title: CvixLer_endosperm_3_mRNASeq

first: Mary

last: Gehring

description: mRNA-seq

data_processing:
Sequencing quality was assessed using fastqc. Low quality reads were removed with fastq_quality_filter using options -q 20 and -p 80 (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered reads were aligned to the TAIR 10 version of the Arabidopsis reference genome (www.arabidopsis.org) using the TopHat v. 2.0.8 read aligner (http://tophat.cbcb.umd.edu/). For 40 bp libraries the options -solexa1.3-quals --segment-length 18 --segment-mismatches 1 --max-segment-intron 11000 were used and for 80 bp libraries the options were --solexa1.3-quals --segment-length 30 --max-segment-intron 11000.
Total read counts for each gene and TE annotated in TAIR10 were quantified using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) with options –m intersection-strict –-stranded=no (for non-strand-specific libraries) or –stranded=yes (for strand-specific libraries).
To generate read counts for each known SNP, reads were first sorted by genome position and then filtered out if two SNP bases within the same read conflicted based on strain classification. Finally the number of reads coming from each strain overlapping a particular SNP were counted using a Perl script and logged in the files that end in _SNP_counts.txt
Allele-specific read counts for each gene and TE were generated by running ht-seq count on the reads classifed by strain with the same options as for total read counts.
FPKM values were calculated using Cufflinks v2.2.1 with a TAIR10 genes and transposons gtf file.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_SNP_counts.txt; tab-delimited text file with number of reads overlapping each covered SNP; columns are the chromosome on which the SNP is located, the 1-based index of the SNP's position on the chromosome, the reference base call -- the DNA base found at SNP_chr, SNP_position in either "col" or "ler" as indicated in the column header, the other base call -- the DNA base found at SNP_chr, SNP_position in either "ler" or "cvi" as indicated in the column header, the number of reads overlapping the SNP of interest (whose base call matches the reference sequence), the number of reads overlapping the SNP of interest (whose base call matches the other sequence), Novel_variant_counts is the number of reads overlapping the SNP of interest, whose base call matches neither the reference nor the other sequence.
Supplementary_files_format_and_content: *_statistics_per_locus.txt, tab-delimited text file with number of reads overlapping every annotated locus in TAIR10; SNP counts are only reported for SNPs that had overlapping reads. The SNPs listed in the _SNP_counts.txt files are thus a subset of the SNPs used to evaluate parent-of-origin effects; columns are: locus_name is the locus model from TAIR10, num_reads is the total number of reads in the library which overlap this gene model, FPKM is the fragments per kilobase per million, which provides a measure of overall transcript abundance at this locus, calculated using Cufflinks, num_X_reads is the number of reads overlapping SNPs found inside locus_name's gene model, for which all base calls unambiguously assign it to the reference base( X = col or ler), num_Y_reads is the number of reads overlapping SNPs found inside locus_name's gene model, for which all base calls unambiguously assign it to the other base  (Y = ler or cvi). CCE, CCN, LLE, LLN, VVE, VVN _statistics_per_locus.txt only include columns 1-3 since there is no notion of an "other" base since all reads come from the same strain.  N.B. There are often many more num_reads mapping to the locus_name as a whole than the sum of num_X_reads + num_Y_reads because of the non-SNP-overlapping reads, which are nevertheless aligned to gene models in TAIR10. All files begin with a 3-letter sequence, which indicates the tissue and the F1 cross, from which they originate.  C = Col-0, L = Ler, V = Cvi (first two letters indicate strain and which parent is female or male)  E = embryo, N = endosperm, S = whole seeds (third letter indicates the tissue in question)  CVE, for example, indicates Col-0 (female) x Cvi (male) embryo, whereas VCN indicates Cvi (female) x Col-0 (male) endosperm.

source_name: endosperm

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected into embryo and endosperm at six DAP (approximately torpedo stage of embryogenesis).

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNaqueous Kit with Plant RNA Isolation Aid or the Ambion RNAqueous Micro Kit.
Libraries were constructed essentially using the Illumina mRNA-seq protocol. 0.6-1 micrograms of total RNA were poly-A selected twice, fragmented, and converted into double-stranded cDNA. The cDNA was end-repaired, adenylated, and adapters ligated. Libraries were PCR amplified for 12 cycles using TruSeq primers.

treatment_protocol: no treatment

value: Cvi female X Ler male

tag: developmental stage

value: 6 days after pollination

value: endosperm


title: LerxCvi_endosperm_3_mRNASeq

status: Public on Jul 08 2014

type: SRA

city: Cambridge

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: mRNA-seq

library_source: transcriptomic

molecule: polyA RNA

organism: Arabidopsis thaliana

tag: genotype

value: Ler female X Cvi male

tag: tissue


title: ∆vib-1 No Carbon #3

city: Berkeley

first: N. Louise

last: Glass

state: CA

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Basecalling performed using Illumina CASAVA_v1.8.0 software
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G  --max-bundle-frags=10000000)
Differential Expression was estimated with Cuffdiff v2.0.2 (options: -u -b -G  --max-bundle-frags=10000000)
Genome_build: N. crassa: OR74A version 10 from the Broad Institute
Supplementary_files_format_and_content: FPKM

molecule: total RNA

organism: Neurospora crassa

source_name: mycelia

growth_protocol: N. crassa strains were innoculated in 100mL Liquid media with 2% sucrose, grown 16 hours at 25ºC 200rpm and constant light. Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-10 or without carbon sources, then grown an additional 4hrs at 25ºC.

extract_protocol:
Mycelia were harvested by filtration and flash frozen in liquid nitrogen. Total RNA was extracted by bead-beating in TRIZOL reagent and purified with RNeasy kit from Qiagen.
mRNA was enriched with oligo-dT magnetic beads, fragmented and reverse transcribed with Superscript II reverse polymerase from Invitrogen. Illumina adapters were added to the cDNA library with the TruSeq DNA kit v2, SetA

tag: strain

value: ∆vib-1 a

tag: treatment

value: No Carbon


title: LerxCvi_endosperm_2_mRNASeq

description: mRNA-seq


title: CvixLer_endosperm_2_mRNASeq

description: mRNA-seq


title: CvixCol_endosperm_3_mRNASeq

description: mRNA-seq

value: Cvi female X Col-0 male


title: LerxCol_endosperm_5_mRNASeq

description: mRNA-seq

value: Ler female X Col-0 male


title: ColxLer_endosperm_5_mRNASeq

description: mRNA-seq

value: Col-0 female X Ler male


title: ColxCvi_endosperm_3_mRNASeq

description: mRNA-seq

value: Col-0 female X Cvi male


title: LerxCol_endosperm_4_mRNASeq

description: mRNA-seq


title: Ler x Col_seeds_rep_1

description: sRNA-seq

data_processing:
Basecalls performed using Illumina Off-Line Basecaller (OLB) version 1.9
trimmed low quality read ends with fastq_quality_trimmer: -t 20, -l 25
removed adapters with fastx_clipper: -a TCGTATGCCGTCTTCTGCTTG -i 18
Reads aligned using Bowtie 1.0.0: -v 2 --best; initial alignment was to a metagenome of both parental genomes, but reads were then converted in all cases to TAIR10 coordinates.
All reads that overlapped annotated tRNAs, snRNAs, rRNAs, or snoRNAs were removed
normalized libraries by converting read values within windows into RPM (reads per million) values
reads were classified for parent of origin using SNP classification approach
Genome_build: TAIR10, resequenced Ler-0 genome, Cvi pseudogenome
Supplementary_files_format_and_content: Files ending in "norm.s.txt" have the chromosome number in the first column, the start and end positions of the 300 base window in the second and third columns respectively, and the normalized number of reads within the window in the units of reads per million in the fourth column.
Supplementary_files_format_and_content: Files ending in "SNP_counts.txt" show the results of the SNP classication, showing the number of reads derived from each strain at each SNP position.

source_name: Whole seeds

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were collected at six DAP (approximately torpedo stage of embryogenesis).

extract_protocol:
Whole seeds were removed from siliques 6 days after pollination.  RNAs smaller than 200 nt were isolated from whole seeds using the mirVana RNA isolation kit (Ambion, Life Technologies Corporation).
Libraries for Illumina sequencing were constructed following the method of Grimson et al., Nature 455, 2008, with only minor modifications.  Multiplexing of libraries was enabled through the use of four different 3' PCR primers during library amplification, each of which was 94 bases in length as opposed to the 44 nt 3' PCR primer from the referenced protocol.  As a result the sequences obtained in the final gel purification step ranged in size from 135-155 nt in length.

value: whole seeds


title: Ler x Col_seeds_rep_2

description: sRNA-seq


title: Col x Ler_seeds_rep_2

description: sRNA-seq


title: Ler x Ler_seeds_rep_1

description: sRNA-seq

value: Ler female X Ler male


title: Col x Ler_seeds_rep_1

description: sRNA-seq


title: Cvi x Cvi_seeds_rep_2

description: sRNA-seq

value: Cvi female X Cvi male


title: Col x Cvi_seeds_rep_2

description: sRNA-seq


title: Col x Cvi_seeds_rep_1

description: sRNA-seq


title: Cvi x Col_seeds_rep_2

description: sRNA-seq


title: ColxLer_endosperm_2_mRNASeq

description: mRNA-seq


title: Cvi x Cvi_seeds_rep_1

description: sRNA-seq


title: LerxCol_endosperm_2_mRNASeq

description: mRNA-seq


title: Cvi x Col_seeds_rep_1

description: sRNA-seq


title: CvixLer_embryo_mRNASeq

description: mRNA-seq

source_name: embryo

value: embryo


title: LerxCvi_endosperm_mRNASeq

description: mRNA-seq


title: CvixLer_endosperm_mRNASeq

description: mRNA-seq


title: LerxCvi_embryo_mRNASeq

description: mRNA-seq


title: CvixCol_whole_seed_mRNASeq

description: mRNA-seq

data_processing:
Sequencing quality was assessed using fastqc. Low quality reads were removed with fastq_quality_filter using options -q 20 and -p 80 (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered reads were aligned to the TAIR 10 version of the Arabidopsis reference genome (www.arabidopsis.org) using the TopHat v. 1.4.1 read aligner (http://tophat.cbcb.umd.edu/). Mapping tolerated at most two mismatches to the reference (or three for the 80 bp Ler x Cvi and Cvi x Ler endosperm libraries). The Tophat option –segment-length 40 was used for the 80 bp libraries.
Total read counts for each annotated gene and TE (found in statistics_per_locus.txt files) were quantified using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) on accepted_hits.sam files (Tophat output) with options -m intersection-strict --stranded=no.
To generate read counts for each known SNP, reads were first sorted by genome position and then filtered out if two SNP bases within the same read conflicted based on strain classification. Finally the number of reads coming from each strain overlapping a particular SNP were counted using a Perl script and logged in the files that end in _SNP_counts.txt
Allele-specific read counts for each gene and TE were generated by running ht-seq count on the reads classifed by strain (–m intersection-strict –-stranded=no).
FPKM values were calculated using Cufflinks with a TAIR10 gtf file.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_SNP_counts.txt; tab-delimited text file with number of reads overlapping each covered SNP; columns are the chromosome on which the SNP is located, the 1-based index of the SNP's position on the chromosome, the reference base call -- the DNA base found at SNP_chr, SNP_position in either "col" or "ler" as indicated in the column header, the other base call -- the DNA base found at SNP_chr, SNP_position in either "ler" or "cvi" as indicated in the column header, the number of reads overlapping the SNP of interest (whose base call matches the reference sequence), the number of reads overlapping the SNP of interest (whose base call matches the other sequence), Novel_variant_counts is the number of reads overlapping the SNP of interest, whose base call matches neither the reference nor the other sequence.
Supplementary_files_format_and_content: *_statistics_per_locus.txt, tab-delimited text file with number of reads overlapping every annotated locus in TAIR10; SNP counts are only reported for SNPs that had overlapping reads. The SNPs listed in the _SNP_counts.txt files are thus a subset of the SNPs used to evaluate parent-of-origin effects; columns are: locus_name is the locus model from TAIR10, num_reads is the total number of reads in the library which overlap this gene model, FPKM is the fragments per kilobase per million, which provides a measure of overall transcript abundance at this locus, calculated using Cufflinks, num_X_reads is the number of reads overlapping SNPs found inside locus_name's gene model, for which all base calls unambiguously assign it to the reference base( X = col or ler), num_Y_reads is the number of reads overlapping SNPs found inside locus_name's gene model, for which all base calls unambiguously assign it to the other base  (Y = ler or cvi). CCE, CCN, LLE, LLN, VVE, VVN _statistics_per_locus.txt only include columns 1-3 since there is no notion of an "other" base since all reads come from the same strain.  N.B. There are often many more num_reads mapping to the locus_name as a whole than the sum of num_X_reads + num_Y_reads because of the non-SNP-overlapping reads, which are nevertheless aligned to gene models in TAIR10. All files begin with a 3-letter sequence, which indicates the tissue and the F1 cross, from which they originate.  C = Col-0, L = Ler, V = Cvi (first two letters indicate strain and which parent is female or male)  E = embryo, N = endosperm, S = whole seeds (third letter indicates the tissue in question)  CVE, for example, indicates Col-0 (female) x Cvi (male) embryo, whereas VCN indicates Cvi (female) x Col-0 (male) endosperm.

