  Samples were purified on a PCR column (Fermentas #K0702) and eluted in 22µl 10 mM Tris pH 8.
Blunt ends were prepared using the DNATerminator® End Repair Kit (Lucigen #40035). Samples were purified using AMPure xp beads (Beckman #A63880) and A-tailing of 3’ ends of eluted cDNA was performed using Exo-minus Klenow DNA polymerase (Epicentre #KL0810259) at 37°C for 30 min. Uniquely tagged Illumina genomic adopters were ligated by Enzymatics T4 DNA ligase (Invitrogen #15224) at RT for 2hrs.  Size visualization was performed using a 2% agarose gel, yielding cDNA libraries ranging in size from 200–250 bp, which were amplified by PCR (5 sec at 98°C; 10 sec at 72°C; 10-20 cycles) using Phusion High-Fidelity DNA Polymerase (ThermoScientific #F530) .

tag: timepoint

value: 6 Weeks


title: Mouse2_IL18RSingPos

description: SMARTer amplification

source_name: IL-10–IL-18R+ FACS-sorted Treg Cells


title: HESC RNAse replicate 1

value: human embryonic stem cells (HESCs)


title: Mbd3_KD_H3_ChIP

tag: cell line

value: Mbd3 KD


title: NHEK59

description: Primary keratinocytes

source_name: Normal human epidermal keratinocyt 59


title: NHEK64

description: Primary keratinocytes

source_name: Normal human epidermal keratinocyt 64


title: UT_SCC91

description: Primary cSCC cells

source_name: Cutaneous squamous cell carcinoma 91


title: Smarca4_KD_histone_INPUT

value: none (histone_INPUT)


title: Mouse1_IL-10SingPos

description: SMARTer amplification

source_name: IL-10+IL-18R– FACS-sorted Treg Cells

tag: genotype


title: HESC RNAse replicate 2

source_name: HESC RNAse

tag: cell type


title: Mbd3_KD_histone_INPUT


title: Mbd3_KD_H2AZ_ChIP


title: SE T10 Days-b

value: 10 Days


title: SE T10 Days-a


title: SE T12 Hours-b

value: 12 Hours


title: HESC Protected replicate 2


title: EGFP_KD_H2AZ_ChIP

value: EGFP KD


title: EGFP_KD_H3_ChIP


title: Mbd3_KD_Klf4_INPUT


title: NHEK70

description: Primary keratinocytes

source_name: Normal human epidermal keratinocyt 70


title: SE T12 Hours-a


title: SE T6 Weeks-a


title: SE T0-a

value: Zero


title: EB control rep2

data_processing:
Libraries were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.0.12.0/RTA 1.17.21.3) with a 2x101 setup in RapidRun mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+. Sequenced reads were mapped using Tophat v2.0.10 with parameter --library-type=fr-firststrand to Ensembl’s GRCh37 whole genome and specifying the corresponding GTF transcript annotation files, both provided by Illumina's iGenomes project (versions as of May, 2014). Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated with Cufflinks v.2.2.0 (with parameter --library-type fr-firststrand) using the same GTF transcript annotation file, and masking the annotated ribosomal RNA and mitochondrial transcripts. The raw FPKM values were filtered for protein coding genes, and the normalized FPKM values (zFPKM) were calculated as described in (Hart et al., 2013).
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include FPKM, log2FPKM, and zFPKM values for each Sample

source_name: HS181-derived embryoid bodies

extract_protocol:
HESCs and HEBs were harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA protocol.


title: EGFP_KD_Klf4_ChIP


title: EGFP_KD_histone_INPUT


title: daf-16(tm6659);daf-2(e1370) rep 1

city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

description: Sample 19

data_processing:
Libraries were sequenced on Illumina HiSeq 2000 sequencer. Illumina CASAVA-1.8.2 was used base calling
Reads were aligned to Worm reference genome using TopHat2 version 2.0.9
Gene expression was quantified with Cufflinks (version 2.1.1)
Genome_build: UCSC Ce10
Supplementary_files_format_and_content: Text file of raw counts and FPKMs

organism: Caenorhabditis elegans

source_name: Day 1 adult whole-animal

growth_protocol: Animals derived from a synchronized 4-hour egglay were grown at 15°C until the L4 larval stage and then shifted to 20°C. Animals were grown for an additional 20-24 hours to day 1 of adulthood. Plates harboring any males were discarded. A subset of the population was picked for life span assays, and the remainder was harvested for total RNA.

extract_protocol:
Animals were washed twice in M9 buffer. Total RNA was isolated using TRIzol reagent (Invitrogen) and purified using an RNeasy kit (QIAGEN Inc., Valencia, CA) according to manufacturers' instructions.
The Agilent TapeStation was used to assess RNA quality. Samples with RINs (RNA Integrity Numbers) of eight or greater were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #RS-122-2001 and RS-122-2002). mRNA was isolated from 0.1-3 ug of total RNA by polyA+ purification, fragmented, and copied into first-strand cDNA using reverse transcriptase and random primers. 3' cDNA ends were then adenylated and adapters ligated. One of the adapters contained a 6-nucleotide barcode to enable multiplexing of samples. Products were purified and enriched by PCR to create the final cDNA library. Libraries were checked for quality and quantity by Agilent TapeStation and qPCR using a library quantification kit for Illumina sequencing platforms (catalog #KK4835, Kapa Biosystems, Wilmington, MA). Clonal clusters were generated using cBot (Illumina, Inc., San Diego, CA). Quadriplexed samples were sequenced using the HiSeq 2000 system (Illumina) with a 100-cycle paired-end run in high output mode using Version 3 reagents according to manufacturer's protocols.


