title: GSM-RNA

status: Public on Oct 19 2014

city: Bei Jing

first: Shilin

last: Tian

address: Xueqing Road

department: genome research

institute: Novogene Bioinformatics Technology CO.ltd

description:
Golden snub-nosed monkey.
Tissues of heart, liver, kidney, spleen, lung, pancreas, muscle and tongue from one individual.

data_processing:
Illumina Casava 1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Golden snub-nosed monkey whole genome using Tophat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Golden snub-nosed monkey genome assembled by WGS reads using SOAPdenovo software (BioProject: PRJNA230020).
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values.

organism: Rhinopithecus roxellana

source_name: mixed tissues

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mixed


title: LB 2.0 B2 TEX pos L2 HS2

status: Public on Oct 18 2014

type: SRA

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

library_source: transcriptomic

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.13 (TRAPL)
Coverage calculation and normalisation (TRAPL)
Genome_build: NC_000913.2
Supplementary_files_format_and_content: wiggle

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 cells

growth_protocol: To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution.

extract_protocol:
Hot phenol (Sharma et al. 2010, Bloomberg 1990, EMBO J)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: Samples were mixed, incubated on ice for 10 min after which cells were collected by centrifugation at 4150 rpm at 4˚C for 10 min.  Cell pellets were snap frozen in an ethanol/dry ice slurry and stored at -80°C until total RNA could be extracted.

tag: strain

tag: medium

value: LB

tag: growth phase

value: stationary


title: nf0h3b

status: Public on Oct 17 2014

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

country: USA

institute: University of Michigan

description: segments.bed file linked to GSM1347657 (merged analysis of nf0h3a, nf0h3b, nf0h4)

data_processing:
genome_build: hg19
supplementary_files_format_and_content: segments.bed = extended BED format file, one record for each HMM transcription segment, where column 4 is a unique identifier for the corresponding fused and revised transcription unit in format chrom:start-end(strand), column 5 is always 0, column 7 is the segment’s HMM state (0..9), column 8 is segment RPKM, and columns 9 is the transcription unit RPKM.
Library strategy: Bru-Seq (variant of RNA-Seq)
Call bases with Illumina Casava v1.8.2.
Subtract reads that align to the reference ribosomal DNA complete repeating unit using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Align remaining reads to the reference genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3.
Determine fractional read coverage for every genome base using Bedtools v.2.16.2 such that a base covered by one read is recorded as having a coverage of 1/read_length.
Calculate fractional RPKM values for annotated genes, where a gene is the span of its various transcript isoforms.
Separately calculate RPKM values for 1 Kb genome bins.
Merge all samples from each cell line by summing their read counts per 1 Kb bin and recalculating bin RPKM values.
Subject merged bin RPKM values to a strand-specific Hidden Markov model (HMM) segmentation algorithm with ten logarithmically distributed output transcription states (indices 0 to 9, bed column 7).
Calculate aggregate RPKM values for each called transcription segment (bed column 8).
Empirically assign HMM transcription states of 0 to 2 a Boolean transcription state of “not transcribed”  and HMM states 3 to 9 a Boolean transcription state of “transcribed”.
Fuse adjacent transcribed segments into preliminary transcription units.
Revise transcription units by comparing them to the Ensembl gene annotation such that transcription units covering at least 80% of any transcript isoform of each of two adjacent genes on the same strand were split at the most proximal transcription start site of all matching transcripts of the downstream gene.
Calculate aggregate RPKM for each fused and revised transcription unit (bed column 9).

organism: Homo sapiens

source_name: UMHF1 hTERT-immortalized fibroblasts

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h.
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized in the presence of Actinomycin D to result in strand specific reads. After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Bromouridine (Bru, Aldrich) was added to the media at a final concentration of 2 mM and cells were incubated at 37°C for 30 min. Cells were then washed 3 times in PBS and harvested. When indicated, cells were pre-treated for 24 hours with 0.4 uM aphidicolin prior to Bru labeling.

tag: Sex

value: male

tag: cell type

value: primary neonatal foreskin fibroblast

tag: cell line

tag: treatment

tag: replicate

tag: sequenced molecule

value: nascent total RNA


title: aphpre0h1

description: segments.bed file linked to GSM1347653 (merged analysis of aphneg0h1, aphpre0h1)

data_processing:
genome_build: hg19
supplementary_files_format_and_content: segments.bed = extended BED format file, one record for each HMM transcription segment, where column 4 is a unique identifier for the corresponding fused and revised transcription unit in format chrom:start-end(strand), column 5 is always 0, column 7 is the segment’s HMM state (0..9), column 8 is segment RPKM, and columns 9 is the transcription unit RPKM.
supplementary_files_format_and_content: genes.bed = BED format file, one record per gene, where column 4 is the gene name and column 5 is its RPKM
Library strategy: Bru-Seq (variant of RNA-Seq)
Call bases with Illumina Casava v1.8.2.
Subtract reads that align to the reference ribosomal DNA complete repeating unit using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Align remaining reads to the reference genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3.
Determine fractional read coverage for every genome base using Bedtools v.2.16.2 such that a base covered by one read is recorded as having a coverage of 1/read_length.
Calculate fractional RPKM values for annotated genes, where a gene is the span of its various transcript isoforms.
Separately calculate RPKM values for 1 Kb genome bins.
Merge all samples from each cell line by summing their read counts per 1 Kb bin and recalculating bin RPKM values.
Subject merged bin RPKM values to a strand-specific Hidden Markov model (HMM) segmentation algorithm with ten logarithmically distributed output transcription states (indices 0 to 9, bed column 7).
Calculate aggregate RPKM values for each called transcription segment (bed column 8).
Empirically assign HMM transcription states of 0 to 2 a Boolean transcription state of “not transcribed”  and HMM states 3 to 9 a Boolean transcription state of “transcribed”.
Fuse adjacent transcribed segments into preliminary transcription units.
Revise transcription units by comparing them to the Ensembl gene annotation such that transcription units covering at least 80% of any transcript isoform of each of two adjacent genes on the same strand were split at the most proximal transcription start site of all matching transcripts of the downstream gene.
Calculate aggregate RPKM for each fused and revised transcription unit (bed column 9).

source_name: 090 hTERT-immortalized fibroblasts

value: female

value: primary adult skin fibroblast

value: 0.4 micromolar aphidicolin for 24 h


title: nf0h4


title: nf0h3a


title: mesaph0h1

description: segments.bed file linked to GSM1347655 (merged analysis of mesnt0h1, mesaph0h1)

data_processing:
genome_build: mm9
supplementary_files_format_and_content: segments.bed = extended BED format file, one record for each HMM transcription segment, where column 4 is a unique identifier for the corresponding fused and revised transcription unit in format chrom:start-end(strand), column 5 is always 0, column 7 is the segment’s HMM state (0..9), column 8 is segment RPKM, and columns 9 is the transcription unit RPKM.
supplementary_files_format_and_content: genes.bed = BED format file, one record per gene, where column 4 is the gene name and column 5 is its RPKM
Library strategy: Bru-Seq (variant of RNA-Seq)
Call bases with Illumina Casava v1.8.2.
Subtract reads that align to the reference ribosomal DNA complete repeating unit using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Align remaining reads to the reference genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3.
Determine fractional read coverage for every genome base using Bedtools v.2.16.2 such that a base covered by one read is recorded as having a coverage of 1/read_length.
Calculate fractional RPKM values for annotated genes, where a gene is the span of its various transcript isoforms.
Separately calculate RPKM values for 1 Kb genome bins.
Merge all samples from each cell line by summing their read counts per 1 Kb bin and recalculating bin RPKM values.
Subject merged bin RPKM values to a strand-specific Hidden Markov model (HMM) segmentation algorithm with ten logarithmically distributed output transcription states (indices 0 to 9, bed column 7).
Calculate aggregate RPKM values for each called transcription segment (bed column 8).
Empirically assign HMM transcription states of 0 to 2 a Boolean transcription state of “not transcribed”  and HMM states 3 to 9 a Boolean transcription state of “transcribed”.
Fuse adjacent transcribed segments into preliminary transcription units.
Revise transcription units by comparing them to the Ensembl gene annotation such that transcription units covering at least 80% of any transcript isoform of each of two adjacent genes on the same strand were split at the most proximal transcription start site of all matching transcripts of the downstream gene.
Calculate aggregate RPKM for each fused and revised transcription unit (bed column 9).

organism: Mus musculus

source_name: mouse embryonic stem cells

value: embryonic stem cells

value: mES


title: mesnt0h1


title: GM128780h1

source_name: GM12878 lymphoblastoid cells

value: EBV-immortalized lymphoblastoid cells


title: aphneg0h1


title: LB 2.0 B2 TEX neg L1 HS1


title: S28.H3K4me3.NeuN_positive

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
All libraries contained single-end 36-bp reads and were mapped to the human genome with Bowtie2 (version 2.1.0). We allowed up to one mismatch and mapped all sequences to the gender appropriate genome hg19. Reads that mapped to multiple locations were discarded.
We analyzed genome-matching reads with the MACS software (version 2.0.10) to identify significant peaks (P < 1 × 10−5) with bw = 230 bp, as defined experimentally by PCR, tSize = 36 bp, and other parameters set at default.
Genome_build: hg19

molecule: genomic DNA

source_name: prefrontal cortex

extract_protocol:
Tissue aliquots (200–500 mg/subject) were extracted in hypotonic lysis buffer, purified by ultracentrifugation and resuspended in 1x PBS, immunotagged with anti-neuronal nucleus (anti-NeuN, Millipore) antibody and sorted into NeuN(+) and NeuN(-) fractions. Mononucleosomal preparations from at least 1×106 sorted nuclei were prepared for subsequent chromatin immunoprecipitation with anti-H3K4me3 antibody (Upstate/Millipore)
ChIPed DNA was first blunt-ended by End-it DNA Repair Kit (Epicentre) at RT for 1hr. Reaction was cleaned by column (Qiagen), and DNA was A-tailed by exo- Klenow DNA Polymerase (Epicentre) at RT for 1hr. Reaction was again cleaned by column, and DNA was ligated to Genomic Adpater Oligo Mix (Illumina) by Fast-link DNA Ligation Kit (Epicentre) at RT for 2 hours followed by 16°C O/N. Reaction was cleaned by column, and ligated DNA was amplified using PfuUltra II Fusion HS DNA Polymerase (Stratagene) with 250µM dNTPs and 1µL of each of the Genomic PCR Primers (Illimina) in 100µL volume with the following cycling conditions: 95°C 1min; 15 cycles of 95°C 50sec, 65°C 1min, 72°C 30sec; 72°C 5min. PCR product was cleaned and volume reduced by column before loading onto a 1.8% agarose gel. Typically a strong smear of 160-230bp (including 92bp from the Illumina primers) was observed.