source_name: whole seeds

value: whole seed


title: ColxCvi_whole_seed_mRNASeq

description: mRNA-seq


title: CvixCol_endosperm_2_mRNASeq

description: mRNA-seq


title: CvixCol_embryo_mRNASeq

description: mRNA-seq


title: ColxCvi_endosperm_2_mRNASeq

description: mRNA-seq


title: ColxLer_endosperm_4_mRNASeq

description: mRNA-seq


title: CvixCol_endosperm_1_mRNASeq

description: mRNA-seq


title: ColxCol_endosperm_mRNASeq

description: mRNA-seq

value: Col-0 female X Col-0 male


title: ColxCvi_embryo_mRNASeq

description: mRNA-seq


title: pool_human

city: Giessen

first: Birgit

last: Samans

address: Heinrich-Buff-Ring 26-28

country: Germany

institute: University of Giessen

library_source: genomic

data_processing:
Alignment: The sequencing reads were aligned to the precompiled bosTau7/hg19 genome using the short read aligner Bowtie
Peak calling: peak calling was done using MACS with the settings: --nomodel -nolambda --shiftsize=75 --bw 140 --name s_1_1 --gsize=3e9 --tsize=50 --keep-dup=1.
The selection of common peaks in two replicate samples was done using Bedtools suite.
Genome_build: hg19
Supplementary_files_format_and_content: bed file: Nucleosome positions

molecule: genomic DNA

organism: Homo sapiens

source_name: four anonymised fertile donors

extract_protocol:
10 million sperm cells were diluted in PBS and incubated with 0.1% Lysolecithin. After 10mM DTT treatment, freed chromatin was digested with 20U microccal nuclease and centrifuged at 10000 rpm to separate nucleosomal (supernatant) from protamine fraction (pellet). Total DNA from nucleosomal fraction was isolated and separated on 2% agarose gel. 146 bp mono-nucleosomal DNA fragment was purified from the gel (NucleoSpin-Gel-clean-up-Kit, Macherey-Nagel) in order to avoid contaminations with high-molecular protamine-DNA and low molecular sub-nucleosomal DNA.
100 ng of mono-nucleosomal DNA were applied for preparation of the DNA library.DNA samples underwent end repair, dA-tailing and adaptor ligation accordingly to providers’ protocol (Library preparation master mix kit, New England Biolabs).

treatment_protocol: We used fresh ejaculates without prior freezing

tag: age

value: two 27 years old and two 28 years

value: sperm


title: Col x Col_seeds_rep_1

description: sRNA-seq

value: 6 days after pollination


title: MNase Sperm spun

city: Worcester

first: Benjamin

middle: R

last: Carone

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: UMass Medical School

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease digestion of sperm chromatin after centrigation of chromatin.

data_processing:
Removal of 3' adapter sequences using eautils 1.1.2.
Alignment of trimmed sequences to genome using Bowtie v2-2.2.2.
Creation of BigWig using standard scripts in Samtools v0.1.16 and bedGraphToBigWig (available at UCSC genome).
Tab-delimited txt files representing alignment of deepseq libraries to Transcriptional Start Site (TSS) in 20bp windows upstream and downstream of TSS 2000bp using the program SeqMiner v1.3.3e.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: BigWig, tab-delimited text files.

organism: Mus musculus

source_name: Sperm, MNase, spun

growth_protocol: E14 ES cells were cultured on gelatin-coated dishes without feeder cells in standard media containing serum and LIF at 37°C with 5% CO2.

extract_protocol:
Permeabilized ES and sperm nuclei were treated with 10 Units/10^6cells and 1 Unit/10^8cells of micrococcal nuclease (Worthington), respectively, for 5 min @ 37°C. Reaction was stopped with the addition of 10 mM EGTA on ice. For ES cells, nuclei were incubated for 4 hrs at 4°C with rotation, pelleted at 5000g for 5 min, and separated into supernatant and pellet (spun) or were treated the same without centrifugation and separation (unspun). After MNase digestion of sperm nuclei, digestion was centrifuged for 5000g for 5 min.
To characterize the entire range of MNase digestion products, we generated paired-end libraries of DNA fragments from both ES and sperm digestions and performed sequencing using Illumina HiSeq technology. Libraries were prepared as described in PMID: 22025700.

treatment_protocol: Sperm were isolated from the caudal epididymis and vas deferens of 10-week-old C57/6J mice by lacerating tissue in 1 mL of 37°C M2 medium (Sigma). Sperm were allowed to swim up for 1 hr, washed 1X in water, 1X PBS, crosslinked at 37°C with 1% formaldehyde for 15 min, quenched with 250mM glycine for 5 min and frozen in liquid nitrogen.

tag: strain/background

value: 10 weeks

tag: chromatin preparation

value: Micrococcal Nuclease

tag: fraction

value: supernatant

tag: antibody


title: MNase ESC spun

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease digestion of E14 chromatin after centrigation of chromatin.

source_name: Embryonic stem cells, MNase, spun

value: 129 X Ola

tag: cell line

tag: cell type

value: embryonic stem cell line


title: CvixCvi_embryo_mRNASeq

description: mRNA-seq


title: CvixCvi_endosperm_mRNASeq

description: mRNA-seq

value: endosperm


title: PC

city: San Diego

first: Shicheng

last: Guo

address: 8730 Costa Verde

institute: MCRI, SHSCI, GHH, UCSD

data_processing:
Illumina Casava1.7 software used for base-calling.
sequence were mapped to the hg19 human genome reference assembly by BWA alignment tools with the default settings.
The peaks (hypermethylatged regions) were identified using MACS software.
human CpG islands (CGIs) were downloaded from the UCSC database. The genomic methylation profile generated was uploaded to a public database (GEO and UCSC)
Genome_build: h19
Supplementary_files_format_and_content: wig

source_name: Pancreatic Cancer

extract_protocol:
DNA preparation from frozen tissues and cell lines was performed using a conventional proteinase K/organic extraction method as previously described GSE33839
MBD enriched cf DNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: 10 pancreatic cancer mix library

value: pancreatic cancer


title: MNase ESC unspun

description: Non-Separated Fraction of DNA fragments resulting from Microccocal nuclease digestion of E14 chromatin.

source_name: Embryonic stem cells, MNase, unspun

value: non-separated


title: ColxCol_embryo_mRNASeq

description: mRNA-seq


title: s_1_1_human

description: Anonymised fertile donor.

data_processing:
Alignment: The sequencing reads were aligned to the precompiled bosTau7/hg19 genome using the short read aligner Bowtie.
Peak calling: peak calling was done using MACS with the settings: --nomodel -nolambda --shiftsize=75 --bw 140 --name s_1_1 --gsize=3e9 --tsize=50 --keep-dup=1.
The selection of common peaks in two replicate samples was done using Bedtools suite.
Genome_build: GRCh37
Genome_build: bosTau7
Supplementary_files_format_and_content: bed file: Nucleosome positions.

source_name: human sperm

growth_protocol: We used fresh ejaculates without prior freezing.

extract_protocol:
10 million sperm cells were diluted in PBS and incubated with 0.1% Lysolecithin. After 10mM DTT treatment, freed chromatin was digested with 20U micrococcal nuclease and centrifuged at 10000 rpm to separate nucleosomal (supernatant) from protamine fraction (pellet). Total DNA from nucleosomal fraction was isolated and separated on 2% agarose gel. 146 bp mono-nucleosomal DNA fragment was purified from the gel (NucleoSpin-Gel-clean-up-Kit, Macherey-Nagel).
100 ng of mono-nucleosomal DNA were applied for preparation of the DNA library. DNA samples underwent end repair, dA-tailing and adaptor ligation according to the provider's protocol (Library preparation master mix kit, New England Biolabs).

tag: gender

value: male

value: 27 years


title: PN

source_name: Pancreatic Normal

value: 10 matched pancreatic cancer adjacent normal tissue mix library

value: normal pancreatic tissue


title: PL

source_name: Pancreatic Cell Line

value: pancreatic cell line mixture library

value: pancreatic cell lines including (BxPC-3, PANC-1 and CFPAC-1)

value: pancreas


title: BS-Seq Ler x Cvi embryo

data_processing:
Adapters and low quality reads (less than 75% quality scores above 25) were discarded after running quality control of sequencing reads with fastqc
Reads were aligned to the TAIR10 reference genome using Bismark (Krueger and Andrews, 2011) with the following parameters: -n 1 -l 50, where n is the maximum number of mismatches and -l the length of seed (first number of nt that are mapped with less than n mismatches).
Libraries prepared from Ler and Ler-Cvi reciprocal crosses were first aligned to Ler-0 genome (Gan et al., 2011). After mapping, a 2-strain alignment was used to convert Ler-0 genome coordinates to TAIR10. coordinates, allowing subsequent pairwise comparisons between libraries.
The mean bisulfite conversion rate for each library was calculated based on the methylation status of each cytosine from reads mapping to the chloroplast genome, which are expected to be unmethylated.
F1 hybrid libraries: parental contribution to methylation was determined by first mapping the reads to one of the parental genomes (Col-Cvi reads to TAIR10 and Ler-Cvi reads to Ler). Reads that failed to map to either the TAIR10 or Ler genomes were mapped against the Cvi pseudogenome (TAIR10 genome with Cvi SNP substitutions) using the same alignment parameters (-n 1 -l 50).
Redundant mapped reads from each library were eliminated starting from a sorted SAM file, keeping only one sequence per strand that mapped to the same positions. To do this, reads were sorted by decreasing prevalence followed by increasing number of mismatches (not counting bisulfite conversions) to the genome. The most prevalent read with the total highest quality string was kept. In the case of a tie, the read with the fewest number of mismatches was retained.
Bismark’s supplementary script, “methylation extractor”, was used to calculate a methylation value for each cytosine.
The genome was divided into 300nt windows that overlapped by 100nt. Using Bismark's methylation extractor output files as input, weighted methylation levels for each window were calculated as described in (Schultz et al., 2012), requiring at least 5-read coverage at each site.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_window.mean.bed; files are in bed format with mean methylation level across each 300 nt window for the three methylation contexts (CG, CHG, CHH). Samples are indicated in the file name, and represent embryo and endosperm for 7 crosses: ColxCol, ColxCvi, CvixCol, CvixCvi, LerxLer, LerxCvi, and CvixLer. Column headings: Chromosome number, window start position (nt), window end position (nt), mean methylation.
Supplementary_files_format_and_content: weighted_summary_*; Files are in bed format with percent methylation for the three methylation contexts (CG, CHG, CHH).  Weighted methylation for each window (300 nt) was calculated as described in (Schultz et al., 2012), requiring at least 5-read coverage at each C site.   Column headings: Chromosome number, window start position (nt), window end position (nt), reads count per window, methylated reads, weighted methylation level.