title: EGFP_KD_Klf4_INPUT


title: XHh

city: Nanchang

first: Chen

last: Biao

state: Jiang Xi

address: Zhimin main street 1101#

department: College of animal science and technology

institute: Jiangxi 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: Breast muscle

growth_protocol: All broilers were reared in cages with a 24-h photoperiod for the first 2 d of age and then changed to a 16-h photoperiod. They were fed with free access to water and fedad libitum with 16.5% CP and 2, 800 kcal of ME/kg.  According to the body weight (BW) records at 7 weeks, three female birds from each of the two-tail groups of WRR and XH were selected, and then four groups including WRRh (the group of Recessive White Rock with high body weight), WRRl (the group of Recessive White Rock with low body weight), XHh (the group of Xinhua Chickens with high body weight) and XHl (the group of Xinhua Chickens with low body weight) were generated. The averages of body weight values were 1,064.0 ± 11.1, 695.0 ± 24.4, 305.8 ± 23.3, and 207.6 ± 11.1 g for WRRh, WRRl, XHh, and XHl group, respectively.

extract_protocol:
Total RNA was extracted from each breast muscle using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions. The quality and concentration of all twelve RNA samples were determined by 1.5% agarose gel electrophoresis and absorbance at A260/280 ratio, and then divided to four mixed RNA pools for WRRh, WRRl, XHh, and XHl.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Breast muscle tissues of the 3 individuals were collected immediately after euthanized, snap frozen in liq nitrogen, then stored at -80°C until RNA extraction.

value: Xing Hua Chicken

tag: phenotype

value: slow-growing

tag: age

value: 7 Weeks

tag: group

value: high body weight


title: daf-16(tm5032);daf-2(e1370) rep 3

description: Sample 18


title: daf-16(tm6659);daf-2(e1370) rep 3

description: Sample 21


title: XHl

value: low body weight


title: Mbd3_KD_Klf4_ChIP

value: ESC line E14

tag: chip antibody


title: daf-16(tm6659);daf-2(e1370) rep 2

description: Sample 20


title: ES control rep2


title: daf-16(tm5032);daf-2(e1370) rep 2

description: Sample 17


title: ES control rep1


title: WRRh

tag: strain

value: Recessive White Rocks

value: fast-growing


title: EB control rep1

tag: cell line (background)

value: HS181-derived embryoid bodies


title: Total RNA extracted from AlHV-1-infected bovine lymphoblastoid cells (LCL718)

city: Liege

first: Benjamin

middle: G

last: Dewals

address: Avenue de Cureghem, 10

country: Belgium

institute: University of liege

description: small RNAs

data_processing:
Illumina Genome Analyzer IIx
Sequenced reads were clipped with the 3’ adaptor TGGAATTCTCGGGTGCCAAGG, and trimmed. The reads were then collapsed into sequence tags and selected by size (>15nt and <35nt).
The sequence tags were then mapped to the genomes from which they may have been derived and to other already annotated RNAs by using Burrows-Wheeler Aligner (http://bio-bwa.sourceforge.net), permitting up to 2 mismatches per tag. The Bos taurus and AlHV-1 genome sequences were downloaded from the Ensembl repository (assembly version UMD3.1.67) and the RefSeq or GenBank database (accession numbers NC 002531 and AF005363 for the C500 strain long unique region and polyrepetitive terminal region, respectively), respectively. The following sources of annotated transcripts were used: miRBase v.16 for miRNAs, Silva database for Bos taurus rRNA, Genomic tRNA database for Bos taurus tRNA, Noncode v2.0 database for Bos taurus small nuclear-small nucleolar RNA (sn-snoRNA), telomerase RNA, Genbank database for Bos taurus small cytoplasmic RNA (scRNA), and Repbase v.17.03 for Bos taurus and common ancestral repeats. By doing so, small RNAs that mapped unambiguously to sequences from one single functional category were easily classified, while the others were identified by applying the following annotation rule based on the abundances of various types of sequences in the cell: rRNA > tRNA > sn-snoRNA > miRNA > piRNA > repeat > pathogen genome > host genome > unknown.
Supplementary_files_format_and_content: tar archive of files with sequences and their respective copy number.   Files in the "viral_candidates" tar archive show the alignment of each sequence tag to miRNAs on AlHV-1 genomic sequence (LUR+prDNA). Sequence tags are ordered by read counts and these are indicated on the left-hand side for each sequence tag.

organism: Bos taurus

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMC were isolated using with Ficoll-Paque premium density gradient medium as described earlier. Single-cell suspension (10e6 cells/ml) were then cultured in Iscove's modified Dulbecco's Medium containing 10% FCS and 10 UI/mL of recombinant human IL-2 (Roche). Medium was renewed every 3 days and cells analysed by flow cytometry and used for RNA extraction and small RNA deep sequencing.