tag: facs population

value: NeuN positive

value: Female

tag: age

value: 69 years


title: WT unstressed rep1 INPUT

status: Public on Oct 16 2014

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Primary analysis off the HiSeq 2000 machine was done with Illumina RTA v1.18.61, HiSeq Control Software v2.2.38, CASAVA version 1.8.2
Chip-seq: Reads were aligned using bowtie2 (2.1.0) with -k 1 to the yeast genome sacCer2 from UCSC.
Chip-seq: BAM files were read into R (3.0.2) and analyzed using packages GenomicRanges (1.14.4), Rsamtools(1.14.2), rtracklayer(1.22.0).
Chip-seq: bigWig files were created in R by calculating RPM (normalized coverage based on total bowtie2 alignments) and coverages were mean-smoothed with 101-base windows.
Mnase-seq: Reads were aligned using bowtie2 (2.1.0) to the yeast genome sacCer2 from UCSC.
Mnase-seq: BAM files were read into R (3.0.2) and analyzed using packages GenomicRanges (1.14.4), Rsamtools(1.14.2), rtracklayer(1.22.0).
Mnase-seq: bigWig files were created in R by calculating the midpoint of each fragment alignment (for fragments between 100 and 200 bases) and extending from the midpoint to end up with a fragment size of 73 bases. RPM normalized coverage was calculated on the 73 base fragments.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig - rpm normalized coverage based on total bowtie2 alignments

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Cells were grown in YPD

extract_protocol:
Yeast whole cell extract were sonicated DNA-protein complexes were isolated with antibody.
ChiP-seq, Mnase-seq libraries were prepared using KAPA High Throughput Library Preparation Kit, Roche

treatment_protocol: To induce stress cells grown in YPD were shifted to YNB + 0.5% dextrose

tag: genotype/variation

value: WT

tag: tissue

value: WCE

tag: antibody

value: INPUT


title: 2R stressed rep1 INPUT


title: WT stressed rep1 INPUT


title: 2R unstressed rep1 INPUT


title: S6.H3K4me3.NeuN_positive

value: Male

value: 0.6 years


title: KSHV Transcriptome in virions produced from 293L with BAC36 deleted ORF59 complemented with DsREd ORF59

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

data_processing:
The libraries were run on Illumina Hi-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to KSHV data base sequence to calculate the RPKM values of each gene using CLC Workbech 7.0
Genome_build: NCBI genome build of KSHV, accession number NC_009333
Supplementary_files_format_and_content: Comma separated (CSV) files have RPKM values of each genes at respective time points.

organism: Human gammaherpesvirus 8

source_name: KSHV virions

growth_protocol: Virions were purfied after induction of respective cells. purified virions were treated with micrococcal nuclease to eliminate surface attached RNA. Total RNA was extracted byTRIzol method.

extract_protocol:
RNA extracted extracted was done by TRIzol method and depleted for contaminating DNA by treatment with DNAse
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Total RNA was treated with DNAse to eliminate DNA contamination.

tag: host cells

tag: sample type

value: total RNA packaged into virions particles

tag: virus genotype/variation

value: BAC36-delORF59 virus complemented with DSRED ORF59


title: LB 2.0 B1 TEX pos L1 GA

tag: strain

value: LB

value: stationary


title: LB 0.4 B1 TEX pos L1 GA

tag: medium

value: exponential


title: KSHV Transcriptome packaged in virions produced from BCBL1 cells

value: BCBL1 cells

value: BCBL1 virus


title: KSHV Transcriptome packaged in the virions produced from 293L with BAC36

value: 293L with BAC36

value: BAC36 wild type virus


title: KSHV Transcriptome at 72hpi in TIVE

source_name: TIVE cells infected with KSHV

growth_protocol: human TIVE cells were cultured in complete medium containing 10% FBS at 37oC in humidified chamber with 5% CO2

extract_protocol:
Infected cells were cultured for indicated time followed by washing them to remove virus attached to the cell surface. RNA was extracted by standard RNA extraction protocol
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: human TIVE cells were infected with KSHV virus prepared from BCBL-1 cells at the MOI of 10.

value: Telomerase Immortalized Vascular Endothelial (TIVE) cells

tag: infected with

value: KSHV virus

tag: time point


title: KSHV Transcriptome at 48hpi in TIVE

tag: cell type


title: KSHV Transcriptome at 120hpi in TIVE


title: KSHV Transcriptome at 72hpi

source_name: PBMCs infected with KSHV

growth_protocol:
Decoded human peripheral blood mononuclear cells (PBMCs) were purchased from ReachBioo and infected with KSHV virus
human PBMCs were cultured in complete RPMI medium containing 10% FBS at 37oC in humidified chamber with 5% CO2

extract_protocol:
Infected cells were cultured for indicated time followed by washing them with to remove virua attached to the cell surface. RNA was extracted by standard RNA extraction protocol
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: human PBMCs were infected with KSHV virus prepared from BCBL-1 cells at MOI of 10.


title: KSHV Transcriptome at 4hpi in TIVE


title: KSHV Transcriptome at 24hpi in TIVE


title: KSHV Transcriptome at 48hpi

value: peripheral blood mononuclear cells (PBMCs)

value: KSHV virus prepared from BCBL-1 cells at MOI of 10


title: KSHV Transcriptome at 120hpi


title: KSHV Transcriptome at 24hpi


title: S10.H3K4me3.NeuN_negative

value: NeuN negative

tag: Sex

value: 4.7 years


title: KSHV Transcriptome at 72hpi in CD14+ cells

source_name: HumanCD14+ cells infected with KSHV

growth_protocol:
Decoded human CD14+ cells were purchased from ReachBioo were infected with KSHV virus
human CD14+ cells were cultured in complete IMDM medium containing 10% FBS at 37oC in humidified chamber with 5% CO2

treatment_protocol: human CD14+ cells were infection with KSHV virus prepared from BCBL-1 cells and infected at MOI of 10.

value: human CD14+ cells

value: Kaposi's sarcoma-associated herpesvirus (KSHV)


title: KSHV Transcriptome at 4hpi in CD14+ cells


title: BAC36-delORF59 Transcriptome at 4hpi

source_name: PBMCs infected with KSHV-BAC

extract_protocol:
Infected cells were cultured for indicated time followed by washing them with to remove virus attached to the cell surface. RNA was extracted by standard RNA extraction protocol
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: human PBMCs were infected with KSHV virus prepared from 293L cells maintaining BAC36 or BAC36-delORF50 completed with DsRed-ORF59 at MOI of 10.

value: ORF59 deleted KSHV


title: BAC36-delORF59 Transcriptome at 24hpi


title: KSHV Transcriptome at 4hpi


title: KSHV Transcriptome at 24hpi in CD14+ cells


title: KSHV Transcriptome at 96hpi in CD14+ cells


title: KSHV Transcriptome at 48hpi in CD14+ cells


title: BAC36 Transcriptome at 48hpi

value: wild type KSHV


title: BAC36-delORF59 Transcriptome at 48hpi


title: BAC36 Transcriptome at 24hpi


title: BAC36 Transcriptome at 4hpi


title: Day 45 rep2

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
base calling was performed using Illumina’s Real Time Analysis (RTA) software
the RNA-Seq reads were mapped to the mouse reference genome (NCBI37/mm9) using TopHat v1.2.0 parameters --mate-inner-dist -40 --num-threads 4.
transcript abundance estimates were calculated uing Cufflinks 1.0.3 parameters -v -p 5 -N
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files of FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated using RNAzol Bee reagent (Tel-Test Inc., Friendswood, TX) per the manufacturer’s protocol.  RNA concentrations were quantified using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) at a wavelength of 260 nm.   Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and the samples with RNA integrity values above 7.0 were used for the following experiments.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (cat#RS-122-2001/RS-122-2002) according to manufacturer's instructions

value: liver

value: Day 45


title: Day 60 rep1

value: Day 60


title: Day 45 rep1


title: Day 45 rep3


title: Day 60 rep3


title: naive CD8+ T-cells

city: Groningen

first: Barbara

last: Hrdlickova

state: the Netherlands

address: PO Box 30 001

department: of Genetics

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

description: CD4- CD8+ CD45RO-

data_processing:
FastQC was used for confirmation of the quality of the raw reads
STAR version 2.1.3 used for reads mapping to the human reference genome (NCBI build 37), allowing for two mismatches and retaining only uniquely mapping reads. The aligner was provided with a file containing junctions from Ensembl GRCh37.65. Reads that corresponded to flag 1796 in the .bam alignment file (flag 1796: read unmapped, not primary alignment, read fail quality check, read is PCR or optical duplicate) were filtered out.
IntersectBed tool from the BEDTools suite was used to qualified reads that overlapped with exons from known transcripts (as described in Gencode version 14) by no less than 30% of the read's length
normalized expression RPKM (reads per kilobase per million mapped reads) values were calculated using the formula RPKMg = 109 x (Cg / (N x Lg)) [ Mortazavi A, et al., Nat Methods 2008, 5:621–8.]
RPKM values for all Gencode version 14 genes were computed at the gene levels obtained for all 7 immune cell types. Gencode version 14 data was used to annotate these regions with protein-coding and long non-coding RNA genes using the IntersectBed tool from BEDTools suite.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: a matrix of raw counts; rows are genes, columns are samples

molecule: polyA RNA

source_name: Venous peripheral blood-healthy volunteer

extract_protocol:
Venous peripheral blood (60 ml) from a healthy donor was collected in a lithium-heparin BD Vacutainer tube (BD, Franklin Lakes, NJ, USA). Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll Paque Plus (GE Healthcare Life Sciences, Uppsala, Sweden) gradient centrifugation and subjected to staining for FACS analysis. The red blood cells in the pellet were lysed with monochloride solution (155 mM NH4Cl, 10 mM KHCO3, 0.1 mM Na2.EDTA.2H2O, pH 7.4) to yield the granulocyte fraction.The PBMCs were incubated with antibodies for 45 minutes at 4°C and sorted in six different populations on the MoFloTM XDP flow cytometer (Beckman Coulter, Brea, CA, USA). RNA was extracted from all seven immune cell types using the MirVana RNA isolation kit (Ambion, Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
sequencing libraries were prepared from 1 µg of total RNA using the TruSeq RNA kit (Illumina) according to the manufacturer’s instructions.

tag: source

value: circulating immune cells

value: naive CD8+ T-cells

tag: marker

value: CD4- CD8+ CD45RO-


title: Granulocytes

value: Granulocytes


title: naive CD4+ T-cells

description: CD4+ CD8- CD45RO-

value: naive CD4+ T-cells

value: CD4+ CD8- CD45RO-


title: Day 25 rep2

value: Day 25


title: Day 25 rep3


title: Day 60 rep2


title: Day 25 rep1


title: Day 30 rep2

value: Day 30


title: Monocytes

value: Monocytes


title: Day 20 rep3

value: Day 20


title: Day 30 rep1


title: Memory T-cells

description: CD4+ CD8- CD45RO+ and CD4- CD8+ CD45RO+

value: Memory T-cells

value: CD4+ CD8- CD45RO+ and CD4- CD8+ CD45RO+


title: NK cells

description: CD4- CD8- CD56/CD16+ CD19-

value: NK cells


title: Day 15 rep2

value: Day 15


title: Day 20 rep1

value: liver


title: Day 20 rep2


title: Day 15 rep1


title: HDAC1 in control ES cells_Mock

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

description: Chromatin IP against Mock

data_processing:
For basecalling, Illumina Casava 1.7 software was used.
Using BWA version 0.5.9-r16, sequenced reads were mapped to mouse mm9 genome
The peaks were called with MACS peak caller using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: embryonic stem cells

growth_protocol: Mouse J1 ES cells were maintained in DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 20% fetal bovine serum (FBS), 2mM of L-glutamine, 100uM of non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 100uM of β-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor (LIF, Chemicon) and 50U/ml of penicillin/streptomycin. ES cells were cultured in 0.1% gelatin coated dishes.