extract_protocol: At least 1 mg of RNAse-treated DNA was used for library preparation. Libraries were made using an Illumina TruSeq kit, with the following modifications. DNA was sheared using a Covaris instrument (settings: peak power 175W, duty factor 10, cycles/burst 200, time 6 min, 6 C), purified using Agencourt AMPure beads (1.4x DNA:beads) (Beckman Coulter, Inc., Brea, CA), and resuspended in 50 ml of water followed by end repair and 3’ end adenylation. Illumina TruSeq DNA adapters, which contain 5-methylcytosines instead of cytosines, were ligated in a 50-μl reaction. DNA was incubated overnight at 16°C with 2.5 ml adapters, 5,000 units T4 DNA Ligase (New England BioLabs, Ipswich, MA), and 1× T4 Ligase buffer with ATP.  DNA was cleaned twice using Agencourt AMPure beads before bisulfite treatment with the MethylCode Bisulfite Conversion as per manual instructions (Invitrogen, Life Technology Corporation, Carlsbad, CA). Bisulfite-treated DNA was eluted in 10 μl. Three μl was used as a template in each of two PCR reactions with 0.5 units Pfu Turbo, Cx Hotstart DNA Polymerase, 1 μl 10mM dNTPs, and 1× Turbo Cx buffer. PCR conditions were: 95°C for 2 min, 12-15 cycles (95°C for 20 sec, 60°C for 30 sec, 72°C for 1 min), and 72°C for 7 min.

value: Ler female X Cvi male

value: 6 days after pollination

value: embryo


title: BS-Seq Ler x Cvi endosperm


title: BS-Seq Cvi x Ler embryo

value: Cvi female X Ler male


title: BS-Seq Cvi x Col endosperm

value: Cvi female X Col-0 male


title: BS-Seq Cvi x Col embryo


title: BS-Seq Cvi embryo

value: Cvi female X Cvi male


title: BS-Seq Col x Cvi endosperm

value: Col-0 female X Cvi male

value: endosperm


title: BS-Seq Col x Cvi embryo


title: BS-Seq Cvi endosperm


title: BS-Seq Ler embryo

value: Ler female X Ler male


title: BS-Seq Ler endosperm


title: ColxCvi_endosperm_1_mRNASeq

description: mRNA-seq


title: Ler smallRNAseq

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
Illumina Casava software used for basecalling.
The raw reads of small RNAs were processed by PERL scripts built in house. Briefly, the raw reads were screened with Illumina’s quality control filter. The reads that passed the filter were separated into different bins according to their barcodes (indexes). The adaptor was trimmed for each read. Reads that match known rRNAs, tRNAs, snRNAs, and snoRNAs were removed. Reads of 20–24 nt were selected as the raw small RNA sequences. For Col-0, sde4-3, and nrpe1-11, which are in the Columbia ecotype, the small RNA reads were mapped to the Tair10 Arabidopsis genome with SOAP2. For Ler and top1a, which are in the Landsberg ecotype, the small RNA reads were mapped to a pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt).
Every chromosome of Arabidopsis was divided into continuous 500 bp windows. Small RNAs whose 5’ nucleotide falls into a 500 bp window were counted as those belonging to this window. The number of reads in every window was recorded and served as the abundance of small RNAs in this window. The reads were normalized to RPM (reads per million)
Genome_build: TAIR10, and pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt)
Supplementary_files_format_and_content: txt file, which has two columns chr_postion, RPM (reads per million)

source_name: Ler smallRNAseq

growth_protocol: Arabidopsis thaliana seeds were surface sterilized by either 30% bleach or fumigated in an airtight container with a solution containing 50 mL of 100% bleach and 8% HCl for six hours. After, the seeds were planted on half-strength MS-agar plates containing 1% sucrose (no sucrose was added in plates used for chemical screening to minimize fungal growth), stratified at 4°C for two days and moved into a growth chamber. Plants were grown under continuous light at 23°C. All experiments were performed with ten-day-old seedlings.

extract_protocol:
Fifty μg total RNA was resolved on a 15% denaturing polyacrylamide gel and a gel slice containing RNAs of 15 to 40 nucleotides (based on the O’ Range Ruler 10 bp RNA ladder (Thermo Scientific)) was extracted and transferred to a 1.5 ml tube. The gel piece was ground, 500μl of 0.4N NaCl (DEPC) was added to the ground mixture, and the tube containing the gel slice was shaken overnight at 4°C. Eluted RNAs were precipitated using ethanol, re-suspended in DEPC water
Library was constructed with the Illumina TruSeq-small RNA sample preparation kit per manufacturer’s instructions (Illumina). In brief, gel-purified small RNAs were ligated sequentially to 3’ and 5’ adaptors. Following reverse transcription, PCR amplification of the cDNA resulted in the small RNA library, which was gel-purified and subjected to high throughput sequencing

tag: ecotype

value: Landsberg erecta

value: ten-day-old seedlings

value: wild type


title: nrpe1-11 smallRNAseq

source_name: nrpe1-11 smallRNAseq

value: Columbia


title: LerxLer_endosperm_mRNASeq

description: mRNA-seq


title: Eu-myc.input.P1

status: Public on Jul 07 2014

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
peak calling performed with MACS version 1.4.1; macs -t samplebam -c inputbam --format="BAM" --off-auto -p 1e-8 --mfold=7,30 --diag --fe-min=2 --fe-max=30 --fe-step=2; the largest file between input and sample is randomly downsampled to the size of the smallest
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

source_name: Primary B-cells

growth_protocol: Splenic B-cells were isolated from young 6-8 weeks old animal by incubation with B220 MicroBeads (Miltenyi Biotech) and enriched by magnetic cell sorting (MACS), according to the manufacturer’s instructions (Miltenyi Biotech).

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

value: B cells from spleen

tag: genotype/variation

value: WT

tag: chip antibody


title: 3T9.mycER.DNAseI.4hOHT.B

source_name: embryonic fibroblasts, E13.5

growth_protocol: DMEM + penicillin/streptomycin + 2mM glutamin + 10% FBS

extract_protocol:
Cells were resuspended in Buffer A (15 mM Tris-HCl pH 8, 15 mM NaCl, 60 mM KCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, freshly supplemented with 0.5 mM spermidine and 0.15 mM spermine). An equal volume of lysis buffer (Buffer A with 0.1% NP40) was added and the cells were incubated on ice for 10 min. Nuclei were pelleted, washed once with buffer A and then resuspended at a concentration of 50x106 nuclei/ml. 107 nuclei were diluted with an equal volume of 2x DNase I reaction buffer (Roche). DNase I (Roche, 04716728001) was added at increasing concentrations (0, 100, 200, 300, 400, 500 U/ml) and DNA was digested for 10 min at 37°C. An equal volume of Stop buffer (50 mM Tris-HCl pH 8, 100 mM NaCl, 0.1% SDS, 100 mM EDTA pH 8, freshly supplemented with 0.5 mM spermidine, 0.15 mM spermine and 10 μg/ml of RNAse A) was added. Samples were incubated at 55°C for 30 min (220 rpm agitation). 0.2μg/μl of Proteinase K were added and samples were incubated at 55°C overnight (220 rpm). DNA was extracted using a standard phenol/chloroform extraction protocol, dissolved in 100μl of TE (55°C, 2h). Small molecular weight DNA was purified using AMPure beads (Agencourt AMPure XP Reagent, A63881). The eluted DNA was purified once more (20μl of beads; 120μl of 20% PEG buffer) and after washing eluted in 20μl of H2O. DNase I performance was checked by qPCR and samples for sequencing were selected based on the highest signal to noise ratio based on selected genomic regions (MycER fibroblasts: 200-300 U/ml of DNase I). Chosen samples were size-selected run on an agarose gel, small molecular weight DNA (<500 bp) was eluted from the gel with a Qiagen Gel purification kit according to the manufacturer. Up to 10ng DNA was prepared for HiSeq2000 sequencing with TruSeq ChIP Sample Prep Kit (Illumina) following manufacturer instructions. As input DNA, sonicated genomic DNA was used.
Libraries were prepared for Illumina sequencing using a standard protocol for ChIP-seq consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

treatment_protocol: 400 nM 4-hydroxytamoxifen

value: mixed

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER


title: Eu-myc.input.C1


title: Col smallRNAseq

source_name: Col smallRNAseq


title: 3T9.mycER.DNAseI.0hOHT.B

treatment_protocol: EtOH


title: 3T9.Serum.input

value: c-mycflox/flox


title: 3T9.Serum.Myc.t2h

treatment_protocol: serum starved (0% FBS for 48h), then serum stimulated (10% FBS for 2h)

value: c-Myc N262 (Santa Cruz, catalog# sc764, lot# G0111)


title: 3T9.Serum.Myc.t0h

treatment_protocol: serum starved (0% FBS for 48h)


title: 3T9.mycER.RNAseq.4hOHT_4sU

description:
Sample 29
nascent RNA

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded -G gtffile reffile fastqfile
removing duplicate reads: samtools rmdup -S bamfile
from Sample 1 to 11: quantifying read counts over features with HTSeq version 0.5.3p9: python -m HTSeq.scripts.count -q --mode=intersection-nonempty --stranded=no --idattr=gene_id
from Sample 12 to 29: quantifying read counts over features with countOverlaps function within Bioconductor GenomicFeatures package
quantifying transcript abundance through ‘Reads Per Kilobase exon model per Million mapped reads’ (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: text file with rpkm

growth_protocol: DMEM + penicillin/streptomycin + 2mM glutamin + 10% FBS; treatment with 4-hydroxytamoxifen (400nM; 4h)

extract_protocol:
B cells: Total RNA was purified using Trizol (Invitrogen), treated with Turbo DNase (Ambion) and purified with RNA Clean XP (Agencourt). 5 mg of purified RNA were then treated with Ribozero rRNA removal kit (Epicentre) and EtOH precipitated. RNA quality and removal of rRNA were checked with the Agilent 2100 Bioanalyser (Agilent Technologies); fibroblasts: RNA was extracted with the Qiagen miRNeasy kit according to the manufacturer. DNA was digested on the columns (Qiagen). 5 μg of purified RNA were then treated with Ribozero rRNA removal kit (Epicentre) and EtOH precipitated. RNA quality and removal of rRNA were checked with the Agilent 2100 Bioanalyser (Agilent Technologies).; samples 28 and 29 (4sU): 4sU-labeling and sequencing of 4sU-labeled RNA of 3T9 MycER fibroblasts was performed as described previously with minor modifications. Briefly, MycER fibroblasts were treated with OHT for 4 hours. Cells were labeled with 300µM of 4-thiouridine (4sU; Sigma T4509) for 10 min. Medium was removed, cells were put on ice, washed 3x with cold PBS. Cells were scraped in cold PBS and pelleted. RNA was extracted with the Qiagen miRNeasy kit according to the manufacturer including the recommended DNase I digest. 50µg of total RNA was used for the biotinylation reaction: RNA was diluted in 100µl of RNAse free water. 100µl of biotinylation buffer (2.5x stock; 25 mM Tris, pH 7.4, 2.5 mM EDTA) and 50µl of EZ-link Biotin-HPDP (1mg/ml in DMF; Pierce/Thermo Scientific 21341) were added and incubated for 2 hours at room temperature. RNA was precipitated and unbound Biotin-HPDP was removed by a combination of chloroform/isamylalcohol (24:1) precipitation with purification using MaXtract high density tubes from Qiagen. Biotinylated RNA was purified using Dynabeads MyOne Streptavidin T1 (Invitrogen). Before addition of RNA, 50µl of beads were washed 2x in washing buffer A (100 mM NaOH, 50 mM NaCl) and once in washing buffer B (100 mM NaCl). Beads were resuspended in 100µl of buffer C (2M NaCl, 10 mM Tris, pH 7.5, 1 mM EDTA, 0.1% Tween-20) to a final concentration of 5 μg/μl. RNA was added in an equal volume and rotated at room temperature for 15 min. Beads were washed 3x with washing buffer D (1M NaCl, 5 mM Tris, pH 7.5, 0.5 mM EDTA, 0.05% Tween-20). RNA was eluted from the beads in 100µl of 10mM EDTA in 95% formamide (65°C, 10 min). RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). The 4sU-sequencing library was prepared with the Tru-Seq Illumina kit following the manufacturer’s instructions starting from RNA fragmentation.
Libraries for RNA-Seq were then prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads).