extract_protocol:
RNAs were extracted from AlHV-1-infected LCLs (10e7) of a calf developing MCF following infection with AlHV-1 infected BT cells injected intravenously. total RNA was extracted using TRI reagent (Ambion) following the manufacturer's instructions. Small RNA cloning was conducted with 30 ug of total RNA as detailed in Pfeffer et al. (2005). Nature methods 2, 269-276 and then directly sent for large-scale sequencing. Small RNA sequencing was performed at the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France, using an Illumina HiSeq 2000 instrument with a read length of 36 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: blood

value: lymphoblastoid T cells

tag: propagation

value: rhinterleukin-2 (10ug/ml)

tag: passages

value: 4 passages


title: daf-16(tm5030);daf-2(e1370) rep 2

description: Sample 14


title: daf-16(tm5032);daf-2(e1370) rep 1

description: Sample 16


title: daf-16(tm5030);daf-2(e1370) rep 1

description: Sample 13


title: WRRl


title: H3k4me3 Eye ChIPSeq

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: wildtype

data_processing:
libraries sequenced usign Illumina GAIIx single end 49nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
reads were trimmed to 36nt using cutadapt v1.7.1
36nt reads were mapped to mouse genome using BWA v0.7.10 with default aln options
Duplicate Reads have been removed using Picard tools v1.97(1540)
Peak Calling was perform with HOTSPOT v4.1.0 using a random simulated Input to calculate FDR
Peaks selected at FDR 0.01
Genome_build: mm9
Supplementary_files_format_and_content: peaks selected at FDR 0.01 in bed format

source_name: 100 eyes from E10.5 mouse embryos

extract_protocol:
100 eyes from E10.5 mouse embryos were pooled and chromatin was cross-linked with 1% formaldehyde for 15 min and fragmented to obtain DNA in the range of 200–500 bp. DNA was divided in two pools (10mg) and precipitated with 2mg anti-H3K4me1 (CS-037-100, Diagenode) and anti-H3K4me3 (pAB-030-050 Diagenode)
Libraries were prepared for sequencing using standard Illumina protocols for genomic DNA

value: eye

tag: developmental stage

tag: antibody

value: Antibody pAB-030-050 Diagenode


title: daf-16(mg54);daf-2(e1370) rep 2

description: Sample 11


title: ChIP-Seq for H3k9me2 Replicate 2

description: ChIP-Seq for H3k9me2 Replicate 2

data_processing:
map with bwa to HG19
counted mapq > 10 reads per 1000bp using python script
Genome_build: HG19
Supplementary_files_format_and_content: bed files with 1kbp

growth_protocol: Human colon cancer cells (HCT116) and the foreskin fibroblast cells (CRL2429,ATCC) were seeded for 48hrs on an 8 well Lab-Tek II Chamber slides (154534, Lab Tek), fixed with 3% monomeric formaldehyde for 15 minutes at room temperature1 and then stored in 70% ethanol at -20Â°C until use.

extract_protocol:
The immune-complex was reverse crosslinked and associated DNA was purified with ChIP DNA Clean and Concentrator (Zymo research, D5205).
Sequencing library construction was performed using Truseq ChIP sample prep kit (Illumina, IP-202-1012) by following the manufacturer’s instruction with 6-8 ng of ChIPed DNA.

treatment_protocol: Cells were fixed with 1 % formaldehyde at room temperature for 10 min and quenched by 0.125 M glycine. DNA-protein complex were imunopurified by antibody against H3K9me2 (Abcam, ab1220) by conventional method with slight modification6.

value: colon cancer


title: ChIP-Seq for H3k9me2 Replicate 1

description: ChIP-Seq for H3k9me2 Replicate 1


title: daf-16(tm5030);daf-2(e1370) rep 3

description: Sample 15


title: daf-16(mg54);daf-2(e1370) rep 1

description: Sample 10


title: H3k4me1 Eye ChIPSeq

description: wildtype

extract_protocol:
100 eyes from E10.5 mouse embryos were pooled and chromatin was cross-linked with 1% formaldehyde for 15 min and fragmented to obtain DNA in the range of 200–500 bp. DNA was divided in two pools (10mg) and precipitated with 2mg anti-H3K4me1 (CS-037-100, Diagenode) and anti-H3K4me3 (pAB-033-050 Diagenode)
Libraries were prepared for sequencing using standard Illumina protocols for genomic DNA

value: Antibody CS-037-100, Diagenode


title: daf-16(mg54);daf-2(e1370) rep 3

description: Sample 12


title: daf-16(mu86);daf-2(e1370) rep 3

description: Sample 9


title: daf-2(e1370) rep 3

description: Sample 6


title: daf-2(e1370) rep 1

description: Sample 4


title: N2 wild-type rep 3

description: Sample 3

value: N2 wild-type


title: WT_RNA-seq

description: wildtype

data_processing:
libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using TMM from edgeR package
Processed_data_file_format_and_content: tab separated file. Contains normalized counts. Samples in columns, Genes in rows
Genome_build: mm10

source_name: mouse optic cups_WT

extract_protocol:
total RNA was purified from 200 optic cups of 10.5 days mouse embryos
RNA libraries were prepared for sequencing using standard Illumina protocols

value: optic cups

tag: Stage

value: 10.5E Embryos


title: N2 wild-type rep 2

description: Sample 2

tag: genotype/variation


title: N2 wild-type rep 1

description: Sample 1


title: daf-16(mu86);daf-2(e1370) rep 1

description: Sample 7


title: 2A small RNA seq

city: Cambridge

first: Yang

middle: Eric

last: Guo

state: MA

address: 455 Main St

institute: Whitehead Institute MIT

data_processing:
Adapter sequence was clipped (CTGTAGGCACCATCAAT) from raw reads. Clipped reads were then converted from fastq to fasta format
Quantification of mature miRNA levels was performed using quantifier.pl from miRDeep2

organism: Callithrix jacchus

source_name: HVS infected marmoset T cells

growth_protocol: T cells from common marmoset (Callithrix jacchus) immortalized by wildtype HVS strain A11 (WT cells) or a deletion mutant lacking HSURs 1 and 2 (Δ2A cells) (Murthy et al., 1989) were cultured as described (Cook et al., 2004).