extract_protocol:
The cells were cross-linked with 1% formaldehyde, followed by sonication to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500bp to 1Kb were immunoprecipitated using different antibodies/beads.
ChIP-sequencing libraries were generated using NEB ChIP-seq library prep kit (E6200L) according to the manufacturer’s instructions.

value: mouse embryonic stem cell

tag: cell line

value: J1 ES cells containing BirA

tag: chip antibody


title: Day 15 rep3

tag: age


title: HDAC1 in Arid3a OE cells_Mock

description: Chromatin IP against Mock


title: Day 30 rep3


title: HDAC1 in Arid3a OE cells_ChIP

description: Chromatin IP against HDAC1

value: HDAC1 (Abcam, ab7028)


title: BirA control

description: Chromatin IP against Mock


title: Day 10 rep3

value: Day 10


title: Day 10 rep2


title: Day 10 rep1


title: Day 5 rep3

value: Day 5


title: Arid3a OE-High

description: Chromatin IP against Arid3a

value: Arid3a Streptavidin-conjugated beads

value: single colony

tag: treatment

value: Arid3a overexpression high


title: Arid3a OE-Low

description: Chromatin IP against Arid3a

value: Arid3a overexpression moderate


title: H3K18ac ChIP-seq in zelda mutant embryos

city: Berkeley

first: Michael

middle: B

last: Eisen

state: CA

address: 379 Stanley Hall, MC 3220

department: MCB

institute: HHMI/Univ. California, Berkeley

description:
Sample name: Dmel-ZLDm-H3K18ac
ChIP DNA for H3K18ac in zelda (germ line clone) mutant Dmel embryo (Oregon R) at mitotic cycles 12-14d.

data_processing:
Basecalls were performed using CASAVA_v1.8.0.
Sequenced reads were mapped jointly to the April 2006 assembly of the D. melanogaster genome [FlyBase Release 5] and the November 2004 assembly of the D. pseudoobscura genome [FlyBase Release 1.0] using Bowtie (Langmead, 2010) with the command-line options "-q -5 5 -3 5 -l 70 -n 2 -a -m 1 -best -strata", thereby trimming 5 bases from each end of the 100 base single reads, and keeping only tags that mapped uniquely to the genomes with at most two mismatches.
We called peaks for each experiment using MACS (Zhang et al., 2008) v1.4.2 with the options "-- nomodel --shiftsize=130", and used Input as controls.
Genome_build: Drosophila melanogaster FlyBase Release 5 (April 2006).
Genome_build: Drosophila pseudoobscura FlyBase Release 1.0 (November 2004).
Supplementary_files_format_and_content: wig files were generated by extending each aligned read based on the average size of the DNA fragments in the libraries, and the values at each position were further normalized based on the number of D. pseudoobscura reads from each sequenced sample, which served as internal control for the ChIP-seq experiments. The peak files were generated from the MACS peak call program (Zhang et al., 2008).

organism: Drosophila melanogaster

source_name: embryos, zelda mutant, H3K18ac ChIP

growth_protocol: D. melanogaster flies were maintained in large population cages in an incubator set at standard conditions (25°C).

extract_protocol:
7.5, 0.7, 0.4, and 0.3 g of embryos at four different stages, respectively, were used to prepare chromatin for immunoprecipitation following the CsCl2 gradient ultracentrifugation protocol as previously described (Harrison et al., 2011).The chromatin obtained was fragmented to sizes ranging from 100 to 300 bp using a Bioruptor (Diagenode, Inc.) for a total processing time of 140 min (15 s on, 45 s off), with power setting at "H". Prior to carrying out chromatin immunoprecipitation, we mixed the chromatin from each sample with a roughly equivalent amount of chromatin isolated from stage 5 (mitotic cycle 14) D. pseudoobscura embryos, and used about 2 µg of total chromatin (1 µg each of the D. melanogaster and D. pseudoobscura chromatin) for each chromatin immunoprecipitation. The chromatin immunoprecipitation reactions were carried out as described previously (Harrison et al., 2011) with 0.5 ug anti-H4K5ac (Millipore, 07-327), 0.5 ug anti-H3K4me3 (Abcam, ab8580), 0.5 ug anti-H3K27ac (Abcam, ab4729), 1 ug anti-H3 (Abcam, ab1791), 0.75 ug anti-H3K4me1 (Abcam, ab8895), 0.75 ug anti-H4K8ac (Abcam, ab15823), 1.5 ul anti-H3K9ac (Activemotif, 39138), 0.75 ug anti-H3K18ac (Abcam, ab1191), 3 ug anti-H3K27me3 (Millipore, 07-449), or 0.75 ug anti-H3K36me3 (Abcam, ab9050).
The sequencing libraries were prepared from the ChIP and Input DNA samples using the Illumina TruSeq DNA Sample Preparation kit following the manufacturer's instructions, and DNA was subjected to ultra-high-throughput sequencing on Illumina HiSeq 2000 DNA sequencers.
The libraries with different indexes were usually combined into pools, and each library pool was sequenced (100 bp single-end read) in a single lane in a flow cell.

treatment_protocol: Embryos were collected for 30 minutes, and then allowed to develop for 55, 85, 120 or 160 additional minutes before being harvested and fixed with formaldehyde. The fixed embryos were hand sorted in small batches using an inverted microscope to remove embryos younger or older than the targeted age range based on morphology of the embryos as previously described (Harrison et al., 2011). After sorting, embryos were stored at -80oC. After all collections were completed, the sorted embryos of each stage were pooled, and a sample of each pool were stained with DAPI. The ages of the embryos and their distribution in the two younger embryo pools (c7-9, and c11-13) were determined based on nuclei density of the stained embryos. The ages of embryos between c14a and c14c, both of which were distinct from c13 based on nuclei density, were determined based on morphology. For the ChIP-seq experiment in zelda mutant embryos, for which wild type (wt) Oregon R embryos were assayed in parallel as control, the flies were allowed to lay eggs for 3 hours and the embryos were aged for one additional hour before being treated with formaldehyde.

tag: strain/background

value: Oregon R

tag: genotype/variation

value: zelda mutant

tag: tissue

value: embryo

tag: developmental stage

value: mitotic cycle 12-c14d

value: anti-H3K18ac (Abcam, ab1191, lot GR46473-1)


title: Day 5 rep2


title: H3K18ac ChIP-seq in wt embryos

description:
Sample name: Dmel-wt-H3K18ac
ChIP DNA for H3K18ac in wt Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, wt, H3K18ac ChIP

value: wild-type


title: B-cells

description: CD4- CD8- CD56/CD16- CD19+

value: circulating immune cells

value: B-cells


title: H3 ChIP-seq in zelda mutant embryos

description:
Sample name: Dmel-ZLDm-H3
ChIP DNA for histone H3 in zelda (germ line clone) mutant Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, zelda mutant, H3 ChIP


title: H3K4me1 ChIP-seq in wt embryos

description:
Sample name: Dmel-wt-H3K4me1
ChIP DNA for H3K4me1 in wt Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, wt, H3K4me1 ChIP

value: anti-H3K4me1 (Abcam, ab8895, lot GR127871-1)


title: Day 3 rep3

value: liver

value: Day 3


title: HDAC1 in control ES cells_ChIP

description: Chromatin IP against HDAC1

value: mouse embryonic stem cell

value: J1 ES cells containing BirA

value: HDAC1 (Abcam, ab7028)


title: 2R stressed rep1 Snf2 mnase

value: WCE


title: H3 ChIP-seq in wt embryos

description:
Sample name: Dmel-wt-H3
ChIP DNA for histone H3 in wt Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, wt, H3 ChIP


title: 2R stressed rep2 Snf2 mnase


title: 2R unstressed rep2 Snf2 mnase


title: Day 3 rep1


title: Zelda ChIP-seq in zelda mutant embryos

description:
Sample name: Dmel-ZLDm-ZLD
ChIP DNA for Zelda in zelda (germ line clone) mutant Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, zelda mutant, Zelda ChIP

value: anti-Zelda antibody (Harrison et al., 2011, PLoS Genet. 7(10):e1002266)


title: Zelda ChIP-seq in wt embryos

description:
Sample name: Dmel-wt-ZLD
ChIP DNA for Zelda in wt Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, wt, Zelda ChIP


title: WT stressed rep2 Snf2 mnase

value: WT


title: WT stressed rep1 Snf2 mnase


title: Day 1 rep3

value: Day 1


title: Input for cycle 14c ChIP-seq samples

description:
Sample name: Dmel-input-c14c
DNA isolated from input chromatin isolated from wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, input

value: Oregon R

value: mitotic cycle 14(c-d)


title: Day 1 rep2


title: H3K4me1 ChIP-seq in zelda mutant embryos

description:
Sample name: Dmel-ZLDm-H3K4me1
ChIP DNA for H3K4me1 in zelda (germ line clone) mutant Dmel embryo (Oregon R) at mitotic cycles 12-14d.