treatment_protocol: 400 nM 4-hydroxytamoxifen, 4h


title: RNA-seq - WT ischemia, AN6

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description:
AN6
WT_Is_1
Patient sample: Control=ALDH2 wild type (wt) #3, following ischemia.

data_processing:
Mapped using Tophat 2.0.10 to the hg19 reference genome.
Cuffmerge 2.1.1
Cuffdiff 2.1.1
Quantification of the FPKM values was first performed by using Tophat to map the reads to the reference genome (hg19), and then using cufflinks, the transcript assembly was performed. CummeRbund was then used to extract the FPKM values for each of the samples to generate the GeneMatrix.txt file.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: GeneMatrix.txt: Tab-delimited text file includes FPKM values for each of the samples.

source_name: hiPSC-CM, WT ischemia

growth_protocol: RPMI with B27 supplementation.

extract_protocol:
Cells were lysed and RNA was extracted using a Qiagen RNeasy kit.
Total RNA was processed using the Ovation RNA-seq v2 kit.

treatment_protocol: Control or ischemia.

value: ischemia

value: monolayer cardiomyocytes

tag: days in culture

value: day 30 of differentiation


title: 3T9.mycER.RNAseq.0hOHT_4sU

description:
Sample 28
nascent RNA


title: RNA-seq - Mutant control, AN4

description:
AN4
MUT_Con_1
Patient sample: Mutation ALDH2*2/1 (E487K genetic polymorphism) #5, control/no ischemia.

source_name: hiPSC-CM, mutant control

value: no ischemia


title: BS-Seq Col embryo

source_name: embryo

tag: genotype

value: Col-0 female X Col-0 male

tag: developmental stage

value: 6 days after pollination

value: embryo


title: top1a-2 smallRNAseq

source_name: top1a-2 smallRNAseq

value: Landsberg erecta

tag: tissue

value: ten-day-old seedlings


title: RNA-seq - Mutant control, AN3

description:
AN3
MUT_Con_0
Patient sample: Mutation ALDH2*2/1 (E487K genetic polymorphism) #5, control/no ischemia.

tag: treatment


title: 3T9.mycER.RNAseq.16hOHT_4

description:
Sample 27
RNA

growth_protocol: DMEM + penicillin/streptomycin + 2mM glutamin + 10% FBS; treatment with 4-hydroxytamoxifen (400nM; 16h)

treatment_protocol: 400 nM 4-hydroxytamoxifen, 16h

tag: strain


title: 3T9.mycER.RNAseq.16hOHT_3

description:
Sample 26
RNA


title: BS-Seq Col endosperm

source_name: endosperm

value: endosperm


title: RNA-seq - WT control, AN2

description:
AN2
WT_Con_1
Patient sample: Control=ALDH2 wild type (wt) #3, control/no ischemia.

source_name: hiPSC-CM, WT control


title: RNA-seq - WT control, AN1

description:
AN1
WT_Con_0
Patient sample: Control=ALDH2 wild type (wt) #3, control/no ischemia.


title: 3T9.mycER.RNAseq.8hOHT_4

description:
Sample 23
RNA

growth_protocol: DMEM + penicillin/streptomycin + 2mM glutamin + 10% FBS; treatment with 4-hydroxytamoxifen (400nM; 8h)

treatment_protocol: 400 nM 4-hydroxytamoxifen, 8h


title: 3T9.Serum.Myc.t1h

treatment_protocol: serum starved (0% FBS for 48h), then serum stimulated (10% FBS for 1h)


title: RNA-seq - Mutant ischemia, AN8

description:
AN8
MUT_Is_1
Patient sample: Mutation ALDH2*2/1 (E487K genetic polymorphism) #5, following ischemia.

source_name: hiPSC-CM, mutant ischemia


title: P493.input

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to hg19 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
peak calling performed with MACS version 1.4.1; macs -t samplebam -c inputbam --format="BAM" --off-auto -p 1e-8 --mfold=7,30 --diag --fe-min=2 --fe-max=30 --fe-step=2; the largest file between input and sample is randomly downsampled to the size of the smallest
Genome_build: hg19
Supplementary_files_format_and_content: bed files with enriched regions

source_name: B-cell lymphoma cell line

growth_protocol: RPMI + 10% Tetracycline-free serum


title: 3T9.mycER.RNAseq.8hOHT_3

description:
Sample 22
RNA


title: RNA-seq - Mutant ischemia, AN7

description:
AN7
MUT_Is_0
Patient sample: Mutation ALDH2*2/1 (E487K genetic polymorphism) #5, following ischemia.


title: P493.H3K27ac.t24h

treatment_protocol: 0.2 µg/mL Tetracycline (Myc transgene repressed) for 72h and then released in fresh medium without Tetracycline for 24h

value: H3K27ac (Abcam, catalog# ab4729, lot# GR45851-1)


title: LerxLer_embryo_mRNASeq

description: mRNA-seq

value: Ler female X Ler male


title: sde4-3 smallRNAseq

source_name: sde4-3 smallRNAseq

value: Columbia


title: RNA-seq - WT ischemia, AN5

description:
AN5
WT_Is_0
Patient sample: Control=ALDH2 wild type (wt) #3, following ischemia.

value: WT


title: P493.Pol2.t24h

value: RNAPII (Santa Cruz, catalog# sc-899, lot# F0112)


title: 3T9.mycER.RNAseq.8hOHT_1

description:
Sample 20
RNA

value: mixed

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER


title: BS-Seq Cvi x Ler endosperm

value: Cvi female X Ler male


title: P493.H3K4me3.t24h

value: H3K4me3 (Active Motif, catalog# 39159, lot# 1609004)


title: P493.Myc.t24h

value: c-Myc N262 (Santa Cruz, catalog# sc764, lot# G0111)


title: 3T9.mycER.RNAseq.4hOHT_3

description:
Sample 18
RNA


title: 3T9.mycER.RNAseq.4hOHT_4

description:
Sample 19
RNA


title: P493.Myc.t1h

treatment_protocol: 0.2 µg/mL Tetracycline (Myc transgene repressed) for 72h and then released in fresh medium without Tetracycline for 1h


title: 3T9.mycER.RNAseq.8hOHT_2

description:
Sample 21
RNA


title: 3T9.mycER.RNAseq.16hOHT_1

description:
Sample 24
RNA


title: 3T9.mycER.RNAseq.16hOHT_2

description:
Sample 25
RNA


title: 3T9.mycER.RNAseq.4hOHT_2

description:
Sample 17
RNA


title: 3T9.mycER.RNAseq.4hOHT_1

description:
Sample 16
RNA


title: siTOX4 rep3

city: East Melbourne

first: Katrina

middle: Joy

last: Falkenberg

state: Victoria

address: St Andrews Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the human reference genome (GRCh37) using Tophat v1.4.1 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl v67 gtf. Counts were normalised using the limma-voom method.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample

source_name: colorectal carcinoma cell line

growth_protocol: Cells were cultured in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% sodium pyruvate, 2.5g/L glucose.

extract_protocol:
RNA was extracted from cells using the Rneasy RNA extraction kit (QIAGEN) as per the manufacturer's protocol.  RNA was quantitated using spectrophotometry (Nanodrop).
2ug RNA was prepared for sequencing using the TruSeq RNA Sample Preparation v2 Guide with all kit reagents purchased from Illumina.

treatment_protocol: Cells were reverse transfected in 12 well plates with the appropriate siRNA (final concentration 40nM, Dharmacon siGENOME SMARTpools, Thermo Fisher) or lipid only as a control (mock transfection). Each well contained 3.5 x 10^5 cells and 1.0ul of Dharmafect 2 (Thermo Fisher).  Media was refreshed after 24hrs and cells harvested by trypsinisation after a total of 48hrs post-transfection.

value: vorinostat-resistant HCT116


title: siTGM5 rep3


title: siSAP130 rep3


title: 3T9.mycER.RNAseq.0hOHT_3

description:
Sample 14
RNA


title: siRGS18 rep3


title: siNFYA rep3

value: siNFYA


title: siJAK2 rep3


title: siGLI1 rep3


title: 3T9.mycER.RNAseq.0hOHT_2

description:
Sample 13
RNA


title: 3T9.mycER.RNAseq.0hOHT_1

description:
Sample 12
RNA


title: Eu-myc.RNAseq.T_3

description:
Sample 11
RNA

growth_protocol: Single cells suspension of tumor cells  were  obtained  by pressing the  lymphnodes through nylon cell strainers without further purification.

value: B cells from lymphnodes

value: Tg


title: Eu-myc.RNAseq.P_5

description:
Sample 8
RNA

value: B cells from spleen


title: Eu-myc.RNAseq.P_4

description:
Sample 7
RNA


title: Eu-myc.RNAseq.P_3

description:
Sample 6
RNA


title: 3T9.mycER.RNAseq.0hOHT_4

description:
Sample 15
RNA


title: siDPPA5 rep3


title: siCDK10 rep3


title: siBEGAIN rep3

value: siBEGAIN


title: Eu-myc.RNAseq.T_1

description:
Sample 9
RNA


title: Eu-myc.RNAseq.C_4

description:
Sample 3
RNA


title: mock rep3

value: mock


title: Eu-myc.RNAseq.C_6

description:
Sample 4
RNA


title: Eu-myc.RNAseq.C_1

description:
Sample 1
RNA


title: Eu-myc.RNAseq.P_2

description:
Sample 5
RNA


title: siTGM5 rep2


title: Eu-myc.H3K4me1.P2

description: Sample 51

value: H3K4me1 (Abcam, catalog# ab8895, lot# GR46388-1)


title: Eu-myc.H3K4me1.C2

description: Sample 50


title: Eu-myc.RNAseq.T_2

description:
Sample 10
RNA


title: siTOX4 rep2


title: Eu-myc.RNAseq.C_3

description:
Sample 2
RNA


title: siSAP130 rep2


title: siPOLR2D rep3


title: siPSMD13 rep2


title: Eu-myc.H3K4me3.C2

description: Sample 48


title: siEIF3L rep3


title: siRGS18 rep2


title: Eu-myc.H3K4me3.P2

description: Sample 49


title: siPSMD13 rep3


title: 3T9.mycER.input.OHT

description: Sample 47


title: siPOLR2D rep2


title: siCCNK rep3

value: siCCNK


title: siJAK2 rep2


title: siGLI1 rep2


title: 3T9.mycER.H3K27ac.4hOHT

description: Sample 46

value: H3K27ac (Abcam, catalog# ab4729, lot# GR45851-1)