extract_protocol: Please see PMID:21139068

value: T cells

tag: agent

value: herpesvirus saimiri A11


title: SE T0-b

tag: timepoint

value: Zero


title: KO_RNA-seq

description: knock out

source_name: mouse optic cups_KO


title: CF

city: Tai'an

first: Xiangshan

last: Ji

address: 61 Daizong street

department: Collenge of animal science and technology

institute: Shandong Agricultural University

data_processing:
Raw sequencing data were processed by Illumina base-calling pipeline.
After filtering the low quality reads, the MeDIP-seq data were aligned to the Nile tilapia reference genome (Orenil 1.1) using SOAP2 (Version 2.21).
The paired-end mapped reads were defined as fragments (BED file) that were used in further analysis.
Genome_build: Oreochromis niloticus (assembly Orenil1.1).
Supplementary_files_format_and_content: The processed data is EXCEL file, which contains chromsome, fragment start site and fragment end site.

organism: Oreochromis niloticus

source_name: control female

growth_protocol:
reared in 40 m3 tanks in experimental base of Shandong agricultural university
The fish were fed pelleted tilapia food of appropriate size once daily

extract_protocol:
DNA was isolated using traditional phenol-chloroform method from gonad of Nile tilapia
Each MeDIP library was subjected to the paired-end sequencing using Illumina HiSeq 2000 and in 50 bp read length. Five µg original DNA was isolated using phenol-chloroform method and was sonicated to about 100 - 500 bp fragments with a Bioruptor sonicator (Diagenode). Then libraries were constructed using the Illumina Paired-End protocol consisting of end repair, base addition and adaptor ligation steps, and were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions. Adaptor-ligated DNA was immunoprecipitated by monoclonal anti-methylcytidine antibody. The specificity of the enrichment were confirmed by qPCR using SYBR green mastermix (Applied Biosystems) and primers for positive and negative internal control DNA of non-human samples were supplied in the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode). Cycling of qPCR validation was 95℃ 5 min, followed by 40 cycles 95℃ 15 s and 60℃ 1 min. The enriched fragments with methylation and 10% input DNA were purified on ZYMO DNA Clean & Concentrator-5 columns following the manufacturer’s instructions. DNA was eluted in 30 µl buffer EB and its concentration was measured. Enriched fragments was amplified by adaptor-mediated PCR in a final reaction volume of 50 µl consisting of 23 µl purified DNA, 25 µl Phusion DNA polymerase mix (NEB) and 2µl PCR primers. Amplification consisted of 94℃ 30 s, 10 cycles of 94℃ 30s, 60℃ 30 s, 72℃ 30 s then prolong with 5 min at 72℃ and products could be hold at 4℃. Amplifications quality and quantity were evaluated by Agilent 2100 Analyzer DNA 1000 chips purified by 2% agarose gel and eluted in 15 µl buffer EB. Ultra-high-throughput 50 bp pair-end sequencing was carried out using the Illumina HiSeq 2000 according to manufacturer instructions. Raw sequencing data were processed by Illumina base-calling pipeline.

treatment_protocol: One group served as control and the larvae were cultivated at 28 °C. The other was high temperature-induced group and the larvae were cultured at 36 °C for 12 days

tag: breed

value: Genetically Improved Farmed Tilapia

value: juvenile

value: gonad


title: IM

source_name: induced male


title: IF

source_name: induced female


title: CM

source_name: control male


title: Meis1_ChIP-seq

description: wildtype

data_processing:
libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
sequencing adaptor contaminations were removed using cutadapt
reads were mapped to reference genome using BWA
peak calling was perform using PICS R package
motive discovery was perform using rGADEM and MotIV R packges
Processed_data_file_format_and_content: bed file format representing PICS peak calling and score
Genome_build: mm10

source_name: mouse optic cups_WT_ChIP

extract_protocol:
200 eyes from embryos at E10.5 days were dissected, Disgregated and the resulting single cell suspension subjected to cross-linking, Sonication and immunoprecipitation.
Libraries were prepared for sequencing using standard Illumina protocols for genomic DNA


title: CGGBP1 shmiR + bisulfite converted genomic DNA+Alu PCR

status: Public on Aug 26 2015

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

institute: IIT Gandhinagar

description:
Amplicon size 220 bps
1064Sk normal human foreskin fibroblasts passage 12 transduced with lentivirus as indicated, genomic DNA extracted and subjected to bisulfite conversion, and used for PCR as indicated

data_processing:
ILLUMINA: Alignment
ILLUMINA: Removal of duplicate reads (mentioned in reports TXT files)
ILLUMINA: Normalization of bisulfite conversion efficiency by using 100% unmethylated Lambda Phage DNA spike in control
PACBIO: Alignment
PACBIO: consideration of only reads 100 bases or longer for methylation calculation
Genome_build: HG 19
Supplementary_files_format_and_content:
*report.txt: Bismarck Alignment Report
*PCR_alignment_to_consensus.txt: Supermatcher Alignment Output