source_name: embryos, zelda mutant, H3K4me1 ChIP

value: zelda mutant

value: embryo

value: mitotic cycle 12-c14d


title: WT unstressed rep2 Snf2 mnase

source_name: yeast


title: Input for cycle 12 ChIP-seq samples

description:
Sample name: Dmel-input-c12
DNA isolated from input chromatin isolated from wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, input

value: wild-type

value: mitotic cycle 11-13


title: Day 0 rep3

value: Day 0


title: Day 5 rep1

value: liver

value: Day 5


title: Input for cycle 14a ChIP-seq samples

description:
Sample name: Dmel-input-c14a
DNA isolated from input chromatin isolated from wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, input

value: mitotic cycle 14(a-b)


title: Day 1 rep1


title: Day 0 rep2


title: 2R delta bromo stressed rep2 INPUT for Snf2 N'ab

value: Snf2 K1493R K1497R delta bromo

tag: antibody

value: INPUT


title: WT unstressed rep1 Snf2 mnase

value: WCE


title: Input for cycle 8 ChIP-seq samples

description:
Sample name: Dmel-input-c8
DNA isolated from input chromatin isolated from wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, input

value: mitotic cycle 7-9


title: 2R delta bromo stressed rep1 INPUT for Snf2 N'ab


title: Day 0 rep1

tag: strain


title: H3 ChIP-seq cycle 14c

description:
Sample name: Dmel-H3-c14c
ChIP for histone H3 of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3 ChIP


title: 2R delta bromo unstressed rep2 INPUT for Snf2 N'ab


title: 2R unstressed rep1 Snf2 mnase


title: Day -2 rep2

source_name: Liver

value: Day -2


title: H3 ChIP-seq cycle 14a

description:
Sample name: Dmel-H3-c14a
ChIP for histone H3 of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3 ChIP


title: 2R delta bromo unstressed rep1 INPUT for Snf2 N'ab


title: H3 ChIP-seq cycle 12

description:
Sample name: Dmel-H3-c12
ChIP for histone H3 of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3 ChIP


title: Day 3 rep2

value: Day 3


title: Day -2 rep3


title: H3 ChIP-seq cycle 8

description:
Sample name: Dmel-H3-c8
ChIP for histone H3 of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3 ChIP

value: Oregon R


title: Day -2 rep1


title: H3K36me3 ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K36me3-c14c
ChIP for H3K36me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K36me3 ChIP

value: mitotic cycle 14(c-d)

value: anti-H3K36me3 (Abcam, ab9050, lot GR52625-1)


title: WT delta bromo stressed rep2 INPUT for Snf2 N'ab

value: Snf2 delta bromo


title: WT delta bromo unstressed rep2 INPUT for Snf2 N'ab


title: H3K36me3 ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K36me3-c14a
ChIP for H3K36me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K36me3 ChIP

value: embryo


title: ChIP-C_WT

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

description: A300-798A Zfp335 ChIP, WT

data_processing:
Base calling was performed using RTA (Real-Time Analysis) 1.13.
Illumina adapter sequences were trimmed from reads using cutadapt 1.4.1. Trimmed reads were aligned to the mm9 genome assembly using bwa 0.7.7, allowing for a maximum of 2 mismatches.
Reads aligned with a MAPQ score of less than 20 were filtered out using samtools.
Peaks were called using MACS2 (parameters: -g mm --bw=300 –q 0.05).
Aligned sequence reads were filtered with samtools rmdup and used for generating normalized pileup tracks with MACS2 callpeak --SPMR (fragment pileup per million reads), which were then converted to the bigWig format.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig: normalized signal tracks; narrowPeak: peaks called by MACS2.

source_name: thymocytes, WT, Zfp335/NIF1 ChIP

growth_protocol: Total thymocytes were isolated by mechanical disaggregation through a 40μm nylon sieve and washed in cold PBS before formaldehyde crosslinking for ChIP.

extract_protocol:
Sonicated nuclei were cleared by centrifugation and incubated overnight with anti-Zfp335 bound to Dynabeads. Beads were washed in low-salt buffer, high-salt buffer, LiCl buffer and TE buffer. Protein/DNA complexes were eluted, reverse-crosslinked overnight at 65°C and treated with RNase A and proteinase K. ChIP DNA was purified using QIAquick PCR Purification kit (Qiagen).
7-10 ng ChIP DNA and 10 ng input DNA were used for library preparation, performed according to Illumina's TruSeq protocol with some modifications. DNA clean-up, removal of adapter dimers and size selection (300-500 bp) were done using Agencourt AMPure XP beads (Beckman Coulter). Libraries were checked for quality using the High Sensitivity DNA Bioanalyzer kit (Agilent Technologies), quantified with the Qubit dsDNA HS Assay kit (Life Technologies), and sequenced as 50 bp single-end reads on the Illumina HiSeq 2000 platform.

value: WT

value: total thymocytes

value: Zfp335/NIF1 (A300-798A, Bethyl Laboratories, lot no. A300-798A-1)


title: WT delta bromo unstressed rep1 INPUT for Snf2 N'ab


title: ChIP-N_bloto

description: A300-797A Zfp335 ChIP, blt/blt

source_name: thymocytes, blt/blt, Zfp335/NIF1 ChIP

value: blt/blt

value: Zfp335/NIF1 (A300-797A, Bethyl Laboratories, lot no. A300-797A-1)


title: ChIP-N_WT

description: A300-797A Zfp335 ChIP, WT


title: ChIP-C_bloto

description: A300-798A Zfp335 ChIP, blt/blt


title: H3K27me3 ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K27me3-c14a
ChIP for H3K27me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K27me3 ChIP

value: wild-type

value: mitotic cycle 14(a-b)

value: anti-H3K27me3 (Millipore, 07-449, lot JBC1873477)


title: H3K27me3 ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K27me3-c14c
ChIP for H3K27me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K27me3 ChIP


title: 2R stressed rep1 Snf2 INPUT for Snf2 N'ab

value: WCE

value: INPUT


title: Input_bloto

description: Input control, blt/blt

source_name: thymocytes, blt/blt, input


title: WT unstressed rep1 Snf2 INPUT for Snf2 N'ab


title: 2R unstressed rep1 Snf2 INPUT for Snf2 N'ab


title: Input_WT

description: Input control, WT

source_name: thymocytes, WT, input


title: H3K9ac ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K9ac-c14c
ChIP for H3K9ac of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K9ac ChIP

value: anti-H3K9ac (ActiveMotif, 39138, lot 981102)


title: H3K27me3 ChIP-seq cycle 12

description:
Sample name: Dmel-H3K27me3-c12
ChIP for H3K27me3 of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K27me3 ChIP

value: mitotic cycle 11-13


title: mESC mettl3 KO Input sample, replicate 2

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Raw reads were uniquely mapped to mouse reference genome (NCBI37/mm9) using TopHat (version 1.1.3) allowing maximum one mismatch.
RPKM and winscore of each 100bp sliding window along the transcritome is calculated using in house generated script
Genome_build: mm9

source_name: mouse embryonic stem cells

growth_protocol: J-1 murine embryonic stem cells were grown under typical feeder free ES cell culture conditions. ES cells were differentiated by culture in media without LIF.

extract_protocol:
RNA was extracted with TRIZOL and purified with Rneasy columns.
library generation with the dUTP strand specific protocol.

treatment_protocol: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody. A strand specific protocol was used to generate cDNA.

value: mouse embryonic stem cells

value: mettl3 KO

value: none (input)


title: H3K9ac ChIP-seq cycle 12

description:
Sample name: Dmel-H3K9ac-c12
ChIP for H3K9ac of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K9ac ChIP

value: Oregon R


title: H3K9ac ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K9ac-c14a
ChIP for H3K9ac of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K9ac ChIP

value: embryo


title: mESC mettl3 KO m6A IP sample, replicate 2

value: anti m6A


title: WT stressed rep1 Snf2 INPUT for Snf2 N'ab

source_name: yeast

value: WT


title: mESC mettl3 KO m6A IP sample, replicate 1


title: H3K9ac ChIP-seq cycle 8

description:
Sample name: Dmel-H3K9ac-c8
ChIP for H3K9ac of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3K9ac ChIP

value: mitotic cycle 7-9


title: 2R delta bromo stressed rep2 Snf2 N'ab

value: Snf2 K1493R K1497R delta bromo

value: Snf2 N' Ab


title: mESC mettl3 KO Input sample, replicate 1


title: 2R delta bromo unstressed rep2 Snf2 N'ab


title: WT delta bromo stressed rep1 INPUT for Snf2 N'ab

value: Snf2 delta bromo


title: H3K4me3 ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K4me3-c14c
ChIP for H3K4me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K4me3 ChIP

value: wild-type

value: mitotic cycle 14(c-d)

value: anti-H3K4me3 (Abcam, ab8580, lot GR65368-1)


title: 2R delta bromo stressed rep1 Snf2 N'ab

value: WCE


title: 2R delta bromo unstressed rep1 Snf2 N'ab


title: H3K36me3 ChIP-seq cycle 12

description:
Sample name: Dmel-H3K36me3-c12
ChIP for H3K36me3 of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K36me3 ChIP

value: anti-H3K36me3 (Abcam, ab9050, lot GR52625-1)


title: mESC m6A IP sample, replicate 2

value: mettl3 WT


title: WT delta bromo stressed rep2 Snf2 N'ab


title: H3K4me3 ChIP-seq cycle 12

description:
Sample name: Dmel-H3K4me3-c12
ChIP for H3K4me3 of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K4me3 ChIP

value: mitotic cycle 11-13


title: mESC Input sample, replicate 2

value: mouse embryonic stem cells


title: WT delta bromo stressed rep1 Snf2 N'ab


title: mESC m6A IP sample, replicate 1


title: WT delta bromo unstressed rep2 Snf2 N'ab


title: H3K4me3 ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K4me3-c14a
ChIP for H3K4me3 of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K4me3 ChIP

value: mitotic cycle 14(a-b)


title: H3K4me3 ChIP-seq cycle 8

description:
Sample name: Dmel-H3K4me3-c8
ChIP for H3K4me3 of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3K4me3 ChIP

value: Oregon R


title: H3K4me1 ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K4me1-c14c
ChIP for H3K4me1 of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K4me1 ChIP

value: embryo

value: anti-H3K4me1 (Abcam, ab8895, lot GR46388)


title: 2R stressed rep1 Snf2 N'ab


title: mESC Input sample, replicate 1

value: none (input)


title: mESC m6A IP sample

data_processing:
Raw reads were uniquely mapped to mouse reference genome (NCBI37/mm9) using TopHat (version 1.1.3) allowing maximum one mismatch.
RPKM and winscore of each 100bp sliding window along the transcriptome is calculated using in house generated script
Genome_build: mm9

value: Rabbit polyclonal anti m6A (N6-methyladenosine) by synaptic systems (catalog number 202 303; lot number:202003/10)


title: WT delta bromo unstressed rep1 Snf2 N'ab


title: 2R unstressed rep1 Snf2 N'ab


title: H3K4me1 ChIP-seq cycle 12

description:
Sample name: Dmel-H3K4me1-c12
ChIP for H3K4me1 of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K4me1 ChIP


title: WT stressed rep1 Snf2 N'ab

value: WT


title: H3K4me1 ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K4me1-c14a
ChIP for H3K4me1 of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K4me1 ChIP


title: WT stressed rep2 INPUT

value: INPUT


title: H3K27ac ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K27ac-c14a
ChIP for H3K27ac of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K27ac ChIP

value: anti-H3K27ac (Abcam, ab4729, lot GR45787-1)


title: H3K27ac ChIP-seq cycle 12

description:
Sample name: Dmel-H3K27ac-c12
ChIP for H3K27ac of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K27ac ChIP

value: wild-type


title: H3K27ac ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K27ac-c14c
ChIP for H3K27ac of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K27ac ChIP

value: mitotic cycle 14(c-d)


title: H3K4me1 ChIP-seq cycle 8

description:
Sample name: Dmel-H3K4me1-c8
ChIP for H3K4me1 of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3K4me1 ChIP

value: mitotic cycle 7-9


title: 2R stressed rep2 INPUT

value: WCE


title: WT unstressed rep2 INPUT


title: H3K27ac ChIP-seq cycle 8

description:
Sample name: Dmel-H3K27ac-c8
ChIP for H3K27ac of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3K27ac ChIP