title: 3T9.mycER.H3K27ac.0hOHT

description: Sample 45


title: siCDK10 rep2


title: siEIF3L rep2


title: 3T9.mycER.H3K4me3.4hOHT

description: Sample 42


title: 3T9.mycER.H3K4me3.0hOHT

description: Sample 41


title: siBEGAIN rep2


title: mock rep2


title: 3T9.mycER.Myc.4hOHT

description: Sample 40

value: c-Myc N262 (Santa Cruz , catalog# sc764, lot#G0111)


title: siTGM5 rep1


title: 3T9.mycER.input.Pol2

description: Sample 38

value: mixed


title: 3T9.mycER.Pol2.4hOHT

description: Sample 37

value: 3T9 fibroblasts

value: RNAPII (Santa Cruz, catalog# sc-899, lot# F0112)


title: 3T9.mycER.Myc.0hOHT

description: Sample 39

value: c-mycflox/flox; in vitro infected with MycER


title: siSAP130 rep1


title: Eu-myc.H3K27ac.T3

description: Sample 27


title: siNFYA rep2


title: Eu-myc.H3K27ac.T2

description: Sample 26


title: Eu-myc.H3K27ac.T1

description: Sample 25


title: siPSMD13 rep1


title: siPOLR2D rep1


title: 3T9.mycER.Pol2.0hOHT

description: Sample 36


title: siNFYA rep1


title: Eu-myc.input.CPT

description: Sample 28

value: WT


title: siDPPA5 rep2


title: Eu-myc.H3K27ac.P

description: Sample 24


title: 3T9.mycER.H3K4me1.0hOHT

description: Sample 43


title: siJAK2 rep1


title: Eu-myc.H3K27ac.C

description: Sample 23


title: siCCNK rep2


title: siGLI1 rep1


title: 3T9.mycER.H3K4me1.4hOHT

description: Sample 44


title: siEIF3L rep1


title: siTOX4 rep1


title: Eu-myc.H3K4me1.T2

description: Sample 21


title: Eu-myc.H3K4me1.T3

description: Sample 22


title: siRGS18 rep1


title: siDPPA5 rep1


title: Eu-myc.H3K4me1.T1

description: Sample 20


title: siBEGAIN rep1


title: siCDK10 rep1


title: Eu-myc.H3K4me1.P1

description: Sample 19


title: Eu-myc.H3K4me3.T3

description: Sample 17

value: H3K4me3 (Active Motif, catalog# 39159, lot# 1609004)


title: Eu-myc.H3K4me1.C1

description: Sample 18


title: siCCNK rep1

value: vorinostat-resistant HCT116


title: mock rep1


title: Eu-myc.H3K4me3.T2

description: Sample 16


title: P493.Pol2.t0h

description: Sample 32

treatment_protocol: 0.2 µg/mL Tetracycline (Myc transgene repressed)


title: P493.Myc.LowMyc

description: Sample 30

treatment_protocol: 200 nM OHT (endogenous Myc activated) and 0.2 µg/mL Tetracyclin (Myc transgene repressed)


title: Eu-myc.H3K4me3.P1

description: Sample 14


title: Eu-myc.H3K4me3.C1

description: Sample 13


title: P493.Myc.HighMyc

description: Sample 31

treatment_protocol: none (Myc transgene expressed)


title: P493.Myc.t0h

description: Sample 29


title: Eu-myc.Pol2.T.3

description: Sample 12


title: Eu-myc.Pol2.P.1

description: Sample 9


title: Eu-myc.Pol2.T.1

description: Sample 10


title: Eu-myc.Myc.C.1

description: Sample 1

value: c-Myc N262 (Santa Cruz, catalog# sc764, lot#G0111)


title: Eu-myc.Myc.T.3

description: Sample 7

value: B cells from lymphnodes


title: Eu-myc.Myc.P.1

description: Sample 2

value: Tg


title: Eu-myc.Pol2.C.1

description: Sample 8

value: B cells from spleen


title: Ler A Bsseq

data_processing:
Illumina Casava software used for basecalling.
Raw data from Illumina sequencing were filtered to remove reads that failed to pass the Illumina quality control and to condense multi-copy reads to a single copy. Hereafter, the reads were mapped to TAIR 10 Arabidopsis genome as well as a C-to-T converted genome using BS_Seeker with default settings. Only perfectly and uniquely mapped reads were retained. The BS_Seeker results were converted to txt files by a perl script built in house.
Genome_build: TAIR10, and pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt)
Supplementary_files_format_and_content: txt file, which has six columns: chr,postion,C context, strand, methylated C number, Total C number

source_name: Ler A Bsseq

extract_protocol:
BSseq: approximately 1μg of genomic DNA was sonicated to 100~300 bp with Diagenode Bioruptor using the following settings: intensity=high, on=30s, off=30s, total time=60min. Sonicated DNA was purified using the PureLink® PCR Purification Kit (Life Sciences). Purified DNA was end-repaired using the End-It kit (Epicentre) except that dCTP was not included in the reaction. The end-repaired DNA was purified with Agencourt AMPure XP beads (Beckman Coulter), A-tailed with dATP and Klenow 3’-5’ exo- (New England Biolabs) for 30 min at 37°C and then purified with Agencourt AMPure XP beads.
BSseq: The purified DNA was ligated overnight at 16°C to genomic DNA adapters from the Illumina Truseq DNA sample preparation kit with T4 DNA Ligase (New England Biolabs).  Ligation products were purified with AMPure XP beads (Beckman) twice.  Less than 400ng ligated product was converted using the MethylCode Kit (Invitrogen) following the manufacturer’s guidelines except that 12ug carrier RNA (Qiagen) was added into the conversion product before column purification. The final conversion product was amplified using PfuTurbo Cx Hotstart DNA Polymerase (Agilent) under the following PCR conditions (2 minutes at 95°C, 9 cycles of 15 seconds at 98°C, 30 seconds at 60°C, 4 minutes at 72°C and 10 minutes at 72°C). The PCR product was purified with AMpure XP beads to obtain the final library DNA. BS-seq libraries were sequenced at 101 cycles using an Illumina HiSeq 2000.

value: Landsberg erecta

value: ten-day-old seedlings

value: wild type


title: top1a-2 A Bsseq

source_name: top1a-2 A Bsseq


title: Pyruvate pH 5.7, Rep B

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Trimmomatic (v0.30)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie  was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis CDC1551 genome
DESeq was used to normalize data by estimating effective library sizes using robust regression
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the DESeq package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .xls spreadsheets and represents the average of 2 biological replicates

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 was grown in standing T-75 flasks in 40 mL of medium seeded an initial OD of 0.1.  Cultures were incubated at 37C for 3 days.

extract_protocol: cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.

treatment_protocol: Mtb cultures were resuspended in minimal medium and examined under four conditions pH 7.0 10 mM glycerol, pH 5.7 10 mM glycerol, pH 7.0 10 mM pyruvate, pH 5.7 10 mM pyruvate.  Following 3 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

tag: ph

tag: carbon source

value: Pyruvate


title: Eu-myc.Myc.T.1

description: Sample 5


title: Eu-myc.Pol2.T.2

description: Sample 11


title: Pyruvate pH 7.0, Rep B


title: Eu-myc.Myc.T.2

description: Sample 6


title: Pyruvate pH 5.7, Rep A


title: nrpe1-11 C Bsseq

source_name: nrpe1-11 C Bsseq

value: Columbia


title: Eu-myc.Myc.P.3

description: Sample 4

source_name: Primary B-cells


title: Pyruvate pH 7.0, Rep A


title: sde4-3 C Bsseq

source_name: sde4-3 C Bsseq


title: nrpe1-11 B Bsseq

source_name: nrpe1-11 B Bsseq


title: Eu-myc.H3K4me3.T1

description: Sample 15


title: Col C BSseq

source_name: Col C BSseq


title: top1a-7 A BSseq

source_name: top1a-7 A BSseq


title: sde4-3 B Bsseq

source_name: sde4-3 B Bsseq


title: Glycerol pH 5.7, Rep A

value: Glycerol


title: Col B BSseq

source_name: Col B BSseq


title: Glycerol pH 7.0, Rep B


title: 3T9.mycER.DNAseI.4hOHT

description: Sample 2

source_name: embryonic fibroblasts, E13.5

value: mixed


title: Col A BSseq

source_name: Col A BSseq


title: 3T9.mycER.input.DNAseI

description: Sample 3

value: 3T9 fibroblasts


title: 3T9.mycER.DNAseI.0hOHT

description: Sample 1


title: Glycerol pH 7.0, Rep A


title: INPUT OHT HS ChipSeq technical replicate 1 and 2

status: Public on Jul 06 2014

city: London

first: Gordon

last: Peters

address: 44 Lincolns Inn Fields

country: United Kingdom

institute: CRUK London Research Institute

description: Chip-Seq

data_processing: Duplicates were removed using the Picard MarkDuplicates program (picard-tools package version 1.81; http://picard.sourceforge.net) with default parameters.

source_name: Cultured fibroblasts

growth_protocol: The Hs68 strain of human foreskin fibroblasts (ATCC: CRL 1635) expressing an HA-tagged AsiSI:ER fusion protein were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 50-51bp single end sequencing on the Illumina HiSeq 2500.

treatment_protocol: Cells expressing the HA-tagged AsiSI:ER fusion protein were treated with 300 nM  4-hydroxy tamoxifen (OHT) or an equivalent amount of solvent (methanol) for 4 h to activate the AsiSI restriction enzyme.

value: normal foreskin

value: 300 nM 4-hydroxy tamoxifen (OHT) for 4 h


title: INPUT METHANOL HS ChipSeq technical replicate 1 and 2

description: Chip-Seq

value: 300 nM solvent (methanol) for 4 h


title: MEL18 OHT HS ChipSeq technical replicate 1 and 2

description: Chip-Seq

value: MEL18 (Santa Cruz sc-10744)


title: MEL18 METHANOL HS ChipSeq technical replicate 1 and 2

description: Chip-Seq


title: Eu-myc.Myc.P.2

description: Sample 3


title: NS_Fezf2_2

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
reads were aligned to the mouse (mm9) reference genome assemblies using Tophat2 using default options.
Aligned reads were used as input for Cuffdiff2 to determine expression levels (FPKM) and differential expression between conditions using the default options.
CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was used to process, index, and visualize the output of the Cuffdiff2 analyses.
Genome_build: mm9
Supplementary_files_format_and_content: CummeRbund diffTable output. Contains log ratios and differential significance test results.

source_name: Dissociated E14.5 cortical neurospheres

growth_protocol: Mice were housed under controlled pathogen-free conditions (Harvard University’s Biological Research Infrastructure) and experiments were approved by the Harvard University Committee on the Use of Animals in Research and Teaching. Primary cortical progenitors were isolated from E14.5 brains and grown as neurospheres in presence of growth factors. Neurospheres were expanded for a maximum of one passages and then plated as a monolayer on dishes coated with poly-D-lysine (VWR) and laminin (BD). E14.5 pregnant dams were deeply anesthetized and the embryos were removed. Presumptive somatosensory area was microdissected in cold Hanks’ medium and mechanically triturated to obtain a single cell suspension. Cells were spun at 5,000 g for 5 min at room temperature and the pellet was resuspended in Neurosphere Media, containing 5,000U Penicillin/streptomycin, 200mM L-glutamine, N2 and B27 supplements (Gibco), as well as 20 ng/ml epidermal growth factor (EGF) (Sigma), and 20 ng/ml β-fibroblast growth factor (FGF) (Millipore) in order to promote the survival of neural stem cells. After quantification of cell density, neural stem cells were plated in 200 ml tissue culture flasks (untreated or low-adherence) (Corning) at 200,000 cells/flask and incubated at 37°C with 5% CO2. The medium was changed every 3–4 days and the cells were expanded as neurospheres for one passage. Subsequently, cells were plated as a monolayer on dishes previously coated with poly-D-lysine (VWR) and laminin (BD).