growth_protocol: 10% FBS (Supplemented with Glutamine) in MEM (SIGMA)

extract_protocol:
DNA extracted using Qiagen Genomic DNA extraction kit.
NEXTflex Bisulfite (cat# 5119-01) Sequencing kit provided by Bioo Scientific for Illumina Seq. PacBio SMARTBLLl for PacBio sequencing
Mate Pairedfor Illumina and SmartBell for PacBio

treatment_protocol: Lentiviral transduction (MoI = 6)

tag: cell line

tag: cell type

value: Normal human foreskin fibroblasts

tag: passage

value: passage 12

value: Lentivirus (shmiR) transduced

tag: molecule subtype

value: PCR product (ALU) from bisulfite converted genomic DNA


title: Control shmiR + bisulfite converted genomic DNA+Alu PCR

source_name: 1064Sk normal human foreskin fibroblasts


title: CGGBP1 shmiR + bisulfite converted genomic DNA+LINE-1 PCR

description:
Amplicon size 429 bps
1064Sk normal human foreskin fibroblasts passage 12 transduced with lentivirus as indicated, genomic DNA extracted and subjected to bisulfite conversion, and used for PCR as indicated

value: PCR product (LINE-1) from bisulfite converted genomic DNA


title: OX9_flg22_R1

city: College Station

first: Libo

last: Shan

state: Texas

address: Norman Borlaug Center 136, TAMU2123

department: Department of Plant Pathology and Microbiology

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings
Sequencer .bcl basecall files were formatted into .fastq files using bcl2fastq 1.8.4 script configureBclToFastq.pl
Samples are demultiplexed during the execution of the configureBclToFastq.pl script. Three metrics are examined upon sample demultiplexing: (1) demultiplexing balance, (2) rate of prefiltering, and (3) the presence of technical adapter sequence at the ends of reads using cutadapt 1.0.
Reads were aligned to the Arabidopsis genome using Tophat v2.0.12 with default parameter settings
Normalized abundance measurements of FPKM value were generated using the Cuffdiff v2.2.1
Genome_build: Arabidopsis TAIR10 genome annotation
Supplementary_files_format_and_content: txt format, gene relative expression level of fragments per kilobase of exon per million fragments mapped (FPKM)

growth_protocol: Seedlings were germinated on ½ Murashige and Skoog (MS) plate containing 1% sucrose, 0.8% Agar.Plants were grown in a growth room at 23°C, 45% humidity and 75μE m-2s-1 light with a 12 hr light/12 hr dark photoperiod.

extract_protocol:
Total RNA from 10-day-old seedlings was extracted by TRIzol reagent (Invitrogen) and quantified with NanoDrop (Thermo Scientific).
cDNA libraries were made using Illumina TruSeq RNA prep kit as per the manufacturer's protocol and 1 μg total RNA was used for one sample.

treatment_protocol: Ten days old seedlings were transferred to a 6-well tissue culture plate with 2 ml water for overnight, and then treated with 100 mM flg22 for 30 min.

tag: genotype

value: 35S:ASR3-HA transgenic line OX9

tag: age

value: 10-day old

value: whole plant


title: daf-16(mu86);daf-2(e1370) rep 2

description: Sample 8


title: OX9_CK_R2


title: OX9_CK_R1


title: OX9_flg22_R2


title: asr3-1_flg22_R1


title: asr3-1_CK_R2


title: WT_flg22_R2

tag: cultivar

value: wildtype


title: daf-2(e1370) rep 2

description: Sample 5


title: asr3-1_CK_R1

tag: tissue


title: asr3-1_flg22_R2


title: WT_flg22_R1


title: WT_CK_R1


title: WT_CK_R2


title: Control shmiR + bisulfite converted genomic DNA+LINE-1 PCR


title: TE9.1

city: London

first: paul

last: blakeley

address: 215 Euston Road

institute: Crick Institute

description: Sample name: Y_TE

data_processing:
Reads alligned to the human genome sequence using TopHat2
Read counts were generated using HTSeq-count
Genome_build: GRCh37.74
Supplementary_files_format_and_content: read counts