title: 2R unstressed rep2 INPUT


title: H3K18ac ChIP-seq cycle 14c

description:
Sample name: Dmel-H3K18ac-c14c
ChIP for H3K18ac of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H3K18ac ChIP

value: anti-H3K18ac (Abcam, ab1191, lot GR46473-1)


title: H3K18ac ChIP-seq cycle 14a

description:
Sample name: Dmel-H3K18ac-c14a
ChIP for H3K18ac of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H3K18ac ChIP


title: H3K18ac ChIP-seq cycle 12

description:
Sample name: Dmel-H3K18ac-c12
ChIP for H3K18ac of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H3K18ac ChIP


title: 2R stressed rep1 H3K9Ac

source_name: yeast

value: H3K9Ac millipore


title: H3K18ac ChIP-seq cycle 8

description:
Sample name: Dmel-H3K18ac-c8
ChIP for H3K18ac of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H3K18ac ChIP


title: H4K8ac ChIP-seq cycle 14c

description:
Sample name: Dmel-H4K8ac-c14c
ChIP for H4K8ac of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H4K8ac ChIP

value: anti-H4K8ac (Abcam, ab15823, lot GR25500-1)


title: mESC Input sample

source_name: mouse embryonic stem cells

value: input

value: mouse embryonic stem cells


title: 2R unstressed rep1H3K9Ac


title: WT stressed rep2 H3K9Ac


title: H4K8ac ChIP-seq cycle 12

description:
Sample name: Dmel-H4K8ac-c12
ChIP for H4K8ac of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H4K8ac ChIP

value: Oregon R

value: mitotic cycle 11-13


title: WT unstressed rep1 Snf2 N'ab

value: Snf2 N' Ab


title: H4K8ac ChIP-seq cycle 14a

description:
Sample name: Dmel-H4K8ac-c14a
ChIP for H4K8ac of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H4K8ac ChIP

value: embryo

value: mitotic cycle 14(a-b)


title: WT unstressed rep1 H3K9Ac

value: WT


title: WT stressed rep1 H3K9Ac


title: H4K5ac ChIP-seq cycle 14a

description:
Sample name: Dmel-H4K5ac-c14a
ChIP for H4K5ac of wt Dmel embryo (Oregon R) at mitotic cycles 14a-b (hand sorted).

source_name: embryos, cycle 14a, H4K5ac ChIP

value: anti-H4K5ac (Millipore, 07-327, lot 1911263)


title: H4K5ac ChIP-seq cycle 14c

description:
Sample name: Dmel-H4K5ac-c14c
ChIP for H4K5ac of wt Dmel embryo (Oregon R) at mitotic cycles 14c-d (hand sorted).

source_name: embryos, cycle 14c, H4K5ac ChIP


title: 2R stressed rep2 Snf2 C'ab

value: Snf2 C' Ab


title: 2R stressed rep1 Snf2 C'ab


title: H4K8ac ChIP-seq cycle 8

description:
Sample name: Dmel-H4K8ac-c8
ChIP for H4K8ac of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H4K8ac ChIP

value: wild-type


title: 2R unstressed rep2 Snf2 C'ab


title: WT stressed rep2 Snf2 C'ab


title: 2R unstressed rep1 Snf2 C'ab


title: H4K5ac ChIP-seq cycle 12

description:
Sample name: Dmel-H4K5ac-c12
ChIP for H4K5ac of wt Dmel embryo (Oregon R) at mitotic cycles 11-13 (hand sorted).

source_name: embryos, cycle 12, H4K5ac ChIP


title: H4K5ac ChIP-seq at cycle 8

description:
Sample name: Dmel-H4K5ac-c8
ChIP for H4K5ac of wt Dmel embryo (Oregon R) at mitotic cycles 7-9 (hand sorted).

source_name: embryos, cycle 8, H4K5ac ChIP


title: WT unstressed rep2 Snf2 C'ab


title: 2R stressed rep2 H3K9Ac


title: WT stressed rep1 Snf2 C'ab


title: 2R unstressed rep2 H3K9Ac


title: WT unstressed rep1 Snf2 C'ab


title: tap+

status: Public on Oct 15 2014

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
Sequencing reads were mapped using Bowtie version 0.12.7 (Langmead et al., 2009) to the C. crescentus NA1000 reference genome (Genbank:  CP001340).  All valid alignments were made, and only reads that mapped to a unique location were used with no mismatches allowed.  The position of each alignment is distributed into to the 5' most base for 5' end mapping
tap+ and tap- aligned sequencing reads were normalization by the total number of non-ribosomal RNA reads for comparison.
The log value of the ratio (θ) between the number of sequencing reads obtained at the 5’ ends of tap+ and tap- libraries was calculated for each mapped genomic location
Genomic locations that meet the following criteria are identified as transcriptional start sites (TSS):  (1) normalized tap+ read > 25 (2)  θ > 0.26 (3) (3) An increase of >35% of RNA-seq density (Schrader et al, 2014) in the region 0-38bp upstream TSS than 1-38bp in the region downstream of TSS.  (4) have been biochemical validated
Genome_build: NA1000: CP001340
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Each line in the processed file tap_TSS.txt has three columns: Col 1: Genomic coordinate of TSS identifed based on CP001340, Col 2:  chromosome strand of TSS, Col 3: normalized tap+ reads, Col 4:  normalized tap- reads

organism: Caulobacter vibrioides NA1000

source_name: Total RNA lystate

growth_protocol: Caulobacter crescentus NA1000 were grown to mid-log (OD600 0.4) at 28C in minimal media M2G (Ely, B. Methods in Enzymology 1991 doi:10.1016/0076-6879(91)04019-K)

extract_protocol:
10 micogram of total RNA was isolated using Trizol® Plus kit (Invitrogen) according to the manufacturer protocol.
Total RNA was treated with MICROBExpressTM (Ambion) to remove ribosomal RNA following the manufacturer protocol followed with the treatment 10 U of Tobacco Acid Pyrophosphatase (TAP) (epicentre) for 1.5 hours at 37°C in tap+.  To tap+ and tap- samples, 10 pmol of RNA adapter (5'-ACACUCUUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated using 25 U of T4 RNA Ligase 1 (New England BioLabs) for 12 h at 16°C.  cDNA was then generated from purified RNA using SuperScript® II Reverse Transcriptase (Invitrogen) with 10 pmol of primer (5'-CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNN-3') following standard manufacturer protocol and treated with 1 Unit of RNase H (Invitrogen) for 20 min at 37°C.  cDNA was PCR amplified for 12 cycles using primers (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', 5'-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3').  DNA was size selected from 100bp to 300bp using agarose gel-electrophoresis, purified using QIAquick Gel Extraction Kit (Qiagen).  100ng of DNA was then treated with duplex-specific nuclease (evrogen) to remove ribosomal cDNA following standard manufacturer protocol and PCR amplified for 10 cycles.

treatment_protocol: Cells were pelleted and immediately frozen in liquid nitrogen


title: tap-


title: WT unstressed rep2 H3K9Ac


title: t=80

data_processing:
Sequencing reads were mapped using Bowtie version 0.12.7 (Langmead et al., 2009) to the C. crescentus NA1000 reference genome (Genbank:  CP001340).  All valid alignments were made, and only reads that mapped to a unique location were used with no mismatches allowed.  The position of each alignment is distributed into to the 5' most base for 5' end mapping
Aligned sequencing reads were normalization by the total number of non-ribosomal RNA reads for comparison.
The value of normalized sequencing reads obtained at each TSS position of each time point library was calculated.
Genome_build: NA1000: CP001340
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Each line in the processed file time_point_TSS.txt has the following organization in columns: Col 1: Genomic coordinate of TSS, Col 2:  chromosome strand of TSS, Col 3: t=0 normalized reads, Col 4: t=20 normalized reads, Col 5: t=40 normalized reads, Col 6: t=60 normalized reads, Col 7: t=80 normalized reads, Col 8: t=100 normalized reads, Col 9: t=120 normalized reads, Col 10: t=140 normalized reads

growth_protocol: Caulobacter crescentus NA1000 were grown to mid-log (OD600 0.4) at 28C in minimal media M2G (Ely, B. Methods in Enzymology 1991).  Cells were then syncrhonized using ludox density centrifugation (Evinger, M., Agabian, N. J. Bacteriol. 1977) and cell cycle time points were collected in 20 minute intervals.

extract_protocol:
10 micogram of total RNA was isolated using Trizol® Plus kit (Invitrogen) according to the manufacturer protocol.
Total RNA was treated with MICROBExpressTM (Ambion) to remove ribosomal RNA following the manufacturer protocol followed with the treatment 10 U of Tobacco Acid Pyrophosphatase (TAP) (epicentre) for 1.5 hours at 37°C.  10 pmol of RNA adapter (5'-ACACUCUUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated using 25 U of T4 RNA Ligase 1 (New England BioLabs) for 12 h at 16°C.  cDNA was then generated from purified RNA using SuperScript® II Reverse Transcriptase (Invitrogen) with 10 pmol of primer (5'-CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNN-3') following standard manufacturer protocol and treated with 1 Unit of RNase H (Invitrogen) for 20 min at 37°C.  cDNA was PCR amplified for 12 cycles using primers (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', 5'-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3').  DNA was size selected from 100bp to 300bp using agarose gel-electrophoresis, purified using QIAquick Gel Extraction Kit (Qiagen).  100ng of DNA was then treated with duplex-specific nuclease (evrogen) to remove ribosomal cDNA following standard manufacturer protocol and PCR amplified for 10 cycles.

tag: timepoint (minutes)


title: t=60


title: t=100


title: t=0


title: t=40


title: t=20


title: wild type

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

country: China

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endosperm

value: 15 DAP

value: wild type


title: opaque2 mutant


title: BM1

city: East Melbourne

first: Alex

last: Hewitt

address: 32 Gisborne St

country: Australia

institute: University of Melbourne

data_processing:
Reads were screened for the presence of any adaptor/overrepresented sequences as well as ambiguous characters and clipped where required.
Cleaned reads were aligned against the human genome using Tophat (http://tophat.cbcb.umd.edu).
Genome_build: human genome (build 37)
Supplementary_files_format_and_content: gtf files containing gene/transcript IDs, FPKM etc

source_name: W8B2+ cell_bone marrow

growth_protocol: Surgical atrial appendage specimens were manually minced into 1-2 mm3 fragments and subjected to enzymatic digestion with collagenase A (1 mg/mL) for 20 min at 370C. The tissue fragments were plated onto fibronectin- (10 μg/mL; Sigma-Aldrich, MO, USA) coated dishes, and cultured in explant media containing IMDM supplemented with 20% fetal calf serum (FCS), 0.1 mM β-mercaptoethanol, 2 mM L-glutamine and 50 U/mL penicillin/streptomycin (all from Invitrogen, CA, USA). After 2-3 weeks, monolayer of adherent cells outgrowth from the adherent tissue fragments were collected using enzymatic digestion with trypsin-EDTA (0.25%; Invitrogen) and expanded on plastic tissue culture substrate in growth media containing 25% endothelial growth media (EGM-2; Lonza, MD, USA) and 75% M199 media (Lonza) supplemented with 10% FCS, 0.1 mM non-essential amino acids and 50 U/mL penicillin/streptomycin. Once confluent, cells were partially enriched for W8B2+ cells by Magnetic Cell Sorting System (W8B2 mouse anti-human IgG1; Miltenyi Biotechnology, CA, USA) and expanded in growth media. After confluence, cells were labeled with W8B2 PE-conjugated antibody (mouse anti-human IgG1; Biolegends, CA, USA), sorted using a FACSAria Flow cytometer and sorter (BD Biosciences, USA) and expanded in growth media as passage 1.