extract_protocol:
Total RNA was isolated using Qiazol (Qiagen)/chloroform extraction followed by spin-column purification (RNeasy mini kit, Qiagen) according to the manufacturer’s instructions. RNA concentration and purity were measured with Nanodrop (Thermo Fisher) and RNA integrity was assessed on a Bioanalyzer (Agilent) using the. High quality RNA samples (RNA Integrity Number ≥ 8) were used for library preparation.
mRNA-seq libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s protocol. 200ng total RNA was used as input for the TruSeq libraries from mouse tissues, and 200ng for the libraries from neural stem cells and neurospheres. Prior to sequencing, libraries were run on a Bioanalyzer DNA7500 chip to assess purity, fragment size, and concentration. Libraries free of adapter dimers and with a peak region area (220-500bp) ≥ 80% of the total area were sequenced. Individually barcoded samples were pooled and sequenced on the Illumina HiSeq 2500 platform.

treatment_protocol: 3XFLAG-Fezf2GFP and 3XFLAGGFP constructs were first cloned into pRETROX-IRES-ZsGreen1 retroviral vectors (Clontech Laboratories, Inc.) to generate high titer, replication-incompetent, VSVg-coated lentiviral particles that were packaged in 293T cells (MOI < 109 PFU/ml). 12-18 hours after plating, neural stem cells were infected with retroviruses. 16–20 h after infection, cells were switched into fresh media. Cells were collected 48 hours after infection

value: Primary cortical neurospheres

tag: passage


title: DNAPKCS OHT HS ChipSeq technical replicate 1 and 2

description: Chip-Seq

value: pDNA-PKcs (Abcam ab18192)


title: NS_GFP_1


title: NS_GFP_2


title: Glycerol pH 5.7, Rep B


title: DNAPKCS METHANOL HS ChipSeq technical replicate 1 and 2

description: Chip-Seq


title: NS_Fezf2_1


title: ChIP-seq induced GFP-3Flag in neurospheres replicate 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Chromatin IP against Flag

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment: sequencing reads were aligned to the mouse genome (version mm9) using Bowtie version 0.12.7 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024", and only uniquely mapping reads were retained for further analysis.
Peak-calling: GEM  was used to detect binding events, using the options “--top 2000 --k_min 7 --k_max 12 --a 20 --q 3 --mrc 1 –constant_model_range --d_l 1000 --d_r 1000 --v 2 --nf --refine_pwm --gc0 0.42”. Reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the scaled read count from the corresponding region in the control experiment (p<10^-6, Binomial test, adjusted for multiple testing using Benjamini & Hochberg’s method).
Genome_build: mm9
Supplementary_files_format_and_content: txt: GEM output files
Supplementary_files_format_and_content: BED: Conversion of GEM output files to BED format, centered on the GEM binding event location
Supplementary_files_format_and_content: BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC)

source_name: Neurospheres

growth_protocol: Primary cortical progenitors were isolated from E14.5 brains and grown as neurospheres in presence of growth factors according to (Ahlenius et al., 2008). Neurospheres were expanded for a maximum of two passages and then plated as a monolayer on dishes coated with poly-D-lysine (VWR) and laminin (BD). Additional details on neurosphere isolation and culture are in Supplemental Experimental Procedures.

extract_protocol:
ChIP analysis was performed on 15x10^7 neural stem cells per condition (3XFlagFezf2IRESZsGFP, 3XFlagIRESZsGFP and untransduced MOCK) as described (Nelson et al., 2006) with modifications as detailed in the Supplemental Experimental Procedures. Briefly, cells were dissociated with 0.25% trypsin (Invitrogen), washed with PBS and chemically cross-linked with formaldehyde solution (1%). Cells were disrupted in lysis buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS;  and protease inhibitors) for 20 min on ice and sonicated with a Bioruptor to shear DNA into 200-700 bp fragments. Dynal magnetic beads (Sheep anti-mouse #M-28, Invitrogen, M2 FLAG) were preblocked with 5 μg of anti-FLAG M2 antibody per reaction (Sigma-Aldrich) overnight inverted at 4° C. Beads were then washed and resuspended in fresh 0.5% BSA diluted in PBS. Bead-antibody complexes were incubated at 4° C overnight with inversion. Beads were resuspended twice in low salt immune complex wash buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.1; and 150 mM NaCl), incubated for 5 min at 4° C, with rotation, and resuspended in LiCl immune complex wash buffer (0.25 M LiCl; 1% NP40; 1% deoxycholate; 1 mM EDTA; and 10 mM Tris-HCl, pH 8.1) twice and incubated for 5 min at 4° C, with rotation. Beads were then rinsed with ice-cold TE and DNA was eluted in 100 μl of elution buffer at 65º for 15 minutes. Reverse crosslinking was performed by incubating the ChIP DNA overnight at 65º. DNA was purified on QIAquick PCR purification columns (Qiagen) for use as template for Solexa library construction.
ChIP-seq libraries prepared using standard Illumina protocols

treatment_protocol: Cortical progenitors were infected with 3XFlagFezf2IRESZsGFP or 3XFlagIRESZsGFP lentiviruses. 3XFlagFezf2IRESZsGFP or 3XFlagIRESZsGFP constructs were first cloned into pRETROX-IRES-ZsGreen1 retroviral vectors (Clontech Laboratories, Inc.) to generate high titer, replication-incompetent, VSVg-coated lentiviral particles that were packaged in 293T cells (MOI < 10^9 PFU/ml). 12-18 hours after plating, neural stem cells were infected with retroviruses. 16–20 h after infection, cells were switched into fresh media. Cells were collected 48 hours after infection for chromatin immunoprecipitation (ChIP).

value: neurosphere

value: Infection with 3XFlagIRESZsGFP

value: anti-FLAG M2 (Sigma, F1804)

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #


title: RNA-Seq-Naive-Donor9

status: Public on Jul 05 2014

city: La Jolla

first: Anna

last: Gerasimova

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description:
Whole Transcriptome Amplification (MDA)
PolyAtail selected messenger RNA

data_processing:
Human RNA-Seq data was mapped against hg19 using tophat46 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/).
49 different RNA-Seq assays were performed and the obtained sam files were converted and merged into separated bam files using samtools.
To identify differential gene expression between cell-types, we performed negative binomial tests for pairwise comparisons of the naïve CD4+, CCR4+, and CCR4- T cells employing the Bioconductor package DESeq and allowing for a false discovery rate of 1%.
Genome_build: hg19
Supplementary_files_format_and_content: For visualization of the RNA-seq data in public genome browsers, sequencing coverage was calculated at genome wide 50bp windows after extending each read to a length of 120bp along the sequencing direction using MEDIPS v.1.10.0 (extend = 120, uniq = F, window_size=50, BSgenome = "BSgenome.Hsapiens.UCSC.hg19")  and the resulting coverage profiles (RPKM) were exported as wiggle files.

source_name: Blood PBMCs

growth_protocol: T cells subtypes were isolated from Peripheral Blood mononuclear cell fraction (PBMC). CD4+ T cells were isolated by a magnetic selection and subsequently stained with an appropriate pannel of surfce markers. CCR4+, CCR4- and naive T cells were then directly sorted by Flow cytometry into lysis buffer (Trizol LS).

extract_protocol:
RNA was extracted using miRNAasy Kit (Qiagen) as described previously (Seumois et al, 2012).
10-15ng of purified total RNA was used for poly A section (Poly(A)Purist Mag kit, Life technologies). Poly A selected RNA was amplified with the Whole Transcriptome Amplification Sequencing Technology kit (SEQR, Sigma) as per manufacturers recommendation. One μg of this amplified cDNA was treated with restriction enzyme (SEQR, Sigma), to remove the primer sequences and then purified using AmpureXP beads (Beckman Coulter). Efficiency of removal of SEQR primer sequences was assessed by PCR. From this step, 250 ng of purified DNA was sonicated with E220 Covaris multiplex sonicator (Covaris) to generate 100-250bp DNA fragments. Sonicated cDNA was used for preparing standard SOLiD sequencing library.

treatment_protocol: No treatment post isolation was applied

tag: cell type

value: Naive T cells

value: CD3+ CD4+ CD45RO- CD45RA+ CD62L+ T cells

tag: disease

value: healthy (tested non-asthmatic)