source_name: Human Embryo

extract_protocol:
Single cells were isolated from blastocyst stage embryos (6-7 days post fertilisation) for subsequent analysis by micromanipulation, with a duration of less than 20 minutes. Embryos were placed in drops of G-MOPS solution (Vitrolife) on a petri dish overlaid with mineral oil. The plate was placed on a microscope stage (Olympus IX70) and the embryos were held with an opposing holding pipette and blastomere biopsy pipette (Research Instruments) using Narishige micromanipulators (Narishige, Japan). The biopsy mode of a Saturn 5 laser (Research Instruments) was used to separate the majority of the mural TE from the ICM and polar TE. The ICM and polar TE were washed quickly in PBS without Ca2+ and Mg2+ (Invitrogen) then placed in 0.05% trypsin/EDTA (Invitrogen) for 5 minutes at room temperature. Trypsin was quenched using Global Media supplemented with 5 mg/mL LifeGlobal Protein Supplement. After quenching, the cell clump was placed back on the stage in a drop of G-MOPS solution and pipetted up and down several times using the blastomere biopsy pipette.
cDNA was generated from single cells using the SMARTer Ultra Low Input RNA kit for Illumina Sequencing?HV (Clontech Laboratories, Inc.) according to maunfacturers? guidelines. Single cells were picked using 100 ?m inner diameter Stripper pipette (Origio) and transferred to individual low bind RNAse-free tube containing 0.25 ?l RNase inhibitor, 4.75 ?l Dilution buffer and 5 ?l nuclease-free water on a -80°C pre-chilled CoolRack (Biocision, CA). Samples were stored at -80°C until ready to be processed. 1 ?l of 3? SMART CDS Primer II A was added to the sample, mixed well and incubated at 72°C for 3 min. First strand cDNA was synthesised by adding 4 ?l 5X First-Strand Buffer, 0.5 ?l 100 mM DTT, 1 ?l 20 mM dNTP mix, 1 ?l SMARTer IIA Oligonucleotide, 0.5 ?l RNase Inhibitor and 2 ?l SMARTScribe Reverse Transcriptase (100 U/?l) directly to a tube containing the sample and incubating at 42°C for 2 hours followed by 10 min at 70°C.
First strand cDNA was purified by adding 36 ?l of room temperature SPRI Ampure XP beads (Beckman Coulter Genomics), mixing well and incubating at room temperature for 8 min. Tubes were placed on a MagnaBot II Magnetic Separation device (Promega) and allowed to stand until all beads were immobilised into a pellet. The supernatant was removed and discarded. Tubes were briefly spun and any residual liquid was removed.
Double stranded cDNA was amplified from the template bound to the beads using Advantage 2 PCR kit (Clontech Laboratories, Inc.). 5 ?l 10X Advantage 2 PCR Buffer, 2 ?l 10 mM dNTP Mix, 2 ?l IS PCR Primer, 2 ?l 50X Advantage 2 Polymerase Mix and 39 ?l Nuclease-Free water were added to the tube containing the sample to give a total volume of 50 ?l. PCR amplification was performed at 95°C for 1 min, followed by 18 cycles of 15 sec at 95°C, 30 sec at 65°C and 6 min at 68°C followed by final extension step of 10 min at 72°C. Amplified cDNA was purified by adding 90 ?l SPRI Ampure XP beads, mixing well and incubating at room temperature for 8 min to allow amplified cDNA bind to the beads. Sample tubes were placed on the magnet and allowed to stand until all beads had been immobilised. Supernatant was removed and discarded and beads were washed twice by adding 200 ?l freshly prepared 80% ethanol and leaving for 30 sec before discarding the supernatant. Tubes were spun briefly to collect residual liquid. The bead pellet was allowed to air dry. 12 ?l of purification buffer was added to rehydrate the pellet and incubated for 2 min at room temperature. cDNA was eluted by pipetting up and down 10 times before returning the tube to the magnet. The clear supernatant containing the cDNA was removed from the immobilised beads and transferred to a new low-bind tube. cDNA was stored at -80°C until library preparation.
cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using QuBit dsDNA HS kit (Life Technologies UK Ltd.) Typical yields from a single cell ranged from 1 ng to 9 ng.
In preparation for library generation cDNA was sheared using Covaris S2 to achieve cDNA in 200-500 bp range. 10 ?l of cDNA sample and 65 ?l purification buffer was added to Covaris AFA Fiber Pre-Slit Snap Cap microTUBE. cDNA was sheared using the settings 10% Duty, Intensity 5, Burst Cycle 200 for 2 min. Sheared cDNA was transferred to a new 0.2 ml low-bind tube.
Libraries were prepared using Low Input Library Prep Kit (Clontech Laboratories, Inc.) according to manufacturer?s instructions. The amount of input cDNA was calculated from the concentration measured by the Bioanalyser assay prior to shearing, taking into account the dilution involved in the shearing step. The appropriate amplification cycle number was selected according to manufacturer?s guidelines. Library quality was assessed by Bioanalyser and the concentration was measured by QuBit assay.  The molar concentration of library was calculated thus: Library molecular weight = average size in bp (from Bioanalyser) x 650 g/mol per bp.

value: Blastocyst

tag: lineage

value: Trophectoderm

tag: embryo number

value: Embryo 9


title: TE8.5

description: Sample name: ICM_B38

tag: developmental stage

value: Embryo 8


title: TE8.6

description: Sample name: ICM_B22


title: TE8.8

description: Sample name: ICM_B45


title: PE8.1

description: Sample name: ICM_B30

value: Primitive Endoderm


title: TE8.2

description: Sample name: ICM_B7


title: TE8.3

description: Sample name: ICM_B4


title: TE3.2

description: Sample name: A23

value: Embryo 3


title: TE3.4

description: Sample name: A3


title: EPI3.1

description: Sample name: ICM_A14

value: Epiblast


title: TE8.7

description: Sample name: ICM_B15


title: TE3.3

description: Sample name: A22


title: TE3.1

description: Sample name: A20


title: TE8.4

description: Sample name: B36


title: TE3.5

description: Sample name: A15


title: MRC5_PD52w_2

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
FASTQ files were extracted using Illumina Casava software v1.8.2 (sample 1-24) or bcl2fastq v1.8.4 (sample 25-60)
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

source_name: total RNA extracted from MRC-5 fibroblasts

growth_protocol: The fibroblasts were maintained in the presence of rotenone throughout their span (from young PD till senescent) in culture in dim light, due to the light sensitive nature of rotenone [Dekker et al., 2011].