extract_protocol:
RNA of freshly sorted positive cells was extracted and purified using RNAeasy minikit (Qiagen, Maryland, USA). The RNA yield and integrity were determined using BioAnalyzer RNA 6000 Nano (Agilent Technologies, CA, USA). The RNA integrity (RIN) scores were at least 9 in all samples.
Libraries were processed with TruSeq RNA Sample Preparation v2 reagents (Illumina, CA, USA) and were quality assessed using electrophoreis (DNA 1K Screen Tape on the TapeStation system, Agilent). Sequencing was performed in a single lane on an Illumina HiSeq-2000 platform with TruSeq Single Reads Cluster Kit v3 and TruSeq Sequencing By Synthesis v3 reagents (by the Australian Genome Research Facility (AGRF), Victoria, Australia).

value: bone marrow

value: W8B2+ cells

tag: passage

value: passage 3


title: wild-type_AB_sphere_rep1

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
Reads were mapped to Zv9 release 68 using Tophat v2.0.5 using the options -p 8 -i 20 -I 380000 --coverage-search --microexon-search
Differential expression was determined using Cufflinks with options -p 4 -u
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each condition, and statistics for differential expression

organism: Danio rerio

source_name: whole sphere stage embryo

growth_protocol: Embryos were grown in E3 embryo medium at 28.5 degrees celcius

extract_protocol:
Total RNA was extracted using Trizol according to manufacturers protocol and treated with Ambion TURBO Dnase.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wt

value: Sphere

value: AB


title: Rattus_Norvegicus - Whole Brain (24hr PMD), H3K27ac ChIP

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

institute: Erasmus MC

data_processing:
Human: Solexa sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best). SOLiD sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
Mice: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p).
Rat: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
genome build: hg19, mm9, rn4
Supplementary_files_format_and_content: bedgraph: Treat pileup MACS2 bedGraph format.
Supplementary_files_format_and_content: bw: Treat pileup in bigWig format, read per million normalized.
Supplementary_files_format_and_content: peaks.txt: Peaks in MACS2 txt format.
Supplementary_files_format_and_content: peaks.bed: Peaks in MACS2 BED format.

source_name: Whole brain 24 hr post mortem delay

extract_protocol: Frozen tissues were dissected at -20ºC, thawed quickly and homogenized. Between 20mm3 and 0.5cm3 was used depending on tissue availability. Tissue was immediately chemically cross-linked by the addition of 2ml one-fifth volume of fresh 11% formaldehyde solution in medium and incubated for 10 minutes while rotating at room temperature. Cells were washed with PBS at 4ºC.Cells were lysed and sonicated. The IP was incubated overnight at 4°C with 50 ul of Dynal Protein G magnetic beads (Invitrogen lot# 90513840) that had been pre-incubated with 5 µg of the appropriate antibody for at least 3 hrs in PBS/0.5% BSA at 4°C. Beads were washed 4 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and at the same time crosslinking was reversed by overnight incubation at 65°C. After removal of the beads immunoprecipitated DNA was diluted 1:1 with TE and then treated with RNAse A for 2 hours at 37°C, followed by proteinase K treatment for 2 hours at 50°C. DNA was purified using two consecutive phenol:chloroform extractions using MaXtract High Density gel tubes. The resulting DNA was used for analysis either on the solexa sequencer (HiSeq 2000 genome sequencer) or the SOLiD sequencer (5500xl /550xlW). The sample prep was preformed  by using the sequencer  corresponding  ChIP-Seq sample prep kit according  to the manufacturers protocol. HiSeq samples were prepped and run by the MIT BioMicro Center (http://openwetware.org/wiki/BioMicroCenter) using the HiSeq 2000 genome sequencer (10 ChIPs multiplexed per lane). Solexa samples were prepped and run in-house using the SOLiD 5500xl or SOLiD 5500xlW.

value: H3K27ac (Abcam, ab4729)

value: Whole brain 24 hr post mortem delay


title: eomesafh105_sphere_rep2


title: wild-type_AB_sphere_rep2


title: MSCA7

source_name: W8B2+ cell_atrial appendages

value: heart; atrial appendages

tag: cell type

value: passage 2


title: SKBR3

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using  cutadapt tools that is part of iMir.
To predict piRNAs, iMir uses piRNABank (tranlib), while miRAnalyzer version 0.3 was used for the identification of miRNAs and other sncRNA.
Differential expression analysis was performed by iMir (p-value ≤ 0.05, Fisher's exact test and absolute fold-change 1.5)
Wicoxon Mann-Whitney test was performed by using MeV version 4.8.1
Biclustering and Principle Component analysis (PCA) was done using DESEQ 1.14.0 package from R Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files represent piRNAs. They were generated using iMir.

source_name: hormone-insensitive, ERα-

extract_protocol: Total RNA was extracted from cell lines using the standard RNA Extraction method with TRI Reagent  (Sigma) method. 7.5μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol.

tag: growth

value: hormone-insensitive, ERα-

value: Breast cancer cells


title: t=120


title: MSCA3


title: ckit7

source_name: c-Kit+ cell_atrial appendages

value: c-Kit+ cells


title: t=140


title: Rattus_Norvegicus - Whole Brain (16hr PMD), H3K27ac ChIP

source_name: Whole brain 16 hr post mortem delay

value: Whole brain 16 hr post mortem delay


title: MSCA6


title: Rattus_Norvegicus - Whole Brain (8hr PMD), H3K27ac ChIP

source_name: Whole brain 8 hr post mortem delay

value: Whole brain 8 hr post mortem delay


title: ckit6


title: ckit5


title: Region_88 - Thalamus and Pulvinar (whole), Brain6, H3K27ac ChIP

data_processing:
Human: Solexa sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best). SOLiD sequencing: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
Bedgraph files were generate by MACS2.
Mice: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) as long as the read, allowing 1 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p).
Rat: ChIP seq reads were mapped with bowtie 0.12.7 with a seed (-l) of 36bp, allowing 3 mismatch(-n) and only 1 alignment(-m) per seed. Best singleton alignment were given (- - best).
Enriched Regions were determent by MACS2 (version2.0.8) with a threshold of 1e-5 (-p), a shiftsize of 200 (--nomodel,--shiftsize), and a large lambda of 100000 (--llocal).
genome build: hg19, mm9, rn4
Supplementary_files_format_and_content: Bedgraph: Tracks of ChIP seq data

source_name: Female Brain: thalamus/pulvinar (whole)

value: Female Brain:thalamus/pulvinar (whole)


title: Region_27 - Central Medial Thalamic Nuclei, Brain1, Input

source_name: Female Brain: central medial thalamic nuclei (contains nucleus medialis dorsalis fasciculosis, commissural nucleus, paraventricular thalamic nucleus, reuniens thalamic nucleus, cucullaris nucleus, paratenial thalamic nucleus)

value: input

value: Female Brain:central medial thalamic nuclei (contains nucleus medialis dorsalis fasciculosis, commissural nucleus, paraventricular thalamic nucleus, reuniens thalamic nucleus, cucullaris nucleus, paratenial thalamic nucleus)


title: Rattus_Norvegicus - Whole Brain (0hr PMD), H3K27ac ChIP

source_name: Whole brain 0 hr post mortem delay

value: Whole brain 0 hr post mortem delay


title: Region_31 - Putamen, Brain1, Input

source_name: Female Brain: putamen

value: Female Brain:putamen


title: Region_13 - Medial Superior Temporal Gyrus, Brain1, Input

source_name: Female Brain: medial superior temporal gyrus (secondary auditory cortex)

value: Female Brain:medial superior temporal gyrus (secondary auditory cortex)


title: Region_74 - Superior Occipital Gyrus, Brain6, H3K27ac ChIP

source_name: Female Brain: superior occipital gyrus

value: Female Brain:superior occipital gyrus


title: Region_52 - Gyrus Rectus, Brain1, Input

source_name: Female Brain: gyrus rectus

value: Female Brain:gyrus rectus


title: eomesafh105_sphere_rep1

value: Sphere

value: AB


title: Region_12 - White Matter, Brain1, Input

source_name: Female Brain: white matter

value: Female Brain:white matter


title: Region_10 - Internal Globus Pallidus, Brain1, Input

source_name: Female Brain: internal globus pallidus

value: Female Brain:internal globus pallidus


title: BM2

source_name: W8B2+ cell_bone marrow

value: bone marrow

value: W8B2+ cells

value: passage 3


title: Region_40 - Cerebellum, Brain1, Input

source_name: Female Brain: cerebellum

value: Female Brain:cerebellum


title: Region_63 - Pituitary Gland, Brain5, H3K27ac ChIP

source_name: Female Brain: pituatary gland

value: H3K27ac (Abcam, ab4729)

value: Female Brain:pituatary gland


title: Region_8 - Superior Temporal Gyrus (planum polare), Brain6, H3K27ac ChIP

source_name: Female Brain: superior temporal gyrus

value: Female Brain:superior temporal gyrus


title: Region_3 - Occipital Pole, Brain1, Input

source_name: Female Brain: occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)

value: input

value: Female Brain:occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)


title: Region_26_31 - Caudate Nucleus (medio superior) and Putamen, Brain5, H3K27ac ChIP

source_name: Female Brain: medio superior caudate nucleus (body)

value: Female Brain:medio superior caudate nucleus (body)


title: Region_1 - Posterior Precentral Gyrus, Brain1, Input

source_name: Female Brain: posterior precentral gyrus (primary motor cortex)

value: Female Brain:posterior precentral gyrus (primary motor cortex)


title: SNAI2DM_input

city: La Jolla

first: George

last: Sen

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

description: Sample 18

data_processing:
Use of Partek Genomics Suite, http://www.partek.com/partekgs to align and analyze data.
ChIP-Seq reads were aligned back to the hg19 assembly of the human genome.
Peaks were called using the Partek Genomic Suite
Genome_build: hg19
Supplementary_files_format_and_content: text files

growth_protocol:
Growth medium conditions involved culturing keratinocytes in KCSFM (Life Technologies)
To induce differentiation, cells were cultured in 1.2mM calcium +100% confluence for 3 days