title: ChIP-seq induced Fezf2-3Flag in neurospheres replicate 2

description: Chromatin IP against Flag

value: Infection with 3XFlagFezf2IRESZsGFP


title: RNA-Seq-Naive-Donor7


title: ChIP-seq uninduced Mock in neurospheres replicate 2

description: Chromatin IP against Flag

value: Uninfected


title: ChIP-seq induced GFP-3Flag in neurospheres replicate 2

description: Chromatin IP against Flag


title: RNA-Seq-Naive-Donor8


title: ChIP-seq uninduced Mock in neurospheres replicate 1

description: Chromatin IP against Flag


title: RNA-Seq-Naive-Donor2


title: RNA-Seq-Naive-Donor20

value: asthmatic


title: RNA-Seq-Naive-Donor16


title: RNA-Seq-Naive-Donor19


title: RNA-Seq-Naive-Donor18


title: RNA-Seq-Naive-Donor14


title: RNA-Seq-Naive-Donor13


title: RNA-Seq-Naive-Donor12


title: ChIP-seq induced Fezf2-3Flag in neurospheres replicate 1

description: Chromatin IP against Flag


title: RNA-Seq-CCR4POS-Donor9

value: CCR4+ T cells

value: CD3+ CD4+ CD45RO+ CD45RA- CCR4+ CD25- T cells


title: RNA-Seq-Naive-Donor10


title: RNA-Seq-Naive-Donor1


title: RNA-Seq-CCR4POS-Donor7


title: RNA-Seq-CCR4POS-Donor6


title: RNA-Seq-Naive-Donor22


title: RNA-Seq-CCR4POS-Donor8


title: RNA-Seq-CCR4POS-Donor22


title: RNA-Seq-CCR4POS-Donor4


title: RNA-Seq-CCR4POS-Donor23


title: RNA-Seq-Naive-Donor23


title: RNA-Seq-CCR4POS-Donor19


title: RNA-Seq-Naive-Donor17


title: RNA-Seq-CCR4POS-Donor18


title: RNA-Seq-CCR4POS-Donor17


title: RNA-Seq-CCR4POS-Donor14


title: RNA-Seq-CCR4POS-Donor13


title: RNA-Seq-Naive-Donor15


title: RNA-Seq-CCR4POS-Donor16


title: RNA-Seq-CCR4POS-Donor12


title: RNA-Seq-CCR4POS-Donor11


title: RNA-Seq-CCR4POS-Donor10


title: RNA-Seq-CCR4POS-Donor20


title: RNA-Seq-CCR4POS-Donor1


title: RNA-Seq-CCR4POS-Donor15


title: RNA-Seq-CCR4NEG-Donor9

value: CCR4- T cells

value: CD3+ CD4+ CD45RO+ CD45RA- CCR4- CD25- T cells


title: RNA-Seq-CCR4NEG-Donor22


title: RNA-Seq-CCR4NEG-Donor8


title: RNA-Seq-CCR4NEG-Donor20


title: RNA-Seq-Naive-Donor11


title: RNA-Seq-CCR4NEG-Donor19


title: RNA-Seq-CCR4NEG-Donor18


title: RNA-Seq-CCR4NEG-Donor17


title: RNA-Seq-CCR4NEG-Donor1


title: RNA-Seq-CCR4NEG-Donor16


title: RNA-Seq-CCR4NEG-Donor13


title: RNA-Seq-CCR4NEG-Donor14


title: RNA-Seq-CCR4NEG-Donor12


title: H3K4me2_ChIPSeq_Naive-Donor23-rep2

data_processing:
ChIP-seq data (csfasta and qual files) were mapped against the human reference genome hg19 (downloaded from the Genome Bioinformatics database of the University of California Santa Cruz) using Bowtie v.0.12.7.
120 different ChIP-Seq assays were performed and the obtained sam files were converted and merged into separated bam files using samtools.
To identify cell type specific differentially enriched regions (DERs), H3K4me2 ChIP-Seq data was grouped according to their cell types: i) naïve CD4+ T cells, (n=42), ii) CCR4+ T cells (n=42), and iii) CCR4− T cells (n=36). Sequencing coverage was calculated for all samples at genome wide 500bp windows, and pairwise differential coverage between groups was calculated using MEDIPS v.1.12.0 (extend = 120, uniq = F, window_size=500, BSgenome = "BSgenome.Hsapiens.UCSC.hg19", minRowSum=1, p.adj = “bonferroni”, diff.method=”edgeR”). Consequently, we performed quantile normalization as a standard prior to identification of differentially enriched regions.
Genome_build: hg19
Supplementary_files_format_and_content: Result Table 1 (MEDIPS.Cell_type_comparison.txt) is a list of all cell-type specific differentially enriched regions (DERs). The table contains adjusted p-values together with fold change for each cell-type pairwise comparison, cell-type mean RPKM values, mean of quantile normalized counts, RPKM values for each sample, and quantile normalized count number for each sample at genome wide 500 bp windows as returned by the MEDIPS software.
Supplementary_files_format_and_content: Result Table 2 (MEDIPS.Asthmatics_vs_Healthy.txt) contains adjusted p-values together with fold change for healthy vs. asthmatic comparisons, mean normalized counts, normalized counts, and RPKM values as returned by the MEDIPS software.

growth_protocol: The base medium for this cell line is ATCC-formulated RPMI-1640 Medium, Catalog No. 30-2001. To make the complete growth medium, add the following components to the base medium: 10% T-STIM with Con A (rat IL-2 culture supplement ) Becton Dickinson, Catalog No. 354115), 10% fetal bovine serum, 0.05 mM 2-mercaptoethanol, 10 pg/ml mouse IL-1 alpha (R&D Systems, Catalog No. 400ML). Subculture actively growing suspension cultures before they have reached 1 X 106 cells/mL or the IL-1 and IL-2 will be rapidly depleted and the cells will lose viability. Use inoculation densities of 2 X 105 viable cells/mL. Medium Renewal:Twice per week.

extract_protocol:
Sorted cells were washed and fixed for 10 min at room temperature with 1:10 dilution of 11% formaldehyde buffer, neutralized 2.5 M glycine, washed twice in ice cold PBS, and cell pellets snap frozen in liquid nitrogen before storing at -80°C. Frozen cells were lysed in 120 μl of SDS lysis buffer containing 1 mM PMSF, 20 mg/ml sodium butyrate and proteinase inhibitor cocktail, and chromatin sheared by sonication, using Bioruptor. 500ng of Chromatin was used for immuno-precipitation. Chromatin was diluted in 1ml of radioimmunoprecipitation assay buffer and immunoprecipitation was done overnight at 4°C by incubating 1 μl of antibody pre-coated on 10 μl protein A coated magnetic beads. Immunocomplexes were captured and washed with RIPA buffer x1, high-salt buffer x1, LiCl buffer x1, and low salt buffer x1. Beads were resuspended in TE transferred to fresh tubes, captured and then resuspended in 1% SDS elution buffer. The crosslinking was reversed by incubating samples for 15 minutes at 65°C, and treated with 2 μl of RNase A for 30 minutes at 37°C, and, with proteinase K for 6 hours at 55°C followed by overnight incubation at 65°C. DNA was purified using affinity. The amount of DNA in the ChIP samples was quantified using picogreen assay. One ng of ChIP DNA was PCR amplified for 18 to 22 cycles using whole genome amplification (WGA). Two μg of this amplified DNA was treated with restriction enzyme to remove the WGA primer sequences and then purified using AmpureXP bead. DNA was sonicated with E220 Covaris multiplex sonicator (Covaris) to generate 100-250bp DNA fragments.
Libraries were prepared according to SOLiD's instructions accompanying the DNA Sample Kit (5500 SOLiD® Fragment 48  Library Core Kit & Fragment Library Barcode Adaptors 1-96).

tag: cell subtype

value: Naïve T cells

tag: cell surface markers

value: H3K4me2 (clone Y47, lot#YH041501C; Abcam)


title: H3K4me2_ChIPSeq_Naive-Donor22-rep2


title: H3K4me2_ChIPSeq_Naive-Donor21-rep3


title: H3K4me2_ChIPSeq_Naive-Donor21-rep2


title: H3K4me2_ChIPSeq_Naive-Donor21-rep1


title: H3K4me2_ChIPSeq_Naive-Donor20-rep2


title: H3K4me2_ChIPSeq_Naive-Donor19-rep1


title: H3K4me2_ChIPSeq_Naive-Donor18-rep1


title: H3K4me2_ChIPSeq_Naive-Donor18-rep2


title: H3K4me2_ChIPSeq_Naive-Donor19-rep2


title: H3K4me2_ChIPSeq_Naive-Donor20-rep1


title: H3K4me2_ChIPSeq_Naive-Donor17-rep2


title: H3K4me2_ChIPSeq_Naive-Donor16-rep1


title: H3K4me2_ChIPSeq_Naive-Donor17-rep1


title: H3K4me2_ChIPSeq_Naive-Donor15-rep2


title: H3K4me2_ChIPSeq_Naive-Donor16-rep2


title: H3K4me2_ChIPSeq_Naive-Donor15-rep1


title: H3K4me2_ChIPSeq_Naive-Donor14-rep2


title: H3K4me2_ChIPSeq_Naive-Donor14-rep1


title: H3K4me2_ChIPSeq_Naive-Donor13-rep2


title: H3K4me2_ChIPSeq_Naive-Donor23-rep1


title: H3K4me2_ChIPSeq_Naive-Donor12-rep2


title: H3K4me2_ChIPSeq_Naive-Donor12-rep1


title: H3K4me2_ChIPSeq_Naive-Donor13-rep1


title: H3K4me2_ChIPSeq_Naive-Donor11-rep1


title: H3K4me2_ChIPSeq_Naive-Donor11-rep2


title: H3K4me2_ChIPSeq_Naive-Donor9-rep1


title: H3K4me2_ChIPSeq_Naive-Donor10-rep1


title: H3K4me2_ChIPSeq_Naive-Donor8-rep2


title: H3K4me2_ChIPSeq_Naive-Donor8-rep1


title: H3K4me2_ChIPSeq_Naive-Donor7-rep2


title: H3K4me2_ChIPSeq_Naive-Donor9-rep2


title: H3K4me2_ChIPSeq_Naive-Donor2-rep2


title: H3K4me2_ChIPSeq_Naive-Donor3-rep2


title: H3K4me2_ChIPSeq_Naive-Donor5-rep2


title: H3K4me2_ChIPSeq_Naive-Donor5-rep1


title: H3K4me2_ChIPSeq_Naive-Donor1-rep3


title: H3K4me2_ChIPSeq_Naive-Donor3-rep1


title: H3K4me2_ChIPSeq_Naive-Donor1-rep2


title: H3K4me2_ChIPSeq_Naive-Donor1-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor23-rep2

value: CCR4+ Tcells


title: H3K4me2_ChIPSeq_CCR4pos-Donor22-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor22-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor23-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor21-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor21-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor20-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor18-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor19-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor19-rep2


title: H3K4me2_ChIPSeq_Naive-Donor7-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor18-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor17-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor17-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor16-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor15-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor15-rep2


title: H3K4me2_ChIPSeq_Naive-Donor2-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor14-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor13-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor13-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor14-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor12-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor10-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor11-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor9-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor9-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor12-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor11-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor20-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor8-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor7-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor8-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor7-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor5-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor5-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor16-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor3-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor4-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor4-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor2-rep1


title: H3K4me2_ChIPSeq_CCR4pos-Donor2-rep2


title: H3K4me2_ChIPSeq_CCR4pos-Donor1-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor23-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor22-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor22-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor21-rep2


title: Nt-iPS52

city: Baoshan

first: Botao

last: Zhao

state: Shanghai

address: 333 Nanchen Rd

department: college of life science

institute: Shanghai University

description:
Small RNA
18-30nt

data_processing:
Remove adaptors, low quality tags and contaminants to get clean reads performed by BGI-Shenzhen, Shenzhen, China.
Tags were annotated by BGI-Shenzhen, Shenzhen, China.
miRNA reads were extracted and subjected to DESeq package in R language.
Normalization and variance stabilizing transformation (VST) were performed by DESeq.
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: Tab-delimited matrix contains the normalized and variance stabilizing transformed values derived by DESeq. The values are log transformed.

source_name: cells established by successively reprogramming of iPSCs by nuclear transfer

growth_protocol: ESCs, Nt-ESs, iPSCs and Nt-iPSCs were cultured on irradiated MEFs, in mESC medium containing leukaemia inhibitory factor (LIF), 15% FBS, nonessential amino acids, L-glutamine, Nucleosides, 2-mercaptoethanol and penicillin/streptomycin. MEFs and feeder cells were cultured in MEF medium containing 10% FBS, nonessential amino acids and penicillin/streptomycin.

extract_protocol:
RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols by BGI-Shenzhen, Shenzhen, China.

tag: strain/background

value: C57B6/129SvJae F1

value: cells established by successively reprogramming of iPSCs (NT-iPSCs)


title: Nt-iPS51

description:
Small RNA
18-30nt


title: H3K4me2_ChIPSeq_CCR4Neg-Donor21-rep1

tag: chip antibody


title: Nt-ES72

description:
Small RNA
18-30nt

source_name: cells established by reprogramming MEF cells using nuclear transfer

value: ESCs established by reprogramming MEF cells (NT-ESCs)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor20-rep1


title: Nt-ES71

description:
Small RNA
18-30nt


title: H3K4me2_ChIPSeq_CCR4Neg-Donor19-rep2


title: iPS62

description:
Small RNA
18-30nt

source_name: induced pluripotent stem cells by OSKM factors

value: induced pluripotent stem cells (iPSCs)