extract_protocol:
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.

treatment_protocol: The media were changed and rotenone was supplemented every 3 days, due to the half-life of rotenone [Cabras et al., 2002].

tag: population doublings

value: fibroblasts

tag: treatment

value: 100 nM rotenone


title: MRC5_PD52w_1


title: MRC5_PD52w_3


title: MRC5_PD48wo_2


title: MRC5_PD48wo_1


title: MRC5_PD52wo_2


title: MRC5_PD48w_2


title: MRC5_PD48w_3


title: MRC5_PD48w_1


title: MRC5_PD48wo_3


title: MRC5_PD52wo_3


title: TE8.1

description: Sample name: ICM_B19


title: MRC5_PD42w_3


title: MRC5_PD42w_2


title: MRC5_PD42wo_3


title: MRC5_PD38w_3


title: MRC5_PD38w_1


title: MRC5_PD42w_1


title: MRC5_PD38wo_3


title: MRC5_PD42wo_2


title: MRC5_PD38w_2


title: MRC5_PD38wo_1


title: MRC5_PD38wo_2


title: 5'Sµ, 53BP1-/- +ATMi. rep3

city: Boston

first: Junchao

last: Dong

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital, Harvard Medical School

description: processed data file: 5'Sm-53BP1+ATMi.txt

data_processing:
library strategy: high-throughput genome-wide translocation sequencing (HTGTS)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 or its derivative reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9, mm9_129IgHC
Supplementary_files_format_and_content: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Tname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Tstart) and end (Tend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: spleen B cells+5'Sµ, 53BP1-/- +ATMi

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using HTGTS.

treatment_protocol: Purified B cells were stimulated with either aCD40/IL4 or LPS/aIgD-dextran; I-SceI infection were performed at day 1 after stimulation with the presence of 4ug/ml polybrene; ATM inhibitor were added at day 1 at final concentration of 10mg/ml.

value: spleen B cells

tag: genetic variation

tag: activation method

tag: treatment protocol

value: cytokine stimulation, 10uM ATM inhibitor

tag: target locus

tag: reference assembly

tag: growth protocol


title: 5'Sµ, 53BP1-/- +ATMi, rep2

tag: cell type


title: 5'Sµ,WT+ATMi-5', rep3

description: processed data file: 5'Sm-WT+ATMi.txt

source_name: spleen B cells+5'Sµ,WT+ATMi-5'

value: WT


title: MRC5_PD52wo_1

tag: cell line


title: 5'Sµ, 53BP1-/- +ATMi, rep1


title: 5'Sµ,WT+ATMi-5', rep1

description: processed data file: 5'Sm-WT+ATMi.txt


title: 5'Sµ,WT+ATMi-5', rep2

description: processed data file: 5'Sm-WT+ATMi.txt


title: 5'Sµ, rif1-/- 5', rep3

description: processed data file: 5'Sm-RIF1.txt

source_name: spleen B cells+5'Sµ, rif1-/- 5'

value: RIF1fl/fl, CD19-Cre

value: cytokine stimulation


title: 5'Sµ, rif1-/- 5', rep2-RE

description: processed data file: 5'Sm-RIF1.txt


title: 5'Sµ, rif1-/- 5', rep2

description: processed data file: 5'Sm-RIF1.txt


title: 5'Sµ, H2AX-/- 5', rep3-RE

description: processed data file: 5'Sm-H2AX.txt

source_name: spleen B cells+5'Sµ, H2AX-/- 5'

value: delta-S-gamma-1_2xI, H2AX-/-

value: resequencing of rep3


title: MRC5_PD42wo_1


title: 5'Sµ, H2AX-/- 5', rep2-RE

description: processed data file: 5'Sm-H2AX.txt

value: resequencing of rep2


title: 5'Sµ, 53BP1-/- 5', rep7

description:
processed data file: 5'Sm-53BP1.txt
processed data file: 5'Sm-53BP1_2.txt

source_name: spleen B cells+5'Sµ, 53BP1-/- 5'

value: cytokine stimulation + DMSO


title: 5'Sµ, rif1-/- 5', rep1

description: processed data file: 5'Sm-RIF1.txt


title: 5'Sµ, H2AX-/- 5', rep2

description: processed data file: 5'Sm-H2AX.txt


title: 5'Sµ, 53BP1-/- 5', rep5

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ, H2AX-/- 5', rep1-RE

description: processed data file: 5'Sm-H2AX.txt

value: resequencing of rep1


title: 5'Sµ, 53BP1-/- 5', rep4

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ, H2AX-/- 5', rep1

description: processed data file: 5'Sm-H2AX.txt


title: 5'Sµ, H2AX-/- 5', rep3

description: processed data file: 5'Sm-H2AX.txt


title: 5'Sµ, 53BP1-/- 5', rep8


title: 5'Sµ, 53BP1-/- 5', rep6


title: 5'Sµ, ATM-/- 5', rep1

description: processed data file: 5'Sm-ATM.txt

source_name: spleen B cells+5'Sµ, ATM-/- 5'

value: ATM-/-


title: 5'Sµ, 53BP1-/- 5', rep3

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ, ATM-/- 5', rep3

description: processed data file: 5'Sm-ATM.txt


title: 5'Sµ, 53BP1-/- 5', rep1-re

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ, 53BP1-/- 5', rep1

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ, 53BP1-/- 5', rep2

description: processed data file: 5'Sm-53BP1.txt


title: 5'Sµ,WT-5', rep4

description: processed data file: 5'Sm-WT.txt

source_name: spleen B cells+5'Sµ,WT-5'