extract_protocol:
Cells were fixed, lysed, and nuclei harvested and then sonicated using a Diogenode water bath sonicator
TruSeq ChIP Sample Prep Kit for ChIP-Seq (illumina)

value: Human keratinocytes

value: overexpressing SNAI2

tag: culture medium

value: differentiation medium


title: SNAI2DM_IPA

description: Sample 13

value: anti-SNAI2 (Slug (C19G7)) Rabbit mAb

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #


title: LacZ_input

description: Sample 15

value: overexpressing LACZ


title: LacZDM_IPA

description: Sample 11

tag: chip antibody


title: LacZDM_input

description: Sample 17


title: LacZDM_IPB

description: Sample 12


title: Region_23 - Substantia Nigra, Brain5, H3K27ac ChIP

source_name: Female Brain: substantia nigra

value: Female Brain:substantia nigra


title: SNAI2_IPB

description: Sample 10

value: growth medium


title: Region_86 - Fastigial Nucleus, Brain2, H3K27ac ChIP

source_name: Female Brain: fastigial nucleus

value: Female Brain:fastigial nucleus


title: SNAI2_IPA

description: Sample 9


title: Region_87 - Subthalamic Nucleus, Brain2, H3K27ac ChIP

source_name: Female Brain: subthalamic nucleus

value: Female Brain:subthalamic nucleus


title: LacZ_IPB

description: Sample 8


title: Input_SNAI2

description: Sample 6

value: SNAI2 knockdown (SNAI2 shRNA)


title: Region_85 - Central Medial Thalamic Nuclei, Brain2, H3K27ac ChIP

source_name: Female Brain: central medial thalamic nuclei

value: H3K27ac (Abcam, ab4729)

value: Female Brain:central medial thalamic nuclei


title: Input_CTL

description: Sample 5

value: control shRNA


title: LacZ_IPA

description: Sample 7


title: SNAI2i_2

description: Sample 4


title: Region_38 - Hypothalamus, Brain6, H3K27ac ChIP

source_name: Female Brain: hypothalamus (whole)

value: Female Brain:hypothalamus (whole)


title: Region_84 - Superior Pariental Lobule, Brain2, H3K27ac ChIP

source_name: Female Brain: superior pariental lobule

value: Female Brain:superior pariental lobule


title: SNAI2DM_IPB

description: Sample 14


title: CTL_2

description: Sample 2


title: SNAI2_input

description: Sample 16


title: Region_40 - Cerebellum, Brain6, H3K27ac ChIP

value: Female Brain:cerebellum


title: SNAI2i_1

description: Sample 3

value: Human keratinocytes


title: Region_83 - Supramarginal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: supramarginal gyrus

value: Female Brain:supramarginal gyrus


title: CTL_1

description: Sample 1


title: Mus_Musculus - Cerebellum, H3K27ac ChIP

source_name: Cerebellum

value: Cerebellum


title: Region_82 - Medial Temporal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: medial temporal gyrus

value: Female Brain:medial temporal gyrus


title: Region_1 - Posterior Precentral Gyrus, Brain4, H3K27ac ChIP

source_name: Male Brain: posterior precentral gyrus (primary motor cortex)

value: Male Brain:posterior precentral gyrus (primary motor cortex)


title: Region_1 - Posterior Precentral Gyrus, Brain3, H3K27ac ChIP


title: Region_74 - Superior Occipital Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: superior occipital gyrus (secondary visual cortex V3/V7a)

value: Female Brain:superior occipital gyrus (secondary visual cortex V3/V7a)


title: Region_80 - Pons (rostral part), Brain2, H3K27ac ChIP

source_name: Female Brain: pons rostal part

value: Female Brain:pons rostal part


title: Region_75 - Caudate Nucleus (anterior), Brain1, H3K27ac ChIP

source_name: Female Brain: anterior caudate nucleus (head)

value: Female Brain:anterior caudate nucleus (head)


title: Region_72 - Subiculum, Brain1, H3K27ac ChIP

source_name: Female Brain: subiculum, postsubicular area, parasubicular area

value: Female Brain:subiculum, postsubicular area, parasubicular area


title: Region_78 - Lingual Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: lingual gyrus

value: Female Brain:lingual gyrus


title: Region_81 - Tectum, Brain2, H3K27ac ChIP

source_name: Female Brain: tectum (superior/inferior colliculus)

value: Female Brain:tectum (superior/inferior colliculus)


title: Region_71 - Long Insular Gyri, Brain1, H3K27ac ChIP

source_name: Female Brain: long insular gyri

value: H3K27ac (Abcam, ab4729)

value: Female Brain:long insular gyri


title: Region_77 - Cuneus, Brain2, H3K27ac ChIP

source_name: Female Brain: cuneus

value: Female Brain:cuneus


title: Region_69 - Uncal cleft, Brain1, H3K27ac ChIP

source_name: Female Brain: uncal cleft (uncus)

value: Female Brain:uncal cleft (uncus)


title: Region_74 - Superior Occipital Gyrus, Brain2, H3K27ac ChIP


title: Region_68 - Nucleus Dendatus, Brain1, H3K27ac ChIP

source_name: Female Brain: nucleus dendatus

value: Female Brain:nucleus dendatus


title: Region_66 - Myelencephalon Nuclei, Brain1, H3K27ac ChIP

source_name: Female Brain: myelencephalon nuclei (including hypoglossal nucleus, vagus nucleus, nucleus gracilis, nucleus cuneatus)

value: Female Brain:myelencephalon nuclei (including hypoglossal nucleus, vagus nucleus, nucleus gracilis, nucleus cuneatus)


title: Region_70 - Medial Geniculate Nucleus, Brain1, H3K27ac ChIP

source_name: Female Brain: medial geniculate nucleus, nucleus limitans, peripeduncular nucleus

value: Female Brain:medial geniculate nucleus, nucleus limitans, peripeduncular nucleus


title: Region_65 - Raphe Nuclei, Brain1, H3K27ac ChIP

source_name: Female Brain: raphe nuclei

value: Female Brain:raphe nuclei


title: Region_63 - Pituitary Gland, Brain1, H3K27ac ChIP

source_name: Female Brain: pituatary gland

value: Female Brain:pituatary gland


title: Region_62 - Lateral Hypothalamic Region, Brain1, H3K27ac ChIP

source_name: Female Brain: lateral hypothalamic area, bed nucleus of the stria terminalis ventral part

value: Female Brain:lateral hypothalamic area, bed nucleus of the stria terminalis ventral part


title: Region_68 - Nucleus Dendatus, Brain2, H3K27ac ChIP


title: Region_61 - Paraventricular Hypothalamic Region, Brain1, H3K27ac ChIP

source_name: Female Brain: paraventricular hypothalamic area, uncinate nucleus, sexual dimorphic nucleus, suprachiasmatic nucleus, diagonal band nucleus, medial preoptic nucleus

value: Female Brain:paraventricular hypothalamic area, uncinate nucleus, sexual dimorphic nucleus, suprachiasmatic nucleus, diagonal band nucleus, medial preoptic nucleus


title: Region_67 - Nucleus Arcuatus, Brain2, H3K27ac ChIP

source_name: Female Brain: nucleus arcuatus

value: Female Brain:nucleus arcuatus


title: Mus_Musculus - Whole Brain, H3K27ac ChIP

source_name: Whole brain

value: Whole brain


title: Region_59 - Anterior Insular Claustrum, Brain1, H3K27ac ChIP

source_name: Female Brain: anterior insular claustrum

value: Female Brain:anterior insular claustrum


title: Region_66 - Myelencephalon Nuclei, Brain2, H3K27ac ChIP


title: Region_60 - Piriform Cortex, Brain1, H3K27ac ChIP

source_name: Female Brain: piriform cortex

value: Female Brain:piriform cortex


title: Region_58 - Nucleus Accumbens, Brain1, H3K27ac ChIP

source_name: Female Brain: nucleus accumbus

value: Female Brain:nucleus accumbus


title: Region_65 - Raphe Nuclei, Brain2, H3K27ac ChIP


title: Region_63 - Pituitary Gland, Brain2, H3K27ac ChIP


title: Region_53 - Bed Nucleus, Brain1, H3K27ac ChIP

source_name: Female Brain: bed nucleus of the stria terminalis medial part, central part, lateral part, prereticular zone

value: Female Brain:bed nucleus of the stria terminalis medial part, central part, lateral part, prereticular zone


title: Region_51 - Superior Frontal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: superior frontal gyrus

value: H3K27ac (Abcam, ab4729)

value: Female Brain:superior frontal gyrus


title: Region_52 - Gyrus Rectus, Brain1, H3K27ac ChIP

source_name: Female Brain: gyrus rectus

value: Female Brain:gyrus rectus


title: Region_50 - Superior Frontal Gyrus (para olfactory region), Brain1, H3K27ac ChIP


title: Region_73 - Anterior Medial Frontal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: anterior medial frontal gyrus

value: Female Brain:anterior medial frontal gyrus


title: Region_67 - Nucleus Arcuatus, Brain1, H3K27ac ChIP


title: Region_49 - Anterior Cingulate Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: anterior cingulate gyrus

value: Female Brain:anterior cingulate gyrus


title: Region_48 - Paraterminal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: paraterminal gyrus/subcallosal area

value: Female Brain:paraterminal gyrus/subcallosal area


title: Region_57 - Septal Nuclei, Brain2, H3K27ac ChIP

source_name: Female Brain: lateral septal nucleus, triangular septal nucleus, septofimbial nucleus, medial septal nucleus

value: Female Brain:lateral septal nucleus, triangular septal nucleus, septofimbial nucleus, medial septal nucleus


title: Region_46 - Supramarginal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: supramarginal gyrus

value: Female Brain:supramarginal gyrus


title: Region_47 - Posterior Cingulate Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: posterior cingulate gyrus

value: Female Brain:posterior cingulate gyrus


title: Region_45 - Pineal Gland, Brain1, H3K27ac ChIP

source_name: Female Brain: pineal gland

value: Female Brain:pineal gland


title: Region_55 - Superior Pariental Lobule, Brain2, H3K27ac ChIP

source_name: Female Brain: superior pariental lobule (secondary sensorimotor cortex)

value: Female Brain:superior pariental lobule (secondary sensorimotor cortex)


title: Region_54 - Mammillary Body, Brain2, H3K27ac ChIP

source_name: Female Brain: mammillary body

value: Female Brain:mammillary body


title: Region_44 - Fusiform Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: fusiform gyrus (occipito temporal gyrus)

value: Female Brain:fusiform gyrus (occipito temporal gyrus)


title: Region_43 - Middle Temporal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: middle temporal gyrus

value: Female Brain:middle temporal gyrus


title: Input2

data_processing:
Sequence reads were aligned to the Zv9 mouse genome release using Bowtie with the following options: -n2 –e120 –l 28 -m2 -k2 -best
Peaks were called in ChIP samples over input using MACS with the following options: −−mfold8 –pvalue 1e-4
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: peak wig files were generated using MACS.  Peak bed files were generated using MACS followed by custom Perl scripts.