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica12

data_processing:
ChIP-seq data (csfasta and qual files) were mapped against the mouse reference genome mm10 (downloaded from the Genome Bioinformatics database of the University of California Santa Cruz) using Bowtie v.0.12.7.
Pairwise Spearman correlation and scatterplots between samples were calculated by comparing the sequencing coverage at genome wide 500bp windows using MEDIPS v.1.10.0 (extend = 120, uniq = F, window_size=500, BSgenome ="BSgenome.Mmusculus.UCSC.mm10")
For the correlation analysis of Standart H3K4me2 ChiP-Seq replicas 1-6, we have trimmed reads from 50bp to 35bp. Row files contain untimmed reads.
Genome_build: mm10
Supplementary_files_format_and_content: For visualization of the ChIP-seq data in public genome browsers, sequencing coverage was calculated at genome wide 50bp windows after extending each read to a length of 120bp along the sequencing direction using MEDIPS v.1.10.0 (extend = 120, uniq = F, window_size=50, BSgenome = "BSgenome.Mmusculus.UCSC.mm10")  and the resulting coverage profiles (RPKM) were exported as wiggle files. Conversion from wiggle to bigwig files using wigToBigWig utility provided by UCSC Genome Browser

source_name: mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC)

extract_protocol:
Cells were washed and fixed for 10 min at room temperature with 1:10 dilution of 11% formaldehyde buffer, neutralized 2.5 M glycine, washed twice in ice cold PBS, and cell pellets snap frozen in liquid nitrogen before storing at -80°C. Frozen cells were lysed in 120 μl of SDS lysis buffer containing 1 mM PMSF, 20 mg/ml sodium butyrate and proteinase inhibitor cocktail, and chromatin sheared by sonication, using Bioruptor. Different amount of chromatin was used for immuno-precipitation. Chromatin was diluted in 1ml of radioimmunoprecipitation assay buffer and immunoprecipitation was done overnight at 4°C by incubating 1 μl of antibody pre-coated on 10 μl protein A coated magnetic beads. Immunocomplexes were captured and washed with RIPA buffer x1, high-salt buffer x1, LiCl buffer x1, and low salt buffer x1. Beads were resuspended in TE transferred to fresh tubes, captured and then resuspended in 1% SDS elution buffer. The crosslinking was reversed by incubating samples for 15 minutes at 65°C, and treated with 2 μl of RNase A for 30 minutes at 37°C, and, with proteinase K for 6 hours at 55°C followed by overnight incubation at 65°C. DNA was purified using affinity. The amount of DNA in the ChIP samples was quantified using picogreen assay. One ng of ChIP DNA was PCR amplified for 18 to 22 cycles using whole genome amplification (WGA). Two μg of this amplified DNA was treated with restriction enzyme to remove the WGA primer sequences and then purified using AmpureXP bead. DNA was sonicated with E220 Covaris multiplex sonicator (Covaris) to generate 100-250bp DNA fragments.
Libraries were prepared according to SOLiD's instructions accompanying the DNA Sample Kit (5500 SOLiD® Fragment 48  Library Core Kit & Fragment Library Barcode Adaptors 1-96).

value: AKR/J

value: D10.G4.1 cells, ATCC

tag: cell count

value: 100K cells


title: iPS63

description:
Small RNA
18-30nt


title: H3K4me2_ChIPSeq_CCR4pos-Donor1-rep2

value: healthy (tested non-asthmatic)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor19-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor18-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor17-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor17-rep2


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica10


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica9


title: H3K4me2_ChIPSeq_CCR4Neg-Donor23-rep1


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica7


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica8


title: H3K4me2_ChIPSeq_CCR4Neg-Donor16-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor15-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor16-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor15-rep1


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica5


title: Standart H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica7

value: 2 million cells


title: H3K4me2_ChIPSeq_CCR4Neg-Donor14-rep1

value: asthmatic


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+03 cells) replica4

value: 1K cells


title: H3K4me2_ChIPSeq_CCR4Neg-Donor13-rep2


title: H3K4me2_ChIPSeq_CCR4Neg-Donor18-rep1


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica4


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+03 cells) replica3


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+03 cells) replica2


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica11


title: H3K4me2_ChIPSeq_CCR4Neg-Donor13-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor12-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor12-rep2


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+04 cells) replica3

value: 10K cells


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+04 cells) replica2


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+04 cells) replica1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor11-rep1

value: CCR4- T cells


title: H3K4me2_ChIPSeq_CCR4Neg-Donor8-rep2

value: CD3+ CD4+ CD45RO+ CD45RA- CCR4- CD25- T cells


title: H3K4me2_ChIPSeq_CCR4Neg-Donor8-rep1


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica6


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica3


title: H3K4me2_ChIPSeq_CCR4Neg-Donor7-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor9-rep1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor6-rep2


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica1


title: H3K4me2_ChIPSeq_CCR4Neg-Donor14-rep2


title: WT_mRNA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Sample 9

data_processing:
ChIP-seq: Reads were mapped to the TAIR8 genome by allowing up to 2 mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed in to one read and analysis performed was done as previously described (Du et al., 2012).
Bisulfite-seq: Analyzed exactly as previously described (Stroud et al., 2013), by allowing up to 2 mismatches using BS seeker (Chen et al., 2010) except that reads were mapped to the TAIR8 genome.
RNA-seq: Reads were mapped using Bowtie (Langmead et al., 2009) allowing up to 2 mismatches, and uniquely mapping reads were retained.
Genome_build: TAIR8
Supplementary_files_format_and_content: ChIP-seq: Sequence of reads, number of reads
Supplementary_files_format_and_content: Bisulfite-seq: Wiggle format files with fractional methylation levels C/(C+T). Methylation levels were calculated only for cytosines covered by >=4 reads. mCG are cytosines methylated in CG contexts. mCHG are those in CHG contexts (H=A T or C). mCHH are those in CHH contexts.
Supplementary_files_format_and_content: RNA-seq: Wiggle format files with normalized read densities calculated in 100 bp bins. Normalized reads were calculated by # reads/0.1kb/uniquely mapping readsx10^6.

source_name: 10 day old seedlings

growth_protocol: plants were grown under long day conditions i.e 16 hours light and 8 hours dark.

extract_protocol:
ChIP-seq: 2 grams of expanded leaves were ground in liquid nitrogen and fixed in 1% formaldehyde for 10 minutes. The reaction was stopped by adding 0.125 M glycine. Nuclei were extracted by filtration through Miracloth and iteratively washed and centrifuged at 2,000g.  Nuclei were lysed in SDS buffer. DNA was sonicated for 10 cycles of 0.5 minute on and 1 minute off with an UCD-200TM-EX Bioruptor (Diagenode) on medium power, at 0 to 4°C. Sonicated chromatin was incubated overnight with either anti-H2As or anti-H3 (ab1791, Abcam) antibodies. After pre-clearing, magnetic protein A-beads (Dynabeads protein A, Invitrogen) were incubated with the antibodies-chromatin mix for 3 hours. After precipitation of the beads on a magnetic rack (MagnaRack, Invitrogen) and washes with increasing stringency, DNA was eluted at 65°C and reverse cross-linked with proteinase K (Fermentas). Immunoprecipitated DNA was treated with RNase A (Fermentas) and purified with the QIAquick purification kit (Qiagen). ChIP-seq libraries were generated as per manufacturer’s instructions (Illumina).
Bisulfite-seq: 0.1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).
RNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. Tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina Truseq).

tag: ecotype

tag: genotype/variation

value: WT

tag: age

value: 10 day

value: seedlings


title: hta6_7_12_mRNA

description: Sample 10

tag: tissue


title: hta6_7_12_BS

description: Sample 8

source_name: 3 wk leaves (mature rosette leaves)

value: 3 wk

value: leaves


title: WT_H2AZ_ChIP

description: Sample 6

source_name: 3 wk leaves (expanded leaves)

value: anti-H2AZ antibody


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 6

tag: strain

value: H3K4me2 (clone Y47, lot#YH041501C; Abcam)


title: WT_H2AX_ChIP

description: Sample 5

value: anti-H2AX antibody


title: H3K4me2_ChIPSeq_CCR4Neg-Donor6-rep1


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 5

value: AKR/J

value: D10.G4.1 cells, ATCC


title: MEF14

description:
Small RNA
18-30nt

source_name: mouse embryonic fibroblasts

value: C57B6/129SvJae F1

value: mouse embryonic fibroblasts (MEFs)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor5-rep1

value: healthy (tested non-asthmatic)


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+03 cells) replica1

value: 1K cells


title: WT_H2AW_ChIP

description: Sample 4

value: anti-H2AW antibody


title: MEF15

description:
Small RNA
18-30nt


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 4

value: 2 million cells


title: WT_H2A_ChIP

description: Sample 3

value: anti-H2A antibody


title: H3K4me2_ChIPSeq_CCR4Neg-Donor4-rep2

value: CCR4- T cells

value: CD3+ CD4+ CD45RO+ CD45RA- CCR4- CD25- T cells


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 3


title: ES4

description:
Small RNA
18-30nt

source_name: embryonic stem cells E14

tag: cell line

value: embryonic stem cells (ESCs)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor4-rep1


title: Micro-scaled H3K4me2 ChiP-Seq (1*1.00E+05 cells) replica2

value: 100K cells


title: MEF13

description:
Small RNA
18-30nt


title: WT_H3_ChIP

description: Sample 2

value: WT

value: 3 wk

value: leaves

value: anti-H3 (ab1791, Abcam)


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 2

value: AKR/J

value: H3K4me2 (clone Y47, lot#YH041501C; Abcam)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor1-rep2


title: ES3

description:
Small RNA
18-30nt


title: Standard H3K4me2 ChIP-Seq (2*1.00E+06 cells) replica 1

value: D10.G4.1 cells, ATCC


title: ES2

description:
Small RNA
18-30nt


title: WT_inputDNA

description: Sample 1

value: none (input)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor1-rep1

value: healthy (tested non-asthmatic)


title: H3K4me2_ChIPSeq_CCR4Neg-Donor5-rep2


title: WT_BS

description: Sample 7


title: UP09003120

status: Public on Jul 04 2014

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

data_processing:
Illumina Casava 1.7 and 1.8 software used for basecalling.
Reads were trimmed by finding longest subsequence with all bases>=Phred20. PolyA tail was removed and reads with minimum length of 50 bp were mapped with TopHat2 (version 2.0.5) taking into account strand specificity (forward strand).
Mapped read counts were collected within 16667 predicted gene models.
Genewise read counts were normalized using TMM method in R package edgeR. Normalized counts were obtained by dividing unnormalized counts by effective library size.
Genome_build: GenBank APLT01000000 (submitted)
Supplementary_files_format_and_content: text file including unnormalized read counts of 16667 genes is linked to each sample records and 'NormalizedCounts.txt' is linked to Series records.

organism: Melitaea cinxia

extract_protocol:
Total RNA was extracted from frozen butterfly thorax with Trizol (Life Technologies Corporation, CA, USA) followed by chloroform, phenol-chloroform-isoamylalcohol and second chloroform purification. RNA was precipitated with isopropanol and washed with ethanol. RNA quality was verified with NanoDrop measurement (Thermo Fischer Scientific Inc., MA, USA) and Bioanalyzer run (Agilent Technologies, CA, USA).
An in-house strand-specific library construction protocol based on polyA-anchoring.

treatment_protocol: The material was collected in the autumn of 2009 as diapausing larvae from four different regional populations in northern Europe: Åland (Finland), Saaremaa (Estonia), Uppland (Sweden) and Öland (Sweden). The larvae overwintered in mixed (within population) groups in a growth chamber under constant temperature of +5°C and 85% relative humidity. In spring 2010, larvae were reared singly under common garden conditions (12:12; L/D; 28/15°C) with fresh leaves of the host plant Plantago lanceolata.  After eclosion the adults were held in the same common garden conditions for three days.

tag: population

value: UP

tag: gender

value: Male


title: UP09003125

value: Female


title: UP09004151


title: UP09004177


title: UP09005207


title: UP09004155


title: SA09004160

value: SA


title: UP09003127


title: UP09003119


title: SA09005235


title: SA09004151


title: SA09004156


title: SA09004193


title: SA09003117


title: SA09003120


title: SA09005216


title: SA09005208


title: SA09003148


title: SA09005240


title: SA09004187


title: UP09004172


title: UP09005205


title: SA09004154


title: SA09003136


title: SA09003121


title: SA09004155


title: UP09004164


title: SA09005212


title: SA09004194


title: SA09002059


title: SA09005244


title: SA09004184


title: SA09003144


title: SA09004165


title: SA09004178


title: SA09003119


title: SA09005211


title: SA09003128


title: SA09004173


title: SA09003127


title: SA09003130


title: SA09005207


title: SA09004168


title: SA09005226


title: SA09005205


title: SA09005231


title: SA09003129


title: SA09004152


title: SA09004196


title: SA09005218


title: SA09005228


title: SA09003113


title: OL09005213

value: OL


title: OL09004181


title: SA09004166


title: SA09004172


title: OL09003119