title: 5'Sµ,WT-5', rep1

description: processed data file: 5'Sm-WT.txt


title: γSµ, 53BP1-/- 5', rep3

description: processed data file: rSm-53BP1.txt

source_name: spleen B cells+γSµ, 53BP1-/- 5'

value: gamma-S-mu, 53BP1-/-

value: delta-S-mu


title: 5'Sµ, ATM-/- 5', rep2

description: processed data file: 5'Sm-ATM.txt


title: γSµ, 53BP1-/- 5', rep2

description: processed data file: rSm-53BP1.txt


title: 5'Sµ,WT-5', rep2

description: processed data file: 5'Sm-WT.txt


title: γSµ, 53BP1-/- 5', rep1-re

description: processed data file: rSm-53BP1.txt


title: γSµ, ATM-/- 5', rep3

description: processed data file: rSm-ATM.txt

source_name: spleen B cells+γSµ, ATM-/- 5'

value: gamma-S-mu, ATM-/-


title: γSµ, ATM-/- 5', rep1

description: processed data file: rSm-ATM.txt


title: 5'Sµ,WT-5', rep3

description: processed data file: 5'Sm-WT.txt


title: γSµ, ATM-/- 5', rep2

description: processed data file: rSm-ATM.txt


title: γSµ_LPS-5', rep2

description: processed data file: rSm-LPS-5'.txt

source_name: spleen B cells+γSµ_LPS-5'

value: gamma-S-mu


title: γSµ_LPS-5', rep3

description: processed data file: rSm-LPS-5'.txt


title: γSµ_LPS-3', rep2

description: processed data file: rSm-LPS-3'.txt

source_name: spleen B cells+γSµ_LPS-3'


title: γSµ_LPS-3', rep1

description: processed data file: rSm-LPS-3'.txt


title: γSµ_αCD40/IL4-3', rep3

description: processed data file: rSm-aCD40IL4-3'.txt

source_name: spleen B cells+γSµ_αCD40/IL4-3'


title: γSµ_αCD40/IL4-3', rep1


title: γSµ_αCD40/IL4-3', rep2


title: γSµ_αCD40/IL4-5', rep3

description: processed data file: rSm-aCD40IL4-5'.txt

source_name: spleen B cells+γSµ_αCD40/IL4-5'


title: 5'Sµ,WT-5', rep5

description: processed data file: 5'Sm-WT.txt


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_5', rep2

description: processed data file: Sm-DEL_Day3_5BE_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_non-productive (Sµ-Sα)Δ, ΔSµ_Day3_5'

value: CH12F3 murine lymphoma cells


title: γSµ_αCD40/IL4-5', rep1


title: γSµ_αCD40/IL4-5', rep2


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_3', rep3

description: processed data file: Sm-DEL_Day3_3BE_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_non-productive (Sµ-Sα)Δ, ΔSµ_Day3_3'


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_3', rep2


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_5', rep3


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_5', rep3

description: processed data file: Sm-DEL_Day2_5BE_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_non-productive (Sµ-Sα)Δ, ΔSµ_Day2_5'


title: γSµ, ATM-/- 5', rep4

description: processed data file: rSm-ATM.txt


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_5', rep1


title: γSµ_LPS-3', rep3

description: processed data file: rSm-LPS-3'.txt


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_3', rep2

description: processed data file: Sm-DEL_Day2_3BE_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_non-productive (Sµ-Sα)Δ, ΔSµ_Day2_3'


title: γSµ, 53BP1-/- 5', rep1

description: processed data file: rSm-53BP1.txt


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_5', rep2


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_3', rep3


title: γSµ_LPS-5', rep1

description: processed data file: rSm-LPS-5'.txt


title: ΔSα_1xI, Sm-INV, rep2

description: processed data file: Sa_1xI-Smu-INV_3BE_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI, Sm-INV

value: delta-S-alpha_1xI-SceI, Sm-inversion

value: I-SceI plasmid nucleofection


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_5', rep1


title: ΔSα_1xI, Sm-INV, rep3


title: ΔSα_1xI, Sm-INV, rep1


title: ΔSα_1xI-5', clone #2, rep3

description: processed data file: Sa_1xI-5BE clone #2_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-5', clone #2


title: ΔSα_1xI-5', clone #2, rep1


title: ΔSα_1xI-3', clone #2, rep2

description: processed data file: Sa_1xI-3BE clone #2_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-3', clone #2


title: ΔSα_1xI-3', clone #2, rep1-re

value: resequencing rep1


title: ΔSα_1xI-5', clone #1, rep2

description: processed data file: Sa_1xI-5BE clone #1_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-5', clone #1


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day3_3', rep1


title: ΔSα_1xI-3', clone #2, rep1


title: ΔSα_1xI-5', clone #1, rep1


title: ΔSα_1xI-3', clone #1, rep3

description: processed data file: Sa_1xI-3BE clone #1_pooled_tlx.txt

source_name: CH12F3 murine lymphoma cells_ΔSα_1xI-3', clone #1


title: non-productive (Sµ-Sα)Δ, ΔSµ_Day2_3', rep1


title: ΔSα_1xI-3', clone #1, rep2


title: ΔSα_1xI-3', clone #1, rep1