source_name: high-sphere stage embryos

growth_protocol: Embryos grown in E3 embryo medium at 28.5 degrees celcius

extract_protocol:
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification from was used to obtain chromatin of appropriate fragment size.  Desired protein-DNA complexes were isolated using antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

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

value: AB

value: high-sphere

value: input


title: Eomesa_ChIP2

value: Eomesa


title: Region_52 - Gyrus Rectus, Brain2, H3K27ac ChIP

value: H3K27ac (Abcam, ab4729)


title: Smad2_ChIP2


title: Region_57 - Septal Nuclei, Brain1, H3K27ac ChIP


title: Region_64 - Olivary Nucleus, Brain2, H3K27ac ChIP

source_name: Female Brain: olivary nucleus

value: Female Brain:olivary nucleus


title: Region_55 - Superior Parietal Lobule, Brain1, H3K27ac ChIP


title: Input1


title: Region_47 - Posterior Cingulate Gyrus, Brain2, H3K27ac ChIP


title: Region_41 - Post Central Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: post central gyrus (superior part)  (secondary sensorimotor cortex)

value: Female Brain:post central gyrus (superior part)  (secondary sensorimotor cortex)


title: Region_42 - Angular Gyrus (superior), Brain1, H3K27ac ChIP

source_name: Female Brain: angular gyrus superior (secondary visual cortex V3/V7a)

value: Female Brain:angular gyrus superior (secondary visual cortex V3/V7a)


title: Eomesa_ChIP1


title: Region_46 - Supramarginal Gyrus, Brain2, H3K27ac ChIP


title: Region_40 - Cerebellum, Brain1, H3K27ac ChIP

source_name: Female Brain: cerebellum

value: Female Brain:cerebellum


title: Region_45 - Pineal Gland, Brain2, H3K27ac ChIP


title: Region_39 - Precuneus, Brain1, H3K27ac ChIP

source_name: Female Brain: precuneus

value: Female Brain:precuneus


title: Region_38 - Hypothalamus, Brain1, H3K27ac ChIP

source_name: Female Brain: hypothalamus

value: Female Brain:hypothalamus


title: Smad2_ChIP1


title: Region_56 - Substantia Nigra Reticular, Brain2, H3K27ac ChIP

source_name: Female Brain: substantia nigra reticular

value: Female Brain:substantia nigra reticular


title: Region_42 - Angular Gyrus (Superior), Brain2, H3K27ac ChIP


title: Region_37 - Angular Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: angular gyrus

value: Female Brain:angular gyrus


title: Region_41 - Post Central Gyrus, Brain2, H3K27ac ChIP


title: Region_36 - Posterior Medial Frontal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: posterior medial frontal gyrus

value: Female Brain:posterior medial frontal gyrus


title: Region_35 - Red Nucleus, Brain1, H3K27ac ChIP

source_name: Female Brain: red nucleus (nucleus rubens)

value: Female Brain:red nucleus (nucleus rubens)


title: Region_40 - Cerebellum, Brain2, H3K27ac ChIP


title: Region_37 - Angular Gyrus, Brain2, H3K27ac ChIP


title: Region_35 - Red Nucleus, Brain2, H3K27ac ChIP


title: Region_51 - Superior Frontal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: superior frontal gyrus

value: Female Brain:superior frontal gyrus


title: Region_31 - Putamen, Brain1, H3K27ac ChIP

source_name: Female Brain: putamen

value: Female Brain:putamen


title: Region_34 - Inferior Temporal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: inferior temporal gyrus

value: Female Brain:inferior temporal gyrus


title: Region_34 - Inferior Temporal Gyrus, Brain1, H3K27ac ChIP


title: Region_32 - Medial Precentral Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: medial precentral gyrus (secondary motor cortex)

value: Female Brain:medial precentral gyrus (secondary motor cortex)


title: Region_32 - Medial Precentral Gyrus, Brain2, H3K27ac ChIP


title: Region_30 - Medial Dorsal Thalamic Nucleus, Brain1, H3K27ac ChIP

source_name: Female Brain: medial dorsal thalamic nucleus (dorsal superficial nucleus)

value: Female Brain:medial dorsal thalamic nucleus (dorsal superficial nucleus)


title: Region_31 - Putamen, Brain2, H3K27ac ChIP


title: Region_28 - Ventral Anterior Thalamic Nucleus, Brain2, H3K27ac ChIP

source_name: Female Brain: ventral anterior thalamic nucleus (anteroprincipal thalamic nucleus)

value: Female Brain:ventral anterior thalamic nucleus (anteroprincipal thalamic nucleus)


title: Region_29 - External Globus Pallidus, Brain2, H3K27ac ChIP

source_name: Female Brain: external globus pallidus

value: H3K27ac (Abcam, ab4729)

value: Female Brain:external globus pallidus


title: Region_29 - External Globus Pallidus, Brain1, H3K27ac ChIP


title: Region_27 - Central Medial Thalamic Nuclei, Brain2, H3K27ac ChIP

source_name: Female Brain: central medial thalamic nuclei (contains nucleus medialis dorsalis fasciculosis, commissural nucleus, paraventricular thalamic nucleus, reuniens thalamic nucleus, cucullaris nucleus, paratenial thalamic nucleus)

value: Female Brain:central medial thalamic nuclei (contains nucleus medialis dorsalis fasciculosis, commissural nucleus, paraventricular thalamic nucleus, reuniens thalamic nucleus, cucullaris nucleus, paratenial thalamic nucleus)


title: Region_43 - Middle Temporal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: middle temporal gyrus

value: Female Brain:middle temporal gyrus


title: Region_28 - Ventral Anterior Thalamic Nucleus, Brain1, H3K27ac ChIP


title: Region_33 - Geniculate Nucleus, Brain1, H3K27ac ChIP

source_name: Female Brain: geniculate nucleus

value: Female Brain:geniculate nucleus


title: Region_26 - Caudate Nucleus (Medio Superior), Brain2, H3K27ac ChIP

source_name: Female Brain: medio superior caudate nucleus (body)

value: Female Brain:medio superior caudate nucleus (body)


title: Region_26 - Caudate Nucleus (medio superior), Brain1, H3K27ac ChIP


title: Region_24 - Amygdala, Brain1, H3K27ac ChIP

source_name: Female Brain: amygdala

value: Female Brain:amygdala


title: Region_22 - Inferior Frontal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: inferior frontal gyrus, pars triangularis (Broca's area)

value: Female Brain:inferior frontal gyrus, pars triangularis (Broca's area)


title: Region_25 - Lateral Occipital Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: lateral occipital gyrus (secondary visual cortex V2, V3)

value: Female Brain:lateral occipital gyrus (secondary visual cortex V2, V3)


title: Region_27 - Central Medial Thalamic Nuclei, Brain1, H3K27ac ChIP


title: Region_20 - Anterior Insular Cortex, Brain2, H3K27ac ChIP

source_name: Female Brain: short insular gyri, anterior insular cortex (gustatory cortex)

value: Female Brain:short insular gyri, anterior insular cortex (gustatory cortex)


title: Region_12 - White Matter, Brain2, H3K27ac ChIP

source_name: Female Brain: white matter

value: Female Brain:white matter


title: Region_13 - Medial Superior Temporal Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: medial superior temporal gyrus (secondary auditory cortex)

value: Female Brain:medial superior temporal gyrus (secondary auditory cortex)


title: Region_23 - Substantia Nigra, Brain1, H3K27ac ChIP

source_name: Female Brain: substantia nigra

value: Female Brain:substantia nigra


title: Region_22 - Inferior Frontal Gyrus (pars triangularis), Brain1, H3K27ac ChIP


title: Region_20 - Anterior Insular Cortex, Brain1, H3K27ac ChIP


title: Region_8 - Superior Temporal Gyrus (planum polare), Brain2, H3K27ac ChIP

source_name: Female Brain: superior temporal gyrus, planum polare

value: Female Brain:superior temporal gyrus, planum polare


title: Region_10 - Internal Globus Pallidus, Brain2, H3K27ac ChIP

source_name: Female Brain: internal globus pallidus

value: Female Brain:internal globus pallidus


title: Region_7 - Hippocampus, Brain2, H3K27ac ChIP

source_name: Female Brain: hippocampus

value: Female Brain:hippocampus


title: Region_19 - Postcentral Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: postcentral gyrus (primary somatosensory cortex )

value: Female Brain:postcentral gyrus (primary somatosensory cortex )


title: Region_18 - Frontal Pole, Brain1, H3K27ac ChIP

source_name: Female Brain: frontal pole

value: H3K27ac (Abcam, ab4729)

value: Female Brain:frontal pole


title: Region_5 - Medial Anterior Cingulate Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: medial anterior cingulate gyrus

value: Female Brain:medial anterior cingulate gyrus


title: Region_17 - Superior Frontal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: superior frontal gyrus

value: Female Brain:superior frontal gyrus


title: Region_3 - Occipital Pole, Brain2, H3K27ac ChIP

source_name: Female Brain: occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)

value: Female Brain:occipital pole, Internal calcarine sulcus,  (primary visual cortex V1)


title: Region_1 - Posterior Precentral Gyrus, Brain2, H3K27ac ChIP

source_name: Female Brain: posterior precentral gyrus (primary motor cortex)

value: Female Brain:posterior precentral gyrus (primary motor cortex)


title: Region_2 - Locus Coeruleus, Brain2, H3K27ac ChIP

source_name: Female Brain: Female Brain: locus coeruleus

value: Female Brain:Female Brain:locus coeruleus


title: Region_16 - Medial Posterior Cingulate Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: medial posterior cingulate gyrus

value: Female Brain:medial posterior cingulate gyrus


title: Region_15 - Hippocampal Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: hippocampal gyrus

value: Female Brain:hippocampal gyrus


title: Region_14 - Orbital Gyrus, Brain1, H3K27ac ChIP

source_name: Female Brain: orbital gyrus

value: Female Brain:orbital gyrus


title: Region_79 - Precuneus, Brain1, H3K27ac ChIP

source_name: Female Brain: precuneus

value: Female Brain:precuneus


title: Region_13 - Medial Superior Temporal Gyrus, Brain1, H3K27ac ChIP

value: Female Brain:medial superior temporal gyrus (secondary auditory cortex)


title: Region_77 - Cuneus, Brain1, H3K27ac ChIP

source_name: Female Brain: cuneus

value: Female Brain:cuneus


title: Region_12 - White Matter, Brain1, H3K27ac ChIP

source_name: Female Brain: white matter

value: Female Brain:white matter


title: Region_21 - Superior Temporal Gyrus (planum temporale), Brain1, H3K27ac ChIP

source_name: Female Brain: superior temporal gyrus, planum temporale (Wernicke's area)

value: Female Brain:superior temporal gyrus, planum temporale (Wernicke's area)


title: Region_10 - Internal Globus Pallidus, Brain1, H3K27ac ChIP

value: Female Brain:internal globus pallidus